From 04f8275df3ca8a8a89581a9b0ee5176eacbca970 Mon Sep 17 00:00:00 2001 From: Pirmin Kaufmann Date: Thu, 23 Feb 2023 16:19:47 +0100 Subject: [PATCH 01/24] Switched to copier template. Note: environment.yml not yet updated, linter configs not yet merged. --- .bumpversion.cfg | 29 -- .copier-answers.yml | 17 ++ .github/workflows/pre-commit.yml | 40 +++ .gitignore | 19 +- .pre-commit-config.yaml | 91 +++++- AUTHORS.md | 9 + AUTHORS.rst | 13 - CONTRIBUTING.md | 183 ++++++++++++ CONTRIBUTING.rst | 224 --------------- HISTORY.md | 5 + HISTORY.rst | 8 - LICENSE | 5 +- MANIFEST.in | 13 +- README.bumpversion.rst | 8 - README.md | 100 +++++++ README.rst | 269 ------------------ USAGE.md | 13 + USAGE.txt | 0 dev-environment.yml | 234 --------------- dev-requirements.in | 20 -- docs/Makefile | 2 +- docs/authors.rst | 2 +- docs/conf.py | 123 ++++---- docs/contributing.rst | 2 +- docs/documentation.inactive | 53 ++++ docs/history.rst | 2 +- docs/index.rst | 3 +- docs/installation.rst | 72 ++--- docs/modules.rst | 6 + docs/readme.rst | 2 +- docs/usage.rst | 2 +- find_py_toml.sh | 1 - jenkins/JenkinsJobPR | 33 +++ jenkins/Jenkinsfile | 130 +++++++++ mypy.ini => old_config/mypy.ini | 0 tox.ini => old_config/tox.ini | 0 pyproject.toml | 172 ++++++++++- requirements.in | 11 - .../environment.yml | 24 +- requirements/requirements.yml | 49 ++++ setup.py | 72 ----- src/pyflexplot/__init__.py | 12 +- {scripts => tools}/find_py_toml.sh | 0 tools/run-mypy.sh | 27 ++ tools/setup_env.sh | 68 +++++ tools/setup_miniconda.sh | 44 +++ 46 files changed, 1185 insertions(+), 1027 deletions(-) delete mode 100644 .bumpversion.cfg create mode 100644 .copier-answers.yml create mode 100644 .github/workflows/pre-commit.yml create mode 100644 AUTHORS.md delete mode 100644 AUTHORS.rst create mode 100644 CONTRIBUTING.md delete mode 100644 CONTRIBUTING.rst create mode 100644 HISTORY.md delete mode 100644 HISTORY.rst delete mode 100644 README.bumpversion.rst create mode 100644 README.md delete mode 100644 README.rst create mode 100644 USAGE.md delete mode 100644 USAGE.txt delete mode 100644 dev-environment.yml delete mode 100644 dev-requirements.in create mode 100644 docs/documentation.inactive create mode 100644 docs/modules.rst delete mode 120000 find_py_toml.sh create mode 100644 jenkins/JenkinsJobPR create mode 100644 jenkins/Jenkinsfile rename mypy.ini => old_config/mypy.ini (100%) rename tox.ini => old_config/tox.ini (100%) delete mode 100644 requirements.in rename environment.yml => requirements/environment.yml (93%) create mode 100644 requirements/requirements.yml delete mode 100644 setup.py rename {scripts => tools}/find_py_toml.sh (100%) create mode 100755 tools/run-mypy.sh create mode 100755 tools/setup_env.sh create mode 100755 tools/setup_miniconda.sh diff --git a/.bumpversion.cfg b/.bumpversion.cfg deleted file mode 100644 index adeb6863..00000000 --- a/.bumpversion.cfg +++ /dev/null @@ -1,29 +0,0 @@ -[bumpversion] -current_version = 1.0.10 -commit = False -tag = False -parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\.(?P[a-z]+)(?P\d+))? -serialize = - {major}.{minor}.{patch}.{release}{build} - {major}.{minor}.{patch} - -[bumpversion:part:release] -first_value = regular -optional_value = regular -values = - dev - regular - -[bumpversion:part:build] - -[bumpversion:file:VERSION] - -[bumpversion:file:setup.py] - -[bumpversion:file:src/pyflexplot/__init__.py] - -[bumpversion:file:src/pyflexplot/cli/__init__.py] - -[bumpversion:file:src/pyflexplot/plotting/__init__.py] - -[bumpversion:file:src/pyflexplot/utils/__init__.py] diff --git a/.copier-answers.yml b/.copier-answers.yml new file mode 100644 index 00000000..f350d68f --- /dev/null +++ b/.copier-answers.yml @@ -0,0 +1,17 @@ +# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY +_commit: a1078ae +_src_path: git@github.com:MeteoSwiss-APN/mch-python-blueprint.git +email: stefan.ruedisuehli@env.ethz.ch +full_name: Stefan Ruedisuehli +github_username: MeteoSwiss-APN +module_name: pyflexplot +project_doc_url: https://github.io/MeteoSwiss-APN/pyflexplot +project_github: https://github.com/MeteoSwiss-APN/pyflexplot +project_keywords: Dispersion, Flexpart, COSMO, mapping, visualization +project_name: PyFlexPlot +project_short_description: Stefan Ruedisuehli's PyFlexPlot +project_slug: pyflexplot +project_ssh_url: git+ssh://git@github.com/MeteoSwiss-APN/pyflexplot.git +python_version: '3.10' +version: 1.0.10 +year: '2023' diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml new file mode 100644 index 00000000..071e0f93 --- /dev/null +++ b/.github/workflows/pre-commit.yml @@ -0,0 +1,40 @@ +name: Run pre-commit in blueprint + +on: + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + blueprint-pre-commit: + runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v2 + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: 3.11.0 + - uses: conda-incubator/setup-miniconda@v2 + with: + miniconda-version: "latest" + channels: conda-forge + channel-priority: flexible + show-channel-urls: true + - name: Create env from unpinned reqs + run: | + conda env create --name dev_env --file requirements/requirements.yml + - name: Install project into env + run: | + conda run --name dev_env pip install --no-deps . + - name: Install pre-commit hooks + run: | + conda run --name dev_env pre-commit install-hooks + - name: Run pre-commit hooks + run: | + conda run --name dev_env pre-commit run --all-files diff --git a/.gitignore b/.gitignore index 8ddf7fc3..725a2d44 100644 --- a/.gitignore +++ b/.gitignore @@ -1,15 +1,3 @@ -# Local files -local/ - -# Default test data link -data - -# Non-permanent data, e.g. test output -scratch/ - -# Batch processing log files -log/ - # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] @@ -58,7 +46,6 @@ nosetests.xml coverage.xml *.cover .hypothesis/ -junit-*.xml .pytest_cache/ # Translations @@ -85,6 +72,9 @@ target/ # Jupyter Notebook .ipynb_checkpoints +# pyenv +.python-version + # celery beat schedule file celerybeat-schedule @@ -96,6 +86,7 @@ celerybeat-schedule # virtualenv .venv +.venvs venv/ venvs/ venv_*/ @@ -112,6 +103,8 @@ venv_*/ # mypy .mypy_cache/ + +# Eclipse .project # VS Code diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c873d54f..e06164af 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,18 +11,91 @@ repos: - id: debug-statements - id: end-of-file-fixer - id: trailing-whitespace -- repo: https://github.com/psf/black - rev: 23.1.0 +- repo: local + hooks: + - id: forbidden-files-copier-rej + name: find copier rejection files + language: fail + entry: "Found copier update rejection file(s): review and remove them" + files: "\\.rej$" + - id: forbidden-files-git-orig + name: find git merge backup files + language: fail + entry: "Found git merge backup file(s): review and remove them" + files: "\\.orig$" +- repo: local + hooks: + - id: rstcheck + name: rstcheck + description: Check REST files for correctness + language: system + entry: rstcheck + types: [rst] +- repo: local + hooks: + - id: codespell + name: codespell + description: Check for spelling errors + language: system + entry: codespell +- repo: local hooks: - id: black - files: ^(.*\.py|(src|tests|docs)/(.*/)*.*\.py)$ -- repo: https://github.com/timothycrosley/isort - rev: 5.12.0 + name: black + description: Format Python code + language: system + entry: black + types_or: [python, pyi] +- repo: local hooks: - id: isort - files: ^(.*\.py|(src|tests|docs)/(.*/)*.*\.py)$ -- repo: https://github.com/PyCQA/pydocstyle - rev: 6.3.0 + name: isort + description: Group and sort Python imports + language: system + entry: isort + types_or: [python, pyi, cython] +- repo: local hooks: - id: pydocstyle - files: ^src/(.*/)*.*\.py$ + name: pydocstyle + description: Check docstrings in Python code for compliance with conventions + language: system + entry: pydocstyle + types: [python] + files: ^src/ +# SR It would be handy to abort if one linter fails b/c the same error often +# SR triggers multiple linters. That way, if flake8 fails, pylint and mypy +# SR (which in large code bases can take some time to run) could be skipped +# SR before fixing the error. Unfortunately, pre-commit only provides the global +# SR option fail_fast, which would abort even after the small fixers and +# SR formatters changed something. A potential solution could be to write a +# SR small bash script run-linters.sh that runs flake8, pylint and run-mypy.sh +# SR in that order and aborts on error. +- repo: local + hooks: + - id: pylint + name: pylint + description: Check Python code for correctness, consistency and adherence to best practices + language: system + entry: pylint + types: [python] +- repo: local + hooks: + - id: flake8 + name: flake8 + description: Check Python code for correctness, consistency and adherence to best practices + language: system + entry: flake8 + types: [python] +- repo: local + hooks: + - id: mypy + name: mypy + description: Perform static type analysis of Python code + language: system + entry: bash tools/run-mypy.sh + require_serial: true + pass_filenames: false + verbose: true + types: [python] + files: ^(src|tests)/ diff --git a/AUTHORS.md b/AUTHORS.md new file mode 100644 index 00000000..2616d9a9 --- /dev/null +++ b/AUTHORS.md @@ -0,0 +1,9 @@ +# Credits + +## Development Lead + +- Stefan Ruedisuehli + +## Contributors + +None yet. Why not be the first? diff --git a/AUTHORS.rst b/AUTHORS.rst deleted file mode 100644 index 2dab79bd..00000000 --- a/AUTHORS.rst +++ /dev/null @@ -1,13 +0,0 @@ -======= -Credits -======= - -Development Lead ----------------- - -* Stefan Ruedisuehli - -Contributors ------------- - -None yet. Why not be the first? diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..d0aececd --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,183 @@ +# Contributing + +Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given. + +## Types of Contributions + +You can contribute in many ways. + +### Report Bugs + +Report bugs as [GitHub issues](https://github.com/MeteoSwiss-APN/pyflexplot/issues). + +If you are reporting a bug, please include + +- your operating system name and version, +- any details about your local setup that might be helpful in troubleshooting, and +- detailed steps to reproduce the bug. + +### Fix Bugs + +Look through the [GitHub issues](https://github.com/MeteoSwiss-APN/pyflexplot/issues) for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it. + +### Implement Features + +Look through the [GitHub issues](https://github.com/MeteoSwiss-APN/pyflexplot/issues) for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it. + +### Write Documentation + +PyFlexPlot could always use more documentation, whether as part of the official PyFlexPlot docs, in docstrings --- or even on the web in blog posts, articles, and such. + +### Submit Feedback + +The best way to send feedback is to file a [GitHub issue]( https://github.com/MeteoSwiss-APN/pyflexplot/issues). + +If you are proposing a feature, + +- explain in detail how it would work; +- keep the scope as narrow as possible, to make it easier to implement; and +- remember that this is a volunteer-driven project, and that contributions are welcome! :) + +## Get Started! + +Ready to contribute? Here's how to set up `pyflexplot` for local development. + +1. Fork the [`pyflexplot` repo](https://github.com/) on GitHub. +2. Clone your fork locally: + + ```bash + git clone git@github.com:your_name_here/pyflexplot.git + ``` + +3. Create a virtual environment and install the dependencies: + + ```bash + cd pyflexplot/ + ./tools/setup_env.sh + ``` + + This will create a conda environment named `pyflexplot` (change with `-n`) and install the pinned runtime and development dependencies in `requirements/environment.yml`. + + Install the package itself in editable mode. + + ```bash + conda activate pyflexplot + pip install --editable . + ``` + + Use `-u` to get the newest package versions (unpinned dependencies in `requirements/requirements.yml`), and additionally `-e` to update the environment files. + +4. Create a branch for local development: + + ```bash + git switch -c name-of-your-bugfix-or-feature + ``` + + Now you can make your changes locally. + +5. When you're done with a change, format and check the code using various installed tools like `black`, `isort`, `mypy`, `flake8` or `pylint`. Those that are set up as pre-commit hooks can be run together with: + + ```bash + pre-commit run -a + ``` + + Next, ensure that the code does what it is supposed to do by running the tests with pytest: + + ```bash + pytest + ``` + +6. Commit your changes and push your branch to GitHub: + + ```bash + git add . + git commit -m "fixed this and did that" + git push origin name-of-your-bugfix-or-feature + ``` + +7. Submit a pull request through the GitHub website. + +## Pull Request Guidelines + +Before you submit a pull request, check that it meets these guidelines: + +1. The pull request should include tests. +2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in `README.md`. +3. The pull request should work for Python 3.6 and 3.7, and for PyPy. Make sure that the tests pass for all supported Python versions. + +## Tips + +For a subset of tests or a specific test, run: + +```bash +pytest tests.test_pyflexplot +pytest tests.test_pyflexplot/test_feature::test_edge_case +``` + +## Versioning + +In order to release a new version of your project, follow these steps: + +- Make sure everything is committed, cleaned up and validating (duh!). Don't forget to keep track of the changes in `HISTORY.md`. +- Increase the version number that is hardcoded in `pyproject.toml` (and only there) and commit. +- Either create a (preferentially annotated) tag with `git tag`, or directly create a release on GitHub. + +## Project Structure + +Following is a description of the most important files and folders in the project in alphabetic order. + +- `.github/workflows/`: [GitHub Actions](https://docs.github.com/en/actions) workflows, e.g., checks that are run when certain branches are pushed. +- `docs/`: Documentation. +- `jenkins/`: Jenkins setup. +- `requirements/`: Project dependencies and environment + - `environment.yml`: Full tree of runtime and development dependencies with fully specified ('pinned') version numbers; created with `conda env export`. + - `requirements.yml`: Top-level runtime and development dependencies with minimal version restrictions (typically a minimum version or a version range); kept manually. +- `src/pyflexplot/`: Source code of the project package. +- `tests/test_pyflexplot/`: Unit tests of the project package; run with `pytest`. +- `tools/`: Scripts primarily for development + - `run-mypy.sh`: Run script for the static type checker `mypy`. + - `setup_env.sh`: Script to create new conda environments; see `tools/setup_env.sh -h` for all available options. + - `setup_miniconda.sh`: Script to install miniconda. +- `.gitignore`: Files and folders ignored by `git`. +- `.pre-commit-config.yaml`: Configuration of pre-commit hooks, which are formatters and checkers run before a successful commit. +- `AUTHORS.md`: Project authors. +- `CONTRIBUTING.md`: Instructions on how to contribute to the project. +- `HISTORY.md`: List of changes for each version of the project. +- `LICENSE`: License of the project. +- `MANIFEST.in`: Files installed alongside the source code. +- `pyproject.toml`: Main package specification file, including build dependencies, metadata and the configurations of development tools like `black`, `pytest`, `mypy` etc. +- `README.md`: Description of the project. +- `USAGE.md`: Information on how to use the package. + +## Managing dependencies + +PyFlexPlot uses [Conda](https://docs.conda.io/en/latest/) to manage dependencies. (Also check out [Mamba](https://mamba.readthedocs.io/en/latest/) if you like your package installations fast.) Dependencies are specified in YAML files, of which there are two: + +- `requirements/requirements.yml`: Top-level runtime and development dependencies with minimal version restrictions (typically a minimum version or a version range); kept manually. +- `requirements/environment.yml`: Full tree of runtime and development dependencies with fully specified ('pinned') version numbers; created with `conda env export`. + +The pinned `environment.yml` file should be used to create reproducible environments for development or deployment. This ensures reproducible results across machines and users. The unpinned `requirements.yml` file has two main purposes: (i) keeping track of the top-level dependencies, and (ii) periodically updating the pinned `environment.yml` file to the latest package versions. + +After introducing new first-level dependencies to your requirements, you have to update the environment files in order to be able to create reproducible environments for deployment and production. +Updating the environment files involves the following steps: + +1. Creating an environment from your top-level dependencies in `requirements/requirements.yml` +2. Exporting this environment to `requirements/environment.yml` + +Alternatively, use the provided script + +```bash +./tools/setup_env.sh -ue +``` + +to create a environment from unpinned (`-u`) runtime and development dependencies and export (`-e`) it (consider throwing in `-m` for good measure to speed things up with `mamba`). + +_Note that the separation of unpinned runtime and development dependencies into separate files (`requirements.yml` and `dev-requirements.yml`, respectively) has been given up because when creating an environment from multiple YAML files (with `conda env create` and `conda env update`), only the version restrictions in the last file are guaranteed to be respected, so when installing devevelopment dependencies from `dev-requirements.yml` into an environment created from `requirements.yml`, the solver does not take version restrictions in the latter file into account anymore, potentially resulting in inconsistent production and development environments. Given the negligible overhead (in terms of memory etc.) of installing development dependencies in production environments, they are only separated from the runtime dependencies in `requirements.yml` by a comment._ + +## How to provide executable scripts + +By default, a single executable script called pyflexplot is provided. It is created when the package is installed. When you call it, the main function (`cli`) in `src/pyflexplot/cli.py` is called. + +When the package is installed, a executable script named `pyflexplot` is created in the bin folder of the active conda environment. Upon calling this script in the shell, the `main` function in `src/pyflexplot/cli.py` is executed. + +The scripts, their names and entry points are specified in `pyproject.toml` in the `[project.scripts]` section. Just add additional entries to provide more scripts to the users of your package. diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst deleted file mode 100644 index d280918b..00000000 --- a/CONTRIBUTING.rst +++ /dev/null @@ -1,224 +0,0 @@ -.. highlight:: shell - -============ -Contributing -============ - -Contributions are welcome, and they are greatly appreciated! -Every little bit helps, and credit will always be given. - -You can contribute in many ways: - -Types of Contributions ----------------------- - -Report Bugs -~~~~~~~~~~~ - -Report bugs at https://github.com/MeteoSwiss-APN/pyflexplot/issues. - -If you are reporting a bug, please include: - -* Your operating system name and version. -* Any details about your local setup that might be helpful in troubleshooting. -* Detailed steps to reproduce the bug. - -Fix Bugs -~~~~~~~~ - -Look through the GitHub issues for bugs. -Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it. - -Implement Features -~~~~~~~~~~~~~~~~~~ - -Look through the GitHub issues for features. -Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it. - -Write Documentation -~~~~~~~~~~~~~~~~~~~ - -PyFlexPlot could always use more documentation, whether as part of the official PyFlexPlot docs, in docstrings, or even on the web in blog posts, articles, and such. - -Submit Feedback -~~~~~~~~~~~~~~~ - -The best way to send feedback is to file an issue at https://github.com/MeteoSwiss-APN/pyflexplot/issues. - -If you are proposing a feature: - -* Explain in detail how it would work. -* Keep the scope as narrow as possible, to make it easier to implement. -* Remember that this is a volunteer-driven project, and that contributions are welcome! :) - -Get Started! ------------- - -Ready to contribute? Here's how to set up `pyflexplot` for local development. - -1. Fork the `pyflexplot` repo on GitHub. -2. Clone your fork locally:: - - $ git clone git@github.com:your_name_here/pyflexplot.git - -3. Install your local copy into a virtualenv. This is how you set up your fork for local development:: - - $ cd pyflexplot/ - $ conda env create -n pyflexplot-dev --file=dev-environment.yml - $ conda activate pyflexplot-dev - $ pip install -e . - -4. Create a branch for local development:: - - $ git checkout -b name-of-your-bugfix-or-feature - - Now you can make your changes locally. - -5. When you're done making changes, format them with black, check that your changes pass the static code analyses with flake8 and the tests with pytest, including testing other Python versions with tox:: - - $ black src - $ tox # runs pytest, pylint, flake8 - -6. Commit your changes and push your branch to GitHub:: - - $ git add . - $ git commit -m "Your detailed description of your changes." - $ git push origin name-of-your-bugfix-or-feature - -7. Submit a pull request through the GitHub website. - -Pull Request Guidelines ------------------------ - -Before you submit a pull request, check that it meets these guidelines: - -1. The pull request should include tests. -2. If the pull request adds functionality, the docs should be updated. - Put your new functionality into a function with a docstring, and add the feature to the list in ``README.rst``. -3. The pull request should work for Python 3.6 and 3.7, and for PyPy. - Make sure that the tests pass for all supported Python versions. - -Tips ----- - -To run a subset of tests:: - - $ pytest tests.test_pyflexplot - -Deploying ---------- - -A reminder for the maintainers on how to deploy. -Make sure all your changes are committed (including an entry in ``HISTORY.rst``). -Then run:: - -$ bumpversion patch # possible: major / minor / patch -$ git push -$ git push --tags - -Jenkins will then deploy to PyPI if tests pass. - -Project Structure ------------------ - -.. list-table:: Structure - :widths: 25 75 - :header-rows: 1 - - * - File or directory - - Description - * - AUTHORS.rst - - Contains information about the lead developer and contributors. - * - .bumpversion.cfg - - Configuration file of bumpversion. - * - CONTRIBUTION.rst - - Contains all the information you need when you contribute to this project. - * - dev-environment.yml - Exported conda environment specifying pinned runtime and development dependencies. - Is based on the pinned runtime dependencies in ``environment.yml`` and the unpinned development dependencies in ``dev-requirements.in``. - * - Exported conda environment specifying pinned runtime dependencies. - Is based on the unpinned runtime dependencies in ``requirements.in``. - * - .gitignore - - Files and directories ignored by git. - * - HISTORY.rst - - Lists the releases and their new features. - * - LICENSE - - License of this project. - * - MANIFEST.in - - Specifies the files and directories which will be added to the Pip package. - * - Makefile - - Build file for cleaning, installing the tool and its dependencies, for testing, formatting and linting code, and much more. - Type ``make help`` to see all available commands. - * - mypy.ini - - Configuration file of mypy. - * - .pre-commit-config.yaml - - Configuration file of pre-commit, which, among other things, runs the formatters black and isort. - * - pyproject.toml - - Project specification file as defined by PEP 518. - * - README.rst - - Short documentation about the package. - It lists features and contains a quick start. - * - setup.py - - Script used to build the package. - It reads the unpinned top-level requirements from ``requirements.in`` into the variable ``requirements``. - * - tox.ini - - A configuration file for tox carring out the test for different Python verions. - The listed versions should be the same as in the file ``setup.py``. - * - USAGE.txt - - Instructions on using pyflexplot. - * - VERSION - - Text file containing the current package version. - Handled by bumpversion. - * - docs/ - - Directory containing the documentation. - * - dev-requirements.in - - A text file containing top-level unpinned development dependencies (critical version restrictions only). - It is managed manually. - * - requirements.in - - A text file containing top-level unpinned runtime dependencies (critical version restrictions only). - It is managed manually and read in ``setup.py``. - * - scripts/ - - Directory containing some small helper scripts. - * - src/ - - Source directory. - * - tests/ - - Directory containing the tests. - The directory structure in this folder follows that in the source folder (src). - For each file in the source folder, there is a file with the same name, but with the prefix ``text_``. - * - various/ - - Directory containing various files. - -Managing dependencies ---------------------- - -Generally, projects make use of other libraries, be it as (production) dependencies (e.g., ``import numpy`` in source code) -Which libraries -- and any critical restrictions of their versions -- have to be listed in different places in the project: - -* Unpinned top-level runtime dependencies, which are required to run the application/library, belong in ``requirements.in`` (from which they are read in ``setup.py``). - The versions of unpinned dependencies are only restricted as necessary, e.g., if a minimum version is required for a certain feature or bugfix. -* Unpinned top-level development dependencies, which are additional packages required during development, belong in ``dev-requirements.in``. -* Pinned runtime and development dependencies, created with ``conda env export``, belong in ``environment.yml`` and ``dev-environment.yml``, respectively. - This allows for the creation of reproducible conda environments. - -How to provide executable scripts ---------------------------------- - -By default, a single executable script called pyflexplot is provided. -It is created when the package is installed. -When you call it, the main function (``cli``) in ``src/pyflexplot/cli/cli.py`` is called. - -How many scripts that are created, their names and which functions are called can be configured in the -``setup.py`` file. -The function ``setup`` has a named argument called ``entry_point`` which is a -dictionary with an element ``console_scripts``. -The element is an array of string. -For Example:: - - entry_points={ - 'console_scripts': [ - 'pyflexplot=pyflexplot.cli.cli:cli', - ], - -When the package is installed, a executable script is created in the Python's bin folder with the name ``pyflexplot``. -If a user calls this script, the function ``cli`` in the file ``src/pyflexplot/cli/cli.py`` is called. -If more scripts should be created, add further entries to array ``console_scripts``. diff --git a/HISTORY.md b/HISTORY.md new file mode 100644 index 00000000..3299de73 --- /dev/null +++ b/HISTORY.md @@ -0,0 +1,5 @@ +# History + +## 1.0.10 (2023-XX-XX) + +- First release on PyPI. diff --git a/HISTORY.rst b/HISTORY.rst deleted file mode 100644 index 45e602d0..00000000 --- a/HISTORY.rst +++ /dev/null @@ -1,8 +0,0 @@ -======= -History -======= - -0.1.0 (2019-05-16) ------------------- - -* First release on PyPI. diff --git a/LICENSE b/LICENSE index 7ae764eb..f0ef528c 100644 --- a/LICENSE +++ b/LICENSE @@ -1,7 +1,4 @@ - - -Copyright (c) 2019 ETH Zürich, - Federal Office of Meteorlogy and Climatology MeteoSwiss +Copyright (c) 2023 Federal Office of Meteorlogy and Climatology MeteoSwiss Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/MANIFEST.in b/MANIFEST.in index ed1c323c..5fc6b01b 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,13 +1,12 @@ -include AUTHORS.rst -include CONTRIBUTING.rst -include HISTORY.rst +include AUTHORS.md +include CONTRIBUTING.md +include HISTORY.md include LICENSE -include README.rst -include *requirements.in -include *environment.yml +include README.md -recursive-include src/*/data * +recursive-include requirements * recursive-include src py.typed +recursive-include src/*/data * recursive-include tests * recursive-exclude * __pycache__ recursive-exclude * *.py[co] diff --git a/README.bumpversion.rst b/README.bumpversion.rst deleted file mode 100644 index 3c47a46c..00000000 --- a/README.bumpversion.rst +++ /dev/null @@ -1,8 +0,0 @@ -Move from regular version to dev version:: - bumpversion --allow-dirty --verbose --no-commit --new-version=1.0.6.dev0 dummy - -Bump build number of dev version:: - bumpversion --allow-dirty --verbose --no-commit build - -Release dev version, returning to regular version number:: - bumpversion --allow-dirty --verbose --commit --tag release diff --git a/README.md b/README.md new file mode 100644 index 00000000..91e94ca9 --- /dev/null +++ b/README.md @@ -0,0 +1,100 @@ +# PyFlexPlot: Stefan Ruedisuehli's PyFlexPlot + +## Start developing + +Once you created or cloned this repository, make sure the installation is running properly. Install the package dependencies with the provided script `setup_env.sh`. +Check available options with +```bash +tools/setup_env.sh -h +``` +We distinguish pinned installations based on exported (reproducible) environments and free installations where the installation +is based on top-level dependencies listed in `requirements/requirements.yml`. If you start developing, you might want to do an unpinned installation and export the environment: + +```bash +tools/setup_env.sh -u -e -n +``` +*Hint*: If you are the package administrator, it is a good idea to understand what this script does, you can do everything manually with `conda` instructions. + +*Hint*: Use the flag `-m` to speed up the installation using mamba. Of course you will have to install mamba first (we recommend to install mamba into your base +environment `conda install -c conda-forge mamba`. If you install mamba in another (maybe dedicated) environment, environments installed with mamba will be located +in `/envs/mamba/envs`, which is not very practical. + +The package itself is installed with `pip`. For development, install in editable mode: + +```bash +conda activate +pip install --editable . +``` + +*Warning:* Make sure you use the right pip, i.e. the one from the installed conda environment (`which pip` should point to something like `path/to/miniconda/envs//bin/pip`). + +Once your package is installed, run the tests by typing: + +``` +conda activate +pytest +``` + +If the tests pass, you are good to go. If not, contact the package administrator Stefan Ruedisuehli. Make sure to update your requirement files and export your environments after installation +every time you add new imports while developing. Check the next section to find some guidance on the development process if you are new to Python and/or APN. + +### Roadmap to your first contribution + +Generally, the source code of your library is located in `src/`. The blueprint will generate some example code in `mutable_number.py`, `utils.py` and `cli.py`. `cli.py` thereby serves as an entry +point for functionalities you want to execute from the command line, it is based on the Click library. If you do not need interactions with the command line, you should remove `cli.py`. Moreover, of course there exist other options for command line interfaces, +a good overview may be found here (https://realpython.com/comparing-python-command-line-parsing-libraries-argparse-docopt-click/), we recommend however to use click. The provided example +code should provide some guidance on how the individual source code files interact within the library. In addition to the example code in `src/`, there are examples for +unit tests in `tests//`, which can be triggered with `pytest` from the command line. Once you implemented a feature (and of course you also +implemented a meaningful test ;-)), you are likely willing to commit it. First, go to the root directory of your package and run pytest. + +```bash +conda activate +cd +pytest +``` + +If you use the tools provided by the blueprint as is, pre-commit will not be triggered locally but only if you push to the main branch +(or push to a PR to the main branch). If you consider it useful, you can set up pre-commit to run locally before every commit by initializing it once. In the root directory of +your package, type: + +```bash +pre-commit install +``` + +If you run `pre-commit` without installing it before (line above), it will fail and the only way to recover it, is to do a forced reinstallation (`conda install --force-reinstall pre-commit`). +You can also just run pre-commit selectively, whenever you want by typing (`pre-commit run --all-files`). Note that mypy and pylint take a bit of time, so it is really +up to you, if you want to use pre-commit locally or not. In any case, after running pytest, you can commit and the linters will run at the latest on the GitHub actions server, +when you push your changes to the main branch. Note that pytest is currently not invoked by pre-commit, so it will not run automatically. Automated testing can be set up with +GitHub Actions or be implemented in a Jenkins pipeline (template for a plan available in `jenkins/`. See the next section for more details. + +## Development tools + +As this package was created with the APN Python blueprint, it comes with a stack of development tools, which are described in more detail on +(https://meteoswiss-apn.github.io/mch-python-blueprint/). Here, we give a brief overview on what is implemented. + +### Testing and coding standards + +Testing your code and compliance with the most important Python standards is a requirement for Python software written in APN. To make the life of package +administrators easier, the most important checks are run automatically on GitHub actions. If your code goes into production, it must additionally be tested on CSCS +machines, which is only possible with a Jenkins pipeline (GitHub actions is running on a GitHub server). + +### Pre-commit on GitHub actions + +`.github/workflows/pre-commit.yml` contains a hook that will trigger the creation of your environment (unpinned) on the GitHub actions server and +then run various formatters and linters through pre-commit. This hook is only triggered upon pushes to the main branch (in general: don't do that) +and in pull requests to the main branch. + +### Jenkins + +Two jenkins plans are available in the `jenkins/` folder. On the one hand `jenkins/Jenkinsfile` controls the nightly (weekly, monthly, ...) builds, on the other hand +`jenkins/JenkinsJobPR` controls the pipeline invoked with the command `launch jenkins` in pull requests on GitHub. Your jenkins pipeline will not be set up +automatically. If you need to run your tests on CSCS machines, contact DevOps to help you with the setup of the pipelines. Otherwise, you can ignore the jenkinsfiles +and exclusively run your tests and checks on GitHub actions. + +## Features + +- TODO + +## Credits + +This package was created with [`copier`](https://github.com/copier-org/copier) and the [`MeteoSwiss-APN/mch-python-blueprint`](https://meteoswiss-apn.github.io/mch-python-blueprint/) project template. diff --git a/README.rst b/README.rst deleted file mode 100644 index a510ac1e..00000000 --- a/README.rst +++ /dev/null @@ -1,269 +0,0 @@ -########## -PyFlexPlot -########## - -PyFlexPlot is a Python-based tool to visualize FLEXPART dispersion simulation -results stored in NetCDF format. - -Installation -============ - -PyFlexPlot is hosted on `Github`_. -For the available releases, see `Releases`_. - -.. _`Github`: https://github.com/MeteoSwiss-APN/pyflexplot -.. _`Releases`: https://github.com/MeteoSwiss-APN/pyflexplot/releases - -With Conda ----------- - -Due to the dependency of cartopy on contemporary system libraries, it is the recommended -to install pyflexplot with conda. Conda is, as opposed to pipx and pip, not only able to -manage Python code, but also other items like system libraries. - -To install conda, look for the latest Miniconda version on -https://docs.conda.io/en/latest/miniconda.html. - -If you are working on a HPC system of the CSCS, consult the next section for more details. - -The installation of pyflexplot needs some packages only available in the `conda-forge` channel. -Check your configured conda channels with:: - - conda config --get channels - -The list should contain 'conda-forge' with highest and 'defaults' with -a lower priority. If 'conda-forge' is missing, add it at the top of the -channel list with:: - - conda config --add channels conda-forge - -The following, although recommended by conda, -is not strictly necessary, and may even prevent conda from solving the environment -if you don't have conda-forge as priority channel:: - - conda config --set channel_priority strict - -When you have installed conda, copy the pyflexplot repository (approx. 260 MB):: - - git clone git@github.com:MeteoSwiss-APN/pyflexplot.git - -Change into the base directory of the repository and check the links `Makefile` and `setup.py`:: - - cd pyflexplot - ls -l Makefile setup.py - -They should point to `Makefile.conda.mk` and `setup.conda.py`. -If they do not, overwrite the links with:: - - ln -sf Makefile.conda.mk Makefile - ln -sf setup.conda.py setup.py - -Check the Python version:: - - python --version - -If the python version provided by the system is < 3.7, -use the conda base environment for the further steps:: - - conda activate - -Display help for make options and targets:: - - make help - -Important: Before starting the installation, make sure none or the conda base -environment is active, otherwise pyflexplot will be installed in the active -conda environment instead of creating its own! - -For the installation of pyflexplot with conda, -continue with the section `Installation from repository` further below. - - -At CSCS -------- - -As contemporary system libraries are not available on the HPC systems -of the CSCS, it is highly recommended to use conda for the installation. -Install the latest Miniconda for 64-bit Linux. Choose a directory within -your `$SCRATCH` file system as installation location to -avoid cluttering the limited space on the user's `$HOME`. - -For the same reason, it is better to clone the git repository to a -location within your `$SCRATCH` file system, although conda uses the -conda installation location to store the environment, unlike pipx and -pip, which by default use a `venv` subdirectory of the repository. - -`More information for MeteoSwiss installation at CSCS `__ - - -Deployment with repository -++++++++++++++++++++++++++ - -The installation, starting with a git clone of the repository, can be achieved as follows:: - - cd - git clone git+ssh://github.com/MeteoSwiss-APN/pyflexplot --branch=v0.9.5 --depth=1 manual/git/pyflexplot/v0.9.5 - cd manual/git/pyflexplot/v0.9.5 - python -m venv manual/venvs/pyflexplot/v0.9.5 - make install VENV_DIR=/manual/venvs/pyflexplot/v0.9.5 - cd - ln -s /manual/venvs/pyflexplot/v0.9.5/bin/pyflexplot pyflexplot_v0.9.5 - pyflexplot_v0.9.5 --version - -Note that without `--depth=1`, the whole git history is downloaded, not just the tagged commit. -Also note that without `VENV_DIR=...`, the conda environment is created with -the default name ``pyflexplot``. If an environment other than base is activated, -pyflexplot is installed in the currently activated environment. - - -Installation from repository ----------------------------- - -The most convenient way to install, test and/or develop PyFlexPlot is by using the -Makefile, which provides commands for the most common operations related to -installation, testing etc. (and may also serve as a reference for the respective -Python commands). - -Type `make help` (or just `make`)) in the root of the project to see all available -commands and options. -(Note that the options must come after `make `, even though they look like -environment variables.) - -Express:: - - git clone git@github.com:MeteoSwiss-APN/pyflexplot.git - cd pyflexplot - make test CHAIN=1 - -(With `CHAIN=1`, the `make test*` commands first run `make install`.) - -Short:: - - git clone git@github.com:MeteoSwiss-APN/pyflexplot.git - cd pyflexplot - make install - make test - - conda activate pyflexplot - pyflexplot --help - - # or (if installed with pip): - ./venv/bin/pyflexplot --help - - # or (if installed with pip): - source ./venv/bin/activate - pyflexplot --help - -Details:: - - # Clone the repository - git clone git@github.com:MeteoSwiss-APN/pyflexplot.git - cd pyflexplot - make # list available commands - - # Create a local virtual environment - # If omitted, called by `make install*` commands - make venv - - # Install tool and dependencies in virtual environment - make install # runtime dependencies only - # or - make install-dev # editable, run + test + dev deps - - # Check if conda environment `pyflexplot` now exists - conda info --env - - # Verify the installation (show help) - conda activate pyflexplot - pyflexplot --help - # or (if installed with pip): - ./venv/bin/pyflexplot --help - # or (if installed with pip): - source ./venv/bin/activate - pyflexplot --help - - # Check if correct version is installed - pyflexplot --version - - # Run tests - make test # all tests - # or - make test-fast # fast tests only - # or - make test-medium # fast and medium-fast tests only - -Usage -===== - -Activate the conda environment:: - - conda activate pyflexplot - -To get a list of all available commands, just type:: - - pyflexplot --help # or -h - -Plots -- including in- and output files -- are defined in setup files written in the `TOML`_ format. -(`TOML`_ files look similar to INI-files common in system configuration, -but with a more well-defined syntax.) -Most command line flags are primarily useful during development and testing. - -_`TOML`: https://github.com/toml-lang/toml - -PyFlexPlot ships with a few sets of predefined plots for both operations and testing. -To get a list of available presets, use:: - - pyflexplot --preset=? - -To see the contents of one of the presets, use:: - - pyflexplot --preset-cat - -The standard operational deterministic dispersion plots based on the COSMO-1E control run -can be produced as follows:: - - pyflexplot --preset=opr/cosmo-1e-ctrl/all_pdf - -This produces the plots defined in `pyflexplot/src/pyflexplot/data/presets/opr/cosmo-1e-ctrl.toml` -(check that file for input data paths etc.). -Specifically, it looks for a file matching `opr/cosmo-1e-ctrl` (suffix omitted) in any preset path, -which by default contains `pyflexplot/src/pyflexplot/data/presets`. - -You can open all produced plots in an image viewer like `eog`:: - - pyflexplot --open-all=eog --preset=test/cosmo-1e-ctrl/concentration - # or - pyflexplot --open-first=eog --preset=test/cosmo-2e/* - -It's always good to double-check what pyflexplot would do before-hand:: - - pyflexplot --dry-run -vv --preset=opr/* - -The presets interface is fairly powerful and useful during testing and development. -Some useful functionality includes:: - - # List available presets (add `-v` or `-vv` for additional details) - pyflexplot --preset=? - - # Use wild cards and multiple preset patterns - pyflexplot --preset=test/cosmo-1e-ctrl/* --preset=test/cosmo-2e/stats - - # Exclude some presets - pyflexplot --preset=test/* --preset-skip=test/cosmo2d/multipanel* - -While the plots are best specified in the setup files, -sometimes you may want to change some parameters:: - - pyflexplot --preset=test/cosmo-1e-ctrl/deposition --setup lang en --setup domain ch - -This will first read the setup files, and then substitute parameters you specified with `--setup` -(removing duplicate specifications in the process). - -Credits -------- - -This package was created with `Cookiecutter`_ and the `MeteoSwiss-APN/mch-python-blueprint`_ -project template. - -.. _`Cookiecutter`: https://github.com/audreyr/cookiecutter -.. _`MeteoSwiss-APN/mch-python-blueprint`: https://github.com/MeteoSwiss-APN/mch-python-blueprint diff --git a/USAGE.md b/USAGE.md new file mode 100644 index 00000000..4bce96d4 --- /dev/null +++ b/USAGE.md @@ -0,0 +1,13 @@ +# Usage + +Use PyFlexPlot in a project: + +```python +import pyflexplot +``` + +Before running, make sure to activate your project environment: + +```bash +conda activate pyflexplot +``` diff --git a/USAGE.txt b/USAGE.txt deleted file mode 100644 index e69de29b..00000000 diff --git a/dev-environment.yml b/dev-environment.yml deleted file mode 100644 index 8a8d149e..00000000 --- a/dev-environment.yml +++ /dev/null @@ -1,234 +0,0 @@ -name: pyflexplot-dev -channels: - - conda-forge - - defaults -dependencies: - - _libgcc_mutex=0.1=conda_forge - - _openmp_mutex=4.5=1_gnu - - alabaster=0.7.12=py_0 - 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- shapely=1.8.0=py39hc7dd4e9_2 - - six=1.16.0=pyh6c4a22f_0 - - snowballstemmer=2.1.0=pyhd8ed1ab_0 - - sphinx=4.3.1=pyh6c4a22f_0 - - sphinx-autobuild=2021.3.14=pyhd8ed1ab_0 - - sphinxcontrib-applehelp=1.0.2=py_0 - - sphinxcontrib-devhelp=1.0.2=py_0 - - sphinxcontrib-htmlhelp=2.0.0=pyhd8ed1ab_0 - - sphinxcontrib-jsmath=1.0.1=py_0 - - sphinxcontrib-qthelp=1.0.3=py_0 - - sphinxcontrib-serializinghtml=1.1.5=pyhd8ed1ab_1 - - sqlite=3.36.0=h9cd32fc_2 - - stack_data=0.2.0=pyhd8ed1ab_0 - - tbb=2021.4.0=h4bd325d_1 - - tk=8.6.11=h27826a3_1 - - toml=0.10.2=pyhd8ed1ab_0 - - tomli=1.2.2=pyhd8ed1ab_0 - - tornado=6.1=py39h3811e60_2 - - tox=3.24.5=py39hf3d152e_0 - - tox-conda=0.9.2=pyhd8ed1ab_0 - - traitlets=5.1.1=pyhd8ed1ab_0 - - typed-ast=1.5.0=py39h3811e60_0 - - types-toml=0.10.4=pyhd8ed1ab_0 - - typing-extensions=3.10.0.2=hd8ed1ab_0 - - typing_extensions=3.10.0.2=pyha770c72_0 - - tzdata=2021e=he74cb21_0 - - urllib3=1.26.7=pyhd8ed1ab_0 - - virtualenv=20.4.7=py39hf3d152e_2 - - wcwidth=0.2.5=pyh9f0ad1d_2 - - wheel=0.37.0=pyhd8ed1ab_1 - - wrapt=1.12.1=py39h3811e60_3 - - xorg-libxau=1.0.9=h7f98852_0 - - xorg-libxdmcp=1.1.3=h7f98852_0 - - xz=5.2.5=h516909a_1 - - yaml=0.2.5=h7f98852_2 - - zipp=3.6.0=pyhd8ed1ab_0 - - zlib=1.2.11=h36c2ea0_1013 - - zstd=1.5.0=ha95c52a_0 diff --git a/dev-requirements.in b/dev-requirements.in deleted file mode 100644 index 2c6657eb..00000000 --- a/dev-requirements.in +++ /dev/null @@ -1,20 +0,0 @@ -black -bump2version -codespell -flake8 -flake8-black -ipdb -ipython -isort >= 5 -mypy -pre-commit -pydocstyle -pylint >= 2.6.0 -pytest -rope -rstcheck -sphinx -sphinx-autobuild -tox -tox-conda -types-toml diff --git a/docs/Makefile b/docs/Makefile index 7c0a7e9e..796baf2d 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line. SPHINXOPTS = -SPHINXBUILD = python -msphinx +SPHINXBUILD = sphinx-build SPHINXPROJ = pyflexplot SOURCEDIR = . BUILDDIR = _build diff --git a/docs/authors.rst b/docs/authors.rst index e122f914..cf16fc49 100644 --- a/docs/authors.rst +++ b/docs/authors.rst @@ -1 +1 @@ -.. include:: ../AUTHORS.rst +.. mdinclude:: ../AUTHORS.md diff --git a/docs/conf.py b/docs/conf.py index 6784d5ff..c064483c 100755 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,44 +1,37 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -""" -pyflexplot documentation build configuration file, created by -sphinx-quickstart on Fri Jun 9 13:47:02 2017. +"""pyflexplot documentation build configuration file. -This file is execfile()d with the current directory set to its -containing dir. +Based on auto-generated file created by sphinx-quickstart on Fri Jun 9 2017. -Note that not all possible configuration values are present in this -autogenerated file. +This file is executed with the current directory set to its containing dir. -All configuration values have a default; values that are commented out -serve to show the default. +Note that not all possible configuration values are present in this file. -If extensions (or modules to document with autodoc) are in another -directory, add these directories to sys.path here. If the directory is -relative to the documentation root, use os.path.abspath to make it -absolute, like shown here. -""" +All configuration values have a default; values that are commented out serve to +show the default. + +If extensions (or modules to document with autodoc) are in another directory, +add these directories to sys.path here. If the directory is relative to the +documentation root, use os.path.abspath to make it absolute, like shown here. +""" # Standard library import os import sys -from typing import Dict # First-party import pyflexplot sys.path.insert(0, os.path.abspath("..")) - # -- General configuration --------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. # -# needs_sphinx = '1.0' +# needs_sphinx = "1.0" # Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode"] +# extensions coming with Sphinx (named "sphinx.ext.*") or your custom ones. +extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode", "sphinx_mdinclude"] # Add any paths that contain templates here, relative to this directory. templates_path = ["_templates"] @@ -46,16 +39,16 @@ # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # -# source_suffix = ['.rst', '.md'] +# source_suffix = [".rst", ".md"] source_suffix = ".rst" # The master toctree document. master_doc = "index" # General information about the project. -project = u"PyFlexPlot" -copyright = u"2019, Stefan Ruedisuehli" -author = u"Stefan Ruedisuehli" +project = "PyFlexPlot" +copyright = "2023, Stefan Ruedisuehli" # pylint: disable=W0622 # redefined-builtin +author = "Stefan Ruedisuehli" # The version info for the project you're documenting, acts as replacement # for |version| and |release|, also used in various other places throughout @@ -71,7 +64,7 @@ # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. -language = None +language = "en" # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. @@ -101,7 +94,7 @@ # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ["_static"] +# html_static_path = ["_static"] # -- Options for HTMLHelp output --------------------------------------- @@ -112,40 +105,62 @@ # -- Options for LaTeX output ------------------------------------------ -latex_elements: Dict[str, str] = { - # The paper size ('letterpaper' or 'a4paper'). +latex_elements: dict[str, str] = { + # The paper size ("letterpaper" or "a4paper"). + # "papersize": "letterpaper", # - # 'papersize': 'letterpaper', - # The font size ('10pt', '11pt' or '12pt'). + # The font size ("10pt", "11pt" or "12pt"). + # "pointsize": "10pt", # - # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. + # "preamble": "", # - # 'preamble': '', # Latex figure (float) alignment - # - # 'figure_align': 'htbp', + # "figure_align": "htbp", } # Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, documentclass -# [howto, manual, or own class]). -latex_documents = [ - ( - master_doc, - "pyflexplot.tex", - u"PyFlexPlot Documentation", - u"Stefan Ruedisuehli", - "manual", - ), -] +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +# latex_documents = [ +# (master_doc, 'copier-pypackage.tex', 'copier-pypackage Documentation', +# 'Audrey Roy Greenfeld', 'manual'), +# ] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +# latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +# latex_use_parts = False + +# If true, show page references after internal links. +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# latex_appendices = [] + +# If false, no module index is generated. +# latex_domain_indices = True # -- Options for manual page output ------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). -man_pages = [(master_doc, "pyflexplot", u"PyFlexPlot Documentation", [author], 1)] +man_pages = [ + ( + master_doc, + "pyflexplot", + "PyFlexPlot Documentation", + [author], + 1, + ) +] # -- Options for Texinfo output ---------------------------------------- @@ -157,10 +172,22 @@ ( master_doc, "pyflexplot", - u"PyFlexPlot Documentation", + "PyFlexPlot Documentation", author, "pyflexplot", "One line description of project.", "Miscellaneous", ), ] + +# Documents to append as an appendix to all manuals. +# texinfo_appendices = [] + +# If false, no module index is generated. +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +# texinfo_no_detailmenu = False diff --git a/docs/contributing.rst b/docs/contributing.rst index e582053e..4fc50161 100644 --- a/docs/contributing.rst +++ b/docs/contributing.rst @@ -1 +1 @@ -.. include:: ../CONTRIBUTING.rst +.. mdinclude:: ../CONTRIBUTING.md diff --git a/docs/documentation.inactive b/docs/documentation.inactive new file mode 100644 index 00000000..6355c16d --- /dev/null +++ b/docs/documentation.inactive @@ -0,0 +1,53 @@ +name: docs + +on: + push: + branches: + - main + pull_request: + branches: + - '*' + +jobs: + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v1 + - uses: C2SM/sphinx-action@sphinx-latest + with: + pre-build-command: '' + docs-folder: "docs/" + # Great extra actions to compose with: + # Create an artifact of the html output. + - uses: actions/upload-artifact@v1 + with: + name: DocumentationHTML + path: docs/_build/ + # Publish built docs to gh-pages branch. + # =============================== + - name: Commit documentation changes + run: | + pwd + ls docs + echo ' ' + ls docs/_build + git clone https://github.com/ammaraskar/sphinx-action-test.git --branch gh-pages --single-branch gh-pages + cp -r docs/_build/html/* gh-pages/ + cd gh-pages + touch .nojekyll + git config --local user.email "action@github.com" + git config --local user.name "GitHub Action" + git add . + git commit -m "Update documentation" -a || true + # The above command will fail if no changes were present, so we ignore + # that. + - name: Push changes + # this commit SHA corresponds to tag `v0.6.0` + uses: ad-m/github-push-action@40bf560936a8022e68a3c00e7d2abefaf01305a6 + with: + force: true + branch: gh-pages + directory: gh-pages + # =============================== diff --git a/docs/history.rst b/docs/history.rst index 25064996..d26e5be8 100644 --- a/docs/history.rst +++ b/docs/history.rst @@ -1 +1 @@ -.. include:: ../HISTORY.rst +.. mdinclude:: ../HISTORY.md diff --git a/docs/index.rst b/docs/index.rst index d5c8a183..11fe8b16 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,5 +1,5 @@ Welcome to PyFlexPlot's documentation! -====================================== +=========================================================== .. toctree:: :maxdepth: 2 @@ -16,5 +16,4 @@ Welcome to PyFlexPlot's documentation! Indices and tables ================== * :ref:`genindex` -* :ref:`modindex` * :ref:`search` diff --git a/docs/installation.rst b/docs/installation.rst index db295ae9..3a50030e 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -4,67 +4,75 @@ Installation ============ +There are two installation types, a production installation, which is static, and a development installation, which is editable. -Stable release --------------- -To install PyFlexPlot, run this command in your terminal: +Preparation +----------- -.. code-block:: console +To install PyFlexPlot you need a miniconda installation. You can either set up your miniconda installation manually or use the script `tools/setup_miniconda.sh`, which will download and install the latest version of miniconda. - $ pip install pyflexplot -This is the preferred method to install PyFlexPlot, as it will always install the most recent stable release. +Installation of dependencies +---------------------------- -If you don't have `pip`_ installed, this `Python installation guide`_ can guide -you through the process. +Dependencies are handled by the conda package manager. The goal of this step is to set up a conda environment according to the requirements of PyFlexPlot. Note that by design, there are some dependencies already when you start developing the package, as the environment includes linters and other development tools. -.. _pip: https://pip.pypa.io -.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/ +The dependencies are handled in requirement files. Free installations are based on the `requirements/requirements.yml` file, where the top-level dependencies of the package are listed. Pinned installations are based on exported environments and stored in the file `requirements/environment.yml`. +Environments (based on either unpinned or pinned requirements) are handled by the script `tools/setup_env.sh`. The optional flag `-u` stands for unpinned installation: -From sources ------------- +.. code-block:: console -The sources for PyFlexPlot can be downloaded from the `Github repo`_. + $ bash tools/setup_env.sh -u -Option 1 -^^^^^^^^ -You can directly install it: +This will create an up-to-date environment that can be exported to `requirements/environment.yml` with the optional flag `-e` (see below). -.. code-block:: console +You can control the environment name with the flag `-n` and the Python version with `-v`. Run :code:`./tools/setup_env -h` for available options and defaults (incl. mamba support). - $ pip install git+https://github.com/MeteoSwiss-APN/pyflexplot#egg=pyflexplot -or in developer mode: +Installation of PyFlexPlot +----------------------------------------------- + +After creating and activating your environment by running .. code-block:: console - $ pip install -e git+https://github.com/MeteoSwiss-APN/pyflexplot#egg=pyflexplot + $ ./tools/setup_env.sh + $ conda activate pyflexplot + +in the root folder of pyflexplot, type -For furhter details see the `pip documentation`_. +.. code-block:: console -Option 2 -^^^^^^^^ -You can either clone the public repository: + $ python -m pip install --no-deps . + +for a (static) production installation and .. code-block:: console - $ git clone git://github.com/ruestefa/pyflexplot + $ pip install --no-deps --editable . + +for a (editable) development installation. + -Or download the `tarball`_: +Maintenance of the environment (for developers) +----------------------------------------------- + +If you need to add new first-level dependencies to your package, make sure to include them in `requirements/requirements.yml`. (Note that pip requirements can be added to these files in the `- pip:` section of the document.) After a (unpinned!) installation, this will change the full dependency tree and you need to export the environment. You can either do this by hand by activating the environment and then running .. code-block:: console - $ curl -OL https://github.com/ruestefa/pyflexplot/tarball/master + $ conda env export pyflexplot requirements/environment.yml -Once you have a copy of the source, you can install it with: +or you can reinstall with the setup script from `requirements/requirements.yml` and directly export the environment with the `-e` flag. .. code-block:: console - $ python setup.py install + $ ./tools/setup_env -ue + +Interaction with Jenkins and Github actions +------------------------------------------- -.. _`pip documentation`: https://pip.pypa.io/en/stable/reference/pip_install/#vcs-support -.. _Github repo: https://github.com/MeteoSwiss-APN/pyflexplot -.. _tarball: https://github.com/MeteoSwiss-APN/pyflexplot/tarball/master +Your package is always built on a Github actions server upon committing to the main branch. If your code goes into production, pinned production installations must be tested with Jenkins on CSCS machines. Templates may be found in the jenkins/ folder. Contact DevOps to help you set up your pipeline. diff --git a/docs/modules.rst b/docs/modules.rst new file mode 100644 index 00000000..d9e2a176 --- /dev/null +++ b/docs/modules.rst @@ -0,0 +1,6 @@ +======= +Modules +======= + +.. automodule:: pyflexplot.mutable_number + :members: diff --git a/docs/readme.rst b/docs/readme.rst index 72a33558..97d49585 100644 --- a/docs/readme.rst +++ b/docs/readme.rst @@ -1 +1 @@ -.. include:: ../README.rst +.. mdinclude:: ../README.md diff --git a/docs/usage.rst b/docs/usage.rst index b7f80c5e..9f4b0dcf 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -1 +1 @@ -.. include:: ../USAGE.rst +.. mdinclude:: ../USAGE.md diff --git a/find_py_toml.sh b/find_py_toml.sh deleted file mode 120000 index ace0daa9..00000000 --- a/find_py_toml.sh +++ /dev/null @@ -1 +0,0 @@ -scripts/find_py_toml.sh \ No newline at end of file diff --git a/jenkins/JenkinsJobPR b/jenkins/JenkinsJobPR new file mode 100644 index 00000000..8a10ef6e --- /dev/null +++ b/jenkins/JenkinsJobPR @@ -0,0 +1,33 @@ +pipelineJob('pyflexplot_PR') { + parameters { + stringParam('sha1', 'main') + } + definition { + cpsScm { + scm { + git { + remote { + github('MeteoSwiss-APN/pyflexplot') + refspec('+refs/pull/*:refs/remotes/origin/pr/*') + credentials('466e4dd5-80af-4935-828f-a9fff24b46de') + } + branch('${sha1}') + } + } + triggers { + githubPullRequest { + orgWhitelist('MeteoSwiss-APN') + triggerPhrase('launch jenkins.*') + onlyTriggerPhrase() + useGitHubHooks() + extensions { + commitStatus { + context('MeteoSwiss Jenkins - pull request') + } + } + } + } + scriptPath('jenkins/Jenkinsfile') + } + } +} diff --git a/jenkins/Jenkinsfile b/jenkins/Jenkinsfile new file mode 100644 index 00000000..6af66015 --- /dev/null +++ b/jenkins/Jenkinsfile @@ -0,0 +1,130 @@ +pipeline { + options { + // the variable $WORKSPACE is assigned dynamically at the beginning of every stage + // and might change depending on the number of concurrent builds active. + // We can only allow 1 concurrent build to have a consistent access to $WORKSPACE + // Otherwise we should use stash/unstash for the miniconda installation + disableConcurrentBuilds() + } + environment { + PATH = "$WORKSPACE/miniconda/bin:$PATH" + } + agent { + label 'tsa' + } + + post { + always{ + echo 'Cleaning up workspace' + deleteDir() + } + } + stages { + stage('setup miniconda') { + steps { + sh '''#!/usr/bin/env bash + set -e + bash tools/setup_miniconda.sh -p ${WORKSPACE} + ''' + } + } + stage('build package') { + steps { + sh '''#!/usr/bin/env bash + set -e + cd ${WORKSPACE}/pyflexplot + source ${WORKSPACE}/miniconda/etc/profile.d/conda.sh + conda init bash --no-user --install --system + conda activate + bash tools/setup_env.sh -n pyflexplot -u + conda activate pyflexplot + pip install --no-deps . + ''' + } + } + stage('test') { + steps { + sh '''#!/usr/bin/env bash + source $WORKSPACE/miniconda/etc/profile.d/conda.sh + conda init bash --no-user --install --system + conda activate pyflexplot + cd ${WORKSPACE}/pyflexplot + pytest tests + ''' + } + } + stage('dev-environment') { + steps { + sh '''#!/usr/bin/env bash + set -e + source $WORKSPACE/miniconda/etc/profile.d/conda.sh + conda init bash --no-user --install --system + conda activate + cd ${WORKSPACE}/pyflexplot + bash tools/setup_env.sh -n dev-pyflexplot -u + conda activate dev-pyflexplot + pip install --no-deps --editable . + ''' + } + } + stage('dev-test') { + steps { + sh '''#!/usr/bin/env bash + source $WORKSPACE/miniconda/etc/profile.d/conda.sh + conda init bash --no-user --install --system + conda activate dev-pyflexplot + cd ${WORKSPACE}/pyflexplot + pytest tests + ''' + } + } + stage('pinned-environment') { + steps { + sh '''#!/usr/bin/env bash + set -e + source $WORKSPACE/miniconda/etc/profile.d/conda.sh + conda init bash --no-user --install --system + conda activate + cd ${WORKSPACE}/pyflexplot + bash tools/setup_env.sh -n pinned-pyflexplot + conda activate pinned-pyflexplot + pip install --no-deps . + ''' + } + } + stage('pinned-test') { + steps { + sh '''#!/usr/bin/env bash + source $WORKSPACE/miniconda/etc/profile.d/conda.sh + conda activate pinned-pyflexplot + cd ${WORKSPACE}/pyflexplot + pytest tests + ''' + } + } + stage('pinned-dev-environment') { + steps { + sh '''#!/usr/bin/env bash + set -e + source $WORKSPACE/miniconda/etc/profile.d/conda.sh + conda init bash --no-user --install --system + conda activate + cd ${WORKSPACE}/pyflexplot + bash tools/setup_env.sh -n pinned-dev-pyflexplot + conda activate pinned-dev-pyflexplot + pip install --no-deps --editable . + ''' + } + } + stage('pinned-dev-test') { + steps { + sh '''#!/usr/bin/env bash + source $WORKSPACE/miniconda/etc/profile.d/conda.sh + conda activate pinned-dev-pyflexplot + cd ${WORKSPACE}/pyflexplot + pytest tests + ''' + } + } + } +} diff --git a/mypy.ini b/old_config/mypy.ini similarity index 100% rename from mypy.ini rename to old_config/mypy.ini diff --git a/tox.ini b/old_config/tox.ini similarity index 100% rename from tox.ini rename to old_config/tox.ini diff --git a/pyproject.toml b/pyproject.toml index 14e385ee..3efe6ccb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,4 +1,172 @@ - [build-system] -requires = ["setuptools >= 35.0.2", "wheel"] +requires = [ + "setuptools>=65", + "wheel>=0.38", +] build-backend = "setuptools.build_meta" + +[project] +name = "pyflexplot" +version = "1.0.10" +description = "Stefan Ruedisuehli's PyFlexPlot" +readme = "README.md" +keywords = [ + "Dispersion", + "Flexpart", + "COSMO", + "mapping", + "visualization", +] +classifiers = [ + "Development Status :: 2 - Pre-Alpha", + "Intended Audience :: Developers", + "Natural Language :: English", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", +] +requires-python = ">=3.10" +authors = [ + {name="Stefan Ruedisuehli", email="stefan.ruedisuehli@env.ethz.ch"}, +] + +[project.urls] +source = "https://github.com/MeteoSwiss-APN/pyflexplot" +documentation = "https://github.io/MeteoSwiss-APN/pyflexplot" + +[project.scripts] +# Format: = ".:" +# pyflexplot = "pyflexplot.cli:main" +pyflexplot = "pyflexplot.cli.cli:cli" +pytrajplot = "pytrajplot.cli:cli" +crop-netcdf = "srtools.crop_netcdf:main" + +[tool.pytest.ini_options] +testpaths = ["tests"] +addopts = [ + "-s", + "-ra", + "--pdbcls=IPython.terminal.debugger:TerminalPdb", + "--tb=short", + # "--cov=pyflexplot", + # "--mypy", +] + +[tool.black] + +[tool.isort] +default_section = "THIRDPARTY" +profile = "black" +force_single_line = true +order_by_type = false +# Set `multi_line_output = 7` to mark too long lines with `# NOQA` (uppercase!) +# instead of spreading them over multiple lines. This leaves lines with long +# trailing comments intact, which may occur if multiple directives are necessary +# (e.g., `# type: ignore [import] # pylint: disable=no-name-in-module`). +# (Note that thanks to `force_single_line = true`, this should be the main +# reason for too long lines because multi-import lines are already broken up.) +multi_line_output = 7 # 7=noqa +# Headings +import_heading_stdlib = "Standard library" +import_heading_thirdparty = "Third-party" +import_heading_firstparty = "First-party" +import_heading_localfolder = "Local" +# Known modules to avoid misclassification +known_standard_library = [ + # Add standard library modules that may be misclassified by isort +] +known_third_party = [ + # Add third-party modules that may be misclassified by isort +] +known_first_party = [ + # Add first-party modules that may be misclassified by isort + "pyflexplot", +] + +[tool.mypy] + +[[tool.mypy.overrides]] +# Note: Only globally ignore missing imports as a matter of last resort! +# See https://blog.wolt.com/engineering/2021/09/30/professional-grade-mypy-configuration/ +module = [ + # Add external modules w/o type hints here +] +ignore_missing_imports = true + +[tool.flake8] +max-line-length = 88 +# max-complexity = 10 +ignore = [ + "E203", # Allow whitespace before ':' (https://github.com/PyCQA/pycodestyle/issues/373) + "F811", # Allow redefinition of unused name (necessary for typing.overload) + "I002", # Don't check for isort configuration + "W503", # Allow line break before binary operator (PEP 8-compatible) +] +per-file-ignores = [ + "__init__.py: F401", # Allow unused imports +] + +[tool.pylint] +recursive = true +ignore-imports = true +max-line-length = 88 +# Tweak valid name formats +# Defaults (http://pylint-messages.wikidot.com/messages:c0103): +# argument-rgx = "^[a-z_][a-z0-9_]{2,30}$" +# attr-rgx = "^[a-z_][a-z0-9_]{2,30}$" +# function-rgx = "^[a-z_][a-z0-9_]{2,30}$" +# method-rgx = "^[a-z_][a-z0-9_]{2,30}$" +# variable-rgx = "^[a-z_][a-z0-9_]{2,30}$" +# class-rgx = "^[A-Z_][a-zA-Z0-9]+$" +# const-rgx = "^(([A-Z_][A-Z0-9_]*)|(__.*__))$" +# module-rgx = "^(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$" +argument-rgx = "^[a-z_][a-z0-9_]{,40}$" +attr-rgx = "^[a-z_][a-z0-9_]{,40}$" +function-rgx = "^[a-z_][a-z0-9_]{,40}$" +method-rgx = "^[a-z_][a-z0-9_]{,40}$" +variable-rgx = "^[a-z_][a-z0-9_]{,40}$" +class-rgx = "^[A-Z_][a-zA-Z0-9]+$" +const-rgx = "^(([a-z_][a-z0-9_]*)|([A-Z_][A-Z0-9_]*)|(__[a-zA-Z0-9]+__))$" +module-rgx = "^(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$" +inlinevar-rgx = "^[A-Za-z_][A-Za-z0-9_]*$" +# Disable selected warnings, errors etc. that conflict with style guide etc. +# Note: To locally ignore certain errors, use "pylint: disable=XXXX" comments instead! +disable = [ + "C0115", # Missing class docstring + "C0116", # Missing function or method docstring + "R0903", # Too few public methods (*/2) (too-few-public-methods) + # "R0801", # Similar lines in 2 files (duplicate-code) + # -> see https://github.com/PyCQA/pylint/issues/214 + "R1705", # Unnecessary "elif" after "return" (no-else-return) + "R1720", # Unnecessary "elif" after "raise" (no-else-raise) + "R1724", # Unnecessary "elif" after "continue" (no-else-continue) + "W1116", # Second argument of isinstance is not a type (isinstance-second-argument-not-valid-type) +] +# Ignore (sub-)modules that trigger errors like E1101 (no-member) or E0611 (no-name-in-module) +ignored-modules = [] + +[tool.pydocstyle] +# All codes: http://www.pydocstyle.org/en/stable/error_codes.html +ignore = [ + # "D100", # Missing docstring in public module + "D101", # Missing docstring in public class + "D102", # Missing docstring in public method + "D103", # Missing docstring in public function + # "D104", # Missing docstring in public package + "D105", # Missing docstring in magic method + # "D105", # Missing docstring in public nested class + # "D107", # Missing docstring in __init__ + "D203", # Blank line required before class docstring + "D213", # Multi-line docstring summary should start at the second line + # "D405", # Section name should be properly capitalized + "D406", # Section name should end with a newline + "D407", # Missing dashed underline after section +] + +[tool.rstcheck] +ignore_directives = [ + "automodule", + "mdinclude", +] + +[tool.codespell] +ignore-words-list = "inout" diff --git a/requirements.in b/requirements.in deleted file mode 100644 index fc0f72a3..00000000 --- a/requirements.in +++ /dev/null @@ -1,11 +0,0 @@ -cartopy >= 0.18 -click >= 6.0 -geopy -matplotlib -netcdf4 -numpy >= 1.20 -pillow >= 8.4.0 -pypdf2 == 1.* -scipy -toml -typing-extensions diff --git a/environment.yml b/requirements/environment.yml similarity index 93% rename from environment.yml rename to requirements/environment.yml index 4cf4aced..6e596d38 100644 --- a/environment.yml +++ b/requirements/environment.yml @@ -1,7 +1,6 @@ name: pyflexplot channels: - conda-forge - - defaults dependencies: - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=1_gnu @@ -9,12 +8,13 @@ dependencies: - alsa-lib=1.2.3=h516909a_0 - appdirs=1.4.4=pyh9f0ad1d_0 - astroid=2.8.5=py39hf3d152e_0 + - asttokens=2.0.5=pyhd8ed1ab_0 - attrs=21.2.0=pyhd8ed1ab_0 - babel=2.9.1=pyh44b312d_0 - backcall=0.2.0=pyh9f0ad1d_0 - backports=1.0=py_2 - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0 - - black=21.12b0=pyhd8ed1ab_0 + - black=22.1.0=pyhd8ed1ab_0 - brotli=1.0.9=h7f98852_6 - brotli-bin=1.0.9=h7f98852_6 - brotlipy=0.7.0=py39h3811e60_1003 @@ -41,10 +41,11 @@ dependencies: - distlib=0.3.3=pyhd8ed1ab_0 - docutils=0.16=py39hf3d152e_3 - editdistance-s=1.0.0=py39h1a9c180_2 + - executing=0.8.3=pyhd8ed1ab_0 - expat=2.4.1=h9c3ff4c_0 - filelock=3.3.2=pyhd8ed1ab_0 - flake8=4.0.1=pyhd8ed1ab_2 - - flake8-black=0.2.3=pyhd8ed1ab_0 + - flake8-black=0.3.0=pyhd8ed1ab_0 - fontconfig=2.13.1=hba837de_1005 - freetype=2.10.4=h0708190_1 - geographiclib=1.52=pyhd8ed1ab_0 @@ -66,7 +67,7 @@ dependencies: - iniconfig=1.1.1=pyh9f0ad1d_0 - intel-openmp=2021.4.0=h06a4308_3561 - ipdb=0.13.9=pyhd8ed1ab_0 - - ipython=7.30.1=py39hf3d152e_0 + - ipython=8.1.1=py39hf3d152e_0 - isort=5.10.1=pyhd8ed1ab_0 - jbig=2.1=h7f98852_2003 - jedi=0.18.0=py39hf3d152e_3 @@ -130,7 +131,7 @@ dependencies: - mccabe=0.6.1=py_1 - more-itertools=8.11.0=pyhd8ed1ab_0 - munkres=1.1.4=pyh9f0ad1d_0 - - mypy=0.910=py39h3811e60_4 + - mypy=0.931=py39h3811e60_2 - mypy_extensions=0.4.3=py39hf3d152e_4 - mysql-common=8.0.27=ha770c72_3 - mysql-libs=8.0.27=hfa10184_3 @@ -153,12 +154,13 @@ dependencies: - pip=21.3.1=pyhd8ed1ab_0 - platformdirs=2.3.0=pyhd8ed1ab_0 - pluggy=0.13.1=py39hf3d152e_4 - - pre-commit=2.16.0=py39hf3d152e_0 + - pre-commit=2.17.0=py39hf3d152e_0 - proj=8.2.0=h277dcde_0 - prompt-toolkit=3.0.22=pyha770c72_0 - psutil=5.8.0=py39h3811e60_2 - pthread-stubs=0.4=h36c2ea0_1001 - ptyprocess=0.7.0=pyhd3deb0d_0 + - pure_eval=0.2.2=pyhd8ed1ab_0 - py=1.11.0=pyh6c4a22f_0 - pycodestyle=2.8.0=pyhd8ed1ab_0 - pycparser=2.21=pyhd8ed1ab_0 @@ -177,7 +179,7 @@ dependencies: - pyqtwebengine=5.12.1=py39h0fcd23e_8 - pyshp=2.1.3=pyh44b312d_0 - pysocks=1.7.1=py39hf3d152e_4 - - pytest=6.2.5=py39hf3d152e_2 + - pytest=7.0.1=py39hf3d152e_0 - python=3.9.7=hb7a2778_3_cpython - python-dateutil=2.8.2=pyhd8ed1ab_0 - python_abi=3.9=2_cp39 @@ -187,7 +189,7 @@ dependencies: - readline=8.1=h46c0cb4_0 - regex=2021.11.10=py39h3811e60_0 - requests=2.26.0=pyhd8ed1ab_1 - - rope=0.22.0=pyhd8ed1ab_0 + - rope=0.23.0=pyhd8ed1ab_0 - rstcheck=3.3.1=pyh9f0ad1d_0 - scipy=1.8.0=py39hee8e79c_1 - setuptools=59.1.1=py39hf3d152e_0 @@ -203,15 +205,17 @@ dependencies: - sphinxcontrib-qthelp=1.0.3=py_0 - sphinxcontrib-serializinghtml=1.1.5=pyhd8ed1ab_1 - sqlite=3.36.0=h9cd32fc_2 + - stack_data=0.2.0=pyhd8ed1ab_0 - tbb=2021.4.0=h4bd325d_1 - tk=8.6.11=h27826a3_1 - toml=0.10.2=pyhd8ed1ab_0 - tomli=1.2.2=pyhd8ed1ab_0 - tornado=6.1=py39h3811e60_2 - - tox=3.24.4=py39hf3d152e_2 + - tox=3.24.5=py39hf3d152e_0 + - tox-conda=0.9.2=pyhd8ed1ab_0 - traitlets=5.1.1=pyhd8ed1ab_0 - typed-ast=1.5.0=py39h3811e60_0 - - types-toml=0.10.1=pyhd8ed1ab_0 + - types-toml=0.10.4=pyhd8ed1ab_0 - typing-extensions=3.10.0.2=hd8ed1ab_0 - typing_extensions=3.10.0.2=pyha770c72_0 - tzdata=2021e=he74cb21_0 diff --git a/requirements/requirements.yml b/requirements/requirements.yml new file mode 100644 index 00000000..d35fdf6e --- /dev/null +++ b/requirements/requirements.yml @@ -0,0 +1,49 @@ +name: pyflexplot +channels: + - conda-forge +dependencies: + - python>=3.10 + - pip>=22.3 + # runtime + - cartopy >= 0.18 + - click >= 6.0 + - geopy + - matplotlib + - netcdf4 + - numpy >= 1.20 + - pillow >= 8.4.0 + - pypdf2 == 1.* + - scipy + - toml + - typing-extensions + # development + - anaconda-client>=1.11 + - black>=22.10 + - boa>=0.14 + - codespell>=2.2 + - conda-build>=3.23 + - flake8>=6.0 + - flake8-black>=0.3 + - ipdb>=0.13 + - ipython>=8.7 + - isort>=5.12 + - mccabe>=0.7 + - mypy>=0.991 + - mamba>=1.1 + - pre-commit>=2.20 + - pydocstyle>=6.1 + - pylint>=2.15 + - pytest>=7.2 + - rich>=12.6 + - rope>=1.6 + - rstcheck>=6.1 + - sphinx>=4.3 + - sphinx-autobuild>=2021.3 + - toml>=0.10 + - types-setuptools>=65.6 + - types-toml>=0.10 + - pip: + # development + - copier>=7.0 + - flake8-pyproject>=1.2 + - sphinx-mdinclude>=0.5 diff --git a/setup.py b/setup.py deleted file mode 100644 index e5f76d24..00000000 --- a/setup.py +++ /dev/null @@ -1,72 +0,0 @@ -"""Set up the project.""" -# Standard library -from typing import List -from typing import Sequence - -# Third-party -from pkg_resources import parse_requirements -from setuptools import find_packages -from setuptools import setup - - -def read_present_files(paths: Sequence[str]) -> str: - """Read the content of those files that are present.""" - contents: List[str] = [] - for path in paths: - try: - with open(path, "r") as f: - contents += ["\n".join(map(str.strip, f.readlines()))] - except FileNotFoundError: - continue - return "\n\n".join(contents) - - -description_files = [ - "README", - "README.md", - "README.rst", - "HISTORY", - "HISTORY.md", - "HISTORY.rst", -] - -metadata = { - "name": "pyflexplot", - "version": "1.0.10", - "description": "PyFlexPlot visualizes FLEXPART particle dispersion simulations.", - "long_description": read_present_files(description_files), - "author": "Stefan Ruedisuehli", - "author_email": "stefan.ruedisuehli@env.ethz.ch", - "url": "https://github.com/ruestefa/pyflexplot", - "keywords": "NWP dispersion ensemble modeling FLEXPART visualization", - "classifiers": [ - "Development Status :: 2 - Pre-Alpha", - "Intended Audience :: Developers", - "Natural Language :: English", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.9", - ], -} - -python = ">= 3.9" - -# Runtime dependencies: top-level and unpinned (only critical version restrictions) -with open("requirements.in") as f: - requirements = list(map(str, parse_requirements(f.readlines()))) - -scripts = [ - "pyflexplot=pyflexplot.cli.cli:cli", - "pytrajplot=pytrajplot.cli:cli", - "crop-netcdf=srtools.crop_netcdf:main", -] - -setup( - python_requires=python, - install_requires=requirements, - entry_points={"console_scripts": scripts}, - packages=find_packages("src"), - package_dir={"": "src"}, - include_package_data=True, - zip_save=False, - **metadata, -) diff --git a/src/pyflexplot/__init__.py b/src/pyflexplot/__init__.py index 15608a3d..86e49de9 100644 --- a/src/pyflexplot/__init__.py +++ b/src/pyflexplot/__init__.py @@ -1,10 +1,7 @@ -"""Top-level package ``pyflexplot``.""" - -__author__ = """Stefan Ruedisuehli""" -__email__ = "stefan.ruedisuehli@env.ethz.ch" -__version__ = "1.0.10" +"""Top-level package for PyFlexPlot.""" # Standard library +import importlib.metadata import logging as _logging import sys as _sys import warnings as _warnings @@ -33,6 +30,11 @@ print(msg, file=_sys.stderr) _sys.exit(1) +__author__ = "Stefan Ruedisuehli" +__email__ = "stefan.ruedisuehli@env.ethz.ch" +__version__ = importlib.metadata.version(__package__) + +del importlib __all__: _List[str] = [] diff --git a/scripts/find_py_toml.sh b/tools/find_py_toml.sh similarity index 100% rename from scripts/find_py_toml.sh rename to tools/find_py_toml.sh diff --git a/tools/run-mypy.sh b/tools/run-mypy.sh new file mode 100755 index 00000000..756c35ca --- /dev/null +++ b/tools/run-mypy.sh @@ -0,0 +1,27 @@ +#!/bin/bash +# +# Run mypy separately over components of the project (source, tests) +# +# Call mypy via this script in pre-commit +# - to always check all files (not just those that changed), +# - to check different components of the project separately (in case of multiple packages), and +# - to give mypy access to all dependencies (by running it locally rather than in isolation). +# +# src: https://jaredkhan.com/blog/mypy-pre-commit + +set -o errexit + +VERBOSE=${VERBOSE:-false} + +SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd ) +cd "${SCRIPT_DIR}/.." + +# Paths relative to project root +paths=( + src/pyflexplot + tests/test_pyflexplot +) +for path in "${paths[@]}"; do + ${VERBOSE} && echo "mypy \"${path}\"" + mypy "${path}" || exit +done diff --git a/tools/setup_env.sh b/tools/setup_env.sh new file mode 100755 index 00000000..f40cbe85 --- /dev/null +++ b/tools/setup_env.sh @@ -0,0 +1,68 @@ +#!/bin/bash +# +# Create conda environment with pinned or unpinned requirements +# +# - 2022-08 (D. Regenass) Write original script +# - 2022-09 (S. Ruedisuehli) Refactor; add some options +# + +# Default env names +DEFAULT_ENV_NAME="pyflexplot" + +# Default options +ENV_NAME="${DEFAULT_ENV_NAME}" +PYVERSION=3.10 +PINNED=true +EXPORT=false +CONDA=conda +HELP=false + +help_msg="Usage: $(basename "${0}") [-n NAME] [-p VER] [-u] [-e] [-m] [-h] + +Options: + -n NAME Env name [default: ${DEFAULT_ENV_NAME} + -p VER Python version [default: ${PYVERSION}] + -u Use unpinned requirements (minimal version restrictions) + -e Export environment files (requires -u) + -m Use mamba instead of conda + -h Print this help message and exit +" + +# Eval command line options +while getopts n:p:defhimu flag; do + case ${flag} in + n) ENV_NAME=${OPTARG};; + p) PYVERSION=${OPTARG};; + e) EXPORT=true;; + h) HELP=true;; + m) CONDA=mamba;; + u) PINNED=false;; + ?) echo -e "\n${help_msg}" >&2; exit 1;; + esac +done + +if ${HELP}; then + echo "${help_msg}" + exit 0 +fi + +echo "Setting up environment for installation" +eval "$(conda shell.bash hook)" || exit # NOT ${CONDA} (doesn't work with mamba) +conda activate || exit # NOT ${CONDA} (doesn't work with mamba) + +# Create new env; pass -f to overwriting any existing one +echo "Creating ${CONDA} environment" +${CONDA} create -n ${ENV_NAME} python=${PYVERSION} --yes || exit + +# Install requirements in new env +if ${PINNED}; then + echo "Pinned installation" + ${CONDA} env update --name ${ENV_NAME} --file requirements/environment.yml || exit +else + echo "Unpinned installation" + ${CONDA} env update --name ${ENV_NAME} --file requirements/requirements.yml || exit + if ${EXPORT}; then + echo "Export pinned prod environment" + ${CONDA} env export --name ${ENV_NAME} --no-builds | \grep -v '^prefix:' > requirements/environment.yml || exit + fi +fi diff --git a/tools/setup_miniconda.sh b/tools/setup_miniconda.sh new file mode 100755 index 00000000..a0fcb59f --- /dev/null +++ b/tools/setup_miniconda.sh @@ -0,0 +1,44 @@ +#!/bin/bash +# +# Install miniconda if necessary +# +# - 2022-08 (D. Regenass) Write original script +# - 2022-09 (S. Ruedisuehli) Refactor +# + +# Default options +INSTALL_PREFIX=${PWD} +USER_INSTALL=false + +# here the conda version is fixed, the sha256 hash has to be set accordingly +MINICONDA_URL=https://repo.anaconda.com/miniconda/Miniconda3-py310_22.11.1-1-Linux-x86_64.sh +SHA256=00938c3534750a0e4069499baf8f4e6dc1c2e471c86a59caa0dd03f4a9269db6 + +# Eval command line options +while getopts p:u flag; do + case ${flag} in + p) INSTALL_PREFIX=${OPTARG};; + u) USER_INSTALL=true;; + esac +done + +# Install conda executable if not yet available +if [[ -f $CONDA_EXE ]]; then + echo "Found a conda executable at: ${CONDA_EXE}" +else + echo "No conda executable available, fetching Miniconda install script" + wget -O ${INSTALL_PREFIX}/miniconda.sh ${MINICONDA_URL} + echo "${SHA256} ${INSTALL_PREFIX}/miniconda.sh" | sha256sum --check || exit 1 + bash ${INSTALL_PREFIX}/miniconda.sh -b -p ${INSTALL_PREFIX}/miniconda + source ${INSTALL_PREFIX}/miniconda/etc/profile.d/conda.sh + conda config --set always_yes yes --set changeps1 no + conda config --add channels conda-forge + if ${USER_INSTALL}; then + conda init bash + else + # this is a workaround as plain --no-user is not working as it should + conda init bash --no-user --install --system + fi + conda activate + rm ${INSTALL_PREFIX}/miniconda.sh +fi From e25cf11afe9a67925da17a08d94352bd196e541a Mon Sep 17 00:00:00 2001 From: Pirmin Kaufmann Date: Thu, 23 Feb 2023 16:44:50 +0100 Subject: [PATCH 02/24] Adapted linter config. --- old_config/mypy.ini | 32 --------- old_config/tox.ini | 155 -------------------------------------------- pyproject.toml | 29 ++++++++- 3 files changed, 27 insertions(+), 189 deletions(-) delete mode 100644 old_config/mypy.ini delete mode 100644 old_config/tox.ini diff --git a/old_config/mypy.ini b/old_config/mypy.ini deleted file mode 100644 index 832a4c29..00000000 --- a/old_config/mypy.ini +++ /dev/null @@ -1,32 +0,0 @@ - -[mypy] - -[mypy-cartopy.*] -ignore_missing_imports = True - -[mypy-click.*] -ignore_missing_imports = True - -[mypy-geopy.*] -ignore_missing_imports = True - -[mypy-IPython.*] -ignore_missing_imports = True - -[mypy-matplotlib.*] -ignore_missing_imports = True - -[mypy-netCDF4.*] -ignore_missing_imports = True - -[mypy-PyPDF2.*] -ignore_missing_imports = True - -[mypy-scipy.*] -ignore_missing_imports = True - -[mypy-shapely.*] -ignore_missing_imports = True - -[mypy-tomlkit.*] -ignore_missing_imports = True diff --git a/old_config/tox.ini b/old_config/tox.ini deleted file mode 100644 index 172aaa03..00000000 --- a/old_config/tox.ini +++ /dev/null @@ -1,155 +0,0 @@ - -[isort] -default_section = THIRDPARTY -force_grid_wrap = 0 -force_single_line = 1 -line_length = 88 -order_by_type = false -# Headings -import_heading_stdlib = Standard library -import_heading_thirdparty = Third-party -import_heading_firstparty = First-party -import_heading_localfolder = Local -# Known modules to avoid misclassification -known_standard_library = -known_first_party = - pyflexplot - srtools - srutils - words -known_third_party = - click - numpy - matplotlib - -[flake8] -exclude = docs -max-line-length = 88 -ignore = - E203, # Allow whitespace before ':' (https://github.com/PyCQA/pycodestyle/issues/373) - F811, # Allow redefinition of unused name (necessary for typing.overload) - I002, # Don't check for isort configuration - W503, # Allow line break before binary operator (PEP 8-compatible) - -[pydocstyle] -# All codes: http://www.pydocstyle.org/en/stable/error_codes.html -ignore = - # D100, # Missing docstring in public module - D101, # Missing docstring in public class - D102, # Missing docstring in public method - D103, # Missing docstring in public function - # D104, # Missing docstring in public package - D105, # Missing docstring in magic method - # D105, # Missing docstring in public nested class - # D107, # Missing docstring in __init__ - D203, # Blank line required before class docstring - D213, # Multi-line docstring summary should start at the second line - D405, # Section name should be properly capitalized - D406, # Section name should end with a newline - D407, # Missing dashed underline after section - -[pylint] -ignore-imports = yes -max-line-length = 88 -# Tweak valid name formats -# Defaults (http://pylint-messages.wikidot.com/messages:c0103): -# argument-rgx = ^[a-z_][a-z0-9_]{2,30}$ -# attr-rgx = ^[a-z_][a-z0-9_]{2,30}$ -# function-rgx = ^[a-z_][a-z0-9_]{2,30}$ -# method-rgx = ^[a-z_][a-z0-9_]{2,30}$ -# variable-rgx = ^[a-z_][a-z0-9_]{2,30}$ -# class-rgx = ^[A-Z_][a-zA-Z0-9]+$ -# const-rgx = ^(([A-Z_][A-Z0-9_]*)|(__.*__))$ -# module-rgx = ^(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$ -argument-rgx = ^[a-z_][a-z0-9_]{,40}$ -attr-rgx = ^[a-z_][a-z0-9_]{,40}$ -function-rgx = ^[a-z_][a-z0-9_]{,40}$ -method-rgx = ^[a-z_][a-z0-9_]{,40}$ -variable-rgx = ^[a-z_][a-z0-9_]{,40}$ -class-rgx = ^[A-Z_][a-zA-Z0-9]+$ -const-rgx = ^(([a-z_][a-z0-9_]*)|([A-Z_][A-Z0-9_]*)|(__[a-zA-Z0-9]+__))$ -module-rgx = ^(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$ -inlinevar-rgx = ^[A-Za-z_][A-Za-z0-9_]*$ -# Disable selected warnings, errors etc. that conflict with style guide etc. -# Note: To locally ignore certain errors, use "pylint: disable=XXXX" comments instead! -disable = - C0115, # Missing class docstring - C0116, # Missing function or method docstring - C0330, # Wrong hanging indentation before block (add 4 spaces) - R0903, # Too few public methods (*/2) (too-few-public-methods) - R0801, # Similar lines in 2 files (duplicate-code) - # -> see https://github.com/PyCQA/pylint/issues/214 - R1705, # Unnecessary "elif" after "return" (no-else-return) - R1720, # Unnecessary "elif" after "raise" (no-else-raise) - R1724, # Unnecessary "elif" after "continue" (no-else-continue) - W1116, # Second argument of isinstance is not a type (isinstance-second-argument-not-valid-type) - W0602, # Using global for '...' but no assignment is done (global-variable-not-assigned) - E0401, # Inable to import '...' (import-error) - # -> Wrongly triggered for relative imports (pylint v2.11.1, 2022-03-09) - # -> TODO Re-enable once fixed (see https://github.com/PyCQA/pylint/issues/3651) -# Ignore (sub-)modules that trigger errors like E1101 (no-member) or E0611 (no-name-in-module) -ignored-modules = - cartopy, # E1101 (no-member) (PlateCarree) - netCDF4, # E1101 (no-member) - -[pytest] -testpaths = tests -addopts = - -s - -ra - --pdbcls=IPython.terminal.debugger:TerminalPdb - --tb=short - -# TODO add pydocstyle & mccabe -[tox] -requires = tox-conda -envlist = - pytest - flake8 - pylint - mypy - -[testenv:pytest] -setenv = - PYTHONPATH = {toxinidir} -conda_channels = - default - conda-forge -conda_env = {toxinidir}/dev-environment.yml -deps = - pytest -commands = pytest --basetemp={envtmpdir} {posargs} - -[testenv:flake8] -skip_install = true -conda_env = {toxinidir}/dev-environment.yml -deps = - flake8 -commands = flake8 src tests - -[testenv:pylint] -conda_channels = - default - conda-forge -conda_env = {toxinidir}/dev-environment.yml -deps = - pylint -commands = pylint --rcfile=tox.ini src - -[testenv:pre-commit] -skip_install = true -deps = - pre-commit -conda_env = {toxinidir}/dev-environment.yml -commands = pre-commit run --all-files - -[testenv:mypy] -skip_install = true -conda_env = {toxinidir}/dev-environment.yml -deps = - mypy - types-toml -# Note: Files in ./tests are currently not checked because they are not found -# Reason: Recursive file discovery in mypy is broken -# (https://github.com/python/mypy/issues/6385) -commands = mypy src # tests diff --git a/pyproject.toml b/pyproject.toml index 3efe6ccb..e73936aa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -80,6 +80,9 @@ known_third_party = [ known_first_party = [ # Add first-party modules that may be misclassified by isort "pyflexplot", + "srtools", + "srutils", + "words", ] [tool.mypy] @@ -89,6 +92,17 @@ known_first_party = [ # See https://blog.wolt.com/engineering/2021/09/30/professional-grade-mypy-configuration/ module = [ # Add external modules w/o type hints here + # Todo: replace by "type: ignore [import]" directives in code + "cartopy.*", + "click.*", + "geopy.*", + "IPython.*", + "matplotlib.*", + "netCDF4.*", + "PyPDF2.*", + "scipy.*", + "shapely.*", + "tomlkit.*", ] ignore_missing_imports = true @@ -140,9 +154,20 @@ disable = [ "R1720", # Unnecessary "elif" after "raise" (no-else-raise) "R1724", # Unnecessary "elif" after "continue" (no-else-continue) "W1116", # Second argument of isinstance is not a type (isinstance-second-argument-not-valid-type) + # Migrated from old blueprint, check if still needed + "W0602", # Using global for '...' but no assignment is done (global-variable-not-assigned) + "E0401", # Inable to import '...' (import-error) + # -> Wrongly triggered for relative imports (pylint v2.11.1, 2022-03-09) + # -> TODO Re-enable once fixed (see https://github.com/PyCQA/pylint/issues/3651) + "C0330", # Wrong hanging indentation before block (add 4 spaces) + "R0801", # Similar lines in 2 files (duplicate-code) ] # Ignore (sub-)modules that trigger errors like E1101 (no-member) or E0611 (no-name-in-module) -ignored-modules = [] +ignored-modules = [ + # Migrated from old blueprint, todo: replace by pylint disable directives in code + "cartopy", # E1101 (no-member) (PlateCarree) + "netCDF4", # E1101 (no-member) +] [tool.pydocstyle] # All codes: http://www.pydocstyle.org/en/stable/error_codes.html @@ -157,7 +182,7 @@ ignore = [ # "D107", # Missing docstring in __init__ "D203", # Blank line required before class docstring "D213", # Multi-line docstring summary should start at the second line - # "D405", # Section name should be properly capitalized + "D405", # Section name should be properly capitalized "D406", # Section name should end with a newline "D407", # Missing dashed underline after section ] From 5b5dc315944d5338c6e8dac45f2ac2eedf08a9ab Mon Sep 17 00:00:00 2001 From: Pirmin Kaufmann Date: Thu, 23 Feb 2023 17:26:56 +0100 Subject: [PATCH 03/24] Fix some linter issues and temporarily disable pylint. --- .pre-commit-config.yaml | 16 +- pyproject.toml | 10 +- requirements/environment.yml | 460 ++++++++++++++++++----------------- 3 files changed, 244 insertions(+), 242 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e06164af..f509ee3a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -71,14 +71,14 @@ repos: # SR formatters changed something. A potential solution could be to write a # SR small bash script run-linters.sh that runs flake8, pylint and run-mypy.sh # SR in that order and aborts on error. -- repo: local - hooks: - - id: pylint - name: pylint - description: Check Python code for correctness, consistency and adherence to best practices - language: system - entry: pylint - types: [python] +#- repo: local +# hooks: +# - id: pylint +# name: pylint +# description: Check Python code for correctness, consistency and adherence to best practices +# language: system +# entry: pylint +# types: [python] - repo: local hooks: - id: flake8 diff --git a/pyproject.toml b/pyproject.toml index e73936aa..aed74203 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -163,11 +163,11 @@ disable = [ "R0801", # Similar lines in 2 files (duplicate-code) ] # Ignore (sub-)modules that trigger errors like E1101 (no-member) or E0611 (no-name-in-module) -ignored-modules = [ - # Migrated from old blueprint, todo: replace by pylint disable directives in code - "cartopy", # E1101 (no-member) (PlateCarree) - "netCDF4", # E1101 (no-member) -] +#ignored-modules = [ +# # Migrated from old blueprint, todo: replace by pylint disable directives in code +# "cartopy", # E1101 (no-member) (PlateCarree) +# "netCDF4", # E1101 (no-member) +#] [tool.pydocstyle] # All codes: http://www.pydocstyle.org/en/stable/error_codes.html diff --git a/requirements/environment.yml b/requirements/environment.yml index 6e596d38..9e842b4a 100644 --- a/requirements/environment.yml +++ b/requirements/environment.yml @@ -2,232 +2,234 @@ name: pyflexplot channels: - conda-forge dependencies: - - _libgcc_mutex=0.1=conda_forge - - _openmp_mutex=4.5=1_gnu - - alabaster=0.7.12=py_0 - - alsa-lib=1.2.3=h516909a_0 - - appdirs=1.4.4=pyh9f0ad1d_0 - - astroid=2.8.5=py39hf3d152e_0 - - asttokens=2.0.5=pyhd8ed1ab_0 - - attrs=21.2.0=pyhd8ed1ab_0 - - babel=2.9.1=pyh44b312d_0 - - backcall=0.2.0=pyh9f0ad1d_0 - - backports=1.0=py_2 - - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0 - - black=22.1.0=pyhd8ed1ab_0 - - brotli=1.0.9=h7f98852_6 - - brotli-bin=1.0.9=h7f98852_6 - - brotlipy=0.7.0=py39h3811e60_1003 - - bump2version=1.0.1=pyh9f0ad1d_0 - - bzip2=1.0.8=h7f98852_4 - - c-ares=1.18.1=h7f98852_0 - - ca-certificates=2021.10.8=ha878542_0 - - cartopy=0.20.1=py39h9134429_3 - - certifi=2021.10.8=py39hf3d152e_1 - - cffi=1.15.0=py39h4bc2ebd_0 - - cfgv=3.3.1=pyhd8ed1ab_0 - - cftime=1.5.1.1=py39hce5d2b2_1 - - chardet=4.0.0=py39hf3d152e_2 - - charset-normalizer=2.0.0=pyhd8ed1ab_0 - - click=8.0.4=py39hf3d152e_0 - - codespell=2.1.0=pyhd8ed1ab_0 - - colorama=0.4.4=pyh9f0ad1d_0 - - cryptography=35.0.0=py39h95dcef6_2 - - curl=7.80.0=h2574ce0_0 - - cycler=0.11.0=pyhd8ed1ab_0 - - dataclasses=0.8=pyhc8e2a94_3 - - dbus=1.13.6=h48d8840_2 - - decorator=5.1.0=pyhd8ed1ab_0 - - distlib=0.3.3=pyhd8ed1ab_0 - - docutils=0.16=py39hf3d152e_3 - - editdistance-s=1.0.0=py39h1a9c180_2 - - executing=0.8.3=pyhd8ed1ab_0 - - expat=2.4.1=h9c3ff4c_0 - - filelock=3.3.2=pyhd8ed1ab_0 - - flake8=4.0.1=pyhd8ed1ab_2 - - flake8-black=0.3.0=pyhd8ed1ab_0 - - fontconfig=2.13.1=hba837de_1005 - - freetype=2.10.4=h0708190_1 - - geographiclib=1.52=pyhd8ed1ab_0 - - geopy=2.2.0=pyhd8ed1ab_0 - - geos=3.10.0=h9c3ff4c_0 - - gettext=0.19.8.1=h73d1719_1008 - - giflib=5.2.1=h36c2ea0_2 - - glib=2.70.0=h780b84a_1 - - glib-tools=2.70.0=h780b84a_1 - - gst-plugins-base=1.18.5=hf529b03_2 - - gstreamer=1.18.5=h9f60fe5_2 - - hdf4=4.2.15=h10796ff_3 - - hdf5=1.12.1=nompi_h2750804_103 - - icu=68.2=h9c3ff4c_0 - - identify=2.3.6=pyhd8ed1ab_0 - - idna=3.1=pyhd3deb0d_0 - - imagesize=1.3.0=pyhd8ed1ab_0 - - importlib-metadata=3.10.1=py39hf3d152e_0 - - iniconfig=1.1.1=pyh9f0ad1d_0 - - intel-openmp=2021.4.0=h06a4308_3561 - - ipdb=0.13.9=pyhd8ed1ab_0 - - ipython=8.1.1=py39hf3d152e_0 - - isort=5.10.1=pyhd8ed1ab_0 - - jbig=2.1=h7f98852_2003 - - jedi=0.18.0=py39hf3d152e_3 - - jinja2=3.0.3=pyhd8ed1ab_0 - - jpeg=9d=h36c2ea0_0 - - keyutils=1.6.1=h166bdaf_0 - - kiwisolver=1.3.2=py39h1a9c180_1 - - krb5=1.19.2=h3790be6_4 - - lazy-object-proxy=1.6.0=py39h3811e60_1 - - lcms2=2.12=hddcbb42_0 - - ld_impl_linux-64=2.36.1=hea4e1c9_2 - - lerc=3.0=h9c3ff4c_0 - - libblas=3.9.0=13_linux64_openblas - - libbrotlicommon=1.0.9=h7f98852_6 - - libbrotlidec=1.0.9=h7f98852_6 - - libbrotlienc=1.0.9=h7f98852_6 - - libcblas=3.9.0=13_linux64_openblas - - libclang=11.1.0=default_ha53f305_1 - - libcurl=7.80.0=h2574ce0_0 - - libdeflate=1.8=h7f98852_0 - - libedit=3.1.20191231=he28a2e2_2 - - libev=4.33=h516909a_1 - - libevent=2.1.10=h9b69904_4 - - libffi=3.4.2=h7f98852_5 - - libgcc-ng=11.2.0=h1d223b6_13 - - libgfortran-ng=11.2.0=h69a702a_13 - - libgfortran5=11.2.0=h5c6108e_13 - - libglib=2.70.0=h174f98d_1 - - libgomp=11.2.0=h1d223b6_13 - - libiconv=1.16=h516909a_0 - - liblapack=3.9.0=13_linux64_openblas - - libllvm11=11.1.0=hf817b99_3 - - libllvm9=9.0.1=default_hc23dcda_7 - - libnetcdf=4.8.1=nompi_hb3fd0d9_101 - - libnghttp2=1.43.0=h812cca2_1 - - libnsl=2.0.0=h7f98852_0 - - libogg=1.3.4=h7f98852_1 - - libopenblas=0.3.18=pthreads_h8fe5266_0 - - libopus=1.3.1=h7f98852_1 - - libpng=1.6.37=h21135ba_2 - - libpq=13.3=hd57d9b9_3 - - libssh2=1.10.0=ha56f1ee_2 - - libstdcxx-ng=11.2.0=he4da1e4_13 - - libtiff=4.3.0=h6f004c6_2 - - libuuid=2.32.1=h7f98852_1000 - - libvorbis=1.3.7=h9c3ff4c_0 - - libwebp=1.2.1=h3452ae3_0 - - libwebp-base=1.2.1=h7f98852_0 - - libxcb=1.13=h7f98852_1004 - - libxkbcommon=1.0.3=he3ba5ed_0 - - libxml2=2.9.12=h72842e0_0 - - libzip=1.8.0=h4de3113_1 - - libzlib=1.2.11=h36c2ea0_1013 - - livereload=2.6.3=pyh9f0ad1d_0 - - llvm-openmp=12.0.1=h4bd325d_1 - - lz4-c=1.9.3=h9c3ff4c_1 - - markupsafe=2.0.1=py39h3811e60_1 - - matplotlib=3.4.3=py39hf3d152e_2 - - matplotlib-base=3.4.3=py39h2fa2bec_2 - - matplotlib-inline=0.1.3=pyhd8ed1ab_0 - - mccabe=0.6.1=py_1 - - more-itertools=8.11.0=pyhd8ed1ab_0 - - munkres=1.1.4=pyh9f0ad1d_0 - - mypy=0.931=py39h3811e60_2 - - mypy_extensions=0.4.3=py39hf3d152e_4 - - mysql-common=8.0.27=ha770c72_3 - - mysql-libs=8.0.27=hfa10184_3 - - ncurses=6.2=h58526e2_4 - - netcdf4=1.5.8=nompi_py39h64b754b_101 - - nodeenv=1.6.0=pyhd8ed1ab_0 - - nspr=4.32=h9c3ff4c_1 - - nss=3.72=hb5efdd6_0 - - numpy=1.22.3=py39h18676bf_0 - - olefile=0.46=pyh9f0ad1d_1 - - openjpeg=2.4.0=hb52868f_1 - - openssl=1.1.1l=h7f98852_0 - - packaging=21.0=pyhd8ed1ab_0 - - parso=0.8.2=pyhd8ed1ab_0 - - pathspec=0.9.0=pyhd8ed1ab_0 - - pcre=8.45=h9c3ff4c_0 - - pexpect=4.8.0=pyh9f0ad1d_2 - - pickleshare=0.7.5=py_1003 - - pillow=8.4.0=py39ha612740_0 - - pip=21.3.1=pyhd8ed1ab_0 - - platformdirs=2.3.0=pyhd8ed1ab_0 - - pluggy=0.13.1=py39hf3d152e_4 - - pre-commit=2.17.0=py39hf3d152e_0 - - proj=8.2.0=h277dcde_0 - - prompt-toolkit=3.0.22=pyha770c72_0 - - psutil=5.8.0=py39h3811e60_2 - - pthread-stubs=0.4=h36c2ea0_1001 - - ptyprocess=0.7.0=pyhd3deb0d_0 - - pure_eval=0.2.2=pyhd8ed1ab_0 - - py=1.11.0=pyh6c4a22f_0 - - pycodestyle=2.8.0=pyhd8ed1ab_0 - - pycparser=2.21=pyhd8ed1ab_0 - - pydocstyle=6.1.1=pyhd8ed1ab_0 - - pyflakes=2.4.0=pyhd8ed1ab_0 - - pygments=2.10.0=pyhd8ed1ab_0 - - pylint=2.11.1=pyhd8ed1ab_0 - - pyopenssl=21.0.0=pyhd8ed1ab_0 - - pyparsing=3.0.6=pyhd8ed1ab_0 - - pypdf2=1.26.0=py_2 - - pyproj=3.2.1=py39h1b810de_5 - - pyqt=5.12.3=py39hf3d152e_8 - - pyqt-impl=5.12.3=py39hde8b62d_8 - - pyqt5-sip=4.19.18=py39he80948d_8 - - pyqtchart=5.12=py39h0fcd23e_8 - - pyqtwebengine=5.12.1=py39h0fcd23e_8 - - pyshp=2.1.3=pyh44b312d_0 - - pysocks=1.7.1=py39hf3d152e_4 - - pytest=7.0.1=py39hf3d152e_0 - - python=3.9.7=hb7a2778_3_cpython - - python-dateutil=2.8.2=pyhd8ed1ab_0 - - python_abi=3.9=2_cp39 - - pytz=2021.3=pyhd8ed1ab_0 - - pyyaml=6.0=py39h3811e60_3 - - qt=5.12.9=hda022c4_4 - - readline=8.1=h46c0cb4_0 - - regex=2021.11.10=py39h3811e60_0 - - requests=2.26.0=pyhd8ed1ab_1 - - rope=0.23.0=pyhd8ed1ab_0 - - rstcheck=3.3.1=pyh9f0ad1d_0 - - scipy=1.8.0=py39hee8e79c_1 - - setuptools=59.1.1=py39hf3d152e_0 - - shapely=1.8.0=py39hc7dd4e9_2 - - six=1.16.0=pyh6c4a22f_0 - - snowballstemmer=2.1.0=pyhd8ed1ab_0 - - sphinx=4.3.1=pyh6c4a22f_0 - - sphinx-autobuild=2021.3.14=pyhd8ed1ab_0 - - sphinxcontrib-applehelp=1.0.2=py_0 - - sphinxcontrib-devhelp=1.0.2=py_0 - - sphinxcontrib-htmlhelp=2.0.0=pyhd8ed1ab_0 - - sphinxcontrib-jsmath=1.0.1=py_0 - - sphinxcontrib-qthelp=1.0.3=py_0 - - sphinxcontrib-serializinghtml=1.1.5=pyhd8ed1ab_1 - - sqlite=3.36.0=h9cd32fc_2 - - stack_data=0.2.0=pyhd8ed1ab_0 - - tbb=2021.4.0=h4bd325d_1 - - tk=8.6.11=h27826a3_1 - - toml=0.10.2=pyhd8ed1ab_0 - - tomli=1.2.2=pyhd8ed1ab_0 - - tornado=6.1=py39h3811e60_2 - - tox=3.24.5=py39hf3d152e_0 - - tox-conda=0.9.2=pyhd8ed1ab_0 - - traitlets=5.1.1=pyhd8ed1ab_0 - - typed-ast=1.5.0=py39h3811e60_0 - - types-toml=0.10.4=pyhd8ed1ab_0 - - typing-extensions=3.10.0.2=hd8ed1ab_0 - - typing_extensions=3.10.0.2=pyha770c72_0 - - tzdata=2021e=he74cb21_0 - - urllib3=1.26.7=pyhd8ed1ab_0 - - virtualenv=20.4.7=py39hf3d152e_2 - - wcwidth=0.2.5=pyh9f0ad1d_2 - - wheel=0.37.0=pyhd8ed1ab_1 - - wrapt=1.12.1=py39h3811e60_3 - - xorg-libxau=1.0.9=h7f98852_0 - - xorg-libxdmcp=1.1.3=h7f98852_0 - - xz=5.2.5=h516909a_1 - - yaml=0.2.5=h7f98852_2 - - zipp=3.6.0=pyhd8ed1ab_0 - - zlib=1.2.11=h36c2ea0_1013 - - zstd=1.5.0=ha95c52a_0 + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - alabaster=0.7.12 + - alsa-lib=1.2.3 + - appdirs=1.4.4 + - astroid=2.8.5 + - asttokens=2.0.5 + - attrs=21.2.0 + - babel=2.9.1 + - backcall=0.2.0 + - backports=1.0 + - backports.functools_lru_cache=1.6.4 + - black=22.1.0 + - brotli=1.0.9 + - brotli-bin=1.0.9 + - brotlipy=0.7.0 + - bump2version=1.0.1 + - bzip2=1.0.8 + - c-ares=1.18.1 + - ca-certificates=2022.12.7 + - cartopy=0.20.1 + - certifi=2022.12.7 + - cffi=1.15.0 + - cfgv=3.3.1 + - cftime=1.5.1.1 + - chardet=4.0.0 + - charset-normalizer=2.0.0 + - click=8.0.4 + - codespell=2.1.0 + - colorama=0.4.4 + - cryptography=35.0.0 + - curl=7.80.0 + - cycler=0.11.0 + - dataclasses=0.8 + - dbus=1.13.6 + - decorator=5.1.0 + - distlib=0.3.3 + - docutils=0.16 + - editdistance-s=1.0.0 + - executing=0.8.3 + - expat=2.4.1 + - filelock=3.3.2 + - flake8-black=0.3.0 + - fontconfig=2.13.1 + - freetype=2.10.4 + - geographiclib=1.52 + - geopy=2.2.0 + - geos=3.10.0 + - gettext=0.19.8.1 + - giflib=5.2.1 + - glib=2.70.0 + - glib-tools=2.70.0 + - gst-plugins-base=1.18.5 + - gstreamer=1.18.5 + - hdf4=4.2.15 + - hdf5=1.12.1 + - icu=68.2 + - identify=2.3.6 + - idna=3.1 + - imagesize=1.3.0 + - importlib-metadata=3.10.1 + - iniconfig=1.1.1 + - intel-openmp=2021.4.0 + - ipdb=0.13.9 + - ipython=8.1.1 + - isort=5.10.1 + - jbig=2.1 + - jedi=0.18.0 + - jinja2=3.0.3 + - jpeg=9d + - keyutils=1.6.1 + - kiwisolver=1.3.2 + - krb5=1.19.2 + - lazy-object-proxy=1.6.0 + - lcms2=2.12 + - ld_impl_linux-64=2.36.1 + - lerc=3.0 + - libblas=3.9.0 + - libbrotlicommon=1.0.9 + - libbrotlidec=1.0.9 + - libbrotlienc=1.0.9 + - libcblas=3.9.0 + - libclang=11.1.0 + - libcurl=7.80.0 + - libdeflate=1.8 + - libedit=3.1.20191231 + - libev=4.33 + - libevent=2.1.10 + - libffi=3.4.2 + - libgcc-ng=11.2.0 + - libgfortran-ng=11.2.0 + - libgfortran5=11.2.0 + - libglib=2.70.0 + - libgomp=11.2.0 + - libiconv=1.16 + - liblapack=3.9.0 + - libllvm11=11.1.0 + - libllvm9=9.0.1 + - libnetcdf=4.8.1 + - libnghttp2=1.43.0 + - libnsl=2.0.0 + - libogg=1.3.4 + - libopenblas=0.3.18 + - libopus=1.3.1 + - libpng=1.6.37 + - libpq=13.3 + - libssh2=1.10.0 + - libstdcxx-ng=11.2.0 + - libtiff=4.3.0 + - libuuid=2.32.1 + - libvorbis=1.3.7 + - libwebp=1.2.1 + - libwebp-base=1.2.1 + - libxcb=1.13 + - libxkbcommon=1.0.3 + - libxml2=2.9.12 + - libzip=1.8.0 + - libzlib=1.2.11 + - livereload=2.6.3 + - llvm-openmp=12.0.1 + - lz4-c=1.9.3 + - markupsafe=2.0.1 + - matplotlib=3.4.3 + - matplotlib-base=3.4.3 + - matplotlib-inline=0.1.3 + - more-itertools=8.11.0 + - munkres=1.1.4 + - mypy=0.931 + - mypy_extensions=0.4.3 + - mysql-common=8.0.27 + - mysql-libs=8.0.27 + - ncurses=6.2 + - netcdf4=1.5.8 + - nodeenv=1.6.0 + - nspr=4.32 + - nss=3.72 + - numpy=1.22.3 + - olefile=0.46 + - openjpeg=2.4.0 + - openssl=1.1.1l + - packaging=21.0 + - parso=0.8.2 + - pathspec=0.9.0 + - pcre=8.45 + - pexpect=4.8.0 + - pickleshare=0.7.5 + - pillow=8.4.0 + - pip=21.3.1 + - platformdirs=2.3.0 + - pluggy=0.13.1 + - pre-commit=2.17.0 + - proj=8.2.0 + - prompt-toolkit=3.0.22 + - psutil=5.8.0 + - pthread-stubs=0.4 + - ptyprocess=0.7.0 + - pure_eval=0.2.2 + - py=1.11.0 + - pycparser=2.21 + - pydocstyle=6.1.1 + - pygments=2.10.0 + - pylint=2.11.1 + - pyopenssl=21.0.0 + - pyparsing=3.0.6 + - pypdf2=1.26.0 + - pyproj=3.2.1 + - pyqt=5.12.3 + - pyqt-impl=5.12.3 + - pyqt5-sip=4.19.18 + - pyqtchart=5.12 + - pyqtwebengine=5.12.1 + - pyshp=2.1.3 + - pysocks=1.7.1 + - pytest=7.0.1 + - python=3.9.7 + - python-dateutil=2.8.2 + - python_abi=3.9 + - pytz=2021.3 + - pyyaml=6.0 + - qt=5.12.9 + - readline=8.1 + - regex=2021.11.10 + - requests=2.26.0 + - rope=0.23.0 + - rstcheck=3.3.1 + - scipy=1.8.0 + - setuptools=59.1.1 + - shapely=1.8.0 + - six=1.16.0 + - snowballstemmer=2.1.0 + - sphinx=4.3.1 + - sphinx-autobuild=2021.3.14 + - sphinxcontrib-applehelp=1.0.2 + - sphinxcontrib-devhelp=1.0.2 + - sphinxcontrib-htmlhelp=2.0.0 + - sphinxcontrib-jsmath=1.0.1 + - sphinxcontrib-qthelp=1.0.3 + - sphinxcontrib-serializinghtml=1.1.5 + - sqlite=3.36.0 + - stack_data=0.2.0 + - tbb=2021.4.0 + - tk=8.6.11 + - toml=0.10.2 + - tomli=1.2.2 + - tornado=6.1 + - tox=3.24.5 + - tox-conda=0.9.2 + - traitlets=5.1.1 + - typed-ast=1.5.0 + - types-toml=0.10.4 + - typing-extensions=3.10.0.2 + - typing_extensions=3.10.0.2 + - tzdata=2021e + - urllib3=1.26.7 + - virtualenv=20.4.7 + - wcwidth=0.2.5 + - wheel=0.37.0 + - wrapt=1.12.1 + - xorg-libxau=1.0.9 + - xorg-libxdmcp=1.1.3 + - xz=5.2.5 + - yaml=0.2.5 + - zipp=3.6.0 + - zlib=1.2.11 + - zstd=1.5.0 + - pip: + - flake8==6.0.0 + - flake8-pyproject==1.2.2 + - mccabe==0.7.0 + - pycodestyle==2.10.0 + - pyflakes==3.0.1 From d3b5bec758c978163c673a68b4d4b2381bfe0d0c Mon Sep 17 00:00:00 2001 From: Pirmin Kaufmann Date: Thu, 23 Feb 2023 17:29:39 +0100 Subject: [PATCH 04/24] Removed obsolete Makefile. --- Makefile | 548 ------------------------------------------------------- 1 file changed, 548 deletions(-) delete mode 100644 Makefile diff --git a/Makefile b/Makefile deleted file mode 100644 index 0dd52464..00000000 --- a/Makefile +++ /dev/null @@ -1,548 +0,0 @@ -SHELL := /bin/bash - -.DEFAULT_GOAL := help - -#============================================================================== -# Options -#============================================================================== - -CHAIN ?= 0#OPT Whether to chain targets, e.g., let test depend on install-test -IGNORE_VENV ?= 0#OPT Don't create and/or use a virtual environment -MSG ?= #OPT Message used as, e.g., tag annotation in version bump commands -PYTHON ?= 3.9.7#OPT Python version used to create conda virtual environment -VENV_DIR ?= #OPT Path to existing or new conda virtual environment (overrides VENV_NAME) -VENV_NAME ?= pyflexplot#OPT Name of conda virtual environment (overridden by VENV_DIR) - -# Default values used below (caution: keep values in sync with above) -DEFAULT_VENV_NAME = pyflexplot# -export DEFAULT_VENV_NAME - -#------------------------------------------------------------------------------ - -# Options for all calls to up-do-date pip (i.e., AFTER `pip install -U pip`) -# Example: `--use-feature=2020-resolver` before the new resolver became the default -PIP_OPTS = # --use-feature=in-tree-build is now default in pip -export PIP_OPTS - -# -# Targets conditional on ${CHAIN}. -# -# Use these to specify the respective targets for post-installation targets -# like ``test``, for which installation is optionally activated with CHAIN=1. -# -# Note that for interdependencies between venv/installation targets -- like -# of ``install`` on ``venv``, or if ``install-dev`` on ``install-test`` -- the -# targets are hard-coded w/o these variables, such that they are always executed -# regardless of ${CHAIN}. -# -ifeq (${CHAIN}, 0) - _INSTALL := venv - _INSTALL_DEV := venv -else - _INSTALL := install - _INSTALL_DEV := install-dev -endif -export _INSTALL -export _INSTALL_DEV - -_TMP_VENV := $(shell date +venv-tmp-%s) -export _TMP_VENV - -# If conda base environment is active, ignore it -ifeq (${CONDA_DEFAULT_ENV},base) - CONDA_DEFAULT_ENV := # - export CONDA_DEFAULT_ENV -endif - -#============================================================================== -# Python script: Print help -#============================================================================== - -define PRINT_HELP_PY -import re -import sys - -def parse_makefile(lines): - options = {} - commands = {} - rx_opt = re.compile( - r"^(?P[A-Z_]+) *\?= *(?P[^ ]*) *#OPT (?P.*)? *$$" - ) - rx_cmd1 = re.compile( - r"^(?P[a-zA-Z_-]+):.*?#CMD (?P.*) *$$" - ) - rx_cmd2 = re.compile( - r"^.PHONY: (?P[a-zA-Z_-]+) *#CMD (?P.*) *$$" - ) - for line in lines: - match_opt = rx_opt.match(line) - match_cmd1 = rx_cmd1.match(line) - match_cmd2 = rx_cmd2.match(line) - if match_opt: - m = match_opt - help = m.group("help").split(r"\n") - options[m.group("name")] = (m.group("value"), help) - elif match_cmd1 or match_cmd2: - m = match_cmd1 if match_cmd1 else match_cmd2 - commands[m.group("name")] = m.group("help").split(r"\n") - return options, commands - -def format_options(items): - s = "" - for name, (value, help) in items.items(): - name_value = f"{name}={value}" - for idx, line in enumerate(help): - s += f" {name_value if idx == 0 else '':25s} {line}\n" - return s.rstrip() - -def format_commands(items): - s = "" - for name, help in items.items(): - for idx, line in enumerate(help): - s += f" {name if idx == 0 else '':25s} {line}\n" - return s.rstrip() - -options, commands = parse_makefile(sys.stdin) - -print(f"""\ -Usage: make COMMAND [OPTIONS] - -Options: -{format_options(options)} - -Commands: -{format_commands(commands)} -""") -endef -export PRINT_HELP_PY - -#============================================================================== -# Python script: Open browser -#============================================================================== - -define BROWSER_PY -import os -import sys -import webbrowser - -try: - from urllib import pathname2url -except: - from urllib.request import pathname2url - -webbrowser.open(f"file://{pathname2url(os.path.abspath(sys.argv[1]))}") -endef -export BROWSER_PY -browser = ${PREFIX}python -c "$$BROWSER_PY" - -#============================================================================== -# Help -#============================================================================== - -.PHONY: help #CMD Print this help page. -help: - @python -c "$$PRINT_HELP_PY" < $(MAKEFILE_LIST) - -#============================================================================== -# Cleanup -#============================================================================== - -.PHONY: clean-all #CMD Remove all build, test, coverage and Python artifacts. -clean-all: clean-venv clean-test clean-build clean-pyc - @echo -e "\n[make clean-all] cleaning up" - -.PHONY: clean-build #CMD Remove build artifacts. -clean-build: - @echo -e "\n[make clean-build] removing build artifacts" - \rm -rf "build/" - \rm -rf "dist/" - \rm -rf ".eggs/" - @\rm -ff $(\find . -not -path './venv*' -and -not -path './ENV*' -name '*.egg' -exec echo "rm -ff '{}'" \;) - @\rm -ff $(\find . -not -path './venv*' -and -not -path './ENV*' -name '*.egg' -exec echo "rm -ff '{}'" \;) - -.PHONY: clean-pyc #CMD Remove Python file artifacts. -clean-pyc: - @echo -e "\n[make clean-pyc] removing Python file artifacts" - @\rm -rf $(\find . -not -path './venv*' -and -not -path './ENV*' -name '*.pyc' -exec echo "rm -rf '{}'" \;) - @\rm -rf $(\find . -not -path './venv*' -and -not -path './ENV*' -name '*.pyo' -exec echo "rm -rf '{}'" \;) - @\rm -rf $(\find . -not -path './venv*' -and -not -path './ENV*' -name '*~' -exec echo "rm -rf '{}'" \;) - @\rm -rf $(\find . -not -path './venv*' -and -not -path './ENV*' -name '__pycache__' -exec echo "rm -rf '{}'" \;) - -.PHONY: clean-test #CMD Remove testing artifacts. -clean-test: - @echo -e "\n[make clean-test] removing testing artifacts" - \rm -rf ".tox/" - \rm -f ".coverage" - \rm -rf "htmlcov/" - \rm -rf ".pytest_cache" - \rm -rf ".mypy_cache" - -.PHONY: clean-venv #CMD Remove virtual environment. -clean-venv: -ifeq (${IGNORE_VENV}, 0) - @# Do not ignore existing venv -ifeq (${VENV_DIR},) - @# Path to conda venv has not been passed -ifneq ($(shell conda list --name $(VENV_NAME) 2>/dev/null 1>&2; echo $$?),0) - @echo -e "\n[make clean-venv] no conda virtual environment '${VENV_NAME}' to remove" -else - @echo -e "\n[make clean-venv] removing conda virtual environment '${VENV_NAME}'" - conda env remove --yes --name ${VENV_NAME} -endif -else - @# Path to conda venv has been passed -ifneq ($(shell conda list --prefix $(VENV_DIR) 2>/dev/null 1>&2; echo $$?),0) - @echo -e "\n[make clean-venv] no conda virtual environment at '${VENV_DIR}' to remove" -else - @echo -e "\n[make clean-venv] removing conda virtual environment at '${VENV_DIR}'" - conda env remove --yes --prefix ${VENV_DIR} -endif -endif -endif - -#============================================================================== -# Version control -#============================================================================== - -# Note: Check if git is initialized by checking error status of git rev-parse -.PHONY: git #CMD Initialize a git repository and make initial commit. -git: - @git rev-parse 2>&1 && $(MAKE) _git_ok || $(MAKE) _git_init - -# Hidden target called when git is already initialized -.PHONY: _git_ok -_git_ok: - @echo -e "\n[make git] git already initialized" - -# Hidden target called when git is not yet initialized -.PHONY: _git_init -_git_init: - $(MAKE) clean-all - @echo -e "\n[make git] initializing git repository" - \git init - \git add . - \git commit -m 'initial commit' - \git --no-pager log -n1 --stat - -#============================================================================== -# Conda Virtual Environment -#============================================================================== - -.PHONY: venv #CMD Create/locate conda virtual environment. -venv: _create_conda_venv - @# Use an active or existing conda env if possible, otherwise create new one -ifneq (${VIRTUAL_ENV},) - @# An active Python virtual environment has been found, so abort this mission! - @echo -e "[make venv] error: active non-conda virtual environment found: ${VIRTUAL_ENV}" - exit 1 -endif # VIRTUAL_ENV -ifeq (${IGNORE_VENV}, 0) - @# Don't ignore an existing conda env, and if there is none, create one -ifeq (${VENV_DIR},) - @# Path VENV_DIR to conda env has NOT been passed - $(eval VENV_DIR = $(shell conda run --name $(VENV_NAME) python -c 'import pathlib, sys; print(pathlib.Path(sys.executable).parent.parent)')) - @export VENV_DIR -else # VENV_DIR - @# Path VENV_DIR to conda venv has been passed - $(eval VENV_DIR = $(shell conda run --prefix $(VENV_DIR) python -c 'import pathlib, sys; print(pathlib.Path(sys.executable).parent.parent)')) - @export VENV_DIR -ifneq (${VENV_NAME},${DEFAULT_VENV_NAME}) - @# Name VENV_NAME of conda env has been passed alongside path VENV_DIR - @echo -e "[make venv] warning: VENV_DIR=${VENV_DIR} overrides VENV_NAME=${VENV_NAME}" -endif # VENV_NAME -endif # VENV_DIR - $(eval PREFIX = ${VENV_DIR}/bin/) - @export PREFIX -endif # IGNORE_VENV - ${PREFIX}python -V - -.PHONY: _create_conda_venv -_create_conda_venv: git - @# If there is an active conda environment, use it, regardless of VENV_NAME and VENV_DIR; - @# if there is an existing env matching VENV_NAME and (if set) VENV_DIR, use that; - @# otherwise create a new one based on VENV_NAME and (if set) VENV_DIR. -ifeq (${IGNORE_VENV}, 0) - @# Do not ignore existing venv -ifneq (${CONDA_DEFAULT_ENV},) - @# There already is an active conda environment, so use it (regardless of its name and path) - @echo -e "\n[make venv] found active conda environment '${CONDA_DEFAULT_ENV}' at '${CONDA_PREFIX}'" -ifneq (${CONDA_DEFAULT_ENV}, ${VENV_NAME}) - @# The name of the active env does not match VENV_NAME, but we assume that's OK over override it - @echo -e "[make venv] warning: name of active venv '${CONDA_DEFAULT_ENV}' overrides VENV_NAME='${VENV_NAME}'" - $(eval VENV_NAME = ${CONDA_DEFAULT_ENV}) - @export VENV_NAME -endif # CONDA_DEFAULT_ENV -ifneq (${CONDA_PREFIX}, ${VENV_DIR}) - @# The path to the active env does not match VENV_DIR (if set), but we assume that's OK and override it -ifneq (${VENV_DIR},) - @echo -e "[make venv] warning: path to active venv '${CONDA_PREFIX}' overrides VENV_DIR='${VENV_DIR}'" -endif # VENV_DIR - $(eval VENV_DIR = ${CONDA_PREFIX}) - @export VENV_DIR -endif # CONDA_PREFIX -else # CONDA_DEFAULT_ENV - @# The is no active conda environment -ifeq (${VENV_DIR},) - @# Path VENV_DIR to conda env has NOT been passed -ifeq ($(shell conda list --name $(VENV_NAME) 2>/dev/null 1>&2; echo $$?),0) - @# Conda venv with name VENV_NAME already exists, so use it - @echo -e "\n[make venv] conda virtual environment '${VENV_NAME}' already exists" -else # shell conda ... - @# Conda env with name VENV_NAME doesn't exist yet, so create it - @echo -e "\n[make venv] creating conda virtual environment '${VENV_NAME}'" - conda create -y --name "${VENV_NAME}" python==${PYTHON} -endif # shell conda ... -else # VENV_DIR - @# Path to conda env VENV_DIR has been passed -ifeq ($(shell conda list --prefix $(VENV_DIR) 2>/dev/null 1>&2; echo $$?),0) - @# Conda env at path VENV_DIR already exists, so use it - @echo -e "\n[make venv] conda virtual environment at '${VENV_DIR}'" -else # shell conda ... - @# Conda env at path VENV_DIR does NOT yet exist, so create it - @echo -e "\n[make venv] creating conda virtual environment at '${VENV_DIR}'" - conda create -y --prefix "${VENV_DIR}" python==${PYTHON} -endif # shell conda ... -endif # VENV_DIR -endif # CONDA_DEFAULT_ENV -endif # IGNORE_VENV - -#============================================================================== -# Installation -#============================================================================== - -.PHONY: install #CMD Install the package with pinned runtime dependencies. -install: venv - @echo -e "\n[make install] installing the package" - conda env update --prefix "${VENV_DIR}" --file=environment.yml - # conda install --yes --prefix "${VENV_DIR}" --file requirements.txt # pinned - # conda install --yes --prefix "${VENV_DIR}" --file requirements.in # unpinned - # ${PREFIX}python -m pip install -U pip - ${PREFIX}python -m pip install . ${PIP_OPTS} - ${PREFIX}pyflexplot -V - -.PHONY: install-dev #CMD Install the package as editable with pinned runtime and\ndevelopment dependencies. -install-dev: venv - @echo -e "\n[make install-dev] installing the package as editable with development dependencies" - conda install --yes --prefix "${VENV_DIR}" --file dev-requirements.yml # pinned - # conda install --yes --prefix "${VENV_DIR}" --file requirements.in # unpinned - # conda install --yes --prefix "${VENV_DIR}" --file dev-requirements.in # unpinned - # ${PREFIX}python -m pip install -U pip - ${PREFIX}python -m pip install --editable . ${PIP_OPTS} - ${PREFIX}pre-commit install - ${PREFIX}pyflexplot -V - -.PHONY: install-dev-unpinned #CMD Install the package as editable with unpinned runtime and\ndevelopment dependencies. -install-dev-unpinned: venv - @echo -e "\n[make install-dev] installing the package as editable with development dependencies" - # conda install --yes --prefix "${VENV_DIR}" --file dev-requirements.txt # pinned - conda install --yes --prefix "${VENV_DIR}" --file requirements.in --file dev-requirements.in # unpinned - # ${PREFIX}python -m pip install -U pip - ${PREFIX}python -m pip install --editable . ${PIP_OPTS} - ${PREFIX}pre-commit install - ${PREFIX}pyflexplot -V - -#============================================================================== -# Dependencies -#============================================================================== - -.PHONY: update-run-deps #CMD Update pinned runtime dependencies based on setup.py;\nshould be followed by update-dev-deps (consider update-run-dev-deps) -update-run-deps: git - @echo -e "\n[make update-run-deps] not yet implemented for conda" - exit 1 - # @echo -e "\n[make update-run-deps] updating pinned runtime dependencies in requirements.txt" - # \rm -f requirements.txt - # @echo -e "temporary virtual environment: ${_TMP_VENV}-run" - # python -m venv ${_TMP_VENV}-run - # ${_TMP_VENV}-run/bin/python -m pip install -U pip - # ${_TMP_VENV}-run/bin/python -m pip install . ${PIP_OPTS} - # ${_TMP_VENV}-run/bin/python -m pip freeze | \grep -v '\ requirements.txt - # \rm -rf ${_TMP_VENV}-run - -.PHONY: update-dev-deps #CMD Update pinned development dependencies based on\ndev-requirements.in; includes runtime dependencies in\nrequirements.txt -update-dev-deps: git - @echo -e "\n[make update-dev-deps] not yet implemented for conda" - exit 1 - # @echo -e "\n[make update-dev-deps] updating pinned development dependencies in requirements.txt" - # \rm -f dev-requirements.txt - # @echo -e "temporary virtual environment: ${_TMP_VENV}-dev" - # python -m venv ${_TMP_VENV}-dev - # ${_TMP_VENV}-dev/bin/python -m pip install -U pip - # ${_TMP_VENV}-dev/bin/python -m pip install -r dev-requirements.in ${PIP_OPTS} - # ${_TMP_VENV}-dev/bin/python -m pip install -r requirements.txt --no-deps ${PIP_OPTS} - # ${_TMP_VENV}-dev/bin/python -m pip freeze > dev-requirements.txt - # \rm -rf ${_TMP_VENV}-dev - -# Note: Updating run and dev deps MUST be done in sequence -.PHONY: update-run-dev-deps #CMD Update pinned runtime and development dependencies -update-run-dev-deps: - $(MAKE) update-run-deps - $(MAKE) update-dev-deps - -.PHONY: update-tox-deps #CMD Update pinned tox testing dependencies based on\ntox-requirements.in -update-tox-deps: git - @echo -e "\n[make update-tox-deps] not yet implemented for conda" - exit 1 - # \rm -f tox-requirements.txt - # @echo -e "\n[make update-tox-deps] updating pinned tox testing dependencies in tox-requirements.txt" - # @echo -e "temporary virtual environment: ${_TMP_VENV}-tox" - # python -m venv ${_TMP_VENV}-tox - # ${_TMP_VENV}-tox/bin/python -m pip install -U pip - # ${_TMP_VENV}-tox/bin/python -m pip install -r tox-requirements.in ${PIP_OPTS} - # ${_TMP_VENV}-tox/bin/python -m pip freeze > tox-requirements.txt - # \rm -rf ${_TMP_VENV}-tox - -.PHONY: update-precommit-deps #CMD Update pinned pre-commit dependencies specified in\n.pre-commit-config.yaml -update-precommit-deps: git - @echo -e "\n[make update-precommit-deps] not yet implemented for conda" - exit 1 - # @echo -e "\n[make update-precommit-deps] updating pinned tox testing dependencies in .pre-commit-config.yaml" - # python -m venv ${_TMP_VENV}-precommit - # ${_TMP_VENV}-precommit/bin/python -m pip install -U pip - # ${_TMP_VENV}-precommit/bin/python -m pip install pre-commit - # ${_TMP_VENV}-precommit/bin/pre-commit autoupdate - # \rm -rf ${_TMP_VENV}-precommit - -.PHONY: update-deps #CMD Update all pinned dependencies (run, dev, tox, precommit) -update-deps: update-run-dev-deps update-tox-deps update-precommit-deps - @echo -e "\n[make update-deps] updating all pinned dependencies (run, dev, tox, precommit)" - -#============================================================================== -# Versioning -#============================================================================== - -# Note: -# Bump2version v1.0.0 is incompatible with pre-commit hook fix-trailing-whitespace -# (https://ithub.com/c4urself/bump2version/issues/124), therefore we pre-commit, -# commit, and tag manually. Once the whitespace problem is fixed, this can again -# be done in one command: -# @read -p "Please annotate new tag: " msg \ -# && ${PREFIX}bumpversion patch --verbose --tag-message="$${msg}" - -.PHONY: bump-patch #CMD Increment patch component Z of version number X.Y.Z,\nincl. git commit and tag -bump-patch: ${_INSTALL_DEV} -ifeq ($(MSG),) - @echo -e "\n[make bump-patch] Error: Please provide a description with MSG='...' (use '"'\\n'"' for multiple lines)" -else - @echo -e "\n[make bump-patch] bumping version number: increment patch component\n" - @echo -e '\nTag annotation:\n\n$(subst ',",$(MSG))\n' - @${PREFIX}bumpversion patch --verbose --no-commit --no-tag && echo - @${PREFIX}pre-commit run --files $$(git diff --name-only) && git add -u - @git commit -m "new version v$$(cat VERSION) (patch bump)"$$'\n\n$(subst ',",$(MSG))' --no-verify && echo - @git tag -a v$$(cat VERSION) -m $$'$(subst ',",$(MSG))' - @echo -e "\ngit tag -n -l v$$(cat VERSION)" && git tag -n -l v$$(cat VERSION) - @echo -e "\ngit log -n1" && git log -n1 -endif -# ' (close quote that vim thinks is still open to get the syntax highlighting back in order) - -.PHONY: bump-minor #CMD Increment minor component Y of version number X.Y.Z,\nincl. git commit and tag -bump-minor: ${_INSTALL_DEV} -ifeq ($(MSG),) - @echo -e "\n[make bump-minor] Error: Please provide a description with MSG='...' (use '"'\\n'"' for multiple lines)" -else - @echo -e '\nTag annotation:\n\n$(subst ',",$(MSG))\n' - @${PREFIX}bumpversion minor --verbose --no-commit --no-tag && echo - @${PREFIX}pre-commit run --files $$(git diff --name-only) && git add -u - @git commit -m "new version v$$(cat VERSION) (minor bump)"$$'\n\n$(subst ',",$(MSG))' --no-verify && echo - @git tag -a v$$(cat VERSION) -m $$'$(subst ',",$(MSG))' - @echo -e "\ngit tag -n -l v$$(cat VERSION)" && git tag -n -l v$$(cat VERSION) - @echo -e "\ngit log -n1" && git log -n1 -endif -# ' (close quote that vim thinks is still open to get the syntax highlighting back in order) - -.PHONY: bump-major #CMD Increment major component X of version number X.Y.Z,\nincl. git commit and tag -bump-major: ${_INSTALL_DEV} -ifeq ($(MSG),) - @echo -e "\n[make bump-major] Error: Please provide a description with MSG='...' (use '"'\\n'"' for multiple lines)" -else - @echo -e '\nTag annotation:\n\n$(subst ',",$(MSG))\n' - @${PREFIX}bumpversion major --verbose --no-commit --no-tag && echo - @${PREFIX}pre-commit run --files $$(git diff --name-only) && git add -u - @git commit -m "new version v$$(cat VERSION) (major bump)"$$'\n\n$(subst ',",$(MSG))' --no-verify && echo - @git tag -a v$$(cat VERSION) -m $$'$(subst ',",$(MSG))' - @echo -e "\ngit tag -n -l v$$(cat VERSION)" && git tag -n -l v$$(cat VERSION) - @echo -e "\ngit log -n1" && git log -n1 -endif -# ' (close quote that vim thinks is still open to get the syntax highlighting back in order) - -#============================================================================== -# Format and check the code -#============================================================================== - -.PHONY: format #CMD Check and fix the code formatting -format: ${_INSTALL_DEV} - @echo -e "\n[make format] checking and fixing code formatting" - ${PREFIX}pre-commit run --all-files - -.PHONY: check #CMD Check the code for correctness and best practices -check: ${_INSTALL_DEV} - @echo -e "\n[make check] checking code correctness and best practices" - ${PREFIX}tox --parallel -e mypy -e flake8 -e pylint - -.PHONY: spellcheck #CMD Check for spelling errors -spellcheck: ${_INSTALL_DEV} - @echo -e "\n[make spellcheck] checking for spelling errors" - ${PREFIX}codespell *.rst - find src tests docs -name '*.rst' -exec ${PREFIX}codespell {} \+ - ${PREFIX}codespell *.md - find src tests docs -name '*.md' -exec ${PREFIX}codespell {} \+ - ${PREFIX}codespell *.py - find src tests docs -name '*.py' -exec ${PREFIX}codespell {} \+ - -#============================================================================== -# Run the tests -#============================================================================== - -.PHONY: test-fast #CMD Run only fast tests in the development environment -test-fast: ${_INSTALL_DEV} - @echo -e "\n[make test-fast] running fast tests locally" - # ${PREFIX}tox -e pytest -- tests/fast - ${PREFIX}pytest tests/fast - -.PHONY: test-medium #CMD Run only medium-fast tests in the development environment -test-medium: venv ${_INSTALL_TEST} - @echo -e "\n[make test-medium] running medium-fast tests locally" - # ${PREFIX}tox -e pytest -- tests/medium - ${PREFIX}pytest tests/medium - -.PHONY: test-slow #CMD Run only slow tests in the development environment -test-slow: ${_INSTALL_DEV} - @echo -e "\n[make test-slow] running slow tests locally" - # ${PREFIX}tox -e pytest -- tests/slow - ${PREFIX}pytest tests/slow - -.PHONY: test #CMD Run all tests in the development environment -test: ${_INSTALL_DEV} - @echo -e "\n[make test] running all tests locally" - # ${PREFIX}tox -e pytest - ${PREFIX}pytest tests - -.PHONY: test-iso #CMD Run all tests in an isolated environment -test-iso: ${_INSTALL_DEV} - @echo -e "\n[make test-iso] running all tests in isolation" - ${PREFIX}tox -e pytest - -.PHONY: test-check #CMD Run tests and checks in an isolated environment -test-check: ${_INSTALL_DEV} - @echo -e "\n[make test-check] running tests and checks in isolated environments" - ${PREFIX}tox --parallel - -#============================================================================== -# Documentation -#============================================================================== - -#.PHONY: docs #CMD Generate HTML documentation, including API docs. -#docs: ${_INSTALL_DEV} -# @echo -e "\n[make docs] generating HTML documentation" -# \rm -f docs/pyflexplot.rst -# \rm -f docs/modules.rst -# ${PREFIX}sphinx-apidoc -o docs/ src/pyflexplot -# $(MAKE) -C docs clean -# $(MAKE) -C docs html -# ${browser} docs/_build/html/index.html - -#.PHONY: servedocs #CMD Compile the docs watching for changes. -#servedocs: docs -# @echo -e "\n[make servedocs] continuously regenerating HTML documentation" -# ${PREFIX}watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D . - -#============================================================================== From 302a0dd18fd5f8fbf19f4aeb0fe84e532b92090e Mon Sep 17 00:00:00 2001 From: Pirmin Kaufmann Date: Thu, 23 Feb 2023 17:36:53 +0100 Subject: [PATCH 05/24] Updated environment. --- requirements/environment.yml | 443 +++++++++++++++++++------------ requirements/environment.yml.bck | 235 ++++++++++++++++ 2 files changed, 507 insertions(+), 171 deletions(-) create mode 100644 requirements/environment.yml.bck diff --git a/requirements/environment.yml b/requirements/environment.yml index 9e842b4a..eeaa0fc4 100644 --- a/requirements/environment.yml +++ b/requirements/environment.yml @@ -4,232 +4,333 @@ channels: dependencies: - _libgcc_mutex=0.1 - _openmp_mutex=4.5 - - alabaster=0.7.12 - - alsa-lib=1.2.3 + - alabaster=0.7.13 + - alsa-lib=1.2.8 + - anaconda-client=1.11.0 + - anyio=3.6.2 - appdirs=1.4.4 - - astroid=2.8.5 - - asttokens=2.0.5 - - attrs=21.2.0 - - babel=2.9.1 + - astroid=2.14.2 + - asttokens=2.2.1 + - attr=2.5.1 + - attrs=22.2.0 + - babel=2.11.0 - backcall=0.2.0 - backports=1.0 - backports.functools_lru_cache=1.6.4 - - black=22.1.0 + - beautifulsoup4=4.11.2 + - black=23.1.0 + - boa=0.14.0 - brotli=1.0.9 - brotli-bin=1.0.9 - brotlipy=0.7.0 - - bump2version=1.0.1 - bzip2=1.0.8 - c-ares=1.18.1 - ca-certificates=2022.12.7 - - cartopy=0.20.1 + - cairo=1.16.0 + - cartopy=0.21.1 - certifi=2022.12.7 - - cffi=1.15.0 + - cffi=1.15.1 - cfgv=3.3.1 - - cftime=1.5.1.1 - - chardet=4.0.0 - - charset-normalizer=2.0.0 - - click=8.0.4 - - codespell=2.1.0 - - colorama=0.4.4 - - cryptography=35.0.0 - - curl=7.80.0 + - cftime=1.6.2 + - chardet=5.1.0 + - charset-normalizer=2.1.1 + - click=8.1.3 + - clyent=1.2.2 + - codespell=2.2.2 + - colorama=0.4.6 + - conda=22.11.1 + - conda-build=3.23.3 + - conda-package-handling=2.0.2 + - conda-package-streaming=0.7.0 + - contourpy=1.0.7 + - cryptography=39.0.1 + - curl=7.88.1 - cycler=0.11.0 - dataclasses=0.8 - dbus=1.13.6 - - decorator=5.1.0 - - distlib=0.3.3 - - docutils=0.16 - - editdistance-s=1.0.0 - - executing=0.8.3 - - expat=2.4.1 - - filelock=3.3.2 - - flake8-black=0.3.0 - - fontconfig=2.13.1 - - freetype=2.10.4 + - decorator=5.1.1 + - dill=0.3.6 + - distlib=0.3.6 + - docutils=0.17.1 + - exceptiongroup=1.1.0 + - executing=1.2.0 + - expat=2.5.0 + - fftw=3.3.10 + - filelock=3.9.0 + - flake8=6.0.0 + - flake8-black=0.3.5 + - fmt=9.1.0 + - font-ttf-dejavu-sans-mono=2.37 + - font-ttf-inconsolata=3.000 + - font-ttf-source-code-pro=2.038 + - font-ttf-ubuntu=0.83 + - fontconfig=2.14.2 + - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 + - fonttools=4.38.0 + - freetype=2.12.1 - geographiclib=1.52 - - geopy=2.2.0 - - geos=3.10.0 - - gettext=0.19.8.1 - - giflib=5.2.1 - - glib=2.70.0 - - glib-tools=2.70.0 - - gst-plugins-base=1.18.5 - - gstreamer=1.18.5 + - geopy=2.3.0 + - geos=3.11.1 + - gettext=0.21.1 + - glib=2.74.1 + - glib-tools=2.74.1 + - glob2=0.7 + - graphite2=1.3.13 + - gst-plugins-base=1.22.0 + - gstreamer=1.22.0 + - gstreamer-orc=0.4.33 + - harfbuzz=6.0.0 - hdf4=4.2.15 - - hdf5=1.12.1 - - icu=68.2 - - identify=2.3.6 - - idna=3.1 - - imagesize=1.3.0 - - importlib-metadata=3.10.1 - - iniconfig=1.1.1 - - intel-openmp=2021.4.0 - - ipdb=0.13.9 - - ipython=8.1.1 - - isort=5.10.1 - - jbig=2.1 - - jedi=0.18.0 - - jinja2=3.0.3 - - jpeg=9d + - hdf5=1.12.2 + - icu=70.1 + - identify=2.5.18 + - idna=3.4 + - imagesize=1.4.1 + - importlib-metadata=4.13.0 + - importlib_resources=5.12.0 + - iniconfig=2.0.0 + - ipdb=0.13.11 + - ipython=8.10.0 + - isort=5.12.0 + - jack=1.9.22 + - jedi=0.18.2 + - jinja2=3.1.2 + - joblib=1.2.0 + - jpeg=9e + - json5=0.9.5 + - jsonschema=4.17.3 + - jupyter_core=5.2.0 - keyutils=1.6.1 - - kiwisolver=1.3.2 - - krb5=1.19.2 - - lazy-object-proxy=1.6.0 - - lcms2=2.12 - - ld_impl_linux-64=2.36.1 - - lerc=3.0 + - kiwisolver=1.4.4 + - krb5=1.20.1 + - lame=3.100 + - lazy-object-proxy=1.9.0 + - lcms2=2.14 + - ld_impl_linux-64=2.40 + - lerc=4.0.0 + - libaec=1.0.6 + - libarchive=3.5.2 - libblas=3.9.0 - libbrotlicommon=1.0.9 - libbrotlidec=1.0.9 - libbrotlienc=1.0.9 + - libcap=2.66 - libcblas=3.9.0 - - libclang=11.1.0 - - libcurl=7.80.0 - - libdeflate=1.8 + - libclang=15.0.7 + - libclang13=15.0.7 + - libcups=2.3.3 + - libcurl=7.88.1 + - libdb=6.2.32 + - libdeflate=1.17 - libedit=3.1.20191231 - libev=4.33 - libevent=2.1.10 - libffi=3.4.2 - - libgcc-ng=11.2.0 - - libgfortran-ng=11.2.0 - - libgfortran5=11.2.0 - - libglib=2.70.0 - - libgomp=11.2.0 - - libiconv=1.16 + - libflac=1.4.2 + - libgcc-ng=12.2.0 + - libgcrypt=1.10.1 + - libgfortran-ng=12.2.0 + - libgfortran5=12.2.0 + - libglib=2.74.1 + - libgomp=12.2.0 + - libgpg-error=1.46 + - libiconv=1.17 - liblapack=3.9.0 - - libllvm11=11.1.0 - - libllvm9=9.0.1 - - libnetcdf=4.8.1 - - libnghttp2=1.43.0 + - liblief=0.12.3 + - libllvm15=15.0.7 + - libmamba=1.1.0 + - libmambapy=1.1.0 + - libnetcdf=4.9.1 + - libnghttp2=1.51.0 - libnsl=2.0.0 - libogg=1.3.4 - - libopenblas=0.3.18 + - libopenblas=0.3.21 - libopus=1.3.1 - - libpng=1.6.37 - - libpq=13.3 + - libpng=1.6.39 + - libpq=15.2 + - libsndfile=1.2.0 + - libsolv=0.7.22 + - libsqlite=3.40.0 - libssh2=1.10.0 - - libstdcxx-ng=11.2.0 - - libtiff=4.3.0 + - libstdcxx-ng=12.2.0 + - libsystemd0=252 + - libtiff=4.5.0 + - libtool=2.4.7 + - libudev1=252 - libuuid=2.32.1 - libvorbis=1.3.7 - - libwebp=1.2.1 - - libwebp-base=1.2.1 + - libwebp-base=1.2.4 - libxcb=1.13 - - libxkbcommon=1.0.3 - - libxml2=2.9.12 - - libzip=1.8.0 - - libzlib=1.2.11 + - libxkbcommon=1.5.0 + - libxml2=2.10.3 + - libzip=1.9.2 + - libzlib=1.2.13 - livereload=2.6.3 - - llvm-openmp=12.0.1 - - lz4-c=1.9.3 - - markupsafe=2.0.1 - - matplotlib=3.4.3 - - matplotlib-base=3.4.3 - - matplotlib-inline=0.1.3 - - more-itertools=8.11.0 + - lz4-c=1.9.4 + - lzo=2.10 + - mamba=1.1.0 + - markdown-it-py=2.2.0 + - markupsafe=2.1.2 + - matplotlib=3.7.0 + - matplotlib-base=3.7.0 + - matplotlib-inline=0.1.6 + - mccabe=0.7.0 + - mdurl=0.1.0 + - mpg123=1.31.2 - munkres=1.1.4 - - mypy=0.931 - - mypy_extensions=0.4.3 - - mysql-common=8.0.27 - - mysql-libs=8.0.27 - - ncurses=6.2 - - netcdf4=1.5.8 - - nodeenv=1.6.0 - - nspr=4.32 - - nss=3.72 - - numpy=1.22.3 - - olefile=0.46 - - openjpeg=2.4.0 - - openssl=1.1.1l - - packaging=21.0 - - parso=0.8.2 - - pathspec=0.9.0 - - pcre=8.45 + - mypy=1.0.1 + - mypy_extensions=1.0.0 + - mysql-common=8.0.32 + - mysql-libs=8.0.32 + - nbformat=5.7.3 + - ncurses=6.3 + - netcdf4=1.6.2 + - nodeenv=1.7.0 + - nspr=4.35 + - nss=3.88 + - numpy=1.24.2 + - openjpeg=2.5.0 + - openssl=3.0.8 + - packaging=23.0 + - parso=0.8.3 + - patch=2.7.6 + - patchelf=0.17.2 + - pathspec=0.11.0 + - pcre2=10.40 - pexpect=4.8.0 - pickleshare=0.7.5 - - pillow=8.4.0 - - pip=21.3.1 - - platformdirs=2.3.0 - - pluggy=0.13.1 - - pre-commit=2.17.0 - - proj=8.2.0 - - prompt-toolkit=3.0.22 - - psutil=5.8.0 + - pillow=9.4.0 + - pip=23.0.1 + - pixman=0.40.0 + - pkginfo=1.9.6 + - pkgutil-resolve-name=1.3.10 + - platformdirs=3.0.0 + - pluggy=1.0.0 + - ply=3.11 + - pooch=1.6.0 + - pre-commit=3.0.4 + - proj=9.1.1 + - prompt-toolkit=3.0.36 + - prompt_toolkit=3.0.36 + - psutil=5.9.4 - pthread-stubs=0.4 - ptyprocess=0.7.0 + - pulseaudio=16.1 - pure_eval=0.2.2 - - py=1.11.0 + - py-lief=0.12.3 + - pybind11-abi=4 + - pycodestyle=2.10.0 + - pycosat=0.6.4 - pycparser=2.21 - - pydocstyle=6.1.1 - - pygments=2.10.0 - - pylint=2.11.1 - - pyopenssl=21.0.0 - - pyparsing=3.0.6 - - pypdf2=1.26.0 - - pyproj=3.2.1 - - pyqt=5.12.3 - - pyqt-impl=5.12.3 - - pyqt5-sip=4.19.18 - - pyqtchart=5.12 - - pyqtwebengine=5.12.1 - - pyshp=2.1.3 + - pydantic=1.10.5 + - pydocstyle=6.3.0 + - pyflakes=3.0.1 + - pygments=2.14.0 + - pylint=2.16.2 + - pyopenssl=23.0.0 + - pyparsing=3.0.9 + - pypdf2=1.28.4 + - pyproj=3.4.1 + - pyqt=5.15.7 + - pyqt5-sip=12.11.0 + - pyrsistent=0.19.3 + - pyshp=2.3.1 - pysocks=1.7.1 - - pytest=7.0.1 - - python=3.9.7 + - pytest=7.2.1 + - python=3.11.0 - python-dateutil=2.8.2 - - python_abi=3.9 - - pytz=2021.3 + - python-fastjsonschema=2.16.2 + - python-libarchive-c=4.0 + - python_abi=3.11 + - pytoolconfig=1.2.5 + - pytz=2022.7.1 - pyyaml=6.0 - - qt=5.12.9 - - readline=8.1 - - regex=2021.11.10 - - requests=2.26.0 - - rope=0.23.0 - - rstcheck=3.3.1 - - scipy=1.8.0 - - setuptools=59.1.1 - - shapely=1.8.0 + - qt-main=5.15.8 + - readline=8.1.2 + - reproc=14.2.4 + - reproc-cpp=14.2.4 + - requests=2.28.2 + - rich=13.3.1 + - ripgrep=13.0.0 + - rope=1.7.0 + - rstcheck=6.1.1 + - rstcheck-core=1.0.3 + - ruamel.yaml=0.17.21 + - ruamel.yaml.clib=0.2.7 + - scipy=1.10.1 + - setuptools=65.6.3 + - shapely=2.0.1 + - shellingham=1.5.1 + - sip=6.7.7 - six=1.16.0 - - snowballstemmer=2.1.0 - - sphinx=4.3.1 + - sniffio=1.3.0 + - snowballstemmer=2.2.0 + - soupsieve=2.3.2.post1 + - sphinx=5.3.0 - sphinx-autobuild=2021.3.14 - - sphinxcontrib-applehelp=1.0.2 + - sphinxcontrib-applehelp=1.0.4 - sphinxcontrib-devhelp=1.0.2 - - sphinxcontrib-htmlhelp=2.0.0 + - sphinxcontrib-htmlhelp=2.0.1 - sphinxcontrib-jsmath=1.0.1 - sphinxcontrib-qthelp=1.0.3 - sphinxcontrib-serializinghtml=1.1.5 - - sqlite=3.36.0 - - stack_data=0.2.0 - - tbb=2021.4.0 - - tk=8.6.11 + - sqlite=3.40.0 + - stack_data=0.6.2 + - tk=8.6.12 - toml=0.10.2 - - tomli=1.2.2 - - tornado=6.1 - - tox=3.24.5 - - tox-conda=0.9.2 - - traitlets=5.1.1 - - typed-ast=1.5.0 - - types-toml=0.10.4 - - typing-extensions=3.10.0.2 - - typing_extensions=3.10.0.2 - - tzdata=2021e - - urllib3=1.26.7 - - virtualenv=20.4.7 - - wcwidth=0.2.5 - - wheel=0.37.0 - - wrapt=1.12.1 + - tomli=2.0.1 + - tomlkit=0.11.6 + - toolz=0.12.0 + - tornado=6.2 + - tqdm=4.64.1 + - traitlets=5.9.0 + - typer=0.4.2 + - types-docutils=0.18.3 + - types-setuptools=67.4.0.1 + - types-toml=0.10.8.5 + - typing=3.10.0.0 + - typing-extensions=4.4.0 + - typing_extensions=4.4.0 + - tzdata=2022g + - ukkonen=1.0.1 + - urllib3=1.26.14 + - virtualenv=20.19.0 + - watchgod=0.8.2 + - wcwidth=0.2.6 + - wheel=0.38.4 + - wrapt=1.14.1 + - xcb-util=0.4.0 + - xcb-util-image=0.4.0 + - xcb-util-keysyms=0.4.0 + - xcb-util-renderutil=0.3.9 + - xcb-util-wm=0.4.1 + - xorg-kbproto=1.0.7 + - xorg-libice=1.0.10 + - xorg-libsm=1.2.3 + - xorg-libx11=1.7.2 - xorg-libxau=1.0.9 - xorg-libxdmcp=1.1.3 - - xz=5.2.5 + - xorg-libxext=1.3.4 + - xorg-libxrender=0.9.10 + - xorg-renderproto=0.11.1 + - xorg-xextproto=7.3.0 + - xorg-xproto=7.0.31 + - xz=5.2.6 - yaml=0.2.5 - - zipp=3.6.0 - - zlib=1.2.11 - - zstd=1.5.0 + - yaml-cpp=0.7.0 + - zipp=3.14.0 + - zlib=1.2.13 + - zstandard=0.19.0 + - zstd=1.5.2 - pip: - - flake8==6.0.0 + - copier==7.0.1 + - dunamai==1.16.0 - flake8-pyproject==1.2.2 - - mccabe==0.7.0 - - pycodestyle==2.10.0 - - pyflakes==3.0.1 + - iteration-utilities==0.11.0 + - jinja2-ansible-filters==1.3.2 + - mistune==2.0.5 + - plumbum==1.8.1 + - pyyaml-include==1.3 + - questionary==1.10.0 + - sphinx-mdinclude==0.5.3 diff --git a/requirements/environment.yml.bck b/requirements/environment.yml.bck new file mode 100644 index 00000000..9e842b4a --- /dev/null +++ b/requirements/environment.yml.bck @@ -0,0 +1,235 @@ +name: pyflexplot +channels: + - conda-forge +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - alabaster=0.7.12 + - alsa-lib=1.2.3 + - appdirs=1.4.4 + - astroid=2.8.5 + - asttokens=2.0.5 + - attrs=21.2.0 + - babel=2.9.1 + - backcall=0.2.0 + - backports=1.0 + - backports.functools_lru_cache=1.6.4 + - black=22.1.0 + - brotli=1.0.9 + - brotli-bin=1.0.9 + - brotlipy=0.7.0 + - bump2version=1.0.1 + - bzip2=1.0.8 + - c-ares=1.18.1 + - ca-certificates=2022.12.7 + - cartopy=0.20.1 + - certifi=2022.12.7 + - cffi=1.15.0 + - cfgv=3.3.1 + - cftime=1.5.1.1 + - chardet=4.0.0 + - charset-normalizer=2.0.0 + - click=8.0.4 + - codespell=2.1.0 + - colorama=0.4.4 + - cryptography=35.0.0 + - curl=7.80.0 + - cycler=0.11.0 + - dataclasses=0.8 + - dbus=1.13.6 + - decorator=5.1.0 + - distlib=0.3.3 + - docutils=0.16 + - editdistance-s=1.0.0 + - executing=0.8.3 + - expat=2.4.1 + - filelock=3.3.2 + - flake8-black=0.3.0 + - fontconfig=2.13.1 + - freetype=2.10.4 + - geographiclib=1.52 + - geopy=2.2.0 + - geos=3.10.0 + - gettext=0.19.8.1 + - giflib=5.2.1 + - glib=2.70.0 + - glib-tools=2.70.0 + - gst-plugins-base=1.18.5 + - gstreamer=1.18.5 + - hdf4=4.2.15 + - hdf5=1.12.1 + - icu=68.2 + - identify=2.3.6 + - idna=3.1 + - imagesize=1.3.0 + - importlib-metadata=3.10.1 + - iniconfig=1.1.1 + - intel-openmp=2021.4.0 + - ipdb=0.13.9 + - ipython=8.1.1 + - isort=5.10.1 + - jbig=2.1 + - jedi=0.18.0 + - jinja2=3.0.3 + - jpeg=9d + - keyutils=1.6.1 + - kiwisolver=1.3.2 + - krb5=1.19.2 + - lazy-object-proxy=1.6.0 + - lcms2=2.12 + - ld_impl_linux-64=2.36.1 + - lerc=3.0 + - libblas=3.9.0 + - libbrotlicommon=1.0.9 + - libbrotlidec=1.0.9 + - libbrotlienc=1.0.9 + - libcblas=3.9.0 + - libclang=11.1.0 + - libcurl=7.80.0 + - libdeflate=1.8 + - libedit=3.1.20191231 + - libev=4.33 + - libevent=2.1.10 + - libffi=3.4.2 + - libgcc-ng=11.2.0 + - libgfortran-ng=11.2.0 + - libgfortran5=11.2.0 + - libglib=2.70.0 + - libgomp=11.2.0 + - libiconv=1.16 + - liblapack=3.9.0 + - libllvm11=11.1.0 + - libllvm9=9.0.1 + - libnetcdf=4.8.1 + - libnghttp2=1.43.0 + - libnsl=2.0.0 + - libogg=1.3.4 + - libopenblas=0.3.18 + - libopus=1.3.1 + - libpng=1.6.37 + - libpq=13.3 + - libssh2=1.10.0 + - libstdcxx-ng=11.2.0 + - libtiff=4.3.0 + - libuuid=2.32.1 + - libvorbis=1.3.7 + - libwebp=1.2.1 + - libwebp-base=1.2.1 + - libxcb=1.13 + - libxkbcommon=1.0.3 + - libxml2=2.9.12 + - libzip=1.8.0 + - libzlib=1.2.11 + - livereload=2.6.3 + - llvm-openmp=12.0.1 + - lz4-c=1.9.3 + - markupsafe=2.0.1 + - matplotlib=3.4.3 + - matplotlib-base=3.4.3 + - matplotlib-inline=0.1.3 + - more-itertools=8.11.0 + - munkres=1.1.4 + - mypy=0.931 + - mypy_extensions=0.4.3 + - mysql-common=8.0.27 + - mysql-libs=8.0.27 + - ncurses=6.2 + - netcdf4=1.5.8 + - nodeenv=1.6.0 + - nspr=4.32 + - nss=3.72 + - numpy=1.22.3 + - olefile=0.46 + - openjpeg=2.4.0 + - openssl=1.1.1l + - packaging=21.0 + - parso=0.8.2 + - pathspec=0.9.0 + - pcre=8.45 + - pexpect=4.8.0 + - pickleshare=0.7.5 + - pillow=8.4.0 + - pip=21.3.1 + - platformdirs=2.3.0 + - pluggy=0.13.1 + - pre-commit=2.17.0 + - proj=8.2.0 + - prompt-toolkit=3.0.22 + - psutil=5.8.0 + - pthread-stubs=0.4 + - ptyprocess=0.7.0 + - pure_eval=0.2.2 + - py=1.11.0 + - pycparser=2.21 + - pydocstyle=6.1.1 + - pygments=2.10.0 + - pylint=2.11.1 + - pyopenssl=21.0.0 + - pyparsing=3.0.6 + - pypdf2=1.26.0 + - pyproj=3.2.1 + - pyqt=5.12.3 + - pyqt-impl=5.12.3 + - pyqt5-sip=4.19.18 + - pyqtchart=5.12 + - pyqtwebengine=5.12.1 + - pyshp=2.1.3 + - pysocks=1.7.1 + - pytest=7.0.1 + - python=3.9.7 + - python-dateutil=2.8.2 + - python_abi=3.9 + - pytz=2021.3 + - pyyaml=6.0 + - qt=5.12.9 + - readline=8.1 + - regex=2021.11.10 + - requests=2.26.0 + - rope=0.23.0 + - rstcheck=3.3.1 + - scipy=1.8.0 + - setuptools=59.1.1 + - shapely=1.8.0 + - six=1.16.0 + - snowballstemmer=2.1.0 + - sphinx=4.3.1 + - sphinx-autobuild=2021.3.14 + - sphinxcontrib-applehelp=1.0.2 + - sphinxcontrib-devhelp=1.0.2 + - sphinxcontrib-htmlhelp=2.0.0 + - sphinxcontrib-jsmath=1.0.1 + - sphinxcontrib-qthelp=1.0.3 + - sphinxcontrib-serializinghtml=1.1.5 + - sqlite=3.36.0 + - stack_data=0.2.0 + - tbb=2021.4.0 + - tk=8.6.11 + - toml=0.10.2 + - tomli=1.2.2 + - tornado=6.1 + - tox=3.24.5 + - tox-conda=0.9.2 + - traitlets=5.1.1 + - typed-ast=1.5.0 + - types-toml=0.10.4 + - typing-extensions=3.10.0.2 + - typing_extensions=3.10.0.2 + - tzdata=2021e + - urllib3=1.26.7 + - virtualenv=20.4.7 + - wcwidth=0.2.5 + - wheel=0.37.0 + - wrapt=1.12.1 + - xorg-libxau=1.0.9 + - xorg-libxdmcp=1.1.3 + - xz=5.2.5 + - yaml=0.2.5 + - zipp=3.6.0 + - zlib=1.2.11 + - zstd=1.5.0 + - pip: + - flake8==6.0.0 + - flake8-pyproject==1.2.2 + - mccabe==0.7.0 + - pycodestyle==2.10.0 + - pyflakes==3.0.1 From 98f9c10bb3298d35cbc9788c17a2183752311f11 Mon Sep 17 00:00:00 2001 From: Pirmin Kaufmann Date: Thu, 6 Apr 2023 15:43:58 +0200 Subject: [PATCH 06/24] Updated pyproject.toml to use Python 3.9 as required by pyflexplot. Reformatted README.meteoswiss from rst to md format. --- README.meteoswiss.md | 346 ++++++++++++++++++++++++ README.meteoswiss.rst | 288 -------------------- pyproject.toml | 8 +- requirements/environment.yml | 443 ++++++++++++------------------- requirements/environment.yml.bck | 235 ---------------- 5 files changed, 521 insertions(+), 799 deletions(-) create mode 100644 README.meteoswiss.md delete mode 100644 README.meteoswiss.rst delete mode 100644 requirements/environment.yml.bck diff --git a/README.meteoswiss.md b/README.meteoswiss.md new file mode 100644 index 00000000..a4d135bd --- /dev/null +++ b/README.meteoswiss.md @@ -0,0 +1,346 @@ +PyFlexPlot +========== + +PyFlexPlot is a Python-based tool to visualize FLEXPART dispersion +simulation results stored in NetCDF format. + +Installation +------------ + +See README.rst for installation instructions. + +Testing +------- + +### Test using pyflexplot-test: this section needs to be updated! + +Compare two versions (old and new) of pyflexplot with pyflexplot-test +pyflexplot-test takes two git tags and compares the resulting plots. + +Install pyflexplot-test from git clone + + git clone git+ssh://git@github.com/MeteoSwiss-APN/pyflexplot-test + cd pyflexplot-test + make install CHAIN=1 + +Make "editable" installation, creating soft links in the venv directory + + make install-dev CHAIN=1 + +Check installation of pyflexplot-test and prepare for tests + + pyflexplot-test --version # show version + pyflexplot-test --help # show help + + +#### Automated test using pyflexplot-test + +Example scripts to run test cases are in examples + + ls examples + +The script run_pyflexplot_test.sh runs the default test cases +Important: Before running any of these scripts, adapt the version +in the variables "old" and "new" as required. + + $EDITOR examples/run_pyflexplot_test.sh + +Run the script in a parallel environment +Submit it as parallel job to SLURM + + batchPP -t 3 -T 10 examples/run_pyflexplot_test.sh + +or run in interactively + + salloc -c 10 + examples/run_pyflexplot_test.sh + exit + + +#### Manual test using pyflexplot-test + +Generic call of pyflexplot-test with placeholders +> Note: the result will be stored in `./pyflexplot-test/work` +``` +pyflexplot-test --old-rev= --new-rev= \ + --preset=opr/cosmo-1e-ctrl/all_png --infile= \ + --preset=opr/ifs-hres-eu/all_png --infile= \ + --preset=opr/ifs-hres/all_png --infile= +``` + +View result (generic call with placeholders) + + eog pyflexplot-test/work/_vs_/*.png + +#### Examples for manual tests + +Allocate parallel resources, e.g. 10 cores + + salloc -c 10 + +Compare 2 git tags based on a flexpart output file + +Settings for call to pyflexplot-test +``` +pyflexplot_test_home=$SCRATCH/pyflexplot-test +data=$SCRATCH/flexpart/job +old_rev=v0.15.3-post +new_rev=v0.15.4-pre +model=cosmo-1e-ctrl +testname=6releases +job=1033 +preset=opr/$model/all_png +infile=$(cd $data ; echo $job/output/grid_conc_*.nc) +``` +Run pyflexplot-test with above variables +``` +pyflexplot-test --num-procs=$SLURM_CPUS_PER_TASK \ + --old-rev=$old_rev --new-rev=$new_rev \ + --install-dir=$pyflexplot_test_home/install \ + --data=$data \ + --preset=$preset \ + --work-dir=$pyflexplot_test_home/work/$model/$testname \ + --infile=$infile +``` +For consecutive calls, you save time when adding the options +(if appropriate) +``` + --reuse-installs + --reuse-plots +``` +Run default test cases manually, +see also `pyflexplot-test/examples/run_pyflexplot_test.sh` +Check if still in parallel environment and if revisions defined +``` +printenv SLURM_CPUS_PER_TASK +echo old-rev=$old_rev new-rev=$new_rev +``` +Run default test cases +``` +pyflexplot-test --num-procs=$SLURM_CPUS_PER_TASK --old-rev=$old_rev --new-rev=$new_rev \ + --install-dir=/scratch/kaufmann/pyflexplot-test/install \ + --data=/scratch/ruestefa/shared/test/pyflexplot/data \ + --preset=opr/cosmo-1e-ctrl/all_png \ + --preset=opr/ifs-hres-eu/all_png \ + --preset=opr/ifs-hres/all_png \ + --preset=opr/cosmo-1e/all_png \ + --preset=opr/cosmo-2e/all_png \ + --work-dir=/scratch/kaufmann/pyflexplot-test/work/cosmo-1e-ctrl/default \ + --work-dir=/scratch/kaufmann/pyflexplot-test/work/ifs-hres-eu/default \ + --work-dir=/scratch/kaufmann/pyflexplot-test/work/ifs-hres/default \ + --work-dir=/scratch/kaufmann/pyflexplot-test/work/cosmo-1e/default \ + --work-dir=/scratch/kaufmann/pyflexplot-test/work/cosmo-2e/default +``` +Release allocated resources +``` +exit +``` + +Run pyflexplot +-------------- + +Activate the conda environment + + conda activate pyflexplot + +To use all allocated cpus, add the following option to the pyflexplot command + + --num-procs=$SLURM_CPUS_PER_TASK + +If you want to run the following examples interatcively, +you may want do allocate parallel resources, e.g. 10 cores + + salloc -c 10 + +Run `pyflexplot` +Important: Free resources when done! + + + exit + +Examples how to run pyflexplot +------------------------------ + +Example using default input file. +This example assumes you are in the pyflexplot directory. + +Default input files are searched for in ./data. +Link the default input files if you want to use these for tests. + + ln -s /store/mch/msopr/pyflexplot_testdata data + +Create an output directory + + exp=test + dest=plot_$exp + mkdir $dest + +Run all presets for pdf graphics format with the default input data + + preset='opr/*/all_pdf' + +or choose an appropriate preset (define the variable preset) + +| Model | Type | Preset | +|------------------|----------------------|----------------------------------| +| FLEXPART-IFS | Global output: | preset=opr/ifs-hres/all_pdf | +| FLEXPART-IFS | Europe output: | preset=opr/ifs-hres-eu/all_pdf | +| FLEXPART-COSMO | deterministic output:| preset=opr/cosmo-1e-ctrl/all_pdf | +| FLEXPART-COSMO | deterministic output:| preset=opr/cosmo-2e-ctrl/all_pdf | +| FLEXPART-COSMO-1E| ensemble output: | preset=opr/cosmo-1e/all_pdf | +| FLEXPART-COSMO-2E| ensemble output: | preset=opr/cosmo-2e/all_pdf | + +and run pyflexplot with the chosen preset interactively + + pyflexplot --preset "$preset" --merge-pdfs --dest=$dest + +or as a batch job (recommended) + + batchPP -t 2 -T 10 -n pfp_$exp -- \ + $CONDA_PREFIX/bin/pyflexplot --preset $preset \ + --merge-pdfs --dest=$dest --num-procs=\$SLURM_CPUS_PER_TASK + +Example using operational Flexpart ensemble output +``` +exp=test-2e +preset=opr/cosmo-2e/all_pdf +basetime=$(date --utc --date="today 00" +%Y%m%d%H) +infile000=$(echo /store/mch/msopr/osm/COSMO-2E/FCST${basetime:2:2}/${basetime:2:8}_5??/flexpart_c/000/grid_conc_*_BEZ.nc) +infile=${infile000/\/000\//\/\{ens_member:03\}\/} +dest=plot_${basetime:2:8} +mkdir $dest +batchPP -t 1 -T 10 -n pfp-$exp -- \ + $CONDA_PREFIX/bin/pyflexplot --preset $preset \ + --merge-pdfs --setup infile $infile --setup base_time $basetime --dest=$dest \ + --num-procs=\$SLURM_CPUS_PER_TASK +``` + +The following expamles use FLEXPART output generated with the test-fp script +in the test subdirectory of the flexpart repository of MeteoSwiss. Define FP_JOBS +as path to the FLEXPART output files, e.g. + + FP_JOBS=/scratch/kaufmann/flexpart/job + +Write output to a location where you have write access, e.g. + + FP_OUT=$SCRATCH/flexpart/job + +After additionally defining preset and exp, create the output directory +and submit a job with + + infile=$(echo $FP_JOBS/$exp/output/*.nc) + basetime=$(cat $FP_JOBS/$exp/output/plot_info) + dest=$FP_OUT/$exp/plots + mkdir -p $dest + +and submit the job with the batchPP command as above + +Example: FLEXPART with COSMO-2E Control Run + + preset=opr/cosmo-2e-ctrl/all_pdf + exp=1074 + +Example: FLEXPART with COSMO-1E Control Run + + preset=opr/cosmo-1e-ctrl/all_pdf + exp=1076 + +Example: FLEXPART with COSMO-2E Ensemble Run. +For ensembles, the infile needs to be a pattern rather than a single file + + preset=opr/cosmo-2e/all_pdf + exp=short-bug + infile000=$(echo $FP_JOBS/$exp/output/000/*.nc) + infile=${infile000/\/000\//\/\{ens_member:03\}\/} + +Example: New test case with clound crossing dateline from both sides + + exp=test + preset=opr/ifs-hres/all_pdf + infile=data/ifs-hres/grid_conc_20220406180000_Chmelnyzkyj.nc + basetime=2022040612 + dest=plot_$exp + mkdir $dest + +submit job with batchPP command above + +After job completion, list and visualize results with + + ls $dest/*pdf + evince $dest/*pdf + + +Commit a new version +-------------------- + +Bring all changes to the dev branch if they are not already there. + + git checkout dev + +Copy or merge changes into dev + +Create a new version number, indicating the prerelease status (--new-version +with release and build tags), regardless of uncommitted files (--allow-dirty) +and without committing it as new tag (--no-commit --no-tag) + + bumpversion --verbose --allow-dirty --no-commit --no-tag --new-version=1.0.6-pre-1 dummy + + +Save environment specificatons to allow for an exact replication of +environment with make install + + make install-dev + conda env export --no-builds --file=environment.yml + +Remove the line specifying the pyflexplot version and the preset + +If plots change, create new reference plots +Situation: make test-slow fails (tests/slow/pyflexplot/test_plots/test_*.py) +Reason: Plot references (summary dicts; tests/slow/pyflexplot/test_plots/ref_*.py) + have changed + +Steps: In [`tests/slow/test_pyflexplot/test_plots/shared.py`](tests/slow/test_pyflexplot/test_plots/shared.py), uncomment the line + + + _TestBase = _TestCreateReference + +at the end of the file and re-install if not installed with install-dev. + +Rerun test to generate new reference + + make test-slow + +Revert tests/slow/pyflexplot/test_plots/shared.py + + git checkout tests/slow/test_pyflexplot/test_plots/shared.py + +Inspect the changes to the reference + + git diff tests/slow/test_pyflexplot/test_plots + +Stage and commit all changes in dev + + git add ... + git commit ... + +Merge changes into master +(unless you have merged them from master) + + git checkout master + git merge dev + +Increase version, commit, push to github including tag +Choose target according to change level: +bump-patch, bump-minor, bump-major + + make bump-patch MSG= + +Push commit and associated tag to GitHub + + git push + git push --tag + +Continue development, preferably in the dev branch + + git checkout dev + git merge master diff --git a/README.meteoswiss.rst b/README.meteoswiss.rst deleted file mode 100644 index 130939cb..00000000 --- a/README.meteoswiss.rst +++ /dev/null @@ -1,288 +0,0 @@ -########## -PyFlexPlot -########## - -PyFlexPlot is a Python-based tool to visualize FLEXPART dispersion -simulation results stored in NetCDF format. - -Installation -============ - -See README.rst for installation instructions. - -Testing -======= - -Test using pyflexplot-test, currently outdated: needs update! -------------------------------------------------------------- - -Compare two versions (old and new) of pyflexplot with pyflexplot-test -pyflexplot-test takes two git tags and compares the resulting plots. - -# Install pyflexplot-test from git clone -git clone git+ssh://git@github.com/MeteoSwiss-APN/pyflexplot-test -cd pyflexplot-test -make install CHAIN=1 - -# Make "editable" installation, creating soft links in the venv directory -make install-dev CHAIN=1 - -# Check installation of pyflexplot-test and prepare for tests -pyflexplot-test --version # show version -pyflexplot-test --help # show help - - -# Automated test using pyflexplot-test - -# Example scripts to run test cases are in examples -ls examples - -# The script run_pyflexplot_test.sh runs the default test cases -# Important: Before running any of these scripts, adapt the version -# in the variables "old" and "new" as required. -$EDITOR examples/run_pyflexplot_test.sh - -# Run the script in a parallel environment -# Submit it as parallel job to SLURM -batchPP -t 3 -T 10 examples/run_pyflexplot_test.sh - -# or run in interatively -salloc -c 10 -examples/run_pyflexplot_test.sh -exit - - -# Manual test using pyflexplot-test - -# Generic call of pyflexplot-test with placeholders -# Note: the result will be stored in ./pyflexplot-test/work -pyflexplot-test --old-rev= --new-rev= \ - --preset=opr/cosmo-1e-ctrl/all_png --infile= \ - --preset=opr/ifs-hres-eu/all_png --infile= \ - --preset=opr/ifs-hres/all_png --infile= -# View result (generic call with placeholders) -eog pyflexplot-test/work/_vs_/*.png - -# Examples for manual tests - -# Allocate parallel resources, e.g. 10 cores -salloc -c 10 - -# Compare 2 git tags based on a flexpart output file - -# Settings for call to pyflexplot-test -pyflexplot_test_home=$SCRATCH/pyflexplot-test -data=$SCRATCH/flexpart/job -old_rev=v0.15.3-post -new_rev=v0.15.4-pre -model=cosmo-1e-ctrl -testname=6releases -job=1033 -preset=opr/$model/all_png -infile=$(cd $data ; echo $job/output/grid_conc_*.nc) -# Run pyflexplot-test with above variables -pyflexplot-test --num-procs=$SLURM_CPUS_PER_TASK \ - --old-rev=$old_rev --new-rev=$new_rev \ - --install-dir=$pyflexplot_test_home/install \ - --data=$data \ - --preset=$preset \ - --work-dir=$pyflexplot_test_home/work/$model/$testname \ - --infile=$infile -# For consecutive calls, you save time when adding the options -# (if appropriate) - --reuse-installs - --reuse-plots - -# Run default test cases manually -# see also pyflexplot-test/examples/run_pyflexplot_test.sh -# Check if still in parallel environment and if revisions defined -printenv SLURM_CPUS_PER_TASK -echo old-rev=$old_rev new-rev=$new_rev -# Run default test cases -pyflexplot-test --num-procs=$SLURM_CPUS_PER_TASK --old-rev=$old_rev --new-rev=$new_rev \ - --install-dir=/scratch/kaufmann/pyflexplot-test/install \ - --data=/scratch/ruestefa/shared/test/pyflexplot/data \ - --preset=opr/cosmo-1e-ctrl/all_png \ - --preset=opr/ifs-hres-eu/all_png \ - --preset=opr/ifs-hres/all_png \ - --preset=opr/cosmo-1e/all_png \ - --preset=opr/cosmo-2e/all_png \ - --work-dir=/scratch/kaufmann/pyflexplot-test/work/cosmo-1e-ctrl/default \ - --work-dir=/scratch/kaufmann/pyflexplot-test/work/ifs-hres-eu/default \ - --work-dir=/scratch/kaufmann/pyflexplot-test/work/ifs-hres/default \ - --work-dir=/scratch/kaufmann/pyflexplot-test/work/cosmo-1e/default \ - --work-dir=/scratch/kaufmann/pyflexplot-test/work/cosmo-2e/default - -# Release allocated resources -exit - - -Usage -===== - -Run pyflexplot --------------- - -Activate the conda environment :: - conda activate pyflexplot - -To use all allocated cpus, add the following option to the pyflexplot command :: - --num-procs=$SLURM_CPUS_PER_TASK - -If you want to run the following examples interatcively, -you may want do allocate parallel resources, e.g. 10 cores :: - salloc -c 10 - -Important: Free resources when done! :: - exit - -Examples how to run pyflexplot ------------------------------- - -Example using default input file. -This example assumes you are in the pyflexplot directory. - -Default input files are searched for in ./data. -Link the default input files if you want to use these for tests. :: - ln -s /store/mch/msopr/pyflexplot_testdata data - -Create an output directory :: - exp=test - dest=plot_$exp - mkdir $dest - -Run all presets for pdf graphics format with the default input data :: - preset='opr/*/all_pdf' - -or choose an appropriate preset (define the variable preset) :: - For FLEXPART-IFS Global output: preset=opr/ifs-hres/all_pdf - For FLEXPART-IFS Europe output: preset=opr/ifs-hres-eu/all_pdf - For FLEXPART-COSMO deterministic output: preset=opr/cosmo-1e-ctrl/all_pdf - For FLEXPART-COSMO deterministic output: preset=opr/cosmo-2e-ctrl/all_pdf - For FLEXPART-COSMO-1E ensemble output: preset=opr/cosmo-1e/all_pdf - For FLEXPART-COSMO-2E ensemble output: preset=opr/cosmo-2e/all_pdf - -and run pyflexplot with the chosen preset interactively :: - pyflexplot --preset "$preset" --merge-pdfs --dest=$dest - -or as a batch job (recommended) :: - batchPP -t 2 -T 10 -n pfp_$exp "$CONDA_PREFIX/bin/pyflexplot --preset $preset --merge-pdfs --dest=$dest --num-procs=\$SLURM_CPUS_PER_TASK" - -Example using operational Flexpart ensemble output :: - exp=test-2e - preset=opr/cosmo-2e/all_pdf - basetime=2021112500 - infile000=$(echo /store/mch/msopr/osm/COSMO-2E/FCST${basetime:2:2}/${basetime:2:8}_5??/flexpart_c/000/grid_conc_*_BEZ.nc) - infile=${infile000/\/000\//\/\{ens_member:03\}\/} - dest=plot_${basetime:2:8} - mkdir $dest - batchPP -t 1 -T 10 -n pfp-$exp "$CONDA_PREFIX/bin/pyflexplot --preset $preset --merge-pdfs --setup infile $infile --setup base_time $basetime --dest=$dest --num-procs=\$SLURM_CPUS_PER_TASK" - -The following expamles use FLEXPART output generated with the test-fp script -in the test subdirectory of the flexpart repository of MeteoSwiss. Define FP_JOBS -as path to the FLEXPART output files, e.g. :: - FP_JOBS=/scratch/kaufmann/flexpart/job - -Write output to a location where you have write access, e.g.:: - FP_OUT=$SCRATCH/flexpart/job - -After additionally defining preset and exp, create the output directory -and submit a job with:: - infile=$(echo $FP_JOBS/$exp/output/*.nc) - basetime=$(cat $FP_JOBS/$exp/output/plot_info) - dest=$FP_OUT/$exp/plots - mkdir -p $dest - -and submit the job with the batchPP command as above - -Example: FLEXPART with COSMO-2E Control Run :: - preset=opr/cosmo-2e-ctrl/all_pdf - exp=1074 - -Example: FLEXPART with COSMO-1E Control Run :: - preset=opr/cosmo-1e-ctrl/all_pdf - exp=1076 - -Example: FLEXPART with COSMO-2E Ensemble Run. -For ensembles, the infile needs to be a pattern rather than a single file :: - preset=opr/cosmo-2e/all_pdf - exp=short-bug - infile000=$(echo $FP_JOBS/$exp/output/000/*.nc) - infile=${infile000/\/000\//\/\{ens_member:03\}\/} - -Example: New test case with clound crossing dateline from both sides :: - exp=test - preset=opr/ifs-hres/all_pdf - infile=data/ifs-hres/grid_conc_20220406180000_Chmelnyzkyj.nc - basetime=2022040612 - dest=plot_$exp - mkdir $dest - -submit job with batchPP command above - -After job completion, list and vizualize results with :: - ls $dest/*pdf - evince $dest/*pdf - - -Commit a new version --------------------- - -Bring all changes to the dev branch if they are not already there. :: - git checkout dev - -Copy or merge changes into dev - -Create a new version number, indicating the prerelease status (--new-version -with release and buld tags), regardless of uncommited files (--allow-dirty) -and without committing it as new tag (--no-commit --no-tag) :: - bumpversion --verbose --allow-dirty --no-commit --no-tag --new-version=1.0.6-pre-1 dummy - - -Save environment specificatons to allow for an exact replication of -environment with make install :: - make install-dev - conda env export --no-builds --file=environment.yml - -Remove the line specifying the pyflexplot version and the preset - -If plots change, create new reference plots -Situation: make test-slow fails (tests/slow/pyflexplot/test_plots/test_*.py) -Reason: Plot references (summary dicts; tests/slow/pyflexplot/test_plots/ref_*.py) - have changed -Steps: In ``tests/slow/test_pyflexplot/test_plots/shared.py``, uncomment the line :: - - _TestBase = _TestCreateReference - -at the end of the file and re-install if not installed with install-dev. - -Rerun test to generate new reference :: - make test-slow - -Revert tests/slow/pyflexplot/test_plots/shared.py :: - git checkout tests/slow/test_pyflexplot/test_plots/shared.py - -Inspect the changes to the reference :: - git diff tests/slow/test_pyflexplot/test_plots - -Stage and commit all changes in dev :: - git add ... - git commit ... - -Merge changes into master -(unless you have merged them from master) :: - git checkout master - git merge dev - -Increase version, commit, push to github including tag -Choose target according to change level: -bump-patch, bump-minor, bump-major :: - make bump-patch MSG= - -Push commit and associated tag to GitHub :: - git push - git push --tag - -Continue development, preferably in the dev branch :: - git checkout dev - git merge master diff --git a/pyproject.toml b/pyproject.toml index aed74203..70844ca9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta" [project] name = "pyflexplot" -version = "1.0.10" +version = "1.0.11" description = "Stefan Ruedisuehli's PyFlexPlot" readme = "README.md" keywords = [ @@ -22,9 +22,9 @@ classifiers = [ "Intended Audience :: Developers", "Natural Language :: English", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.9", ] -requires-python = ">=3.10" +requires-python = ">=3.9" authors = [ {name="Stefan Ruedisuehli", email="stefan.ruedisuehli@env.ethz.ch"}, ] @@ -194,4 +194,4 @@ ignore_directives = [ ] [tool.codespell] -ignore-words-list = "inout" +ignore-words-list = "ue,fo" diff --git a/requirements/environment.yml b/requirements/environment.yml index eeaa0fc4..9e842b4a 100644 --- a/requirements/environment.yml +++ b/requirements/environment.yml @@ -4,333 +4,232 @@ channels: dependencies: - _libgcc_mutex=0.1 - _openmp_mutex=4.5 - - alabaster=0.7.13 - - alsa-lib=1.2.8 - - anaconda-client=1.11.0 - - anyio=3.6.2 + - alabaster=0.7.12 + - alsa-lib=1.2.3 - appdirs=1.4.4 - - astroid=2.14.2 - - asttokens=2.2.1 - - attr=2.5.1 - - attrs=22.2.0 - - babel=2.11.0 + - astroid=2.8.5 + - asttokens=2.0.5 + - attrs=21.2.0 + - babel=2.9.1 - backcall=0.2.0 - backports=1.0 - backports.functools_lru_cache=1.6.4 - - beautifulsoup4=4.11.2 - - black=23.1.0 - - boa=0.14.0 + - black=22.1.0 - brotli=1.0.9 - brotli-bin=1.0.9 - brotlipy=0.7.0 + - bump2version=1.0.1 - bzip2=1.0.8 - c-ares=1.18.1 - ca-certificates=2022.12.7 - - cairo=1.16.0 - - cartopy=0.21.1 + - cartopy=0.20.1 - certifi=2022.12.7 - - cffi=1.15.1 + - cffi=1.15.0 - cfgv=3.3.1 - - cftime=1.6.2 - - chardet=5.1.0 - - charset-normalizer=2.1.1 - - click=8.1.3 - - clyent=1.2.2 - - codespell=2.2.2 - - colorama=0.4.6 - - conda=22.11.1 - - conda-build=3.23.3 - - conda-package-handling=2.0.2 - - conda-package-streaming=0.7.0 - - contourpy=1.0.7 - - cryptography=39.0.1 - - curl=7.88.1 + - cftime=1.5.1.1 + - chardet=4.0.0 + - charset-normalizer=2.0.0 + - click=8.0.4 + - codespell=2.1.0 + - colorama=0.4.4 + - cryptography=35.0.0 + - curl=7.80.0 - cycler=0.11.0 - dataclasses=0.8 - dbus=1.13.6 - - decorator=5.1.1 - - dill=0.3.6 - - distlib=0.3.6 - - docutils=0.17.1 - - exceptiongroup=1.1.0 - - executing=1.2.0 - - expat=2.5.0 - - fftw=3.3.10 - - filelock=3.9.0 - - flake8=6.0.0 - - flake8-black=0.3.5 - - fmt=9.1.0 - - font-ttf-dejavu-sans-mono=2.37 - - font-ttf-inconsolata=3.000 - - font-ttf-source-code-pro=2.038 - - font-ttf-ubuntu=0.83 - - fontconfig=2.14.2 - - fonts-conda-ecosystem=1 - - fonts-conda-forge=1 - - fonttools=4.38.0 - - freetype=2.12.1 + - decorator=5.1.0 + - distlib=0.3.3 + - docutils=0.16 + - editdistance-s=1.0.0 + - executing=0.8.3 + - expat=2.4.1 + - filelock=3.3.2 + - flake8-black=0.3.0 + - fontconfig=2.13.1 + - freetype=2.10.4 - geographiclib=1.52 - - geopy=2.3.0 - - geos=3.11.1 - - gettext=0.21.1 - - glib=2.74.1 - - glib-tools=2.74.1 - - glob2=0.7 - - graphite2=1.3.13 - - gst-plugins-base=1.22.0 - - gstreamer=1.22.0 - - gstreamer-orc=0.4.33 - - harfbuzz=6.0.0 + - geopy=2.2.0 + - geos=3.10.0 + - gettext=0.19.8.1 + - giflib=5.2.1 + - glib=2.70.0 + - glib-tools=2.70.0 + - gst-plugins-base=1.18.5 + - gstreamer=1.18.5 - hdf4=4.2.15 - - hdf5=1.12.2 - - icu=70.1 - - identify=2.5.18 - - idna=3.4 - - imagesize=1.4.1 - - importlib-metadata=4.13.0 - - importlib_resources=5.12.0 - - iniconfig=2.0.0 - - ipdb=0.13.11 - - ipython=8.10.0 - - isort=5.12.0 - - jack=1.9.22 - - jedi=0.18.2 - - jinja2=3.1.2 - - joblib=1.2.0 - - jpeg=9e - - json5=0.9.5 - - jsonschema=4.17.3 - - jupyter_core=5.2.0 + - hdf5=1.12.1 + - icu=68.2 + - identify=2.3.6 + - idna=3.1 + - imagesize=1.3.0 + - importlib-metadata=3.10.1 + - iniconfig=1.1.1 + - intel-openmp=2021.4.0 + - ipdb=0.13.9 + - ipython=8.1.1 + - isort=5.10.1 + - jbig=2.1 + - jedi=0.18.0 + - jinja2=3.0.3 + - jpeg=9d - keyutils=1.6.1 - - kiwisolver=1.4.4 - - krb5=1.20.1 - - lame=3.100 - - lazy-object-proxy=1.9.0 - - lcms2=2.14 - - ld_impl_linux-64=2.40 - - lerc=4.0.0 - - libaec=1.0.6 - - libarchive=3.5.2 + - kiwisolver=1.3.2 + - krb5=1.19.2 + - lazy-object-proxy=1.6.0 + - lcms2=2.12 + - ld_impl_linux-64=2.36.1 + - lerc=3.0 - libblas=3.9.0 - libbrotlicommon=1.0.9 - libbrotlidec=1.0.9 - libbrotlienc=1.0.9 - - libcap=2.66 - libcblas=3.9.0 - - libclang=15.0.7 - - libclang13=15.0.7 - - libcups=2.3.3 - - libcurl=7.88.1 - - libdb=6.2.32 - - libdeflate=1.17 + - libclang=11.1.0 + - libcurl=7.80.0 + - libdeflate=1.8 - libedit=3.1.20191231 - libev=4.33 - libevent=2.1.10 - libffi=3.4.2 - - libflac=1.4.2 - - libgcc-ng=12.2.0 - - libgcrypt=1.10.1 - - libgfortran-ng=12.2.0 - - libgfortran5=12.2.0 - - libglib=2.74.1 - - libgomp=12.2.0 - - libgpg-error=1.46 - - libiconv=1.17 + - libgcc-ng=11.2.0 + - libgfortran-ng=11.2.0 + - libgfortran5=11.2.0 + - libglib=2.70.0 + - libgomp=11.2.0 + - libiconv=1.16 - liblapack=3.9.0 - - liblief=0.12.3 - - libllvm15=15.0.7 - - libmamba=1.1.0 - - libmambapy=1.1.0 - - libnetcdf=4.9.1 - - libnghttp2=1.51.0 + - libllvm11=11.1.0 + - libllvm9=9.0.1 + - libnetcdf=4.8.1 + - libnghttp2=1.43.0 - libnsl=2.0.0 - libogg=1.3.4 - - libopenblas=0.3.21 + - libopenblas=0.3.18 - libopus=1.3.1 - - libpng=1.6.39 - - libpq=15.2 - - libsndfile=1.2.0 - - libsolv=0.7.22 - - libsqlite=3.40.0 + - libpng=1.6.37 + - libpq=13.3 - libssh2=1.10.0 - - libstdcxx-ng=12.2.0 - - libsystemd0=252 - - libtiff=4.5.0 - - libtool=2.4.7 - - libudev1=252 + - libstdcxx-ng=11.2.0 + - libtiff=4.3.0 - libuuid=2.32.1 - libvorbis=1.3.7 - - libwebp-base=1.2.4 + - libwebp=1.2.1 + - libwebp-base=1.2.1 - libxcb=1.13 - - libxkbcommon=1.5.0 - - libxml2=2.10.3 - - libzip=1.9.2 - - libzlib=1.2.13 + - libxkbcommon=1.0.3 + - libxml2=2.9.12 + - libzip=1.8.0 + - libzlib=1.2.11 - livereload=2.6.3 - - lz4-c=1.9.4 - - lzo=2.10 - - mamba=1.1.0 - - markdown-it-py=2.2.0 - - markupsafe=2.1.2 - - matplotlib=3.7.0 - - matplotlib-base=3.7.0 - - matplotlib-inline=0.1.6 - - mccabe=0.7.0 - - mdurl=0.1.0 - - mpg123=1.31.2 + - llvm-openmp=12.0.1 + - lz4-c=1.9.3 + - markupsafe=2.0.1 + - matplotlib=3.4.3 + - matplotlib-base=3.4.3 + - matplotlib-inline=0.1.3 + - more-itertools=8.11.0 - munkres=1.1.4 - - mypy=1.0.1 - - mypy_extensions=1.0.0 - - mysql-common=8.0.32 - - mysql-libs=8.0.32 - - nbformat=5.7.3 - - ncurses=6.3 - - netcdf4=1.6.2 - - nodeenv=1.7.0 - - nspr=4.35 - - nss=3.88 - - numpy=1.24.2 - - openjpeg=2.5.0 - - openssl=3.0.8 - - packaging=23.0 - - parso=0.8.3 - - patch=2.7.6 - - patchelf=0.17.2 - - pathspec=0.11.0 - - pcre2=10.40 + - mypy=0.931 + - mypy_extensions=0.4.3 + - mysql-common=8.0.27 + - mysql-libs=8.0.27 + - ncurses=6.2 + - netcdf4=1.5.8 + - nodeenv=1.6.0 + - nspr=4.32 + - nss=3.72 + - numpy=1.22.3 + - olefile=0.46 + - openjpeg=2.4.0 + - openssl=1.1.1l + - packaging=21.0 + - parso=0.8.2 + - pathspec=0.9.0 + - pcre=8.45 - pexpect=4.8.0 - pickleshare=0.7.5 - - pillow=9.4.0 - - pip=23.0.1 - - pixman=0.40.0 - - pkginfo=1.9.6 - - pkgutil-resolve-name=1.3.10 - - platformdirs=3.0.0 - - pluggy=1.0.0 - - ply=3.11 - - pooch=1.6.0 - - pre-commit=3.0.4 - - proj=9.1.1 - - prompt-toolkit=3.0.36 - - prompt_toolkit=3.0.36 - - psutil=5.9.4 + - pillow=8.4.0 + - pip=21.3.1 + - platformdirs=2.3.0 + - pluggy=0.13.1 + - pre-commit=2.17.0 + - proj=8.2.0 + - prompt-toolkit=3.0.22 + - psutil=5.8.0 - pthread-stubs=0.4 - ptyprocess=0.7.0 - - pulseaudio=16.1 - pure_eval=0.2.2 - - py-lief=0.12.3 - - pybind11-abi=4 - - pycodestyle=2.10.0 - - pycosat=0.6.4 + - py=1.11.0 - pycparser=2.21 - - pydantic=1.10.5 - - pydocstyle=6.3.0 - - pyflakes=3.0.1 - - pygments=2.14.0 - - pylint=2.16.2 - - pyopenssl=23.0.0 - - pyparsing=3.0.9 - - pypdf2=1.28.4 - - pyproj=3.4.1 - - pyqt=5.15.7 - - pyqt5-sip=12.11.0 - - pyrsistent=0.19.3 - - pyshp=2.3.1 + - pydocstyle=6.1.1 + - pygments=2.10.0 + - pylint=2.11.1 + - pyopenssl=21.0.0 + - pyparsing=3.0.6 + - pypdf2=1.26.0 + - pyproj=3.2.1 + - pyqt=5.12.3 + - pyqt-impl=5.12.3 + - pyqt5-sip=4.19.18 + - pyqtchart=5.12 + - pyqtwebengine=5.12.1 + - pyshp=2.1.3 - pysocks=1.7.1 - - pytest=7.2.1 - - python=3.11.0 + - pytest=7.0.1 + - python=3.9.7 - python-dateutil=2.8.2 - - python-fastjsonschema=2.16.2 - - python-libarchive-c=4.0 - - python_abi=3.11 - - pytoolconfig=1.2.5 - - pytz=2022.7.1 + - python_abi=3.9 + - pytz=2021.3 - pyyaml=6.0 - - qt-main=5.15.8 - - readline=8.1.2 - - reproc=14.2.4 - - reproc-cpp=14.2.4 - - requests=2.28.2 - - rich=13.3.1 - - ripgrep=13.0.0 - - rope=1.7.0 - - rstcheck=6.1.1 - - rstcheck-core=1.0.3 - - ruamel.yaml=0.17.21 - - ruamel.yaml.clib=0.2.7 - - scipy=1.10.1 - - setuptools=65.6.3 - - shapely=2.0.1 - - shellingham=1.5.1 - - sip=6.7.7 + - qt=5.12.9 + - readline=8.1 + - regex=2021.11.10 + - requests=2.26.0 + - rope=0.23.0 + - rstcheck=3.3.1 + - scipy=1.8.0 + - setuptools=59.1.1 + - shapely=1.8.0 - six=1.16.0 - - sniffio=1.3.0 - - snowballstemmer=2.2.0 - - soupsieve=2.3.2.post1 - - sphinx=5.3.0 + - snowballstemmer=2.1.0 + - sphinx=4.3.1 - sphinx-autobuild=2021.3.14 - - sphinxcontrib-applehelp=1.0.4 + - sphinxcontrib-applehelp=1.0.2 - sphinxcontrib-devhelp=1.0.2 - - sphinxcontrib-htmlhelp=2.0.1 + - sphinxcontrib-htmlhelp=2.0.0 - sphinxcontrib-jsmath=1.0.1 - sphinxcontrib-qthelp=1.0.3 - sphinxcontrib-serializinghtml=1.1.5 - - sqlite=3.40.0 - - stack_data=0.6.2 - - tk=8.6.12 + - sqlite=3.36.0 + - stack_data=0.2.0 + - tbb=2021.4.0 + - tk=8.6.11 - toml=0.10.2 - - tomli=2.0.1 - - tomlkit=0.11.6 - - toolz=0.12.0 - - tornado=6.2 - - tqdm=4.64.1 - - traitlets=5.9.0 - - typer=0.4.2 - - types-docutils=0.18.3 - - types-setuptools=67.4.0.1 - - types-toml=0.10.8.5 - - typing=3.10.0.0 - - typing-extensions=4.4.0 - - typing_extensions=4.4.0 - - tzdata=2022g - - ukkonen=1.0.1 - - urllib3=1.26.14 - - virtualenv=20.19.0 - - watchgod=0.8.2 - - wcwidth=0.2.6 - - wheel=0.38.4 - - wrapt=1.14.1 - - xcb-util=0.4.0 - - xcb-util-image=0.4.0 - - xcb-util-keysyms=0.4.0 - - xcb-util-renderutil=0.3.9 - - xcb-util-wm=0.4.1 - - xorg-kbproto=1.0.7 - - xorg-libice=1.0.10 - - xorg-libsm=1.2.3 - - xorg-libx11=1.7.2 + - tomli=1.2.2 + - tornado=6.1 + - tox=3.24.5 + - tox-conda=0.9.2 + - traitlets=5.1.1 + - typed-ast=1.5.0 + - types-toml=0.10.4 + - typing-extensions=3.10.0.2 + - typing_extensions=3.10.0.2 + - tzdata=2021e + - urllib3=1.26.7 + - virtualenv=20.4.7 + - wcwidth=0.2.5 + - wheel=0.37.0 + - wrapt=1.12.1 - xorg-libxau=1.0.9 - xorg-libxdmcp=1.1.3 - - xorg-libxext=1.3.4 - - xorg-libxrender=0.9.10 - - xorg-renderproto=0.11.1 - - xorg-xextproto=7.3.0 - - xorg-xproto=7.0.31 - - xz=5.2.6 + - xz=5.2.5 - yaml=0.2.5 - - yaml-cpp=0.7.0 - - zipp=3.14.0 - - zlib=1.2.13 - - zstandard=0.19.0 - - zstd=1.5.2 + - zipp=3.6.0 + - zlib=1.2.11 + - zstd=1.5.0 - pip: - - copier==7.0.1 - - dunamai==1.16.0 + - flake8==6.0.0 - flake8-pyproject==1.2.2 - - iteration-utilities==0.11.0 - - jinja2-ansible-filters==1.3.2 - - mistune==2.0.5 - - plumbum==1.8.1 - - pyyaml-include==1.3 - - questionary==1.10.0 - - sphinx-mdinclude==0.5.3 + - mccabe==0.7.0 + - pycodestyle==2.10.0 + - pyflakes==3.0.1 diff --git a/requirements/environment.yml.bck b/requirements/environment.yml.bck deleted file mode 100644 index 9e842b4a..00000000 --- a/requirements/environment.yml.bck +++ /dev/null @@ -1,235 +0,0 @@ -name: pyflexplot -channels: - - conda-forge -dependencies: - - _libgcc_mutex=0.1 - - _openmp_mutex=4.5 - - alabaster=0.7.12 - - alsa-lib=1.2.3 - - appdirs=1.4.4 - - astroid=2.8.5 - - asttokens=2.0.5 - - attrs=21.2.0 - - babel=2.9.1 - - backcall=0.2.0 - - backports=1.0 - - backports.functools_lru_cache=1.6.4 - - black=22.1.0 - - brotli=1.0.9 - - brotli-bin=1.0.9 - - brotlipy=0.7.0 - - bump2version=1.0.1 - - bzip2=1.0.8 - - c-ares=1.18.1 - - ca-certificates=2022.12.7 - - cartopy=0.20.1 - - certifi=2022.12.7 - - cffi=1.15.0 - - cfgv=3.3.1 - - cftime=1.5.1.1 - - chardet=4.0.0 - - charset-normalizer=2.0.0 - - click=8.0.4 - - codespell=2.1.0 - - colorama=0.4.4 - - cryptography=35.0.0 - - curl=7.80.0 - - cycler=0.11.0 - - dataclasses=0.8 - - dbus=1.13.6 - - decorator=5.1.0 - - distlib=0.3.3 - - docutils=0.16 - - editdistance-s=1.0.0 - - executing=0.8.3 - - expat=2.4.1 - - filelock=3.3.2 - - flake8-black=0.3.0 - - fontconfig=2.13.1 - - freetype=2.10.4 - - geographiclib=1.52 - - geopy=2.2.0 - - geos=3.10.0 - - gettext=0.19.8.1 - - giflib=5.2.1 - - glib=2.70.0 - - glib-tools=2.70.0 - - gst-plugins-base=1.18.5 - - gstreamer=1.18.5 - - hdf4=4.2.15 - - hdf5=1.12.1 - - icu=68.2 - - identify=2.3.6 - - idna=3.1 - - imagesize=1.3.0 - - importlib-metadata=3.10.1 - - iniconfig=1.1.1 - - intel-openmp=2021.4.0 - - ipdb=0.13.9 - - ipython=8.1.1 - - isort=5.10.1 - - jbig=2.1 - - jedi=0.18.0 - - jinja2=3.0.3 - - jpeg=9d - - keyutils=1.6.1 - - kiwisolver=1.3.2 - - krb5=1.19.2 - - lazy-object-proxy=1.6.0 - - lcms2=2.12 - - ld_impl_linux-64=2.36.1 - - lerc=3.0 - - libblas=3.9.0 - - libbrotlicommon=1.0.9 - - libbrotlidec=1.0.9 - - libbrotlienc=1.0.9 - - libcblas=3.9.0 - - libclang=11.1.0 - - libcurl=7.80.0 - - libdeflate=1.8 - - libedit=3.1.20191231 - - libev=4.33 - - libevent=2.1.10 - - libffi=3.4.2 - - libgcc-ng=11.2.0 - - libgfortran-ng=11.2.0 - - libgfortran5=11.2.0 - - libglib=2.70.0 - - libgomp=11.2.0 - - libiconv=1.16 - - liblapack=3.9.0 - - libllvm11=11.1.0 - - libllvm9=9.0.1 - - libnetcdf=4.8.1 - - libnghttp2=1.43.0 - - libnsl=2.0.0 - - libogg=1.3.4 - - libopenblas=0.3.18 - - libopus=1.3.1 - - libpng=1.6.37 - - libpq=13.3 - - libssh2=1.10.0 - - libstdcxx-ng=11.2.0 - - libtiff=4.3.0 - - libuuid=2.32.1 - - libvorbis=1.3.7 - - libwebp=1.2.1 - - libwebp-base=1.2.1 - - libxcb=1.13 - - libxkbcommon=1.0.3 - - libxml2=2.9.12 - - libzip=1.8.0 - - libzlib=1.2.11 - - livereload=2.6.3 - - llvm-openmp=12.0.1 - - lz4-c=1.9.3 - - markupsafe=2.0.1 - - matplotlib=3.4.3 - - matplotlib-base=3.4.3 - - matplotlib-inline=0.1.3 - - more-itertools=8.11.0 - - munkres=1.1.4 - - mypy=0.931 - - mypy_extensions=0.4.3 - - mysql-common=8.0.27 - - mysql-libs=8.0.27 - - ncurses=6.2 - - netcdf4=1.5.8 - - nodeenv=1.6.0 - - nspr=4.32 - - nss=3.72 - - numpy=1.22.3 - - olefile=0.46 - - openjpeg=2.4.0 - - openssl=1.1.1l - - packaging=21.0 - - parso=0.8.2 - - pathspec=0.9.0 - - pcre=8.45 - - pexpect=4.8.0 - - pickleshare=0.7.5 - - pillow=8.4.0 - - pip=21.3.1 - - platformdirs=2.3.0 - - pluggy=0.13.1 - - pre-commit=2.17.0 - - proj=8.2.0 - - prompt-toolkit=3.0.22 - - psutil=5.8.0 - - pthread-stubs=0.4 - - ptyprocess=0.7.0 - - pure_eval=0.2.2 - - py=1.11.0 - - pycparser=2.21 - - pydocstyle=6.1.1 - - pygments=2.10.0 - - pylint=2.11.1 - - pyopenssl=21.0.0 - - pyparsing=3.0.6 - - pypdf2=1.26.0 - - pyproj=3.2.1 - - pyqt=5.12.3 - - pyqt-impl=5.12.3 - - pyqt5-sip=4.19.18 - - pyqtchart=5.12 - - pyqtwebengine=5.12.1 - - pyshp=2.1.3 - - pysocks=1.7.1 - - pytest=7.0.1 - - python=3.9.7 - - python-dateutil=2.8.2 - - python_abi=3.9 - - pytz=2021.3 - - pyyaml=6.0 - - qt=5.12.9 - - readline=8.1 - - regex=2021.11.10 - - requests=2.26.0 - - rope=0.23.0 - - rstcheck=3.3.1 - - scipy=1.8.0 - - setuptools=59.1.1 - - shapely=1.8.0 - - six=1.16.0 - - snowballstemmer=2.1.0 - - sphinx=4.3.1 - - sphinx-autobuild=2021.3.14 - - sphinxcontrib-applehelp=1.0.2 - - sphinxcontrib-devhelp=1.0.2 - - sphinxcontrib-htmlhelp=2.0.0 - - sphinxcontrib-jsmath=1.0.1 - - sphinxcontrib-qthelp=1.0.3 - - sphinxcontrib-serializinghtml=1.1.5 - - sqlite=3.36.0 - - stack_data=0.2.0 - - tbb=2021.4.0 - - tk=8.6.11 - - toml=0.10.2 - - tomli=1.2.2 - - tornado=6.1 - - tox=3.24.5 - - tox-conda=0.9.2 - - traitlets=5.1.1 - - typed-ast=1.5.0 - - types-toml=0.10.4 - - typing-extensions=3.10.0.2 - - typing_extensions=3.10.0.2 - - tzdata=2021e - - urllib3=1.26.7 - - virtualenv=20.4.7 - - wcwidth=0.2.5 - - wheel=0.37.0 - - wrapt=1.12.1 - - xorg-libxau=1.0.9 - - xorg-libxdmcp=1.1.3 - - xz=5.2.5 - - yaml=0.2.5 - - zipp=3.6.0 - - zlib=1.2.11 - - zstd=1.5.0 - - pip: - - flake8==6.0.0 - - flake8-pyproject==1.2.2 - - mccabe==0.7.0 - - pycodestyle==2.10.0 - - pyflakes==3.0.1 From ab4d7244cf58a3820b2f9d71e237156730b186af Mon Sep 17 00:00:00 2001 From: Pirmin Kaufmann Date: Tue, 30 May 2023 08:35:55 +0200 Subject: [PATCH 07/24] First step towards newer Python with unpinned requirements. --- README.meteoswiss.md | 14 +- requirements/environment.yml | 468 ++++++++++++++++++++------------ src/pyflexplot/input/species.py | 19 +- tools/setup_env.sh | 2 +- 4 files changed, 309 insertions(+), 194 deletions(-) diff --git a/README.meteoswiss.md b/README.meteoswiss.md index a4d135bd..1f3167fa 100644 --- a/README.meteoswiss.md +++ b/README.meteoswiss.md @@ -7,7 +7,7 @@ simulation results stored in NetCDF format. Installation ------------ -See README.rst for installation instructions. +See [README.md](README.md) for installation instructions. Testing ------- @@ -92,7 +92,7 @@ job=1033 preset=opr/$model/all_png infile=$(cd $data ; echo $job/output/grid_conc_*.nc) ``` -Run pyflexplot-test with above variables +Run `pyflexplot-test` with above variables ``` pyflexplot-test --num-procs=$SLURM_CPUS_PER_TASK \ --old-rev=$old_rev --new-rev=$new_rev \ @@ -132,9 +132,9 @@ pyflexplot-test --num-procs=$SLURM_CPUS_PER_TASK --old-rev=$old_rev --new-rev=$n --work-dir=/scratch/kaufmann/pyflexplot-test/work/cosmo-2e/default ``` Release allocated resources -``` -exit -``` + + exit + Run pyflexplot -------------- @@ -164,7 +164,7 @@ Examples how to run pyflexplot Example using default input file. This example assumes you are in the pyflexplot directory. -Default input files are searched for in ./data. +Default input files are searched for in `./data`. Link the default input files if you want to use these for tests. ln -s /store/mch/msopr/pyflexplot_testdata data @@ -253,7 +253,7 @@ For ensembles, the infile needs to be a pattern rather than a single file infile000=$(echo $FP_JOBS/$exp/output/000/*.nc) infile=${infile000/\/000\//\/\{ens_member:03\}\/} -Example: New test case with clound crossing dateline from both sides +Example: New test case with cloud crossing dateline from both sides exp=test preset=opr/ifs-hres/all_pdf diff --git a/requirements/environment.yml b/requirements/environment.yml index 9e842b4a..fd6074f5 100644 --- a/requirements/environment.yml +++ b/requirements/environment.yml @@ -1,235 +1,343 @@ name: pyflexplot channels: - conda-forge + - defaults dependencies: - _libgcc_mutex=0.1 - _openmp_mutex=4.5 - - alabaster=0.7.12 - - alsa-lib=1.2.3 - - appdirs=1.4.4 - - astroid=2.8.5 - - asttokens=2.0.5 - - attrs=21.2.0 - - babel=2.9.1 + - alabaster=0.7.13 + - alsa-lib=1.2.8 + - anaconda-client=1.11.2 + - anaconda-project=0.11.1 + - anyio=3.6.2 + - astroid=2.15.5 + - asttokens=2.2.1 + - attr=2.5.1 + - attrs=23.1.0 + - babel=2.12.1 - backcall=0.2.0 - backports=1.0 - backports.functools_lru_cache=1.6.4 - - black=22.1.0 + - beautifulsoup4=4.12.2 + - black=23.3.0 + - blosc=1.21.4 + - boa=0.14.0 + - boltons=23.0.0 - brotli=1.0.9 - brotli-bin=1.0.9 - brotlipy=0.7.0 - - bump2version=1.0.1 - bzip2=1.0.8 - - c-ares=1.18.1 - - ca-certificates=2022.12.7 - - cartopy=0.20.1 - - certifi=2022.12.7 - - cffi=1.15.0 + - c-ares=1.19.1 + - ca-certificates=2023.5.7 + - cairo=1.16.0 + - cartopy=0.21.1 + - certifi=2023.5.7 + - cffi=1.15.1 - cfgv=3.3.1 - - cftime=1.5.1.1 - - chardet=4.0.0 - - charset-normalizer=2.0.0 - - click=8.0.4 - - codespell=2.1.0 - - colorama=0.4.4 - - cryptography=35.0.0 - - curl=7.80.0 + - cftime=1.6.2 + - chardet=5.1.0 + - charset-normalizer=3.1.0 + - click=8.1.3 + - clyent=1.2.2 + - codespell=2.2.4 + - colorama=0.4.6 + - conda=23.3.1 + - conda-build=3.24.0 + - conda-pack=0.7.0 + - conda-package-handling=2.0.2 + - conda-package-streaming=0.8.0 + - contourpy=1.0.7 + - cryptography=40.0.2 + - curl=8.1.1 - cycler=0.11.0 - dataclasses=0.8 - dbus=1.13.6 - - decorator=5.1.0 - - distlib=0.3.3 - - docutils=0.16 - - editdistance-s=1.0.0 - - executing=0.8.3 - - expat=2.4.1 - - filelock=3.3.2 - - flake8-black=0.3.0 - - fontconfig=2.13.1 - - freetype=2.10.4 + - decorator=5.1.1 + - defusedxml=0.7.1 + - dill=0.3.6 + - distlib=0.3.6 + - docutils=0.18.1 + - exceptiongroup=1.1.1 + - executing=1.2.0 + - expat=2.5.0 + - filelock=3.12.0 + - flake8=6.0.0 + - flake8-black=0.3.6 + - fmt=9.1.0 + - font-ttf-dejavu-sans-mono=2.37 + - font-ttf-inconsolata=3.000 + - font-ttf-source-code-pro=2.038 + - font-ttf-ubuntu=0.83 + - fontconfig=2.14.2 + - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 + - fonttools=4.39.4 + - freetype=2.12.1 - geographiclib=1.52 - - geopy=2.2.0 - - geos=3.10.0 - - gettext=0.19.8.1 - - giflib=5.2.1 - - glib=2.70.0 - - glib-tools=2.70.0 - - gst-plugins-base=1.18.5 - - gstreamer=1.18.5 + - geopy=2.3.0 + - geos=3.11.2 + - gettext=0.21.1 + - glib=2.76.3 + - glib-tools=2.76.3 + - glob2=0.7 + - graphite2=1.3.13 + - gst-plugins-base=1.22.3 + - gstreamer=1.22.3 + - harfbuzz=7.3.0 - hdf4=4.2.15 - - hdf5=1.12.1 - - icu=68.2 - - identify=2.3.6 - - idna=3.1 - - imagesize=1.3.0 - - importlib-metadata=3.10.1 - - iniconfig=1.1.1 - - intel-openmp=2021.4.0 - - ipdb=0.13.9 - - ipython=8.1.1 - - isort=5.10.1 - - jbig=2.1 - - jedi=0.18.0 - - jinja2=3.0.3 - - jpeg=9d + - hdf5=1.14.0 + - icu=72.1 + - identify=2.5.24 + - idna=3.4 + - imagesize=1.4.1 + - importlib-metadata=4.13.0 + - importlib_resources=5.12.0 + - iniconfig=2.0.0 + - ipdb=0.13.13 + - ipython=8.13.2 + - isort=5.12.0 + - jedi=0.18.2 + - jinja2=3.1.2 + - joblib=1.2.0 + - json5=0.9.5 + - jsonpatch=1.32 + - jsonpointer=2.0 + - jsonschema=4.17.3 + - jupyter_core=5.3.0 - keyutils=1.6.1 - - kiwisolver=1.3.2 - - krb5=1.19.2 - - lazy-object-proxy=1.6.0 - - lcms2=2.12 - - ld_impl_linux-64=2.36.1 - - lerc=3.0 + - kiwisolver=1.4.4 + - krb5=1.20.1 + - lame=3.100 + - lazy-object-proxy=1.9.0 + - lcms2=2.15 + - ld_impl_linux-64=2.40 + - lerc=4.0.0 + - libaec=1.0.6 + - libarchive=3.6.2 - libblas=3.9.0 - libbrotlicommon=1.0.9 - libbrotlidec=1.0.9 - libbrotlienc=1.0.9 + - libcap=2.67 - libcblas=3.9.0 - - libclang=11.1.0 - - libcurl=7.80.0 - - libdeflate=1.8 + - libclang=16.0.4 + - libclang13=16.0.4 + - libcups=2.3.3 + - libcurl=8.1.1 + - libdeflate=1.18 - libedit=3.1.20191231 - libev=4.33 - - libevent=2.1.10 + - libevent=2.1.12 + - libexpat=2.5.0 - libffi=3.4.2 - - libgcc-ng=11.2.0 - - libgfortran-ng=11.2.0 - - libgfortran5=11.2.0 - - libglib=2.70.0 - - libgomp=11.2.0 - - libiconv=1.16 + - libflac=1.4.2 + - libgcc-ng=12.2.0 + - libgcrypt=1.10.1 + - libgfortran-ng=12.2.0 + - libgfortran5=12.2.0 + - libglib=2.76.3 + - libgomp=12.2.0 + - libgpg-error=1.46 + - libiconv=1.17 + - libjpeg-turbo=2.1.5.1 - liblapack=3.9.0 - - libllvm11=11.1.0 - - libllvm9=9.0.1 - - libnetcdf=4.8.1 - - libnghttp2=1.43.0 + - liblief=0.12.3 + - libllvm16=16.0.4 + - libmamba=1.4.2 + - libmambapy=1.4.2 + - libnetcdf=4.9.2 + - libnghttp2=1.52.0 - libnsl=2.0.0 - libogg=1.3.4 - - libopenblas=0.3.18 + - libopenblas=0.3.21 - libopus=1.3.1 - - libpng=1.6.37 - - libpq=13.3 + - libpng=1.6.39 + - libpq=15.3 + - libsndfile=1.2.0 + - libsolv=0.7.23 + - libsqlite=3.42.0 - libssh2=1.10.0 - - libstdcxx-ng=11.2.0 - - libtiff=4.3.0 - - libuuid=2.32.1 + - libstdcxx-ng=12.2.0 + - libsystemd0=253 + - libtiff=4.5.0 + - libuuid=2.38.1 - libvorbis=1.3.7 - - libwebp=1.2.1 - - libwebp-base=1.2.1 - - libxcb=1.13 - - libxkbcommon=1.0.3 - - libxml2=2.9.12 - - libzip=1.8.0 - - libzlib=1.2.11 + - libwebp-base=1.3.0 + - libxcb=1.15 + - libxkbcommon=1.5.0 + - libxml2=2.11.4 + - libzip=1.9.2 + - libzlib=1.2.13 - livereload=2.6.3 - - llvm-openmp=12.0.1 - - lz4-c=1.9.3 - - markupsafe=2.0.1 - - matplotlib=3.4.3 - - matplotlib-base=3.4.3 - - matplotlib-inline=0.1.3 - - more-itertools=8.11.0 + - lz4-c=1.9.4 + - lzo=2.10 + - mamba=1.4.2 + - markdown-it-py=2.2.0 + - markupsafe=2.1.2 + - matplotlib=3.7.1 + - matplotlib-base=3.7.1 + - matplotlib-inline=0.1.6 + - mccabe=0.7.0 + - mdurl=0.1.0 + - mpg123=1.31.3 - munkres=1.1.4 - - mypy=0.931 - - mypy_extensions=0.4.3 - - mysql-common=8.0.27 - - mysql-libs=8.0.27 - - ncurses=6.2 - - netcdf4=1.5.8 - - nodeenv=1.6.0 - - nspr=4.32 - - nss=3.72 - - numpy=1.22.3 - - olefile=0.46 - - openjpeg=2.4.0 - - openssl=1.1.1l - - packaging=21.0 - - parso=0.8.2 - - pathspec=0.9.0 - - pcre=8.45 + - mypy=1.3.0 + - mypy_extensions=1.0.0 + - mysql-common=8.0.32 + - mysql-libs=8.0.32 + - nbformat=5.8.0 + - ncurses=6.3 + - netcdf4=1.6.3 + - nodeenv=1.8.0 + - nspr=4.35 + - nss=3.89 + - numpy=1.24.3 + - openjpeg=2.5.0 + - openssl=3.1.0 + - packaging=23.1 + - parso=0.8.3 + - patch=2.7.6 + - patchelf=0.18.0 + - pathspec=0.11.1 + - pcre2=10.40 - pexpect=4.8.0 - pickleshare=0.7.5 - - pillow=8.4.0 - - pip=21.3.1 - - platformdirs=2.3.0 - - pluggy=0.13.1 - - pre-commit=2.17.0 - - proj=8.2.0 - - prompt-toolkit=3.0.22 - - psutil=5.8.0 + - pillow=9.5.0 + - pip=23.1.2 + - pixman=0.40.0 + - pkginfo=1.9.6 + - pkgutil-resolve-name=1.3.10 + - platformdirs=3.5.1 + - pluggy=1.0.0 + - ply=3.11 + - pooch=1.7.0 + - pre-commit=3.3.2 + - proj=9.2.0 + - prompt-toolkit=3.0.38 + - prompt_toolkit=3.0.38 + - psutil=5.9.5 - pthread-stubs=0.4 - ptyprocess=0.7.0 + - pulseaudio-client=16.1 - pure_eval=0.2.2 - - py=1.11.0 + - py-lief=0.12.3 + - pybind11-abi=4 + - pycodestyle=2.10.0 + - pycosat=0.6.4 - pycparser=2.21 - - pydocstyle=6.1.1 - - pygments=2.10.0 - - pylint=2.11.1 - - pyopenssl=21.0.0 - - pyparsing=3.0.6 - - pypdf2=1.26.0 - - pyproj=3.2.1 - - pyqt=5.12.3 - - pyqt-impl=5.12.3 - - pyqt5-sip=4.19.18 - - pyqtchart=5.12 - - pyqtwebengine=5.12.1 - - pyshp=2.1.3 + - pydantic=1.10.8 + - pydocstyle=6.3.0 + - pyflakes=3.0.1 + - pygments=2.15.1 + - pylint=2.17.4 + - pyopenssl=23.1.1 + - pyparsing=3.0.9 + - pypdf2=1.28.4 + - pyproj=3.5.0 + - pyqt=5.15.7 + - pyqt5-sip=12.11.0 + - pyrsistent=0.19.3 + - pyshp=2.3.1 - pysocks=1.7.1 - - pytest=7.0.1 - - python=3.9.7 + - pytest=7.3.1 + - python=3.10.11 - python-dateutil=2.8.2 - - python_abi=3.9 - - pytz=2021.3 + - python-fastjsonschema=2.17.1 + - python-libarchive-c=4.0 + - python_abi=3.10 + - pytoolconfig=1.2.5 + - pytz=2023.3 - pyyaml=6.0 - - qt=5.12.9 - - readline=8.1 - - regex=2021.11.10 - - requests=2.26.0 - - rope=0.23.0 - - rstcheck=3.3.1 - - scipy=1.8.0 - - setuptools=59.1.1 - - shapely=1.8.0 + - qt-main=5.15.8 + - readline=8.2 + - reproc=14.2.4 + - reproc-cpp=14.2.4 + - requests=2.31.0 + - requests-toolbelt=1.0.0 + - rich=13.3.5 + - ripgrep=13.0.0 + - rope=1.8.0 + - rstcheck=6.1.2 + - rstcheck-core=1.0.3 + - ruamel.yaml=0.17.27 + - ruamel.yaml.clib=0.2.7 + - ruamel_yaml=0.15.80 + - scipy=1.10.1 + - setuptools=67.7.2 + - shapely=2.0.1 + - shellingham=1.5.1 + - sip=6.7.9 - six=1.16.0 - - snowballstemmer=2.1.0 - - sphinx=4.3.1 + - snappy=1.1.10 + - sniffio=1.3.0 + - snowballstemmer=2.2.0 + - soupsieve=2.3.2.post1 + - sphinx=7.0.1 - sphinx-autobuild=2021.3.14 - - sphinxcontrib-applehelp=1.0.2 + - sphinxcontrib-applehelp=1.0.4 - sphinxcontrib-devhelp=1.0.2 - - sphinxcontrib-htmlhelp=2.0.0 + - sphinxcontrib-htmlhelp=2.0.1 - sphinxcontrib-jsmath=1.0.1 - sphinxcontrib-qthelp=1.0.3 - sphinxcontrib-serializinghtml=1.1.5 - - sqlite=3.36.0 - - stack_data=0.2.0 - - tbb=2021.4.0 - - tk=8.6.11 + - sqlite=3.42.0 + - stack_data=0.6.2 + - tk=8.6.12 - toml=0.10.2 - - tomli=1.2.2 - - tornado=6.1 - - tox=3.24.5 - - tox-conda=0.9.2 - - traitlets=5.1.1 - - typed-ast=1.5.0 - - types-toml=0.10.4 - - typing-extensions=3.10.0.2 - - typing_extensions=3.10.0.2 - - tzdata=2021e - - urllib3=1.26.7 - - virtualenv=20.4.7 - - wcwidth=0.2.5 - - wheel=0.37.0 - - wrapt=1.12.1 - - xorg-libxau=1.0.9 + - tomli=2.0.1 + - tomlkit=0.11.8 + - toolz=0.12.0 + - tornado=6.3.2 + - tqdm=4.65.0 + - traitlets=5.9.0 + - typer=0.4.2 + - types-docutils=0.18.3 + - types-setuptools=67.8.0.0 + - types-toml=0.10.8.6 + - typing-extensions=4.6.2 + - typing_extensions=4.6.2 + - tzdata=2023c + - ukkonen=1.0.1 + - unicodedata2=15.0.0 + - urllib3=1.26.15 + - virtualenv=20.23.0 + - watchgod=0.8.2 + - wcwidth=0.2.6 + - wheel=0.40.0 + - wrapt=1.15.0 + - xcb-util=0.4.0 + - xcb-util-image=0.4.0 + - xcb-util-keysyms=0.4.0 + - xcb-util-renderutil=0.3.9 + - xcb-util-wm=0.4.1 + - xkeyboard-config=2.38 + - xorg-kbproto=1.0.7 + - xorg-libice=1.0.10 + - xorg-libsm=1.2.3 + - xorg-libx11=1.8.4 + - xorg-libxau=1.0.11 - xorg-libxdmcp=1.1.3 - - xz=5.2.5 + - xorg-libxext=1.3.4 + - xorg-libxrender=0.9.10 + - xorg-renderproto=0.11.1 + - xorg-xextproto=7.3.0 + - xorg-xf86vidmodeproto=2.3.1 + - xorg-xproto=7.0.31 + - xz=5.2.6 - yaml=0.2.5 - - zipp=3.6.0 - - zlib=1.2.11 - - zstd=1.5.0 + - yaml-cpp=0.7.0 + - zipp=3.15.0 + - zlib=1.2.13 + - zstandard=0.19.0 + - zstd=1.5.2 - pip: - - flake8==6.0.0 - - flake8-pyproject==1.2.2 - - mccabe==0.7.0 - - pycodestyle==2.10.0 - - pyflakes==3.0.1 + - copier==7.2.0 + - dunamai==1.17.0 + - flake8-pyproject==1.2.3 + - funcy==2.0 + - jinja2-ansible-filters==1.3.2 + - mistune==2.0.5 + - plumbum==1.8.1 + - pyyaml-include==1.3 + - questionary==1.10.0 + - sphinx-mdinclude==0.5.3 diff --git a/src/pyflexplot/input/species.py b/src/pyflexplot/input/species.py index 111bdc3f..e6f5fe42 100644 --- a/src/pyflexplot/input/species.py +++ b/src/pyflexplot/input/species.py @@ -50,18 +50,18 @@ class Species: id_cosmo: int = -99 id_ifs: int = -99 name: str = "N/A" - weight: SpeciesAttribute = dc.field(default=SpeciesAttribute(-99.9, "g mol-1")) - half_life: SpeciesAttribute = dc.field(default=SpeciesAttribute(-99.9, "a")) + weight: SpeciesAttribute = dc.field(default=SpeciesAttribute) + half_life: SpeciesAttribute = dc.field(default=SpeciesAttribute) deposition_velocity: SpeciesAttribute = dc.field( - default=SpeciesAttribute(-99.9, "m s-1") + default=SpeciesAttribute ) sedimentation_velocity: SpeciesAttribute = dc.field( - default=SpeciesAttribute(-99.9, "m s-1") + default=SpeciesAttribute ) washout_coefficient: SpeciesAttribute = dc.field( - default=SpeciesAttribute(-99.9, "s-1") + default=SpeciesAttribute ) - washout_exponent: SpeciesAttribute = dc.field(default=SpeciesAttribute(-99.9)) + washout_exponent: SpeciesAttribute = dc.field(default=SpeciesAttribute) @classmethod def create(cls, **params: Any) -> "Species": @@ -77,6 +77,13 @@ def create(cls, **params: Any) -> "Species": params_prep[param] = value return cls(**params_prep) + def __post_init__(self): + self.weight = SpeciesAttribute(-99.9, "g mol-1") + self.half_life = SpeciesAttribute(-99.9, "a") + self.deposition_velocity = SpeciesAttribute(-99.9, "m s-1") + self.sedimentation_velocity = SpeciesAttribute(-99.9, "m s-1") + self.washout_coefficient = SpeciesAttribute(-99.9, "s-1") + self.washout_exponent = SpeciesAttribute(-99.9) # See `flexpart/options/SPECIES/SPECIES_???` # Corresponding parameters: diff --git a/tools/setup_env.sh b/tools/setup_env.sh index f40cbe85..50bd5e80 100755 --- a/tools/setup_env.sh +++ b/tools/setup_env.sh @@ -20,7 +20,7 @@ HELP=false help_msg="Usage: $(basename "${0}") [-n NAME] [-p VER] [-u] [-e] [-m] [-h] Options: - -n NAME Env name [default: ${DEFAULT_ENV_NAME} + -n NAME Env name [default: ${DEFAULT_ENV_NAME}] -p VER Python version [default: ${PYVERSION}] -u Use unpinned requirements (minimal version restrictions) -e Export environment files (requires -u) From f2c7d10df013d7bb63bfed57d0ca0c00fceb796c Mon Sep 17 00:00:00 2001 From: Tobias Wicky Date: Thu, 1 Jun 2023 13:52:46 +0200 Subject: [PATCH 08/24] fix on dataclasses wrapper --- src/srutils/dataclasses.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/srutils/dataclasses.py b/src/srutils/dataclasses.py index 1cc20909..8501042a 100644 --- a/src/srutils/dataclasses.py +++ b/src/srutils/dataclasses.py @@ -5,7 +5,7 @@ import dataclasses as dc from datetime import datetime from datetime import timedelta -from typing import Any +from typing import Any, get_args from typing import Callable from typing import Collection from typing import get_type_hints @@ -133,6 +133,12 @@ def cast_field_value(cls: Type, name: str, value: Any, **kwargs: Any) -> Any: exc = InvalidParameterValueError msg = f"value incompatible with type {type_name}" elif isinstance(e, UnsupportedTypeError): + for arg in get_args(type_): + try: + if isinstance(value, arg): + return value + except TypeError as e: + pass exc = InvalidParameterNameError msg = f"type {type_name} not supported" else: From 872adf070db9c5ed0f0331901abfe2b8c32ae819 Mon Sep 17 00:00:00 2001 From: Pirmin Kaufmann Date: Thu, 8 Jun 2023 15:41:09 +0200 Subject: [PATCH 09/24] Added working environment.yml: using unpinned installation does currently not yield a working environment. --- requirements/environment.yml | 464 +++++++++++++---------------------- 1 file changed, 175 insertions(+), 289 deletions(-) diff --git a/requirements/environment.yml b/requirements/environment.yml index fd6074f5..965b144b 100644 --- a/requirements/environment.yml +++ b/requirements/environment.yml @@ -5,339 +5,225 @@ channels: dependencies: - _libgcc_mutex=0.1 - _openmp_mutex=4.5 - - alabaster=0.7.13 - - alsa-lib=1.2.8 - - anaconda-client=1.11.2 - - anaconda-project=0.11.1 - - anyio=3.6.2 - - astroid=2.15.5 - - asttokens=2.2.1 - - attr=2.5.1 - - attrs=23.1.0 - - babel=2.12.1 + - alabaster=0.7.12 + - alsa-lib=1.2.3 + - appdirs=1.4.4 + - astroid=2.8.5 + - attrs=21.2.0 + - babel=2.9.1 - backcall=0.2.0 - backports=1.0 - backports.functools_lru_cache=1.6.4 - - beautifulsoup4=4.12.2 - - black=23.3.0 - - blosc=1.21.4 - - boa=0.14.0 - - boltons=23.0.0 + - black=21.12b0 - brotli=1.0.9 - brotli-bin=1.0.9 - brotlipy=0.7.0 + - bump2version=1.0.1 - bzip2=1.0.8 - - c-ares=1.19.1 - - ca-certificates=2023.5.7 - - cairo=1.16.0 - - cartopy=0.21.1 - - certifi=2023.5.7 - - cffi=1.15.1 + - c-ares=1.18.1 + - ca-certificates=2021.10.8 + - cartopy=0.20.1 + - certifi=2021.10.8 + - cffi=1.15.0 - cfgv=3.3.1 - - cftime=1.6.2 - - chardet=5.1.0 - - charset-normalizer=3.1.0 - - click=8.1.3 - - clyent=1.2.2 - - codespell=2.2.4 - - colorama=0.4.6 - - conda=23.3.1 - - conda-build=3.24.0 - - conda-pack=0.7.0 - - conda-package-handling=2.0.2 - - conda-package-streaming=0.8.0 - - contourpy=1.0.7 - - cryptography=40.0.2 - - curl=8.1.1 + - cftime=1.5.1.1 + - chardet=4.0.0 + - charset-normalizer=2.0.0 + - click=8.0.4 + - codespell=2.1.0 + - colorama=0.4.4 + - cryptography=35.0.0 + - curl=7.80.0 - cycler=0.11.0 - dataclasses=0.8 - dbus=1.13.6 - - decorator=5.1.1 - - defusedxml=0.7.1 - - dill=0.3.6 - - distlib=0.3.6 - - docutils=0.18.1 - - exceptiongroup=1.1.1 - - executing=1.2.0 - - expat=2.5.0 - - filelock=3.12.0 - - flake8=6.0.0 - - flake8-black=0.3.6 - - fmt=9.1.0 - - font-ttf-dejavu-sans-mono=2.37 - - font-ttf-inconsolata=3.000 - - font-ttf-source-code-pro=2.038 - - font-ttf-ubuntu=0.83 - - fontconfig=2.14.2 - - fonts-conda-ecosystem=1 - - fonts-conda-forge=1 - - fonttools=4.39.4 - - freetype=2.12.1 + - decorator=5.1.0 + - distlib=0.3.3 + - docutils=0.16 + - editdistance-s=1.0.0 + - expat=2.4.1 + - filelock=3.3.2 + - flake8=4.0.1 + - flake8-black=0.2.3 + - fontconfig=2.13.1 + - freetype=2.10.4 - geographiclib=1.52 - - geopy=2.3.0 - - geos=3.11.2 - - gettext=0.21.1 - - glib=2.76.3 - - glib-tools=2.76.3 - - glob2=0.7 - - graphite2=1.3.13 - - gst-plugins-base=1.22.3 - - gstreamer=1.22.3 - - harfbuzz=7.3.0 + - geopy=2.2.0 + - geos=3.10.0 + - gettext=0.19.8.1 + - giflib=5.2.1 + - glib=2.70.0 + - glib-tools=2.70.0 + - gst-plugins-base=1.18.5 + - gstreamer=1.18.5 - hdf4=4.2.15 - - hdf5=1.14.0 - - icu=72.1 - - identify=2.5.24 - - idna=3.4 - - imagesize=1.4.1 - - importlib-metadata=4.13.0 - - importlib_resources=5.12.0 - - iniconfig=2.0.0 - - ipdb=0.13.13 - - ipython=8.13.2 - - isort=5.12.0 - - jedi=0.18.2 - - jinja2=3.1.2 - - joblib=1.2.0 - - json5=0.9.5 - - jsonpatch=1.32 - - jsonpointer=2.0 - - jsonschema=4.17.3 - - jupyter_core=5.3.0 + - hdf5=1.12.1 + - icu=68.2 + - identify=2.3.6 + - idna=3.1 + - imagesize=1.3.0 + - importlib-metadata=3.10.1 + - iniconfig=1.1.1 + - intel-openmp=2021.4.0 + - ipdb=0.13.9 + - ipython=7.30.1 + - isort=5.10.1 + - jbig=2.1 + - jedi=0.18.0 + - jinja2=3.0.3 + - jpeg=9d - keyutils=1.6.1 - - kiwisolver=1.4.4 - - krb5=1.20.1 - - lame=3.100 - - lazy-object-proxy=1.9.0 - - lcms2=2.15 - - ld_impl_linux-64=2.40 - - lerc=4.0.0 - - libaec=1.0.6 - - libarchive=3.6.2 + - kiwisolver=1.3.2 + - krb5=1.19.2 + - lazy-object-proxy=1.6.0 + - lcms2=2.12 + - ld_impl_linux-64=2.36.1 + - lerc=3.0 - libblas=3.9.0 - libbrotlicommon=1.0.9 - libbrotlidec=1.0.9 - libbrotlienc=1.0.9 - - libcap=2.67 - libcblas=3.9.0 - - libclang=16.0.4 - - libclang13=16.0.4 - - libcups=2.3.3 - - libcurl=8.1.1 - - libdeflate=1.18 + - libclang=11.1.0 + - libcurl=7.80.0 + - libdeflate=1.8 - libedit=3.1.20191231 - libev=4.33 - - libevent=2.1.12 - - libexpat=2.5.0 + - libevent=2.1.10 - libffi=3.4.2 - - libflac=1.4.2 - - libgcc-ng=12.2.0 - - libgcrypt=1.10.1 - - libgfortran-ng=12.2.0 - - libgfortran5=12.2.0 - - libglib=2.76.3 - - libgomp=12.2.0 - - libgpg-error=1.46 - - libiconv=1.17 - - libjpeg-turbo=2.1.5.1 + - libgcc-ng=11.2.0 + - libgfortran-ng=11.2.0 + - libgfortran5=11.2.0 + - libglib=2.70.0 + - libgomp=11.2.0 + - libiconv=1.16 - liblapack=3.9.0 - - liblief=0.12.3 - - libllvm16=16.0.4 - - libmamba=1.4.2 - - libmambapy=1.4.2 - - libnetcdf=4.9.2 - - libnghttp2=1.52.0 + - libllvm11=11.1.0 + - libllvm9=9.0.1 + - libnetcdf=4.8.1 + - libnghttp2=1.43.0 - libnsl=2.0.0 - libogg=1.3.4 - - libopenblas=0.3.21 + - libopenblas=0.3.18 - libopus=1.3.1 - - libpng=1.6.39 - - libpq=15.3 - - libsndfile=1.2.0 - - libsolv=0.7.23 - - libsqlite=3.42.0 + - libpng=1.6.37 + - libpq=13.3 - libssh2=1.10.0 - - libstdcxx-ng=12.2.0 - - libsystemd0=253 - - libtiff=4.5.0 - - libuuid=2.38.1 + - libstdcxx-ng=11.2.0 + - libtiff=4.3.0 + - libuuid=2.32.1 - libvorbis=1.3.7 - - libwebp-base=1.3.0 - - libxcb=1.15 - - libxkbcommon=1.5.0 - - libxml2=2.11.4 - - libzip=1.9.2 - - libzlib=1.2.13 + - libwebp=1.2.1 + - libwebp-base=1.2.1 + - libxcb=1.13 + - libxkbcommon=1.0.3 + - libxml2=2.9.12 + - libzip=1.8.0 + - libzlib=1.2.11 - livereload=2.6.3 - - lz4-c=1.9.4 - - lzo=2.10 - - mamba=1.4.2 - - markdown-it-py=2.2.0 - - markupsafe=2.1.2 - - matplotlib=3.7.1 - - matplotlib-base=3.7.1 - - matplotlib-inline=0.1.6 - - mccabe=0.7.0 - - mdurl=0.1.0 - - mpg123=1.31.3 + - llvm-openmp=12.0.1 + - lz4-c=1.9.3 + - markupsafe=2.0.1 + - matplotlib=3.4.3 + - matplotlib-base=3.4.3 + - matplotlib-inline=0.1.3 + - mccabe=0.6.1 + - more-itertools=8.11.0 - munkres=1.1.4 - - mypy=1.3.0 - - mypy_extensions=1.0.0 - - mysql-common=8.0.32 - - mysql-libs=8.0.32 - - nbformat=5.8.0 - - ncurses=6.3 - - netcdf4=1.6.3 - - nodeenv=1.8.0 - - nspr=4.35 - - nss=3.89 - - numpy=1.24.3 - - openjpeg=2.5.0 - - openssl=3.1.0 - - packaging=23.1 - - parso=0.8.3 - - patch=2.7.6 - - patchelf=0.18.0 - - pathspec=0.11.1 - - pcre2=10.40 + - mypy=0.910 + - mypy_extensions=0.4.3 + - mysql-common=8.0.27 + - mysql-libs=8.0.27 + - ncurses=6.2 + - netcdf4=1.5.8 + - nodeenv=1.6.0 + - nspr=4.32 + - nss=3.72 + - numpy=1.22.3 + - olefile=0.46 + - openjpeg=2.4.0 + - openssl=1.1.1l + - packaging=21.0 + - parso=0.8.2 + - pathspec=0.9.0 + - pcre=8.45 - pexpect=4.8.0 - pickleshare=0.7.5 - - pillow=9.5.0 - - pip=23.1.2 - - pixman=0.40.0 - - pkginfo=1.9.6 - - pkgutil-resolve-name=1.3.10 - - platformdirs=3.5.1 - - pluggy=1.0.0 - - ply=3.11 - - pooch=1.7.0 - - pre-commit=3.3.2 - - proj=9.2.0 - - prompt-toolkit=3.0.38 - - prompt_toolkit=3.0.38 - - psutil=5.9.5 + - pillow=8.4.0 + - pip=21.3.1 + - platformdirs=2.3.0 + - pluggy=0.13.1 + - pre-commit=2.16.0 + - proj=8.2.0 + - prompt-toolkit=3.0.22 + - psutil=5.8.0 - pthread-stubs=0.4 - ptyprocess=0.7.0 - - pulseaudio-client=16.1 - - pure_eval=0.2.2 - - py-lief=0.12.3 - - pybind11-abi=4 - - pycodestyle=2.10.0 - - pycosat=0.6.4 + - py=1.11.0 + - pycodestyle=2.8.0 - pycparser=2.21 - - pydantic=1.10.8 - - pydocstyle=6.3.0 - - pyflakes=3.0.1 - - pygments=2.15.1 - - pylint=2.17.4 - - pyopenssl=23.1.1 - - pyparsing=3.0.9 - - pypdf2=1.28.4 - - pyproj=3.5.0 - - pyqt=5.15.7 - - pyqt5-sip=12.11.0 - - pyrsistent=0.19.3 - - pyshp=2.3.1 + - pydocstyle=6.1.1 + - pyflakes=2.4.0 + - pygments=2.10.0 + - pylint=2.11.1 + - pyopenssl=21.0.0 + - pyparsing=3.0.6 + - pypdf2=1.26.0 + - pyproj=3.2.1 + - pyqt=5.12.3 + - pyqt-impl=5.12.3 + - pyqt5-sip=4.19.18 + - pyqtchart=5.12 + - pyqtwebengine=5.12.1 + - pyshp=2.1.3 - pysocks=1.7.1 - - pytest=7.3.1 - - python=3.10.11 + - pytest=6.2.5 + - python=3.9.7 - python-dateutil=2.8.2 - - python-fastjsonschema=2.17.1 - - python-libarchive-c=4.0 - - python_abi=3.10 - - pytoolconfig=1.2.5 - - pytz=2023.3 + - python_abi=3.9 + - pytz=2021.3 - pyyaml=6.0 - - qt-main=5.15.8 - - readline=8.2 - - reproc=14.2.4 - - reproc-cpp=14.2.4 - - requests=2.31.0 - - requests-toolbelt=1.0.0 - - rich=13.3.5 - - ripgrep=13.0.0 - - rope=1.8.0 - - rstcheck=6.1.2 - - rstcheck-core=1.0.3 - - ruamel.yaml=0.17.27 - - ruamel.yaml.clib=0.2.7 - - ruamel_yaml=0.15.80 - - scipy=1.10.1 - - setuptools=67.7.2 - - shapely=2.0.1 - - shellingham=1.5.1 - - sip=6.7.9 + - qt=5.12.9 + - readline=8.1 + - regex=2021.11.10 + - requests=2.26.0 + - rope=0.22.0 + - rstcheck=3.3.1 + - scipy=1.8.0 + - setuptools=59.1.1 + - shapely=1.8.0 - six=1.16.0 - - snappy=1.1.10 - - sniffio=1.3.0 - - snowballstemmer=2.2.0 - - soupsieve=2.3.2.post1 - - sphinx=7.0.1 + - snowballstemmer=2.1.0 + - sphinx=4.3.1 - sphinx-autobuild=2021.3.14 - - sphinxcontrib-applehelp=1.0.4 + - sphinxcontrib-applehelp=1.0.2 - sphinxcontrib-devhelp=1.0.2 - - sphinxcontrib-htmlhelp=2.0.1 + - sphinxcontrib-htmlhelp=2.0.0 - sphinxcontrib-jsmath=1.0.1 - sphinxcontrib-qthelp=1.0.3 - sphinxcontrib-serializinghtml=1.1.5 - - sqlite=3.42.0 - - stack_data=0.6.2 - - tk=8.6.12 + - sqlite=3.36.0 + - tbb=2021.4.0 + - tk=8.6.11 - toml=0.10.2 - - tomli=2.0.1 - - tomlkit=0.11.8 - - toolz=0.12.0 - - tornado=6.3.2 - - tqdm=4.65.0 - - traitlets=5.9.0 - - typer=0.4.2 - - types-docutils=0.18.3 - - types-setuptools=67.8.0.0 - - types-toml=0.10.8.6 - - typing-extensions=4.6.2 - - typing_extensions=4.6.2 - - tzdata=2023c - - ukkonen=1.0.1 - - unicodedata2=15.0.0 - - urllib3=1.26.15 - - virtualenv=20.23.0 - - watchgod=0.8.2 - - wcwidth=0.2.6 - - wheel=0.40.0 - - wrapt=1.15.0 - - xcb-util=0.4.0 - - xcb-util-image=0.4.0 - - xcb-util-keysyms=0.4.0 - - xcb-util-renderutil=0.3.9 - - xcb-util-wm=0.4.1 - - xkeyboard-config=2.38 - - xorg-kbproto=1.0.7 - - xorg-libice=1.0.10 - - xorg-libsm=1.2.3 - - xorg-libx11=1.8.4 - - xorg-libxau=1.0.11 + - tomli=1.2.2 + - tornado=6.1 + - tox=3.24.4 + - traitlets=5.1.1 + - typed-ast=1.5.0 + - types-toml=0.10.1 + - typing-extensions=3.10.0.2 + - typing_extensions=3.10.0.2 + - tzdata=2021e + - urllib3=1.26.7 + - virtualenv=20.4.7 + - wcwidth=0.2.5 + - wheel=0.37.0 + - wrapt=1.12.1 + - xorg-libxau=1.0.9 - xorg-libxdmcp=1.1.3 - - xorg-libxext=1.3.4 - - xorg-libxrender=0.9.10 - - xorg-renderproto=0.11.1 - - xorg-xextproto=7.3.0 - - xorg-xf86vidmodeproto=2.3.1 - - xorg-xproto=7.0.31 - - xz=5.2.6 + - xz=5.2.5 - yaml=0.2.5 - - yaml-cpp=0.7.0 - - zipp=3.15.0 - - zlib=1.2.13 - - zstandard=0.19.0 - - zstd=1.5.2 - - pip: - - copier==7.2.0 - - dunamai==1.17.0 - - flake8-pyproject==1.2.3 - - funcy==2.0 - - jinja2-ansible-filters==1.3.2 - - mistune==2.0.5 - - plumbum==1.8.1 - - pyyaml-include==1.3 - - questionary==1.10.0 - - sphinx-mdinclude==0.5.3 + - zipp=3.6.0 + - zlib=1.2.11 + - zstd=1.5.0 From 2e9d6c6b8d401ff698b99b1efdc1d3cc4dd1b382 Mon Sep 17 00:00:00 2001 From: Pirmin Kaufmann Date: Thu, 8 Jun 2023 17:19:17 +0200 Subject: [PATCH 10/24] Updated to new blueprint using copier. --- .copier-answers.yml | 2 +- README.md | 4 +-- docs/documentation.inactive | 2 +- jenkins/JenkinsJobPR | 33 ------------------- jenkins/Jenkinsfile | 8 ----- pyproject.toml | 5 +-- src/pyflexplot/cli/main.py | 2 -- src/pyflexplot/input/meta_data.py | 1 - src/pyflexplot/input/species.py | 13 +++----- src/pyflexplot/output.py | 1 - src/pyflexplot/plots.py | 2 -- src/pyflexplot/plotting/ref_dist_indicator.py | 3 -- src/pyflexplot/plotting/text_box_axes.py | 1 - src/pyflexplot/setups/plot_panel_setup.py | 1 - src/pyflexplot/setups/plot_setup.py | 1 - src/pyflexplot/utils/formatting.py | 1 - src/srutils/dataclasses.py | 3 +- src/srutils/dict.py | 2 -- src/srutils/testing.py | 2 +- .../test_dict/nested/test_decompress.py | 1 - tests/fast/test_words/test_test.py | 1 - .../fast/test_words/test_translated_words.py | 1 - .../test_deterministic.py | 1 - 23 files changed, 14 insertions(+), 77 deletions(-) delete mode 100644 jenkins/JenkinsJobPR diff --git a/.copier-answers.yml b/.copier-answers.yml index f350d68f..9ac0d897 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,5 +1,5 @@ # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY -_commit: a1078ae +_commit: cc8b3de _src_path: git@github.com:MeteoSwiss-APN/mch-python-blueprint.git email: stefan.ruedisuehli@env.ethz.ch full_name: Stefan Ruedisuehli diff --git a/README.md b/README.md index 91e94ca9..ae72a0b2 100644 --- a/README.md +++ b/README.md @@ -86,8 +86,8 @@ and in pull requests to the main branch. ### Jenkins -Two jenkins plans are available in the `jenkins/` folder. On the one hand `jenkins/Jenkinsfile` controls the nightly (weekly, monthly, ...) builds, on the other hand -`jenkins/JenkinsJobPR` controls the pipeline invoked with the command `launch jenkins` in pull requests on GitHub. Your jenkins pipeline will not be set up +A jenkinsfile is available in the `jenkins/` folder. It can be used for a multibranch jenkins project, which builds +both commits on branches and PRs. Your jenkins pipeline will not be set up automatically. If you need to run your tests on CSCS machines, contact DevOps to help you with the setup of the pipelines. Otherwise, you can ignore the jenkinsfiles and exclusively run your tests and checks on GitHub actions. diff --git a/docs/documentation.inactive b/docs/documentation.inactive index 6355c16d..ad133f3f 100644 --- a/docs/documentation.inactive +++ b/docs/documentation.inactive @@ -17,7 +17,7 @@ jobs: - uses: actions/checkout@v1 - uses: C2SM/sphinx-action@sphinx-latest with: - pre-build-command: '' + pre-build-command: "pip install ." docs-folder: "docs/" # Great extra actions to compose with: # Create an artifact of the html output. diff --git a/jenkins/JenkinsJobPR b/jenkins/JenkinsJobPR deleted file mode 100644 index 8a10ef6e..00000000 --- a/jenkins/JenkinsJobPR +++ /dev/null @@ -1,33 +0,0 @@ -pipelineJob('pyflexplot_PR') { - parameters { - stringParam('sha1', 'main') - } - definition { - cpsScm { - scm { - git { - remote { - github('MeteoSwiss-APN/pyflexplot') - refspec('+refs/pull/*:refs/remotes/origin/pr/*') - credentials('466e4dd5-80af-4935-828f-a9fff24b46de') - } - branch('${sha1}') - } - } - triggers { - githubPullRequest { - orgWhitelist('MeteoSwiss-APN') - triggerPhrase('launch jenkins.*') - onlyTriggerPhrase() - useGitHubHooks() - extensions { - commitStatus { - context('MeteoSwiss Jenkins - pull request') - } - } - } - } - scriptPath('jenkins/Jenkinsfile') - } - } -} diff --git a/jenkins/Jenkinsfile b/jenkins/Jenkinsfile index 6af66015..0d421026 100644 --- a/jenkins/Jenkinsfile +++ b/jenkins/Jenkinsfile @@ -32,7 +32,6 @@ pipeline { steps { sh '''#!/usr/bin/env bash set -e - cd ${WORKSPACE}/pyflexplot source ${WORKSPACE}/miniconda/etc/profile.d/conda.sh conda init bash --no-user --install --system conda activate @@ -48,7 +47,6 @@ pipeline { source $WORKSPACE/miniconda/etc/profile.d/conda.sh conda init bash --no-user --install --system conda activate pyflexplot - cd ${WORKSPACE}/pyflexplot pytest tests ''' } @@ -60,7 +58,6 @@ pipeline { source $WORKSPACE/miniconda/etc/profile.d/conda.sh conda init bash --no-user --install --system conda activate - cd ${WORKSPACE}/pyflexplot bash tools/setup_env.sh -n dev-pyflexplot -u conda activate dev-pyflexplot pip install --no-deps --editable . @@ -73,7 +70,6 @@ pipeline { source $WORKSPACE/miniconda/etc/profile.d/conda.sh conda init bash --no-user --install --system conda activate dev-pyflexplot - cd ${WORKSPACE}/pyflexplot pytest tests ''' } @@ -85,7 +81,6 @@ pipeline { source $WORKSPACE/miniconda/etc/profile.d/conda.sh conda init bash --no-user --install --system conda activate - cd ${WORKSPACE}/pyflexplot bash tools/setup_env.sh -n pinned-pyflexplot conda activate pinned-pyflexplot pip install --no-deps . @@ -97,7 +92,6 @@ pipeline { sh '''#!/usr/bin/env bash source $WORKSPACE/miniconda/etc/profile.d/conda.sh conda activate pinned-pyflexplot - cd ${WORKSPACE}/pyflexplot pytest tests ''' } @@ -109,7 +103,6 @@ pipeline { source $WORKSPACE/miniconda/etc/profile.d/conda.sh conda init bash --no-user --install --system conda activate - cd ${WORKSPACE}/pyflexplot bash tools/setup_env.sh -n pinned-dev-pyflexplot conda activate pinned-dev-pyflexplot pip install --no-deps --editable . @@ -121,7 +114,6 @@ pipeline { sh '''#!/usr/bin/env bash source $WORKSPACE/miniconda/etc/profile.d/conda.sh conda activate pinned-dev-pyflexplot - cd ${WORKSPACE}/pyflexplot pytest tests ''' } diff --git a/pyproject.toml b/pyproject.toml index 70844ca9..2c9450a1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -156,7 +156,7 @@ disable = [ "W1116", # Second argument of isinstance is not a type (isinstance-second-argument-not-valid-type) # Migrated from old blueprint, check if still needed "W0602", # Using global for '...' but no assignment is done (global-variable-not-assigned) - "E0401", # Inable to import '...' (import-error) + "E0401", # Unable to import '...' (import-error) # -> Wrongly triggered for relative imports (pylint v2.11.1, 2022-03-09) # -> TODO Re-enable once fixed (see https://github.com/PyCQA/pylint/issues/3651) "C0330", # Wrong hanging indentation before block (add 4 spaces) @@ -194,4 +194,5 @@ ignore_directives = [ ] [tool.codespell] -ignore-words-list = "ue,fo" +ignore-words-list = "ende,ue,fo,activ,nd,feld,nd" +skip = "requirements/*,*.pdf" diff --git a/src/pyflexplot/cli/main.py b/src/pyflexplot/cli/main.py index a2c444dc..cee08748 100644 --- a/src/pyflexplot/cli/main.py +++ b/src/pyflexplot/cli/main.py @@ -238,7 +238,6 @@ def prepare_setups( suffixes: Optional[Union[str, Collection[str]]], only: Optional[int], ) -> List[PlotSetupGroup]: - # Extend preset setup file paths setup_file_paths = list(setup_file_paths) @@ -437,7 +436,6 @@ def merge_pdf_plots( keep_merged: bool = True, dry_run: bool = False, ) -> List[str]: - # Collect PDFs pdf_paths: List[str] = [] for path in paths: diff --git a/src/pyflexplot/input/meta_data.py b/src/pyflexplot/input/meta_data.py index 9a43a2f5..2fd922ac 100644 --- a/src/pyflexplot/input/meta_data.py +++ b/src/pyflexplot/input/meta_data.py @@ -487,7 +487,6 @@ def from_file( integrate: bool, add_ts0: bool, ) -> "SimulationMetaData": - # Start and end timesteps of simulation start = init_datetime( str(getncattr(fi, "ibdate")) + str(getncattr(fi, "ibtime")) diff --git a/src/pyflexplot/input/species.py b/src/pyflexplot/input/species.py index e6f5fe42..3e01bdd8 100644 --- a/src/pyflexplot/input/species.py +++ b/src/pyflexplot/input/species.py @@ -52,15 +52,9 @@ class Species: name: str = "N/A" weight: SpeciesAttribute = dc.field(default=SpeciesAttribute) half_life: SpeciesAttribute = dc.field(default=SpeciesAttribute) - deposition_velocity: SpeciesAttribute = dc.field( - default=SpeciesAttribute - ) - sedimentation_velocity: SpeciesAttribute = dc.field( - default=SpeciesAttribute - ) - washout_coefficient: SpeciesAttribute = dc.field( - default=SpeciesAttribute - ) + deposition_velocity: SpeciesAttribute = dc.field(default=SpeciesAttribute) + sedimentation_velocity: SpeciesAttribute = dc.field(default=SpeciesAttribute) + washout_coefficient: SpeciesAttribute = dc.field(default=SpeciesAttribute) washout_exponent: SpeciesAttribute = dc.field(default=SpeciesAttribute) @classmethod @@ -85,6 +79,7 @@ def __post_init__(self): self.washout_coefficient = SpeciesAttribute(-99.9, "s-1") self.washout_exponent = SpeciesAttribute(-99.9) + # See `flexpart/options/SPECIES/SPECIES_???` # Corresponding parameters: # Species() : SPECIES_??? diff --git a/src/pyflexplot/output.py b/src/pyflexplot/output.py index 7becb7e9..d1c3895c 100644 --- a/src/pyflexplot/output.py +++ b/src/pyflexplot/output.py @@ -190,7 +190,6 @@ def _replace_format_keys(template: str, kwargs: Mapping[str, Any]) -> str: rxs = r"{" + key + r"(:[^}]*)?}" re.finditer(rxs, path) for m in re.finditer(rxs, path): - # Obtain format specifier (if there is one) try: f = m.group(1) or "" diff --git a/src/pyflexplot/plots.py b/src/pyflexplot/plots.py index 8d566230..e4662d11 100644 --- a/src/pyflexplot/plots.py +++ b/src/pyflexplot/plots.py @@ -1640,7 +1640,6 @@ def format_vertical_level_range( value_top: Union[float, Sequence[float]], unit: str, ) -> Optional[str]: - if (value_bottom, value_top) == (-1, -1): return None @@ -1723,7 +1722,6 @@ def format_coord_label(direction: str, words: TranslatedWords, symbols: Words) - def colors_flexplot(n_levels: int, extend: str) -> Sequence[ColorType]: - color_under = "darkgray" color_over = "lightgray" diff --git a/src/pyflexplot/plotting/ref_dist_indicator.py b/src/pyflexplot/plotting/ref_dist_indicator.py index 6500be19..ce59d1c4 100644 --- a/src/pyflexplot/plotting/ref_dist_indicator.py +++ b/src/pyflexplot/plotting/ref_dist_indicator.py @@ -108,7 +108,6 @@ def add_to(self, ax: Axes, zorder: int) -> None: self._add_to(ax, zorder) def _add_to(self, ax: Axes, zorder: int) -> None: - # Draw box ax.add_patch( mpl.patches.Rectangle( @@ -264,7 +263,6 @@ def run(self, x0, y0, dist, dir_="east"): iter_max = 9999 for _ in range(iter_max): - # Step away from point until target distance exceeded path, dists = self._overstep(x, y, dist0, step_ax_rel) @@ -305,7 +303,6 @@ def _overstep(self, x0_ax, y0_ax, dist0, step_ax_rel): dist = 0.0 x1_ax, y1_ax = x0_ax, y0_ax while dist < self.dist - dist0: - # Move one step farther away from starting point x1_ax += self._dx_unit * step_ax_rel y1_ax += self._dy_unit * step_ax_rel diff --git a/src/pyflexplot/plotting/text_box_axes.py b/src/pyflexplot/plotting/text_box_axes.py index 93ee4da1..6159eeeb 100644 --- a/src/pyflexplot/plotting/text_box_axes.py +++ b/src/pyflexplot/plotting/text_box_axes.py @@ -424,7 +424,6 @@ def text_blocks( @staticmethod def _prepare_line_colors(blocks, colors, default_color): - if colors is None: colors_blocks = [None] * len(blocks) elif len(colors) == len(blocks): diff --git a/src/pyflexplot/setups/plot_panel_setup.py b/src/pyflexplot/setups/plot_panel_setup.py index fa4d51f2..32c3272f 100644 --- a/src/pyflexplot/setups/plot_panel_setup.py +++ b/src/pyflexplot/setups/plot_panel_setup.py @@ -109,7 +109,6 @@ class PlotPanelSetup(BaseSetup): # pylint: disable=R0912 # too-many-branches (>12) def __post_init__(self) -> None: - self._check_types() # Check plot_variable diff --git a/src/pyflexplot/setups/plot_setup.py b/src/pyflexplot/setups/plot_setup.py index 64bc782c..98c6e806 100644 --- a/src/pyflexplot/setups/plot_setup.py +++ b/src/pyflexplot/setups/plot_setup.py @@ -90,7 +90,6 @@ class PlotSetup(BaseSetup): ) def __post_init__(self) -> None: - # Wrap check in function to locally disable pylint check # pylint: disable=E1101 # no-member ("Instance of 'Field' has no '...' member") def _check_plot_type(): diff --git a/src/pyflexplot/utils/formatting.py b/src/pyflexplot/utils/formatting.py index 9669dbca..0275a6e0 100644 --- a/src/pyflexplot/utils/formatting.py +++ b/src/pyflexplot/utils/formatting.py @@ -599,7 +599,6 @@ def __init__( ) def _format_closed(self, lvl0: float, lvl1: float) -> Components: - if self.include == "lower": op0_fmtd = r"$\tt \geq$" op1_fmtd = r"$\tt <$ " diff --git a/src/srutils/dataclasses.py b/src/srutils/dataclasses.py index 8501042a..1ac79c1e 100644 --- a/src/srutils/dataclasses.py +++ b/src/srutils/dataclasses.py @@ -5,9 +5,10 @@ import dataclasses as dc from datetime import datetime from datetime import timedelta -from typing import Any, get_args +from typing import Any from typing import Callable from typing import Collection +from typing import get_args from typing import get_type_hints from typing import Iterable from typing import Optional diff --git a/src/srutils/dict.py b/src/srutils/dict.py index 52517886..588708b3 100644 --- a/src/srutils/dict.py +++ b/src/srutils/dict.py @@ -545,7 +545,6 @@ def run(self, branch_end_criterion=None): return linears def _run_rec(self, dct=None): - if dct is None: dct = self.dct @@ -595,7 +594,6 @@ def __post_init__(self): self.head = self.active def _core_rec(result, dct, state=None): - if state is None: state = _State(dct) diff --git a/src/srutils/testing.py b/src/srutils/testing.py index 76edace2..a95109b3 100644 --- a/src/srutils/testing.py +++ b/src/srutils/testing.py @@ -46,6 +46,7 @@ def property_obj(cls, *args, **kwargs): ... w = property_obj(en='train', de='Zug') """ + # pylint: disable=W0613 # unused-argument (self) def create_obj(self): return cls(*args, **kwargs) @@ -323,7 +324,6 @@ def is_list_like( def _check_children(obj, t_children, f_children, kwargs, raise_): - if t_children is not None: for idx, child in enumerate(obj): if not isinstance(child, t_children): diff --git a/tests/fast/test_srutils/test_dict/nested/test_decompress.py b/tests/fast/test_srutils/test_dict/nested/test_decompress.py index 21785e50..b1e10352 100644 --- a/tests/fast/test_srutils/test_dict/nested/test_decompress.py +++ b/tests/fast/test_srutils/test_dict/nested/test_decompress.py @@ -56,7 +56,6 @@ def test_return_paths(): class Test_MatchEnd: - dct = { "_zz": { "a": 1, diff --git a/tests/fast/test_words/test_test.py b/tests/fast/test_words/test_test.py index 47ffe902..fdf7fa1f 100644 --- a/tests/fast/test_words/test_test.py +++ b/tests/fast/test_words/test_test.py @@ -11,7 +11,6 @@ class _Test_Basic: - ws = property_words(["foo", "bar", "baz"]) def test_all_implicit(self): diff --git a/tests/fast/test_words/test_translated_words.py b/tests/fast/test_words/test_translated_words.py index e4d114fe..228ff3dd 100644 --- a/tests/fast/test_words/test_translated_words.py +++ b/tests/fast/test_words/test_translated_words.py @@ -223,7 +223,6 @@ def test_format(self): class Test_Interface_AddWords: - sol = { ("train", None, "en"): "train", ("train", None, "de"): "Zug", diff --git a/tests/medium/test_pyflexplot/test_input/test_read_flexpart_fields/test_deterministic.py b/tests/medium/test_pyflexplot/test_input/test_read_flexpart_fields/test_deterministic.py index 144769ac..34b9a906 100644 --- a/tests/medium/test_pyflexplot/test_input/test_read_flexpart_fields/test_deterministic.py +++ b/tests/medium/test_pyflexplot/test_input/test_read_flexpart_fields/test_deterministic.py @@ -578,7 +578,6 @@ def test_multiple(datadir, config): # noqa:F811 for var_setups in decompress_twice( setups, "dimensions.time", skip=["model.ens_member_id"] ): - # Read input fields var_setups_dicts_pre = var_setups.dicts() field_groups = read_fields( From ca91e3ca0bb6e40bf5cfbf23cbbc626dc19fe780 Mon Sep 17 00:00:00 2001 From: Pirmin Kaufmann Date: Fri, 9 Jun 2023 08:56:58 +0200 Subject: [PATCH 11/24] Updated reference for slow tests. --- .../test_plots/ref_cosmo-1_affected_area.py | 26 +++---- .../ref_cosmo-1_cloud_arrival_time.py | 26 +++---- .../test_plots/ref_cosmo-1_concentration.py | 26 +++---- .../ref_cosmo-1_integrated_concentration.py | 26 +++---- .../ref_cosmo-1_total_deposition.py | 26 +++---- .../ref_cosmo-1e-ctrl_affected_area.py | 26 +++---- ...o-1e-ctrl_concentration_multipanel_time.py | 72 +++++++++--------- ...-1e-ctrl_tot_deposition_multipanel_time.py | 72 +++++++++--------- .../ref_cosmo-1e_total_deposition_dummy.py | 24 +++--- .../ref_cosmo-2e_ens_cloud_arrival_time.py | 26 +++---- .../ref_cosmo-2e_ens_cloud_departure_time.py | 26 +++---- ...ltipanel_ens_stats_integr_concentration.py | 74 +++++++++---------- .../ref_cosmo-e_ens_cloud_arrival_time.py | 26 +++---- .../ref_cosmo-e_ens_cloud_departure_time.py | 30 ++++---- ...osmo-e_ens_max_integrated_concentration.py | 30 ++++---- .../ref_cosmo-e_ens_mean_concentration.py | 30 ++++---- .../ref_cosmo-e_ens_mean_total_deposition.py | 30 ++++---- .../ref_cosmo-e_ens_min_affected_area.py | 26 +++---- ..._cosmo-e_ens_probability_wet_deposition.py | 26 +++---- .../ref_ifs-hres-eu_affected_area.py | 24 +++--- ...ef_ifs-hres-eu_integrated_concentration.py | 24 +++--- .../ref_ifs-hres-eu_total_deposition.py | 24 +++--- .../test_plots/ref_ifs-hres_affected_area.py | 26 +++---- .../ref_ifs-hres_cloud_departure_time.py | 26 +++---- .../test_plots/ref_ifs-hres_concentration.py | 26 +++---- .../ref_ifs-hres_total_deposition.py | 24 +++--- 26 files changed, 411 insertions(+), 411 deletions(-) diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_affected_area.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_affected_area.py index e3497fba..359abd40 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_affected_area.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_affected_area.py @@ -137,15 +137,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "", @@ -462,7 +462,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$21'$\\,$N (47.3659$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9668$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-09-30 12:00 UTC\nEnd:\t2019-09-30 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t30$\\,$a\nDeposit. vel.:\t0.0015$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t7e-05$\\,$s$^{-1}$\nWashout exponent:\t0.8\n", + "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$21'$\\,$N (47.3659$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9668$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-09-30 12:00 UTC\nEnd:\t2019-09-30 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -690,15 +690,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "", @@ -4128,7 +4128,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4157,7 +4157,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4215,7 +4215,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4244,7 +4244,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_cloud_arrival_time.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_cloud_arrival_time.py index 268317ad..a8036d9d 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_cloud_arrival_time.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_cloud_arrival_time.py @@ -137,15 +137,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "h", @@ -470,7 +470,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$21'$\\,$N (47.3659$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9668$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-09-30 12:00 UTC\nEnd:\t2019-09-30 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t30$\\,$a\nDeposit. vel.:\t0.0015$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t7e-05$\\,$s$^{-1}$\nWashout exponent:\t0.8\n", + "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$21'$\\,$N (47.3659$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9668$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-09-30 12:00 UTC\nEnd:\t2019-09-30 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -698,15 +698,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "h", @@ -4517,7 +4517,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4546,7 +4546,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4604,7 +4604,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4633,7 +4633,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_concentration.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_concentration.py index 4216960e..1ce764d5 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_concentration.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_concentration.py @@ -135,15 +135,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -473,7 +473,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tG$\\mathrm{\\"o}$sgen\nBreite:\t47$^\\circ$$\\,$21\'$\\,$N (47.3659$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$58\'$\\,$O (7.9668$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2019-09-30 12:00 UTC\nEnde:\t2019-09-30 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotale Masse:\t1e+09$\\,$Bq\n\n\nSubstanz:\tCs-137\nHalbwertszeit:\t30$\\,$a\nDeposit.-Geschw.:\t0.0015$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t7e-05$\\,$s$^{-1}$\nAuswaschexponent:\t0.8\n', + "lines_str": 'Ort:\tG$\\mathrm{\\"o}$sgen\nBreite:\t47$^\\circ$$\\,$21\'$\\,$N (47.3659$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$58\'$\\,$O (7.9668$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2019-09-30 12:00 UTC\nEnde:\t2019-09-30 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotale Masse:\t1e+09$\\,$Bq\n\n\nSubstanz:\tCs-137\nHalbwertszeit:\t-1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -701,15 +701,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -4566,7 +4566,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4595,7 +4595,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4653,7 +4653,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4682,7 +4682,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_integrated_concentration.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_integrated_concentration.py index 2aacae8c..8823e1ff 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_integrated_concentration.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_integrated_concentration.py @@ -135,15 +135,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -473,7 +473,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$21'$\\,$N (47.3659$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9668$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-09-30 12:00 UTC\nEnd:\t2019-09-30 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t30$\\,$a\nDeposit. vel.:\t0.0015$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t7e-05$\\,$s$^{-1}$\nWashout exponent:\t0.8\n", + "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$21'$\\,$N (47.3659$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9668$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-09-30 12:00 UTC\nEnd:\t2019-09-30 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -701,15 +701,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -4600,7 +4600,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4629,7 +4629,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4687,7 +4687,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4716,7 +4716,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_total_deposition.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_total_deposition.py index 67dc96c3..7e2e849e 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_total_deposition.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_total_deposition.py @@ -135,15 +135,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -480,7 +480,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tG$\\mathrm{\\"o}$sgen\nBreite:\t47$^\\circ$$\\,$21\'$\\,$N (47.3659$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$58\'$\\,$O (7.9668$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2019-09-30 12:00 UTC\nEnde:\t2019-09-30 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotale Masse:\t1e+09$\\,$Bq\n\n\nSubstanz:\tCs-137\nHalbwertszeit:\t30$\\,$a\nDeposit.-Geschw.:\t0.0015$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t7e-05$\\,$s$^{-1}$\nAuswaschexponent:\t0.8\n', + "lines_str": 'Ort:\tG$\\mathrm{\\"o}$sgen\nBreite:\t47$^\\circ$$\\,$21\'$\\,$N (47.3659$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$58\'$\\,$O (7.9668$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2019-09-30 12:00 UTC\nEnde:\t2019-09-30 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotale Masse:\t1e+09$\\,$Bq\n\n\nSubstanz:\tCs-137\nHalbwertszeit:\t-1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -708,15 +708,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -4628,7 +4628,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4657,7 +4657,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4715,7 +4715,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4744,7 +4744,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_affected_area.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_affected_area.py index 38f88fd9..988498ba 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_affected_area.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_affected_area.py @@ -137,15 +137,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "", @@ -462,7 +462,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tBugey\nLatitude:\t45$^\\circ$$\\,$47'$\\,$N (45.7992$^\\circ$$\\,$N)\nLongitude:\t5$^\\circ$$\\,$16'$\\,$E (5.2700$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2021-04-08 00:00 UTC\nEnd:\t2021-04-08 08:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t30$\\,$a\nDeposit. vel.:\t0.0015$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t7e-05$\\,$s$^{-1}$\nWashout exponent:\t0.8\n", + "lines_str": "Site:\tBugey\nLatitude:\t45$^\\circ$$\\,$47'$\\,$N (45.7992$^\\circ$$\\,$N)\nLongitude:\t5$^\\circ$$\\,$16'$\\,$E (5.2700$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2021-04-08 00:00 UTC\nEnd:\t2021-04-08 08:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -690,15 +690,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "", @@ -4116,7 +4116,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4145,7 +4145,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4203,7 +4203,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4232,7 +4232,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_concentration_multipanel_time.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_concentration_multipanel_time.py index 07365f88..fd52d37e 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_concentration_multipanel_time.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_concentration_multipanel_time.py @@ -135,15 +135,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -339,15 +339,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -543,15 +543,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -747,15 +747,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -1492,7 +1492,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tCruas\nBreite:\t44$^\\circ$$\\,$38\'$\\,$N (44.6353$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t4$^\\circ$$\\,$45\'$\\,$O (4.7506$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2020-10-21 05:00 UTC\nEnde:\t2020-10-21 17:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotale Masse:\t4.3e+11$\\,$Bq\n\n\nSubstanz:\tXe-133\nHalbwertszeit:\t5.245$\\,$d\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t0$\\,$s$^{-1}$\nAuswaschexponent:\t0\n', + "lines_str": 'Ort:\tCruas\nBreite:\t44$^\\circ$$\\,$38\'$\\,$N (44.6353$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t4$^\\circ$$\\,$45\'$\\,$O (4.7506$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2020-10-21 05:00 UTC\nEnde:\t2020-10-21 17:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotale Masse:\t4.3e+11$\\,$Bq\n\n\nSubstanz:\tXe-133\nHalbwertszeit:\t-1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -1720,15 +1720,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -2423,15 +2423,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -3126,15 +3126,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -3829,15 +3829,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -9654,7 +9654,7 @@ "va": "top", "ha": "right", }, - "s": "5.245$\\,$d", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -9741,7 +9741,7 @@ "va": "top", "ha": "right", }, - "s": "0$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -9770,7 +9770,7 @@ "va": "top", "ha": "right", }, - "s": "0", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_tot_deposition_multipanel_time.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_tot_deposition_multipanel_time.py index 61488fc5..d5e1aa78 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_tot_deposition_multipanel_time.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e-ctrl_tot_deposition_multipanel_time.py @@ -137,15 +137,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -341,15 +341,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -545,15 +545,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -749,15 +749,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -1537,7 +1537,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tCruas\nLatitude:\t44$^\\circ$$\\,$38'$\\,$N (44.6353$^\\circ$$\\,$N)\nLongitude:\t4$^\\circ$$\\,$45'$\\,$E (4.7506$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2020-10-21 05:00 UTC\nEnd:\t2020-10-21 17:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotal mass:\t4.3e+11$\\,$Bq\n\n\nSubstance:\tXe-133\nHalf-life:\t5.245$\\,$d\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t0$\\,$s$^{-1}$\nWashout exponent:\t0\n", + "lines_str": "Site:\tCruas\nLatitude:\t44$^\\circ$$\\,$38'$\\,$N (44.6353$^\\circ$$\\,$N)\nLongitude:\t4$^\\circ$$\\,$45'$\\,$E (4.7506$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2020-10-21 05:00 UTC\nEnd:\t2020-10-21 17:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotal mass:\t4.3e+11$\\,$Bq\n\n\nSubstance:\tXe-133\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -1765,15 +1765,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -2568,15 +2568,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -3371,15 +3371,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -4174,15 +4174,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -10554,7 +10554,7 @@ "va": "top", "ha": "right", }, - "s": "5.245$\\,$d", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -10641,7 +10641,7 @@ "va": "top", "ha": "right", }, - "s": "0$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -10670,7 +10670,7 @@ "va": "top", "ha": "right", }, - "s": "0", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e_total_deposition_dummy.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e_total_deposition_dummy.py index fbfe5e91..5e13f82c 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e_total_deposition_dummy.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1e_total_deposition_dummy.py @@ -137,15 +137,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -482,7 +482,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tCruas\nBreite:\t44$^\\circ$$\\,$38\'$\\,$N (44.6353$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t4$^\\circ$$\\,$45\'$\\,$O (4.7506$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2020-10-21 05:00 UTC\nEnde:\t2020-10-21 17:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotale Masse:\t4.3e+11$\\,$Bq\n\n\nSubstanz:\tXe-133\nHalbwertszeit:\t5.245$\\,$d\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t0$\\,$s$^{-1}$\nAuswaschexponent:\t0\n', + "lines_str": 'Ort:\tCruas\nBreite:\t44$^\\circ$$\\,$38\'$\\,$N (44.6353$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t4$^\\circ$$\\,$45\'$\\,$O (4.7506$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2020-10-21 05:00 UTC\nEnde:\t2020-10-21 17:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotale Masse:\t4.3e+11$\\,$Bq\n\n\nSubstanz:\tXe-133\nHalbwertszeit:\t-1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -710,15 +710,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -4906,7 +4906,7 @@ "va": "top", "ha": "right", }, - "s": "5.245$\\,$d", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4993,7 +4993,7 @@ "va": "top", "ha": "right", }, - "s": "0$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5022,7 +5022,7 @@ "va": "top", "ha": "right", }, - "s": "0", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_ens_cloud_arrival_time.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_ens_cloud_arrival_time.py index 830c2600..eb614679 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_ens_cloud_arrival_time.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_ens_cloud_arrival_time.py @@ -141,15 +141,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -490,7 +490,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tM$\\mathrm{\\\"u}$hleberg\nLatitude:\t46$^\\circ$$\\,$58'$\\,$N (46.9690$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$16'$\\,$E (7.2685$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2021-03-05 03:00 UTC\nEnd:\t2021-03-05 09:00 UTC\nRate:\t1$\\,$Bq s$^{-1}$\nTotal mass:\t21600$\\,$Bq\n\n\nSubstance:\tNorm\nHalf-life:\t30$\\,$a\nDeposit. vel.:\t0.0015$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t7e-05$\\,$s$^{-1}$\nWashout exponent:\t0.8\n", + "lines_str": "Site:\tM$\\mathrm{\\\"u}$hleberg\nLatitude:\t46$^\\circ$$\\,$58'$\\,$N (46.9690$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$16'$\\,$E (7.2685$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2021-03-05 03:00 UTC\nEnd:\t2021-03-05 09:00 UTC\nRate:\t1$\\,$Bq s$^{-1}$\nTotal mass:\t21600$\\,$Bq\n\n\nSubstance:\tNorm\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -722,15 +722,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -4864,7 +4864,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4893,7 +4893,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4951,7 +4951,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4980,7 +4980,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_ens_cloud_departure_time.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_ens_cloud_departure_time.py index 0ffdef0b..78c8b5c0 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_ens_cloud_departure_time.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_ens_cloud_departure_time.py @@ -141,15 +141,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -490,7 +490,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tM$\\mathrm{\\"u}$hleberg\nBreite:\t46$^\\circ$$\\,$58\'$\\,$N (46.9690$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$16\'$\\,$O (7.2685$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2021-03-05 03:00 UTC\nEnde:\t2021-03-05 09:00 UTC\nRate:\t1$\\,$Bq s$^{-1}$\nTotale Masse:\t21600$\\,$Bq\n\n\nSubstanz:\tNorm\nHalbwertszeit:\t30$\\,$a\nDeposit.-Geschw.:\t0.0015$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t7e-05$\\,$s$^{-1}$\nAuswaschexponent:\t0.8\n', + "lines_str": 'Ort:\tM$\\mathrm{\\"u}$hleberg\nBreite:\t46$^\\circ$$\\,$58\'$\\,$N (46.9690$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$16\'$\\,$O (7.2685$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2021-03-05 03:00 UTC\nEnde:\t2021-03-05 09:00 UTC\nRate:\t1$\\,$Bq s$^{-1}$\nTotale Masse:\t21600$\\,$Bq\n\n\nSubstanz:\tNorm\nHalbwertszeit:\t-1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -722,15 +722,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -4798,7 +4798,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4827,7 +4827,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4885,7 +4885,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4914,7 +4914,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_multipanel_ens_stats_integr_concentration.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_multipanel_ens_stats_integr_concentration.py index 1bd67001..3c1b317b 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_multipanel_ens_stats_integr_concentration.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-2e_multipanel_ens_stats_integr_concentration.py @@ -139,15 +139,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -347,15 +347,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -555,15 +555,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -763,15 +763,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -1516,7 +1516,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tM$\\mathrm{\\"u}$hleberg\nBreite:\t46$^\\circ$$\\,$58\'$\\,$N (46.9690$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$16\'$\\,$O (7.2685$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2021-03-05 03:00 UTC\nEnde:\t2021-03-05 09:00 UTC\nRate:\t1$\\,$Bq s$^{-1}$\nTotale Masse:\t21600$\\,$Bq\n\n\nSubstanz:\tNorm\nHalbwertszeit:\t30$\\,$a\nDeposit.-Geschw.:\t0.0015$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t7e-05$\\,$s$^{-1}$\nAuswaschexponent:\t0.8\n', + "lines_str": 'Ort:\tM$\\mathrm{\\"u}$hleberg\nBreite:\t46$^\\circ$$\\,$58\'$\\,$N (46.9690$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$16\'$\\,$O (7.2685$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2021-03-05 03:00 UTC\nEnde:\t2021-03-05 09:00 UTC\nRate:\t1$\\,$Bq s$^{-1}$\nTotale Masse:\t21600$\\,$Bq\n\n\nSubstanz:\tNorm\nHalbwertszeit:\t-1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -1748,15 +1748,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -2155,15 +2155,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -2562,15 +2562,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -2969,15 +2969,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -8498,7 +8498,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -8527,7 +8527,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -8585,7 +8585,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -8614,7 +8614,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_cloud_arrival_time.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_cloud_arrival_time.py index bce0382e..b38fbbde 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_cloud_arrival_time.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_cloud_arrival_time.py @@ -137,15 +137,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -485,7 +485,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$22'$\\,$N (47.3700$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9700$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-07-27 12:00 UTC\nEnd:\t2019-07-27 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t30$\\,$a\nDeposit. vel.:\t0.0015$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t7e-05$\\,$s$^{-1}$\nWashout exponent:\t0.8\n", + "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$22'$\\,$N (47.3700$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9700$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-07-27 12:00 UTC\nEnd:\t2019-07-27 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -713,15 +713,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -4819,7 +4819,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4848,7 +4848,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4906,7 +4906,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4935,7 +4935,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_cloud_departure_time.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_cloud_departure_time.py index 392d32fe..13249748 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_cloud_departure_time.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_cloud_departure_time.py @@ -137,15 +137,15 @@ }, "species": { "name": ["Cs-137", "I-131a"], - "half_life": [30.0, 8.04], - "half_life_unit": ["a", "d"], - "deposition_velocity": [0.0015, 0.0015], + "half_life": [-99.9, -99.9], + "half_life_unit": ["a", "a"], + "deposition_velocity": [0.0, 0.0], "deposition_velocity_unit": ["m s-1", "m s-1"], "sedimentation_velocity": [0.0, 0.0], "sedimentation_velocity_unit": ["m s-1", "m s-1"], - "washout_coefficient": [7e-05, 7e-05], + "washout_coefficient": [-99.9, -99.9], "washout_coefficient_unit": ["s-1", "s-1"], - "washout_exponent": [0.8, 0.8], + "washout_exponent": [-99.9, -99.9], }, "variable": { "unit": "Bq h m-3", @@ -485,7 +485,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tG$\\mathrm{\\"o}$sgen\nBreite:\t47$^\\circ$$\\,$22\'$\\,$N (47.3700$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$58\'$\\,$O (7.9700$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2019-07-27 12:00 UTC\nEnde:\t2019-07-27 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$ / 1e+07$\\,$Bq s$^{-1}$\nTotale Masse:\t1e+09$\\,$Bq / 2.9e+11$\\,$Bq\n\n\nSubstanz:\tCs-137 / I-131a\nHalbwertszeit:\t30$\\,$a / 8.04$\\,$d\nDeposit.-Geschw.:\t0.0015$\\,$m s$^{-1}$ / 0.0015$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t7e-05$\\,$s$^{-1}$ / 7e-05$\\,$s$^{-1}$\nAuswaschexponent:\t0.8 / 0.8\n', + "lines_str": 'Ort:\tG$\\mathrm{\\"o}$sgen\nBreite:\t47$^\\circ$$\\,$22\'$\\,$N (47.3700$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$58\'$\\,$O (7.9700$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2019-07-27 12:00 UTC\nEnde:\t2019-07-27 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$ / 1e+07$\\,$Bq s$^{-1}$\nTotale Masse:\t1e+09$\\,$Bq / 2.9e+11$\\,$Bq\n\n\nSubstanz:\tCs-137 / I-131a\nHalbwertszeit:\t-1e+02$\\,$a / -1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$ / -1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02 / -1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -713,15 +713,15 @@ }, "species": { "name": ["Cs-137", "I-131a"], - "half_life": [30.0, 8.04], - "half_life_unit": ["a", "d"], - "deposition_velocity": [0.0015, 0.0015], + "half_life": [-99.9, -99.9], + "half_life_unit": ["a", "a"], + "deposition_velocity": [0.0, 0.0], "deposition_velocity_unit": ["m s-1", "m s-1"], "sedimentation_velocity": [0.0, 0.0], "sedimentation_velocity_unit": ["m s-1", "m s-1"], - "washout_coefficient": [7e-05, 7e-05], + "washout_coefficient": [-99.9, -99.9], "washout_coefficient_unit": ["s-1", "s-1"], - "washout_exponent": [0.8, 0.8], + "washout_exponent": [-99.9, -99.9], }, "variable": { "unit": "Bq h m-3", @@ -4831,7 +4831,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a / 8.04$\\,$d", + "s": "-1e+02$\\,$a / -1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4860,7 +4860,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$ / 0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4918,7 +4918,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$ / 7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$ / -1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4947,7 +4947,7 @@ "va": "top", "ha": "right", }, - "s": "0.8 / 0.8", + "s": "-1e+02 / -1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_max_integrated_concentration.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_max_integrated_concentration.py index 21186261..4b3ce16b 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_max_integrated_concentration.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_max_integrated_concentration.py @@ -135,15 +135,15 @@ }, "species": { "name": "I-131a", - "half_life": 8.04, - "half_life_unit": "d", - "deposition_velocity": 0.0015, + "half_life": -99.9, + "half_life_unit": "a", + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -481,7 +481,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tG$\\mathrm{\\"o}$sgen\nBreite:\t47$^\\circ$$\\,$22\'$\\,$N (47.3700$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$58\'$\\,$O (7.9700$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2019-07-27 12:00 UTC\nEnde:\t2019-07-27 20:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotale Masse:\t2.9e+11$\\,$Bq\n\n\nSubstanz:\tI-131a\nHalbwertszeit:\t8.04$\\,$d\nDeposit.-Geschw.:\t0.0015$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t7e-05$\\,$s$^{-1}$\nAuswaschexponent:\t0.8\n', + "lines_str": 'Ort:\tG$\\mathrm{\\"o}$sgen\nBreite:\t47$^\\circ$$\\,$22\'$\\,$N (47.3700$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$58\'$\\,$O (7.9700$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2019-07-27 12:00 UTC\nEnde:\t2019-07-27 20:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotale Masse:\t2.9e+11$\\,$Bq\n\n\nSubstanz:\tI-131a\nHalbwertszeit:\t-1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -709,15 +709,15 @@ }, "species": { "name": "I-131a", - "half_life": 8.04, - "half_life_unit": "d", - "deposition_velocity": 0.0015, + "half_life": -99.9, + "half_life_unit": "a", + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -4791,7 +4791,7 @@ "va": "top", "ha": "right", }, - "s": "8.04$\\,$d", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4820,7 +4820,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4878,7 +4878,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4907,7 +4907,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_mean_concentration.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_mean_concentration.py index caf778e2..5a1e172f 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_mean_concentration.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_mean_concentration.py @@ -135,15 +135,15 @@ }, "species": { "name": ["Cs-137", "I-131a"], - "half_life": [30.0, 8.04], - "half_life_unit": ["a", "d"], - "deposition_velocity": [0.0015, 0.0015], + "half_life": [-99.9, -99.9], + "half_life_unit": ["a", "a"], + "deposition_velocity": [0.0, 0.0], "deposition_velocity_unit": ["m s-1", "m s-1"], "sedimentation_velocity": [0.0, 0.0], "sedimentation_velocity_unit": ["m s-1", "m s-1"], - "washout_coefficient": [7e-05, 7e-05], + "washout_coefficient": [-99.9, -99.9], "washout_coefficient_unit": ["s-1", "s-1"], - "washout_exponent": [0.8, 0.8], + "washout_exponent": [-99.9, -99.9], }, "variable": { "unit": "Bq m-3", @@ -481,7 +481,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$22'$\\,$N (47.3700$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9700$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-07-27 12:00 UTC\nEnd:\t2019-07-27 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$ / 1e+07$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq / 2.9e+11$\\,$Bq\n\n\nSubstance:\tCs-137 / I-131a\nHalf-life:\t30$\\,$a / 8.04$\\,$d\nDeposit. vel.:\t0.0015$\\,$m s$^{-1}$ / 0.0015$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$\nWashout coeff.:\t7e-05$\\,$s$^{-1}$ / 7e-05$\\,$s$^{-1}$\nWashout exponent:\t0.8 / 0.8\n", + "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$22'$\\,$N (47.3700$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9700$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-07-27 12:00 UTC\nEnd:\t2019-07-27 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$ / 1e+07$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq / 2.9e+11$\\,$Bq\n\n\nSubstance:\tCs-137 / I-131a\nHalf-life:\t-1e+02$\\,$a / -1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$ / -1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02 / -1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -709,15 +709,15 @@ }, "species": { "name": ["Cs-137", "I-131a"], - "half_life": [30.0, 8.04], - "half_life_unit": ["a", "d"], - "deposition_velocity": [0.0015, 0.0015], + "half_life": [-99.9, -99.9], + "half_life_unit": ["a", "a"], + "deposition_velocity": [0.0, 0.0], "deposition_velocity_unit": ["m s-1", "m s-1"], "sedimentation_velocity": [0.0, 0.0], "sedimentation_velocity_unit": ["m s-1", "m s-1"], - "washout_coefficient": [7e-05, 7e-05], + "washout_coefficient": [-99.9, -99.9], "washout_coefficient_unit": ["s-1", "s-1"], - "washout_exponent": [0.8, 0.8], + "washout_exponent": [-99.9, -99.9], }, "variable": { "unit": "Bq m-3", @@ -4779,7 +4779,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a / 8.04$\\,$d", + "s": "-1e+02$\\,$a / -1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4808,7 +4808,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$ / 0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4866,7 +4866,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$ / 7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$ / -1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4895,7 +4895,7 @@ "va": "top", "ha": "right", }, - "s": "0.8 / 0.8", + "s": "-1e+02 / -1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_mean_total_deposition.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_mean_total_deposition.py index 63f511d9..bd111a63 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_mean_total_deposition.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_mean_total_deposition.py @@ -135,15 +135,15 @@ }, "species": { "name": ["Cs-137", "I-131a"], - "half_life": [30.0, 8.04], - "half_life_unit": ["a", "d"], - "deposition_velocity": [0.0015, 0.0015], + "half_life": [-99.9, -99.9], + "half_life_unit": ["a", "a"], + "deposition_velocity": [0.0, 0.0], "deposition_velocity_unit": ["m s-1", "m s-1"], "sedimentation_velocity": [0.0, 0.0], "sedimentation_velocity_unit": ["m s-1", "m s-1"], - "washout_coefficient": [7e-05, 7e-05], + "washout_coefficient": [-99.9, -99.9], "washout_coefficient_unit": ["s-1", "s-1"], - "washout_exponent": [0.8, 0.8], + "washout_exponent": [-99.9, -99.9], }, "variable": { "unit": "Bq m-2", @@ -491,7 +491,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$22'$\\,$N (47.3700$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9700$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-07-27 12:00 UTC\nEnd:\t2019-07-27 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$ / 1e+07$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq / 2.9e+11$\\,$Bq\n\n\nSubstance:\tCs-137 / I-131a\nHalf-life:\t30$\\,$a / 8.04$\\,$d\nDeposit. vel.:\t0.0015$\\,$m s$^{-1}$ / 0.0015$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$\nWashout coeff.:\t7e-05$\\,$s$^{-1}$ / 7e-05$\\,$s$^{-1}$\nWashout exponent:\t0.8 / 0.8\n", + "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$22'$\\,$N (47.3700$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9700$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-07-27 12:00 UTC\nEnd:\t2019-07-27 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$ / 1e+07$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq / 2.9e+11$\\,$Bq\n\n\nSubstance:\tCs-137 / I-131a\nHalf-life:\t-1e+02$\\,$a / -1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$ / -1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02 / -1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -719,15 +719,15 @@ }, "species": { "name": ["Cs-137", "I-131a"], - "half_life": [30.0, 8.04], - "half_life_unit": ["a", "d"], - "deposition_velocity": [0.0015, 0.0015], + "half_life": [-99.9, -99.9], + "half_life_unit": ["a", "a"], + "deposition_velocity": [0.0, 0.0], "deposition_velocity_unit": ["m s-1", "m s-1"], "sedimentation_velocity": [0.0, 0.0], "sedimentation_velocity_unit": ["m s-1", "m s-1"], - "washout_coefficient": [7e-05, 7e-05], + "washout_coefficient": [-99.9, -99.9], "washout_coefficient_unit": ["s-1", "s-1"], - "washout_exponent": [0.8, 0.8], + "washout_exponent": [-99.9, -99.9], }, "variable": { "unit": "Bq m-2", @@ -4786,7 +4786,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a / 8.04$\\,$d", + "s": "-1e+02$\\,$a / -1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4815,7 +4815,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$ / 0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$ / 0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4873,7 +4873,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$ / 7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$ / -1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4902,7 +4902,7 @@ "va": "top", "ha": "right", }, - "s": "0.8 / 0.8", + "s": "-1e+02 / -1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_min_affected_area.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_min_affected_area.py index 9ca433b9..03f71844 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_min_affected_area.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_min_affected_area.py @@ -141,15 +141,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "", @@ -476,7 +476,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tM$\\mathrm{\\"u}$hleberg\nBreite:\t46$^\\circ$$\\,$58\'$\\,$N (46.9690$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$16\'$\\,$O (7.2685$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2021-03-05 03:00 UTC\nEnde:\t2021-03-05 09:00 UTC\nRate:\t1$\\,$Bq s$^{-1}$\nTotale Masse:\t21600$\\,$Bq\n\n\nSubstanz:\tNorm\nHalbwertszeit:\t30$\\,$a\nDeposit.-Geschw.:\t0.0015$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t7e-05$\\,$s$^{-1}$\nAuswaschexponent:\t0.8\n', + "lines_str": 'Ort:\tM$\\mathrm{\\"u}$hleberg\nBreite:\t46$^\\circ$$\\,$58\'$\\,$N (46.9690$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t7$^\\circ$$\\,$16\'$\\,$O (7.2685$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2021-03-05 03:00 UTC\nEnde:\t2021-03-05 09:00 UTC\nRate:\t1$\\,$Bq s$^{-1}$\nTotale Masse:\t21600$\\,$Bq\n\n\nSubstanz:\tNorm\nHalbwertszeit:\t-1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -708,15 +708,15 @@ }, "species": { "name": "Norm", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "", @@ -4320,7 +4320,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4349,7 +4349,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4407,7 +4407,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4436,7 +4436,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_probability_wet_deposition.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_probability_wet_deposition.py index 2e331d9d..ef9cc2e7 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_probability_wet_deposition.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-e_ens_probability_wet_deposition.py @@ -135,15 +135,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -478,7 +478,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$22'$\\,$N (47.3700$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9700$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-07-27 12:00 UTC\nEnd:\t2019-07-27 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t30$\\,$a\nDeposit. vel.:\t0.0015$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t7e-05$\\,$s$^{-1}$\nWashout exponent:\t0.8\n", + "lines_str": "Site:\tG$\\mathrm{\\\"o}$sgen\nLatitude:\t47$^\\circ$$\\,$22'$\\,$N (47.3700$^\\circ$$\\,$N)\nLongitude:\t7$^\\circ$$\\,$58'$\\,$E (7.9700$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2019-07-27 12:00 UTC\nEnd:\t2019-07-27 20:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -706,15 +706,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -4671,7 +4671,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4700,7 +4700,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4758,7 +4758,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4787,7 +4787,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_affected_area.py b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_affected_area.py index 59987ce3..bde61dd0 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_affected_area.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_affected_area.py @@ -142,15 +142,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "", @@ -465,7 +465,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tBeznau\nLatitude:\t47$^\\circ$$\\,$33'$\\,$N (47.5519$^\\circ$$\\,$N)\nLongitude:\t8$^\\circ$$\\,$13'$\\,$E (8.2284$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2020-11-13 14:00 UTC\nEnd:\t2020-11-14 02:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotal mass:\t4.3e+11$\\,$Bq\n\n\nSubstance:\tXe-133\nHalf-life:\t5.245$\\,$d\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t0$\\,$s$^{-1}$\nWashout exponent:\t0\n", + "lines_str": "Site:\tBeznau\nLatitude:\t47$^\\circ$$\\,$33'$\\,$N (47.5519$^\\circ$$\\,$N)\nLongitude:\t8$^\\circ$$\\,$13'$\\,$E (8.2284$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2020-11-13 14:00 UTC\nEnd:\t2020-11-14 02:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotal mass:\t4.3e+11$\\,$Bq\n\n\nSubstance:\tXe-133\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -704,15 +704,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "", @@ -5030,7 +5030,7 @@ "va": "top", "ha": "right", }, - "s": "5.245$\\,$d", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5117,7 +5117,7 @@ "va": "top", "ha": "right", }, - "s": "0$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5146,7 +5146,7 @@ "va": "top", "ha": "right", }, - "s": "0", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_integrated_concentration.py b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_integrated_concentration.py index ef9087d7..3c8163be 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_integrated_concentration.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_integrated_concentration.py @@ -140,15 +140,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -476,7 +476,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tBeznau\nLatitude:\t47$^\\circ$$\\,$33'$\\,$N (47.5519$^\\circ$$\\,$N)\nLongitude:\t8$^\\circ$$\\,$13'$\\,$E (8.2284$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2020-11-13 14:00 UTC\nEnd:\t2020-11-14 02:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotal mass:\t4.3e+11$\\,$Bq\n\n\nSubstance:\tXe-133\nHalf-life:\t5.245$\\,$d\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t0$\\,$s$^{-1}$\nWashout exponent:\t0\n", + "lines_str": "Site:\tBeznau\nLatitude:\t47$^\\circ$$\\,$33'$\\,$N (47.5519$^\\circ$$\\,$N)\nLongitude:\t8$^\\circ$$\\,$13'$\\,$E (8.2284$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2020-11-13 14:00 UTC\nEnd:\t2020-11-14 02:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotal mass:\t4.3e+11$\\,$Bq\n\n\nSubstance:\tXe-133\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -715,15 +715,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq h m-3", @@ -5502,7 +5502,7 @@ "va": "top", "ha": "right", }, - "s": "5.245$\\,$d", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5589,7 +5589,7 @@ "va": "top", "ha": "right", }, - "s": "0$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5618,7 +5618,7 @@ "va": "top", "ha": "right", }, - "s": "0", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_total_deposition.py b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_total_deposition.py index 93c52e33..757a3c5c 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_total_deposition.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres-eu_total_deposition.py @@ -142,15 +142,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -485,7 +485,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tBeznau\nBreite:\t47$^\\circ$$\\,$33\'$\\,$N (47.5519$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t8$^\\circ$$\\,$13\'$\\,$O (8.2284$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2020-11-13 14:00 UTC\nEnde:\t2020-11-14 02:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotale Masse:\t4.3e+11$\\,$Bq\n\n\nSubstanz:\tXe-133\nHalbwertszeit:\t5.245$\\,$d\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t0$\\,$s$^{-1}$\nAuswaschexponent:\t0\n', + "lines_str": 'Ort:\tBeznau\nBreite:\t47$^\\circ$$\\,$33\'$\\,$N (47.5519$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t8$^\\circ$$\\,$13\'$\\,$O (8.2284$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2020-11-13 14:00 UTC\nEnde:\t2020-11-14 02:00 UTC\nRate:\t1e+07$\\,$Bq s$^{-1}$\nTotale Masse:\t4.3e+11$\\,$Bq\n\n\nSubstanz:\tXe-133\nHalbwertszeit:\t-1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -724,15 +724,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -5798,7 +5798,7 @@ "va": "top", "ha": "right", }, - "s": "5.245$\\,$d", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5885,7 +5885,7 @@ "va": "top", "ha": "right", }, - "s": "0$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5914,7 +5914,7 @@ "va": "top", "ha": "right", }, - "s": "0", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_affected_area.py b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_affected_area.py index 6fb151c8..b43aff4d 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_affected_area.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_affected_area.py @@ -142,15 +142,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "", @@ -465,7 +465,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tPunggye-ri\nLatitude:\t41$^\\circ$$\\,$16'$\\,$N (41.2800$^\\circ$$\\,$N)\nLongitude:\t129$^\\circ$$\\,$5'$\\,$E (129.0900$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2020-03-17 00:00 UTC\nEnd:\t2020-03-17 08:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t30$\\,$a\nDeposit. vel.:\t0.0015$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t7e-05$\\,$s$^{-1}$\nWashout exponent:\t0.8\n", + "lines_str": "Site:\tPunggye-ri\nLatitude:\t41$^\\circ$$\\,$16'$\\,$N (41.2800$^\\circ$$\\,$N)\nLongitude:\t129$^\\circ$$\\,$5'$\\,$E (129.0900$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2020-03-17 00:00 UTC\nEnd:\t2020-03-17 08:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -704,15 +704,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "", @@ -4438,7 +4438,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4467,7 +4467,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4525,7 +4525,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4554,7 +4554,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_cloud_departure_time.py b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_cloud_departure_time.py index 8ee518e6..ea10e362 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_cloud_departure_time.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_cloud_departure_time.py @@ -142,15 +142,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "h", @@ -475,7 +475,7 @@ }, "release_info": { "title": "Release", - "lines_str": "Site:\tPunggye-ri\nLatitude:\t41$^\\circ$$\\,$16'$\\,$N (41.2800$^\\circ$$\\,$N)\nLongitude:\t129$^\\circ$$\\,$5'$\\,$E (129.0900$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2020-03-17 00:00 UTC\nEnd:\t2020-03-17 08:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t30$\\,$a\nDeposit. vel.:\t0.0015$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t7e-05$\\,$s$^{-1}$\nWashout exponent:\t0.8\n", + "lines_str": "Site:\tPunggye-ri\nLatitude:\t41$^\\circ$$\\,$16'$\\,$N (41.2800$^\\circ$$\\,$N)\nLongitude:\t129$^\\circ$$\\,$5'$\\,$E (129.0900$^\\circ$$\\,$E)\nHeight:\t100$\\,$$\\,$m AGL\n\n\nStart:\t2020-03-17 00:00 UTC\nEnd:\t2020-03-17 08:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotal mass:\t1e+09$\\,$Bq\n\n\nSubstance:\tCs-137\nHalf-life:\t-1e+02$\\,$a\nDeposit. vel.:\t0$\\,$m s$^{-1}$\nSediment. vel.:\t0$\\,$m s$^{-1}$\nWashout coeff.:\t-1e+02$\\,$s$^{-1}$\nWashout exponent:\t-1e+02\n", }, }, "fig_size": [12.5, 8.0], @@ -714,15 +714,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "h", @@ -4964,7 +4964,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -4993,7 +4993,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5051,7 +5051,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5080,7 +5080,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_concentration.py b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_concentration.py index 54c52c07..58edec1d 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_concentration.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_concentration.py @@ -140,15 +140,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -476,7 +476,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tPunggye-ri\nBreite:\t41$^\\circ$$\\,$16\'$\\,$N (41.2800$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t129$^\\circ$$\\,$5\'$\\,$O (129.0900$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2020-03-17 00:00 UTC\nEnde:\t2020-03-17 08:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotale Masse:\t1e+09$\\,$Bq\n\n\nSubstanz:\tCs-137\nHalbwertszeit:\t30$\\,$a\nDeposit.-Geschw.:\t0.0015$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t7e-05$\\,$s$^{-1}$\nAuswaschexponent:\t0.8\n', + "lines_str": 'Ort:\tPunggye-ri\nBreite:\t41$^\\circ$$\\,$16\'$\\,$N (41.2800$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t129$^\\circ$$\\,$5\'$\\,$O (129.0900$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2020-03-17 00:00 UTC\nEnde:\t2020-03-17 08:00 UTC\nRate:\t34722.2$\\,$Bq s$^{-1}$\nTotale Masse:\t1e+09$\\,$Bq\n\n\nSubstanz:\tCs-137\nHalbwertszeit:\t-1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -715,15 +715,15 @@ }, "species": { "name": "Cs-137", - "half_life": 30.0, + "half_life": -99.9, "half_life_unit": "a", - "deposition_velocity": 0.0015, + "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 7e-05, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.8, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-3", @@ -4990,7 +4990,7 @@ "va": "top", "ha": "right", }, - "s": "30$\\,$a", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5019,7 +5019,7 @@ "va": "top", "ha": "right", }, - "s": "0.0015$\\,$m s$^{-1}$", + "s": "0$\\,$m s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5077,7 +5077,7 @@ "va": "top", "ha": "right", }, - "s": "7e-05$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5106,7 +5106,7 @@ "va": "top", "ha": "right", }, - "s": "0.8", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { diff --git a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_total_deposition.py b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_total_deposition.py index b4b15c18..d390c4ec 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_total_deposition.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_ifs-hres_total_deposition.py @@ -142,15 +142,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -485,7 +485,7 @@ }, "release_info": { "title": "Freisetzung", - "lines_str": 'Ort:\tPunggye-ri\nBreite:\t41$^\\circ$$\\,$16\'$\\,$N (41.2800$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t129$^\\circ$$\\,$5\'$\\,$O (129.0900$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2020-09-21 00:00 UTC\nEnde:\t2020-09-21 08:00 UTC\nRate:\t1e+09$\\,$Bq s$^{-1}$\nTotale Masse:\t2.9e+13$\\,$Bq\n\n\nSubstanz:\tXe-133\nHalbwertszeit:\t5.245$\\,$d\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t0$\\,$s$^{-1}$\nAuswaschexponent:\t0\n', + "lines_str": 'Ort:\tPunggye-ri\nBreite:\t41$^\\circ$$\\,$16\'$\\,$N (41.2800$^\\circ$$\\,$N)\nL$\\mathrm{\\"a}$nge:\t129$^\\circ$$\\,$5\'$\\,$O (129.0900$^\\circ$$\\,$O)\nH$\\mathrm{\\"o}$he:\t100$\\,$$\\,$m $\\mathrm{\\"u}$.G.\n\n\nStart:\t2020-09-21 00:00 UTC\nEnde:\t2020-09-21 08:00 UTC\nRate:\t1e+09$\\,$Bq s$^{-1}$\nTotale Masse:\t2.9e+13$\\,$Bq\n\n\nSubstanz:\tXe-133\nHalbwertszeit:\t-1e+02$\\,$a\nDeposit.-Geschw.:\t0$\\,$m s$^{-1}$\nSediment.-Geschw.:\t0$\\,$m s$^{-1}$\nAuswaschkoeff.:\t-1e+02$\\,$s$^{-1}$\nAuswaschexponent:\t-1e+02\n', }, }, "fig_size": [12.5, 8.0], @@ -724,15 +724,15 @@ }, "species": { "name": "Xe-133", - "half_life": 5.245, - "half_life_unit": "d", + "half_life": -99.9, + "half_life_unit": "a", "deposition_velocity": 0.0, "deposition_velocity_unit": "m s-1", "sedimentation_velocity": 0.0, "sedimentation_velocity_unit": "m s-1", - "washout_coefficient": 0.0, + "washout_coefficient": -99.9, "washout_coefficient_unit": "s-1", - "washout_exponent": 0.0, + "washout_exponent": -99.9, }, "variable": { "unit": "Bq m-2", @@ -5414,7 +5414,7 @@ "va": "top", "ha": "right", }, - "s": "5.245$\\,$d", + "s": "-1e+02$\\,$a", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5501,7 +5501,7 @@ "va": "top", "ha": "right", }, - "s": "0$\\,$s$^{-1}$", + "s": "-1e+02$\\,$s$^{-1}$", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { @@ -5530,7 +5530,7 @@ "va": "top", "ha": "right", }, - "s": "0", + "s": "-1e+02", "replace_edge_spaces": False, "edge_spaces_replacement_char": "␣", "kwargs": { From f4310b20cc150a12b898b6dddc17c43cdc48c64b Mon Sep 17 00:00:00 2001 From: Marco Ketzel Date: Mon, 10 Jul 2023 17:13:22 +0200 Subject: [PATCH 12/24] Changed function, so it is covers the inversion of both coordinates in lon (-180, 180) --> (180, -180) --- src/pyflexplot/plotting/coord_trans.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/pyflexplot/plotting/coord_trans.py b/src/pyflexplot/plotting/coord_trans.py index 010aa503..11eb8689 100644 --- a/src/pyflexplot/plotting/coord_trans.py +++ b/src/pyflexplot/plotting/coord_trans.py @@ -133,20 +133,20 @@ def axes_to_map(self, x, y): """Transform from axes to map coordinates.""" # pylint: disable=E0633 # unpacking-non-sequence x_geo, y_geo = self.axes_to_geo(x, y) - x, y = self.geo_to_map(x_geo, y_geo) + x_map, y_map = self.geo_to_map(x_geo, y_geo) if ( isinstance(self.proj_map, PlateCarree) - and not isinstance(x, float) + and not isinstance(x_map, float) and len(x) == 2 - and np.isclose(x[0], x[1], atol=0.5) - and np.isclose(np.abs(x[0]), 180, atol=0.5) ): - # Fix edge case where lon range (-180, 180) is turned into (-180, -180) + # Fix edge case where lon range (-180, 180) can invert to (180, -180) # during the transformation - x[0] = -180.0 - x[1] = +180.0 - return (x, y) + if np.isclose(np.abs(x_map[0]), 180, atol=0.5) and np.isclose(x_map[0], -x[0], atol=0.5): + x_map[0] = np.sign(x[0])*180.0 + if np.isclose(np.abs(x_map[1]), 180, atol=0.5) and np.isclose(x_map[1], -x[1], atol=0.5): + x_map[1] = np.sign(x[1])*180.0 + return (x_map, y_map) @overload def data_to_axes(self, x: float, y: float) -> tuple[float, float]: From 040ee5aa6f9f4368e85ce02e632192b12b7047bc Mon Sep 17 00:00:00 2001 From: Marco Ketzel Date: Fri, 14 Jul 2023 14:55:45 +0200 Subject: [PATCH 13/24] Changed type hint comparison for the casting and Properties of the TextBoxAxes --- src/srutils/dataclasses.py | 119 +++++++++--------- .../test_plotting/test_text_box_axes.py | 4 +- 2 files changed, 58 insertions(+), 65 deletions(-) diff --git a/src/srutils/dataclasses.py b/src/srutils/dataclasses.py index 1ac79c1e..43176a4b 100644 --- a/src/srutils/dataclasses.py +++ b/src/srutils/dataclasses.py @@ -10,6 +10,7 @@ from typing import Collection from typing import get_args from typing import get_type_hints +from typing import get_origin from typing import Iterable from typing import Optional from typing import Sequence @@ -17,6 +18,7 @@ from typing import TypeVar from typing import Union + # First-party from srutils.datetime import derive_datetime_fmt from srutils.exceptions import IncompatibleTypesError @@ -123,17 +125,17 @@ def cast_field_value(cls: Type, name: str, value: Any, **kwargs: Any) -> Any: """ try: type_ = get_type_hints(cls)[name] - except KeyError as e: - raise InvalidParameterNameError(name) from e + except KeyError as ex: + raise InvalidParameterNameError(name) from ex try: return cast_value(type_, value, **kwargs) - except Exception as e: + except Exception as ex: exc: Type[Exception] type_name = type_.__name__ if isinstance(type_, type) else type - if isinstance(e, IncompatibleTypesError): + if isinstance(ex, IncompatibleTypesError): exc = InvalidParameterValueError msg = f"value incompatible with type {type_name}" - elif isinstance(e, UnsupportedTypeError): + elif isinstance(ex, UnsupportedTypeError): for arg in get_args(type_): try: if isinstance(value, arg): @@ -143,8 +145,8 @@ def cast_field_value(cls: Type, name: str, value: Any, **kwargs: Any) -> Any: exc = InvalidParameterNameError msg = f"type {type_name} not supported" else: - raise e - raise exc(f"{msg}: {cls.__name__}.{name} = {sfmt(value)}") from e + raise ex + raise exc(f"{msg}: {cls.__name__}.{name} = {sfmt(value)}") from ex # pylint: disable=R0911 # too-many-return-statements (>6) @@ -186,10 +188,11 @@ def cast_value( sequence of one-character strings, as is their default behavior. """ + type_name = None try: - type_ = type_.__name__ # type: ignore + type_name = type_.__name__ # type: ignore except AttributeError: - type_ = str(type_) + type_ = str(type_name) if bool_mode not in ["native", "intuitive"]: raise ValueError(f"bool_mode neither 'native' nor 'intuitive': {bool_mode}") timedelta_unit_choices = [ @@ -276,17 +279,17 @@ def prepare_wrapped_value( raise error(value, type_, msg) return value - if type_ == "typing.Any": + if type_name == "Any": return value - elif type_ == "NoneType": + elif type_name == "NoneType": if isinstance(value, type(None)) or value == "None": return None - raise error(value, type_) + raise error(value, type_name) - elif type_ == "bool": + elif type_name == "bool": if isinstance(value, Collection) and not isinstance(value, str): - raise error(value, type_, "is a collection") + raise error(value, type_name, "is a collection") if bool_mode == "intuitive": try: value = int(value) @@ -299,45 +302,43 @@ def prepare_wrapped_value( }.get(str(value).lower(), value) return bool(value) - elif type_ == "str": + elif type_name == "str": if isinstance(value, Collection) and not isinstance(value, str): - raise error(value, type_, "is a collection") + raise error(value, type_name, "is a collection") return str(value) - elif type_ in ["int", "float"]: + elif type_name in ["int", "float"]: try: - return {"int": int, "float": float}[type_](value) + return {"int": int, "float": float}[type_name](value) except (TypeError, ValueError) as e: - raise error(value, type_) from e + raise error(value, type_name) from e - elif type_.startswith("typing.Union["): - inner_types = split_outside_parens( - type_[len("typing.Union[") : -len("]")], ", ", parens="[]" - ) + elif "Union" in type_name: + inner_types = get_args(type_) if "NoneType" in inner_types: inner_types.remove("NoneType") inner_types.insert(0, "NoneType") for inner_type in inner_types: - if has_same_type(value, inner_type): + if type(value) == inner_type: return value for inner_type in inner_types: try: return cast_value(inner_type, value, **kwargs) except IncompatibleTypesError: pass - raise error(value, type_, f"no compatible inner type: {inner_types}") + raise error(value, type_name, f"no compatible inner type: {inner_types}") - elif type_.startswith("typing.Optional["): + elif "Optional" in type_name: if value in [None, "None"]: return None - inner_type = type_[len("typing.Optional[") : -len("]")] + inner_type = [i for i in get_args(type_) if not i==type(None)][0] try: return cast_value(inner_type, value, **kwargs) except IncompatibleTypesError: pass - raise error(value, type_, f"incompatible inner type: {inner_type}") + raise error(value, type_name, f"incompatible inner type: {inner_type}") - elif type_ in ["datetime", "datetime.datetime"]: + elif type_name in ["datetime", "datetime.datetime"]: if isinstance(datetime_fmt, str): datetime_fmt = (datetime_fmt,) # type: ignore assert isinstance(datetime_fmt, Sequence) # mypy @@ -347,56 +348,48 @@ def prepare_wrapped_value( try: fmt = derive_datetime_fmt(value) except ValueError as e: - raise error(value, type_, "cannot derive datetime_fmt") from e + raise error(value, type_name, "cannot derive datetime_fmt") from e try: return datetime.strptime(str(value), fmt) except ValueError: pass - raise error(value, type_, f"no compatible datetime_fmt: {datetime_fmt}") + raise error(value, type_name, f"no compatible datetime_fmt: {datetime_fmt}") - elif type_ in ["timedelta", "datetime.timedelta"]: + elif type_name in ["timedelta", "datetime.timedelta"]: try: return timedelta(**{timedelta_unit: value}) except TypeError as e: - raise error(value, type_, f"timedelta_unit: {timedelta_unit}") from e - - if type_ in ["tuple", "typing.Tuple"]: - return prepare_wrapped_value(value, type_, tuple) - - elif type_.startswith("typing.Tuple["): - value = prepare_wrapped_value(value, type_, tuple) - if type_.endswith(", ...]"): - inner_type = type_[len("typing.Tuple[") : -len(", ...]")] + raise error(value, type_name, f"timedelta_unit: {timedelta_unit}") from e + + elif "Tuple" in type_name: + value = prepare_wrapped_value(value, type_name, tuple) + inner_types = [t for t in get_args(type_) if t is not Ellipsis] + if len(inner_types)==0: + return prepare_wrapped_value(value, type_name) + if len(inner_types)==1: + inner_type = inner_types[0] inner_values = [ cast_value(inner_type, inner_value, **kwargs) for inner_value in value ] return tuple(inner_values) - else: - inner_types = split_outside_parens( - type_[len("typing.Tuple[") : -len("]")], ", ", parens="[]" - ) - if len(value) != len(inner_types): - raise error(value, type_, "wrong length") + elif len(inner_types)>1: inner_values = [ cast_value(inner_type, inner_value, **kwargs) for inner_type, inner_value in zip(inner_types, value) ] return tuple(inner_values) - if type_ in ["list", "typing.List"]: - return prepare_wrapped_value(value, type_, list) - - elif type_.startswith("typing.List["): - value = prepare_wrapped_value(value, type_, list) - inner_type = type_[len("typing.List[") : -len("]")] - return [cast_value(inner_type, inner_value, **kwargs) for inner_value in value] - - elif type_ == "typing.Sequence": - return prepare_wrapped_value(value, type_) - - elif type_.startswith("typing.Sequence["): - value = prepare_wrapped_value(value, type_) - inner_type = type_[len("typing.Sequence[") : -len("]")] + elif "List" in type_name: + value = prepare_wrapped_value(value, type_name, list) + inner_type = get_args(type_)[0] + return [cast_value(inner_type, inner_value, **kwargs) for inner_value in value] + + elif "Sequence" in type_name: + value = prepare_wrapped_value(value, type_name) + inner_types = get_args(type_) + if len(inner_types)==0: + return prepare_wrapped_value(value, type_name) + inner_type = inner_types[0] cls: Callable[[Iterable], Sequence] = ( list if isinstance(value, str) else type(value) # type: ignore ) @@ -404,8 +397,8 @@ def prepare_wrapped_value( [cast_value(inner_type, inner_value, **kwargs) for inner_value in value] ) - elif type_ == type(value).__name__: + elif type_name == type(value).__name__: return value else: - raise UnsupportedTypeError(f"{type_}") + raise UnsupportedTypeError(f"{type_name}") diff --git a/tests/fast/test_pyflexplot/test_plotting/test_text_box_axes.py b/tests/fast/test_pyflexplot/test_plotting/test_text_box_axes.py index 895637c3..8edff3f0 100644 --- a/tests/fast/test_pyflexplot/test_plotting/test_text_box_axes.py +++ b/tests/fast/test_pyflexplot/test_plotting/test_text_box_axes.py @@ -23,8 +23,8 @@ def create_text_box(self, name, **kwargs): "fig": { "type": "Figure", "bbox": {"type": "TransformedBbox", "bounds": (0.0, 0.0, 100.0, 100.0)}, - "axes": [ - {"type": "AxesSubplot"}, + "axes": [{}, + #{"type": "AxesSubplot"}, { "type": "Axes", "bbox": { From 40c2288380858cdaf96903b034660776b5cb4512 Mon Sep 17 00:00:00 2001 From: Karko93 Date: Mon, 17 Jul 2023 14:49:07 +0200 Subject: [PATCH 14/24] Removed obsolete class in the Textbox Test --- src/pyflexplot/plotting/text_box_axes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pyflexplot/plotting/text_box_axes.py b/src/pyflexplot/plotting/text_box_axes.py index 6159eeeb..3128ffbb 100644 --- a/src/pyflexplot/plotting/text_box_axes.py +++ b/src/pyflexplot/plotting/text_box_axes.py @@ -79,7 +79,7 @@ def __init__( self.replace_edge_spaces = replace_edge_spaces self.edge_spaces_replacement_char = edge_spaces_replacement_char self.kwargs = kwargs - + print("TEXTBOXELEMENTTEXT ", s, self.kwargs.keys()) # SR_TMP < TODO consider removing this # Add alignment parameters, unless specified in input kwargs self.kwargs["ha"] = self.kwargs.get( From 125729d6f237a16e90ef2d78ee815a4b780cc4b4 Mon Sep 17 00:00:00 2001 From: Karko93 Date: Mon, 17 Jul 2023 14:52:24 +0200 Subject: [PATCH 15/24] Removed obsolete class in the textbox axes tests --- tests/fast/test_pyflexplot/test_plotting/test_text_box_axes.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/fast/test_pyflexplot/test_plotting/test_text_box_axes.py b/tests/fast/test_pyflexplot/test_plotting/test_text_box_axes.py index 8edff3f0..5d9c324c 100644 --- a/tests/fast/test_pyflexplot/test_plotting/test_text_box_axes.py +++ b/tests/fast/test_pyflexplot/test_plotting/test_text_box_axes.py @@ -24,7 +24,6 @@ def create_text_box(self, name, **kwargs): "type": "Figure", "bbox": {"type": "TransformedBbox", "bounds": (0.0, 0.0, 100.0, 100.0)}, "axes": [{}, - #{"type": "AxesSubplot"}, { "type": "Axes", "bbox": { From 0c005b18c7d47d65060651b06263ff33f3a4fab5 Mon Sep 17 00:00:00 2001 From: Karko93 Date: Mon, 24 Jul 2023 17:17:51 +0200 Subject: [PATCH 16/24] Removed obsolete code --- src/pyflexplot/plotting/text_box_axes.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/pyflexplot/plotting/text_box_axes.py b/src/pyflexplot/plotting/text_box_axes.py index 3128ffbb..42241c60 100644 --- a/src/pyflexplot/plotting/text_box_axes.py +++ b/src/pyflexplot/plotting/text_box_axes.py @@ -79,7 +79,6 @@ def __init__( self.replace_edge_spaces = replace_edge_spaces self.edge_spaces_replacement_char = edge_spaces_replacement_char self.kwargs = kwargs - print("TEXTBOXELEMENTTEXT ", s, self.kwargs.keys()) # SR_TMP < TODO consider removing this # Add alignment parameters, unless specified in input kwargs self.kwargs["ha"] = self.kwargs.get( From 797ed2a4d85d7a5769a888643db8c506b5c44906 Mon Sep 17 00:00:00 2001 From: Karko93 Date: Mon, 24 Jul 2023 17:55:59 +0200 Subject: [PATCH 17/24] Removed DeprecationWarning coming from new matplotlib version due to changing in the colormapping --- src/pyflexplot/plots.py | 5 ++++- src/srutils/plotting.py | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/src/pyflexplot/plots.py b/src/pyflexplot/plots.py index e4662d11..35ea3a33 100644 --- a/src/pyflexplot/plots.py +++ b/src/pyflexplot/plots.py @@ -902,7 +902,10 @@ def cmap2colors( n_colors += 1 if extend in ["max", "both"] and not color_over: n_colors += 1 - cmap = mpl.cm.get_cmap(cmap, lut=n_colors) + cmap = mpl.pyplot.get_cmap(cmap) + if n_colors > 1: + cmap = mpl.colors.ListedColormap(cmap(np.linspace(0, 1, n_colors))) + colors: list[ColorType] try: colors = cmap.colors.tolist() diff --git a/src/srutils/plotting.py b/src/srutils/plotting.py index 8e1c685e..5a004e6c 100644 --- a/src/srutils/plotting.py +++ b/src/srutils/plotting.py @@ -21,7 +21,7 @@ def truncate_cmap( """ if isinstance(cmap, str): - cmap = mpl.cm.get_cmap(cmap) + cmap = mpl.pyplot.get_cmap(cmap) return mpl.colors.LinearSegmentedColormap.from_list( f"truncated({cmap.name}, {minval:.2f}, {maxval:.2f})", cmap(np.linspace(minval, maxval, n)), From 7950291ad9d16447499b04cebd79fc688dd06056 Mon Sep 17 00:00:00 2001 From: Karko93 Date: Mon, 24 Jul 2023 18:02:03 +0200 Subject: [PATCH 18/24] Updated the references in the slow test of the different models --- .../test_plots/ref_cosmo-1_affected_area.py | 1800 ++++----- .../ref_cosmo-1_cloud_arrival_time.py | 1800 ++++----- .../test_plots/ref_cosmo-1_concentration.py | 1787 ++++----- .../ref_cosmo-1_integrated_concentration.py | 1811 ++++----- .../ref_cosmo-1_total_deposition.py | 1784 ++++----- .../ref_cosmo-1e-ctrl_affected_area.py | 1776 ++++----- ...o-1e-ctrl_concentration_multipanel_time.py | 3116 +++++++-------- ...-1e-ctrl_tot_deposition_multipanel_time.py | 3472 ++++++++--------- .../ref_cosmo-1e_total_deposition_dummy.py | 1780 ++++----- .../ref_cosmo-2e_ens_cloud_arrival_time.py | 1848 ++++----- .../ref_cosmo-2e_ens_cloud_departure_time.py | 1824 ++++----- ...ltipanel_ens_stats_integr_concentration.py | 3092 +++++++-------- .../ref_cosmo-e_ens_cloud_arrival_time.py | 1776 ++++----- .../ref_cosmo-e_ens_cloud_departure_time.py | 1896 ++++----- ...osmo-e_ens_max_integrated_concentration.py | 1907 ++++----- .../ref_cosmo-e_ens_mean_concentration.py | 1787 ++++----- .../ref_cosmo-e_ens_mean_total_deposition.py | 1782 ++++----- .../ref_cosmo-e_ens_min_affected_area.py | 1848 ++++----- ..._cosmo-e_ens_probability_wet_deposition.py | 1776 ++++----- .../ref_ifs-hres-eu_affected_area.py | 1848 ++++----- ...ef_ifs-hres-eu_integrated_concentration.py | 1859 ++++----- .../ref_ifs-hres-eu_total_deposition.py | 1852 ++++----- .../test_plots/ref_ifs-hres_affected_area.py | 1728 ++++---- .../ref_ifs-hres_cloud_departure_time.py | 1824 ++++----- .../test_plots/ref_ifs-hres_concentration.py | 1835 ++++----- .../ref_ifs-hres_total_deposition.py | 1852 ++++----- 26 files changed, 25793 insertions(+), 25667 deletions(-) diff --git a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_affected_area.py b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_affected_area.py index 359abd40..99f63d77 100644 --- a/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_affected_area.py +++ b/tests/slow/test_pyflexplot/test_plots/ref_cosmo-1_affected_area.py @@ -982,32 +982,32 @@ "xlabel": "", "xlim": (0.19550009091695134, 1.8204999319712316), "xmajorticklabels": [ - 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"Text(0, 0, '')", - "Text(0, 0, '')", - "Text(0, 0, '')", - "Text(0, 0, '')", - "Text(0, 0, '')", - "Text(0, 0, '')", + "Text(0.0, 0, '0.0')", + "Text(0.2, 0, '0.2')", + "Text(0.4, 0, '0.4')", + "Text(0.6000000000000001, 0, '0.6')", + "Text(0.8, 0, '0.8')", + "Text(1.0, 0, '1.0')", ], "xticks": [0.0, 0.2, 0.4, 0.6000000000000001, 0.8, 1.0], "ylabel": "", "ylim": (0.0, 1.0), - "ymajorticklabels": ["Text(0, 0, '')", "Text(0, 0, '')"], + "ymajorticklabels": ["Text(0, 0.0, '0')", "Text(0, 1.0, '1')"], "yminorticklabels": [], "yscale": "linear", - "yticklabels": ["Text(0, 0, '')", "Text(0, 0, '')"], + "yticklabels": ["Text(0, 0.0, '0')", "Text(0, 1.0, '1')"], "yticks": [0.0, 1.0], "zorder": 0, }, From 2eba1aead558a495167dc862863ebc958c02f706 Mon Sep 17 00:00:00 2001 From: Karko93 Date: Tue, 25 Jul 2023 10:56:15 +0200 Subject: [PATCH 19/24] Formatted Code --- src/pyflexplot/plotting/coord_trans.py | 12 ++++++++---- src/srutils/dataclasses.py | 12 ++++++------ 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/src/pyflexplot/plotting/coord_trans.py b/src/pyflexplot/plotting/coord_trans.py index 11eb8689..a0e4c28a 100644 --- a/src/pyflexplot/plotting/coord_trans.py +++ b/src/pyflexplot/plotting/coord_trans.py @@ -142,10 +142,14 @@ def axes_to_map(self, x, y): ): # Fix edge case where lon range (-180, 180) can invert to (180, -180) # during the transformation - if np.isclose(np.abs(x_map[0]), 180, atol=0.5) and np.isclose(x_map[0], -x[0], atol=0.5): - x_map[0] = np.sign(x[0])*180.0 - if np.isclose(np.abs(x_map[1]), 180, atol=0.5) and np.isclose(x_map[1], -x[1], atol=0.5): - x_map[1] = np.sign(x[1])*180.0 + if np.isclose(np.abs(x_map[0]), 180, atol=0.5) and np.isclose( + x_map[0], -x[0], atol=0.5 + ): + x_map[0] = np.sign(x[0]) * 180.0 + if np.isclose(np.abs(x_map[1]), 180, atol=0.5) and np.isclose( + x_map[1], -x[1], atol=0.5 + ): + x_map[1] = np.sign(x[1]) * 180.0 return (x_map, y_map) @overload diff --git a/src/srutils/dataclasses.py b/src/srutils/dataclasses.py index 43176a4b..62ee08eb 100644 --- a/src/srutils/dataclasses.py +++ b/src/srutils/dataclasses.py @@ -331,7 +331,7 @@ def prepare_wrapped_value( elif "Optional" in type_name: if value in [None, "None"]: return None - inner_type = [i for i in get_args(type_) if not i==type(None)][0] + inner_type = [i for i in get_args(type_) if not i == type(None)][0] try: return cast_value(inner_type, value, **kwargs) except IncompatibleTypesError: @@ -364,15 +364,15 @@ def prepare_wrapped_value( elif "Tuple" in type_name: value = prepare_wrapped_value(value, type_name, tuple) inner_types = [t for t in get_args(type_) if t is not Ellipsis] - if len(inner_types)==0: + if len(inner_types) == 0: return prepare_wrapped_value(value, type_name) - if len(inner_types)==1: + if len(inner_types) == 1: inner_type = inner_types[0] inner_values = [ cast_value(inner_type, inner_value, **kwargs) for inner_value in value ] return tuple(inner_values) - elif len(inner_types)>1: + elif len(inner_types) > 1: inner_values = [ cast_value(inner_type, inner_value, **kwargs) for inner_type, inner_value in zip(inner_types, value) @@ -382,12 +382,12 @@ def prepare_wrapped_value( elif "List" in type_name: value = prepare_wrapped_value(value, type_name, list) inner_type = get_args(type_)[0] - return [cast_value(inner_type, inner_value, **kwargs) for inner_value in value] + return [cast_value(inner_type, inner_value, **kwargs) for inner_value in value] elif "Sequence" in type_name: value = prepare_wrapped_value(value, type_name) inner_types = get_args(type_) - if len(inner_types)==0: + if len(inner_types) == 0: return prepare_wrapped_value(value, type_name) inner_type = inner_types[0] cls: Callable[[Iterable], Sequence] = ( From c91ce0ab9be9a08daa5992ed7284053cac3efab7 Mon Sep 17 00:00:00 2001 From: Karko93 Date: Wed, 26 Jul 2023 11:30:58 +0200 Subject: [PATCH 20/24] Updated to pypdf because pyPDF2 is deprecated --- src/srutils/pdf.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/srutils/pdf.py b/src/srutils/pdf.py index 687cb7d4..4f706bbc 100644 --- a/src/srutils/pdf.py +++ b/src/srutils/pdf.py @@ -7,10 +7,10 @@ from typing import Sequence # Third-party -from PyPDF2 import PdfFileReader -from PyPDF2 import PdfFileWriter -from PyPDF2.pdf import PageObject -from PyPDF2.utils import PdfReadError +from pypdf import PdfReader +from pypdf import PdfWriter +from pypdf._page import PageObject +from pypdf.errors import PdfReadError @dc.dataclass @@ -21,9 +21,9 @@ class MultiPagePDF: def write(self, path: str) -> None: """Write the file to disk.""" - writer = PdfFileWriter() + writer = PdfWriter() for page in self.pages: - writer.addPage(page) + writer.add_page(page) dir_path = os.path.dirname(path) if dir_path: os.makedirs(dir_path, exist_ok=True) @@ -36,11 +36,11 @@ def _read_pages(paths: Sequence[str]) -> list[PageObject]: pages: list[PageObject] = [] for path_i in paths: try: - file = PdfFileReader(path_i) + file = PdfReader(path_i) except (ValueError, TypeError, PdfReadError) as e: # Occur sporadically; likely a file system issue raise PdfReadError(path_i) from e - page = file.getPage(0) + page = file.pages[0] pages.append(page) return pages From 103b0c7fab79cd0536b0dc7d130f5d5466260cf2 Mon Sep 17 00:00:00 2001 From: Karko93 Date: Thu, 27 Jul 2023 08:37:58 +0200 Subject: [PATCH 21/24] Updated environment and version information --- environment.yml | 350 ++++++++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 6 +- 2 files changed, 353 insertions(+), 3 deletions(-) create mode 100644 environment.yml diff --git a/environment.yml b/environment.yml new file mode 100644 index 00000000..2f759867 --- /dev/null +++ b/environment.yml @@ -0,0 +1,350 @@ +name: pyflexplot +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - alabaster=0.7.13 + - alsa-lib=1.2.8 + - anaconda-client=1.11.3 + - anaconda-project=0.11.1 + - anyio=3.7.1 + - astroid=2.15.6 + - asttokens=2.2.1 + - attr=2.5.1 + - attrs=23.1.0 + - aws-c-auth=0.7.0 + - aws-c-cal=0.6.0 + - aws-c-common=0.8.23 + - aws-c-compression=0.2.17 + - aws-c-event-stream=0.3.1 + - aws-c-http=0.7.11 + - aws-c-io=0.13.28 + - aws-c-mqtt=0.8.14 + - aws-c-s3=0.3.13 + - aws-c-sdkutils=0.1.11 + - aws-checksums=0.1.16 + - aws-crt-cpp=0.20.3 + - aws-sdk-cpp=1.10.57 + - babel=2.12.1 + - backcall=0.2.0 + - backports=1.0 + - backports.functools_lru_cache=1.6.5 + - beautifulsoup4=4.12.2 + - black=23.3.0 + - blosc=1.21.4 + - boa=0.14.0 + - boltons=23.0.0 + - brotli=1.0.9 + - brotli-bin=1.0.9 + - brotlipy=0.7.0 + - bzip2=1.0.8 + - c-ares=1.19.1 + - ca-certificates=2023.7.22 + - cairo=1.16.0 + - cartopy=0.21.1 + - certifi=2023.7.22 + - cffi=1.15.1 + - cfgv=3.3.1 + - cftime=1.6.2 + - chardet=5.1.0 + - charset-normalizer=3.2.0 + - click=8.1.3 + - clyent=1.2.2 + - codespell=2.2.5 + - colorama=0.4.6 + - conda=23.5.0 + - conda-build=3.24.0 + - conda-pack=0.7.0 + - conda-package-handling=2.0.2 + - conda-package-streaming=0.8.0 + - contourpy=1.1.0 + - cryptography=41.0.2 + - cycler=0.11.0 + - dataclasses=0.8 + - dbus=1.13.6 + - decorator=5.1.1 + - defusedxml=0.7.1 + - dill=0.3.7 + - distlib=0.3.7 + - docutils=0.18.1 + - exceptiongroup=1.1.2 + - executing=1.2.0 + - expat=2.5.0 + - filelock=3.12.2 + - flake8=6.0.0 + - flake8-black=0.3.6 + - fmt=9.1.0 + - font-ttf-dejavu-sans-mono=2.37 + - font-ttf-inconsolata=3.000 + - font-ttf-source-code-pro=2.038 + - font-ttf-ubuntu=0.83 + - fontconfig=2.14.2 + - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 + - fonttools=4.41.1 + - freetype=2.12.1 + - geographiclib=1.52 + - geopy=2.3.0 + - geos=3.11.2 + - gettext=0.21.1 + - glib=2.76.4 + - glib-tools=2.76.4 + - glob2=0.7 + - graphite2=1.3.13 + - gst-plugins-base=1.22.3 + - gstreamer=1.22.3 + - harfbuzz=7.3.0 + - hdf4=4.2.15 + - hdf5=1.14.1 + - icu=72.1 + - identify=2.5.26 + - idna=3.4 + - imagesize=1.4.1 + - importlib-metadata=4.13.0 + - importlib_resources=6.0.0 + - iniconfig=2.0.0 + - ipdb=0.13.13 + - ipython=8.14.0 + - isort=5.12.0 + - jedi=0.18.2 + - jinja2=3.1.2 + - joblib=1.3.0 + - json5=0.9.14 + - jsonpatch=1.32 + - jsonpointer=2.0 + - jsonschema=4.18.4 + - jsonschema-specifications=2023.7.1 + - jupyter_core=5.3.1 + - keyutils=1.6.1 + - kiwisolver=1.4.4 + - krb5=1.20.1 + - lame=3.100 + - lazy-object-proxy=1.9.0 + - lcms2=2.15 + - ld_impl_linux-64=2.40 + - lerc=4.0.0 + - libaec=1.0.6 + - libarchive=3.6.2 + - libblas=3.9.0 + - libbrotlicommon=1.0.9 + - libbrotlidec=1.0.9 + - libbrotlienc=1.0.9 + - libcap=2.67 + - libcblas=3.9.0 + - libclang=16.0.6 + - libclang13=16.0.6 + - libcups=2.3.3 + - libcurl=8.1.2 + - libdeflate=1.18 + - libedit=3.1.20191231 + - libev=4.33 + - libevent=2.1.12 + - libexpat=2.5.0 + - libffi=3.4.2 + - libflac=1.4.3 + - libgcc-ng=13.1.0 + - libgcrypt=1.10.1 + - libgfortran-ng=13.1.0 + - libgfortran5=13.1.0 + - libglib=2.76.4 + - libgomp=13.1.0 + - libgpg-error=1.47 + - libiconv=1.17 + - libjpeg-turbo=2.1.5.1 + - liblapack=3.9.0 + - liblief=0.12.3 + - libllvm16=16.0.6 + - libmamba=1.4.7 + - libmambapy=1.4.7 + - libnetcdf=4.9.2 + - libnghttp2=1.52.0 + - libnsl=2.0.0 + - libogg=1.3.4 + - libopenblas=0.3.23 + - libopus=1.3.1 + - libpng=1.6.39 + - libpq=15.3 + - libsndfile=1.2.0 + - libsolv=0.7.24 + - libsqlite=3.42.0 + - libssh2=1.11.0 + - libstdcxx-ng=13.1.0 + - libsystemd0=253 + - libtiff=4.5.1 + - libuuid=2.38.1 + - libvorbis=1.3.7 + - libwebp-base=1.3.1 + - libxcb=1.15 + - libxkbcommon=1.5.0 + - libxml2=2.11.4 + - libzip=1.9.2 + - libzlib=1.2.13 + - livereload=2.6.3 + - lz4-c=1.9.4 + - lzo=2.10 + - mamba=1.4.7 + - markdown-it-py=3.0.0 + - markupsafe=2.1.3 + - matplotlib=3.7.0 + - matplotlib-base=3.7.0 + - matplotlib-inline=0.1.6 + - mccabe=0.7.0 + - mdurl=0.1.0 + - mpg123=1.31.3 + - munkres=1.1.4 + - mypy=1.4.1 + - mypy_extensions=1.0.0 + - mysql-common=8.0.33 + - mysql-libs=8.0.33 + - nbformat=5.9.1 + - ncurses=6.4 + - netcdf4=1.6.4 + - nodeenv=1.8.0 + - nspr=4.35 + - nss=3.89 + - numpy=1.25.0 + - openjpeg=2.5.0 + - openssl=3.1.1 + - packaging=23.1 + - parso=0.8.3 + - patch=2.7.6 + - patchelf=0.17.2 + - pathspec=0.11.1 + - pcre2=10.40 + - pexpect=4.8.0 + - pickleshare=0.7.5 + - pillow=10.0.0 + - pip=23.1.2 + - pixman=0.40.0 + - pkginfo=1.9.6 + - pkgutil-resolve-name=1.3.10 + - platformdirs=3.9.1 + - pluggy=1.2.0 + - ply=3.11 + - pooch=1.7.0 + - pre-commit=3.3.3 + - proj=9.2.1 + - prompt-toolkit=3.0.39 + - prompt_toolkit=3.0.39 + - psutil=5.9.5 + - pthread-stubs=0.4 + - ptyprocess=0.7.0 + - pulseaudio-client=16.1 + - pure_eval=0.2.2 + - py-lief=0.12.3 + - pybind11-abi=4 + - pycodestyle=2.10.0 + - pycosat=0.6.4 + - pycparser=2.21 + - pydantic=1.10.11 + - pydocstyle=6.3.0 + - pyflakes=3.0.1 + - pygments=2.15.1 + - pylint=2.17.4 + - pyopenssl=23.2.0 + - pyparsing=3.1.0 + - pypdf=3.13.0 + - pyproj=3.6.0 + - pyqt=5.15.9 + - pyqt5-sip=12.12.2 + - pyshp=2.3.1 + - pysocks=1.7.1 + - pytest=7.4.0 + - python=3.10.12 + - python-dateutil=2.8.2 + - python-fastjsonschema=2.18.0 + - python-libarchive-c=5.0 + - python_abi=3.10 + - pytoolconfig=1.2.5 + - pytz=2023.3 + - pyyaml=6.0 + - qt-main=5.15.8 + - readline=8.2 + - referencing=0.30.0 + - reproc=14.2.4 + - reproc-cpp=14.2.4 + - requests=2.31.0 + - requests-toolbelt=1.0.0 + - rich=13.4.2 + - ripgrep=13.0.0 + - rope=1.9.0 + - rpds-py=0.9.2 + - rstcheck=6.1.2 + - rstcheck-core=1.0.3 + - ruamel.yaml=0.17.32 + - ruamel.yaml.clib=0.2.7 + - ruamel_yaml=0.15.80 + - s2n=1.3.46 + - scipy=1.11.1 + - setuptools=68.0.0 + - shapely=2.0.1 + - shellingham=1.5.1 + - sip=6.7.10 + - six=1.16.0 + - snappy=1.1.10 + - sniffio=1.3.0 + - snowballstemmer=2.2.0 + - soupsieve=2.3.2.post1 + - sphinx=7.0.1 + - sphinx-autobuild=2021.3.14 + - sphinxcontrib-applehelp=1.0.4 + - sphinxcontrib-devhelp=1.0.2 + - sphinxcontrib-htmlhelp=2.0.1 + - sphinxcontrib-jsmath=1.0.1 + - sphinxcontrib-qthelp=1.0.3 + - sphinxcontrib-serializinghtml=1.1.5 + - sqlite=3.42.0 + - stack_data=0.6.2 + - tk=8.6.12 + - toml=0.10.2 + - tomli=2.0.1 + - tomlkit=0.11.8 + - toolz=0.12.0 + - tornado=6.3.2 + - tqdm=4.65.0 + - traitlets=5.9.0 + - typer=0.4.2 + - types-docutils=0.18.3 + - types-setuptools=68.0.0.1 + - types-toml=0.10.8.6 + - typing-extensions=4.7.1 + - typing_extensions=4.7.1 + - tzdata=2023c + - ukkonen=1.0.1 + - unicodedata2=15.0.0 + - urllib3=1.26.15 + - virtualenv=20.24.2 + - watchgod=0.8.2 + - wcwidth=0.2.6 + - wheel=0.41.0 + - wrapt=1.15.0 + - xcb-util=0.4.0 + - xcb-util-image=0.4.0 + - xcb-util-keysyms=0.4.0 + - xcb-util-renderutil=0.3.9 + - xcb-util-wm=0.4.1 + - xkeyboard-config=2.39 + - xorg-kbproto=1.0.7 + - xorg-libice=1.1.1 + - xorg-libsm=1.2.4 + - xorg-libx11=1.8.6 + - xorg-libxau=1.0.11 + - xorg-libxdmcp=1.1.3 + - xorg-libxext=1.3.4 + - xorg-libxrender=0.9.11 + - xorg-renderproto=0.11.1 + - xorg-xextproto=7.3.0 + - xorg-xf86vidmodeproto=2.3.1 + - xorg-xproto=7.0.31 + - xz=5.2.6 + - yaml=0.2.5 + - yaml-cpp=0.7.0 + - zipp=3.16.2 + - zlib=1.2.13 + - zstandard=0.19.0 + - zstd=1.5.2 + - pip: + - pyflexplot==1.0.11 +prefix: /users/mketzel/miniconda3/envs/pyflexplot diff --git a/pyproject.toml b/pyproject.toml index 2c9450a1..f1c2fad4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta" [project] name = "pyflexplot" -version = "1.0.11" +version = "1.0.12" description = "Stefan Ruedisuehli's PyFlexPlot" readme = "README.md" keywords = [ @@ -22,9 +22,9 @@ classifiers = [ "Intended Audience :: Developers", "Natural Language :: English", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", ] -requires-python = ">=3.9" +requires-python = ">=3.10" authors = [ {name="Stefan Ruedisuehli", email="stefan.ruedisuehli@env.ethz.ch"}, ] From 01654a2666004a79a8af51a735f87c6587110de6 Mon Sep 17 00:00:00 2001 From: Karko93 Date: Thu, 5 Oct 2023 09:42:31 +0200 Subject: [PATCH 22/24] Update Readme --- README.md | 138 +++++++++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 117 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index ae72a0b2..cf997499 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,29 @@ -# PyFlexPlot: Stefan Ruedisuehli's PyFlexPlot +# PyFlexPlot +PyFlexPlot is a Python-based tool to visualize FLEXPART dispersion simulation results stored in NetCDF format. +## Table of Contents +- [Prerequisites and Cloning the Repository](#prerequisites-and-cloning-the-repository) +- [Getting Started](#getting-started) +- [Usage](#usage) + - [Usage Example](#usage-example) +- [Developer Notes](#developer-notes) + - [Implemented Debugging Features](#implemented-debugging-features) + - [Roadmap to your first Contribution](#roadmap-to-your-first-contribution) + - [Testing and Coding Standards](#testing-and-coding-standards) + - [Pre-commit on GitHub Actions](#pre-commit-on-github-actions) + - [Jenkins](#jenkins) +- [Features](#features) +- [Credits](#credits) +- [External Links](#external-links) +- [License](#license) +## Prerequisites and Cloning the Repository +Before you get started with this repository, ensure you have the following software/tools installed on your system: Git, Python and conda/mamba. +To get a local copy of this repository, run following commands and naviate into the repository: +```bash +git clone https://github.com/MeteoSwiss-APN/pyflexplot +cd +``` -## Start developing +## Getting Started Once you created or cloned this repository, make sure the installation is running properly. Install the package dependencies with the provided script `setup_env.sh`. Check available options with @@ -11,7 +34,7 @@ We distinguish pinned installations based on exported (reproducible) environment is based on top-level dependencies listed in `requirements/requirements.yml`. If you start developing, you might want to do an unpinned installation and export the environment: ```bash -tools/setup_env.sh -u -e -n +tools/setup_env.sh -u -e -n ``` *Hint*: If you are the package administrator, it is a good idea to understand what this script does, you can do everything manually with `conda` instructions. @@ -22,34 +45,101 @@ in `/envs/mamba/envs`, which is not very practical. The package itself is installed with `pip`. For development, install in editable mode: ```bash -conda activate +conda activate pip install --editable . ``` -*Warning:* Make sure you use the right pip, i.e. the one from the installed conda environment (`which pip` should point to something like `path/to/miniconda/envs//bin/pip`). +*Warning:* Make sure you use the right pip, i.e. the one from the installed conda environment (`which pip` should point to something like `path/to/miniconda/envs//bin/pip`). -Once your package is installed, run the tests by typing: +Once your package is installed, navigate to the root directory and run the tests by typing: -``` -conda activate +```bash +cd +conda activate pytest ``` If the tests pass, you are good to go. If not, contact the package administrator Stefan Ruedisuehli. Make sure to update your requirement files and export your environments after installation -every time you add new imports while developing. Check the next section to find some guidance on the development process if you are new to Python and/or APN. +every time you add new imports while developing. Check the next section to find some guidance on the development process if you are new to Python and/or SEN. + +## Usage +To utilize pyflexplot, first ensure you are in the root directory of the project and have activated the necessary conda environment: +```bash +cd +conda activate +``` +The primary command for pyflexplot follows this structure: +```bash +pyflexplot [OPTIONS] CONFIG_FILE_DIRECTORY +``` +To see the available options, run: + ```bash + pyflexplot -h + ``` +To utilize all available CPUs for the command, use the option: +```bash +--num-procs=$SLURM_CPUS_PER_TASK +``` + +### Usage Example +After you've set up pyflexplot ([Prerequisites and cloning the repository](#prerequisites-and-cloning-the-repository) and [Getting started](#getting-started)), +you'll need to specify a configuration file and an output directory. +Create an output directory using: +```bash +dest=test_output/ +``` +Note: The directory will be automatically created if it doesn't already exist. + +There are several default config files available under ```src/pyflexplot/data/presets/opr```. +Furthermore, there are already several default config files available in the directory ```src/pyflexplot/data/presets/opr```. +To run the program for all presets in the PDF graphics format with the default input data, use: + ```bash +preset='opr/*/all_pdf' +``` +Alternatively, select a specific preset from the table below: +| Model | Type | Preset | +|------------------|----------------------|----------------------------------| +| FLEXPART-IFS | Global output: | preset=opr/ifs-hres/all_pdf | +| FLEXPART-IFS | Europe output: | preset=opr/ifs-hres-eu/all_pdf | +| FLEXPART-COSMO | deterministic output:| preset=opr/cosmo-1e-ctrl/all_pdf | +| FLEXPART-COSMO | deterministic output:| preset=opr/cosmo-2e-ctrl/all_pdf | +| FLEXPART-COSMO-1E| ensemble output: | preset=opr/cosmo-1e/all_pdf | +| FLEXPART-COSMO-2E| ensemble output: | preset=opr/cosmo-2e/all_pdf | + +After selecting a preset, run pyflexplot interactively: + ```bash +pyflexplot --preset "$preset" --merge-pdfs --dest=$dest +``` + +## Developer Notes + +As this package was created with the SEN Python blueprint, it comes with a stack of development tools, which are described in more detail on the [Website](https://meteoswiss-apn.github.io/mch-python-blueprint/). Here, we give a brief overview on what is implemented. + +### Implemented Debugging Features +pyflexplot offers several debugging options to assist in troubleshooting and +refining your workflow (see ```pyflexplot -h```). +Here are some of the key debugging features: + ``` +--pdb / --no-pdb Drop into debugger when an exception is raised. [default: no-pdb] +--preset-cat PATTERN Show the contents of preset setup files +--only N Only create the first N plots based on the given setup. +--raise / --no-raise Raise exception in place of user-friendly but uninformative error message. +--dry-run Perform a trial run with no changes made. +--merge-pdfs-dry Merge PDF plots even in a dry run. +``` -### Roadmap to your first contribution +### Roadmap to your first Contribution Generally, the source code of your library is located in `src/`. The blueprint will generate some example code in `mutable_number.py`, `utils.py` and `cli.py`. `cli.py` thereby serves as an entry point for functionalities you want to execute from the command line, it is based on the Click library. If you do not need interactions with the command line, you should remove `cli.py`. Moreover, of course there exist other options for command line interfaces, -a good overview may be found here (https://realpython.com/comparing-python-command-line-parsing-libraries-argparse-docopt-click/), we recommend however to use click. The provided example +a good overview may be found [here](https://realpython.com/comparing-python-command-line-parsing-libraries-argparse-docopt-click/), we recommend however to use click. The provided example code should provide some guidance on how the individual source code files interact within the library. In addition to the example code in `src/`, there are examples for unit tests in `tests//`, which can be triggered with `pytest` from the command line. Once you implemented a feature (and of course you also implemented a meaningful test ;-)), you are likely willing to commit it. First, go to the root directory of your package and run pytest. ```bash -conda activate -cd +conda activate +cd pytest ``` @@ -67,18 +157,14 @@ up to you, if you want to use pre-commit locally or not. In any case, after runn when you push your changes to the main branch. Note that pytest is currently not invoked by pre-commit, so it will not run automatically. Automated testing can be set up with GitHub Actions or be implemented in a Jenkins pipeline (template for a plan available in `jenkins/`. See the next section for more details. -## Development tools - -As this package was created with the APN Python blueprint, it comes with a stack of development tools, which are described in more detail on -(https://meteoswiss-apn.github.io/mch-python-blueprint/). Here, we give a brief overview on what is implemented. -### Testing and coding standards +### Testing and Coding Standards -Testing your code and compliance with the most important Python standards is a requirement for Python software written in APN. To make the life of package +Testing your code and compliance with the most important Python standards is a requirement for Python software written in SEN. To make the life of package administrators easier, the most important checks are run automatically on GitHub actions. If your code goes into production, it must additionally be tested on CSCS machines, which is only possible with a Jenkins pipeline (GitHub actions is running on a GitHub server). -### Pre-commit on GitHub actions +### Pre-commit on GitHub Actions `.github/workflows/pre-commit.yml` contains a hook that will trigger the creation of your environment (unpinned) on the GitHub actions server and then run various formatters and linters through pre-commit. This hook is only triggered upon pushes to the main branch (in general: don't do that) @@ -97,4 +183,14 @@ and exclusively run your tests and checks on GitHub actions. ## Credits -This package was created with [`copier`](https://github.com/copier-org/copier) and the [`MeteoSwiss-APN/mch-python-blueprint`](https://meteoswiss-apn.github.io/mch-python-blueprint/) project template. +This package was created with [`copier`](https://github.com/copier-org/copier) and the [`MeteoSwiss-APN/mch-python-blueprint`](https://github.com/MeteoSwiss-APN/mch-python-blueprint) project template. + +## External Links + +* [copier](https://github.com/copier-org/copier) - Based library and CLI app for rendering project templates. +* [mch-python-blueprint](https://github.com/MeteoSwiss-APN/mch-python-blueprint) - Project template embedded in this project based on copier. + + +## License +This project is licensed under the terms of the MeteoSwiss. The full license text can be found in the [LICENSE](LICENSE) file. +In essence, you are free to use, modify, and distribute the software, provided the associated copyright notice and disclaimers are included. From 28a1c80a935a1b1ae3c2119436bf9da4b1cf4e69 Mon Sep 17 00:00:00 2001 From: Karko93 <41451360+Karko93@users.noreply.github.com> Date: Fri, 13 Oct 2023 13:29:53 +0200 Subject: [PATCH 23/24] Delete environment.yml --- environment.yml | 350 ------------------------------------------------ 1 file changed, 350 deletions(-) delete mode 100644 environment.yml diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 2f759867..00000000 --- a/environment.yml +++ /dev/null @@ -1,350 +0,0 @@ -name: pyflexplot -channels: - - conda-forge - - defaults -dependencies: - - _libgcc_mutex=0.1 - - _openmp_mutex=4.5 - - alabaster=0.7.13 - - alsa-lib=1.2.8 - - anaconda-client=1.11.3 - - anaconda-project=0.11.1 - - anyio=3.7.1 - - astroid=2.15.6 - - asttokens=2.2.1 - - attr=2.5.1 - - attrs=23.1.0 - - aws-c-auth=0.7.0 - - aws-c-cal=0.6.0 - - aws-c-common=0.8.23 - - aws-c-compression=0.2.17 - - aws-c-event-stream=0.3.1 - - aws-c-http=0.7.11 - - aws-c-io=0.13.28 - - aws-c-mqtt=0.8.14 - - aws-c-s3=0.3.13 - - aws-c-sdkutils=0.1.11 - - aws-checksums=0.1.16 - - aws-crt-cpp=0.20.3 - - aws-sdk-cpp=1.10.57 - - babel=2.12.1 - - backcall=0.2.0 - - backports=1.0 - - backports.functools_lru_cache=1.6.5 - - beautifulsoup4=4.12.2 - - black=23.3.0 - - blosc=1.21.4 - - boa=0.14.0 - - boltons=23.0.0 - - brotli=1.0.9 - - brotli-bin=1.0.9 - - brotlipy=0.7.0 - - bzip2=1.0.8 - - c-ares=1.19.1 - - ca-certificates=2023.7.22 - - cairo=1.16.0 - - cartopy=0.21.1 - - certifi=2023.7.22 - - cffi=1.15.1 - - cfgv=3.3.1 - - cftime=1.6.2 - - chardet=5.1.0 - - charset-normalizer=3.2.0 - - click=8.1.3 - - clyent=1.2.2 - - codespell=2.2.5 - - colorama=0.4.6 - - conda=23.5.0 - - conda-build=3.24.0 - - conda-pack=0.7.0 - - conda-package-handling=2.0.2 - - conda-package-streaming=0.8.0 - - contourpy=1.1.0 - - cryptography=41.0.2 - - cycler=0.11.0 - - dataclasses=0.8 - - dbus=1.13.6 - - decorator=5.1.1 - - defusedxml=0.7.1 - - dill=0.3.7 - - distlib=0.3.7 - - docutils=0.18.1 - - exceptiongroup=1.1.2 - - executing=1.2.0 - - expat=2.5.0 - 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- wheel=0.41.0 - - wrapt=1.15.0 - - xcb-util=0.4.0 - - xcb-util-image=0.4.0 - - xcb-util-keysyms=0.4.0 - - xcb-util-renderutil=0.3.9 - - xcb-util-wm=0.4.1 - - xkeyboard-config=2.39 - - xorg-kbproto=1.0.7 - - xorg-libice=1.1.1 - - xorg-libsm=1.2.4 - - xorg-libx11=1.8.6 - - xorg-libxau=1.0.11 - - xorg-libxdmcp=1.1.3 - - xorg-libxext=1.3.4 - - xorg-libxrender=0.9.11 - - xorg-renderproto=0.11.1 - - xorg-xextproto=7.3.0 - - xorg-xf86vidmodeproto=2.3.1 - - xorg-xproto=7.0.31 - - xz=5.2.6 - - yaml=0.2.5 - - yaml-cpp=0.7.0 - - zipp=3.16.2 - - zlib=1.2.13 - - zstandard=0.19.0 - - zstd=1.5.2 - - pip: - - pyflexplot==1.0.11 -prefix: /users/mketzel/miniconda3/envs/pyflexplot From d01db1613c5cbfdab3a6f0e319d7c6083d3e91de Mon Sep 17 00:00:00 2001 From: Karko93 <41451360+Karko93@users.noreply.github.com> Date: Fri, 13 Oct 2023 15:34:02 +0200 Subject: [PATCH 24/24] Update README, Added Quick start section --- README.md | 99 ++++++++++++++++++++++++++++++------------------------- 1 file changed, 54 insertions(+), 45 deletions(-) diff --git a/README.md b/README.md index cf997499..d7ff8384 100644 --- a/README.md +++ b/README.md @@ -2,10 +2,11 @@ PyFlexPlot is a Python-based tool to visualize FLEXPART dispersion simulation results stored in NetCDF format. ## Table of Contents - [Prerequisites and Cloning the Repository](#prerequisites-and-cloning-the-repository) -- [Getting Started](#getting-started) +- [Quick Start](#quick-start) - [Usage](#usage) - [Usage Example](#usage-example) -- [Developer Notes](#developer-notes) +- [The Developer's Guide through the Project](#the-developers-guide-through-the-project) + - [Getting Started](#getting-started) - [Implemented Debugging Features](#implemented-debugging-features) - [Roadmap to your first Contribution](#roadmap-to-your-first-contribution) - [Testing and Coding Standards](#testing-and-coding-standards) @@ -22,45 +23,15 @@ To get a local copy of this repository, run following commands and naviate into git clone https://github.com/MeteoSwiss-APN/pyflexplot cd ``` - -## Getting Started - -Once you created or cloned this repository, make sure the installation is running properly. Install the package dependencies with the provided script `setup_env.sh`. -Check available options with -```bash -tools/setup_env.sh -h -``` -We distinguish pinned installations based on exported (reproducible) environments and free installations where the installation -is based on top-level dependencies listed in `requirements/requirements.yml`. If you start developing, you might want to do an unpinned installation and export the environment: - -```bash -tools/setup_env.sh -u -e -n -``` -*Hint*: If you are the package administrator, it is a good idea to understand what this script does, you can do everything manually with `conda` instructions. - -*Hint*: Use the flag `-m` to speed up the installation using mamba. Of course you will have to install mamba first (we recommend to install mamba into your base -environment `conda install -c conda-forge mamba`. If you install mamba in another (maybe dedicated) environment, environments installed with mamba will be located -in `/envs/mamba/envs`, which is not very practical. - -The package itself is installed with `pip`. For development, install in editable mode: - -```bash -conda activate -pip install --editable . -``` - -*Warning:* Make sure you use the right pip, i.e. the one from the installed conda environment (`which pip` should point to something like `path/to/miniconda/envs//bin/pip`). - -Once your package is installed, navigate to the root directory and run the tests by typing: - +## Quick Start +For a quick setup to use pyflexplot, run the following commands within the root folder: +1. Install pinned environment: ```tools/setup_env.sh``` +2. Activate the environment and build the package: ```bash -cd -conda activate -pytest +conda activate pyflexplot +pip install --no-deps . ``` - -If the tests pass, you are good to go. If not, contact the package administrator Stefan Ruedisuehli. Make sure to update your requirement files and export your environments after installation -every time you add new imports while developing. Check the next section to find some guidance on the development process if you are new to Python and/or SEN. +3. To check if the tool runs properly you can run the tests by running ```pytest tests``` ## Usage To utilize pyflexplot, first ensure you are in the root directory of the project and have activated the necessary conda environment: @@ -84,13 +55,12 @@ To utilize all available CPUs for the command, use the option: ### Usage Example After you've set up pyflexplot ([Prerequisites and cloning the repository](#prerequisites-and-cloning-the-repository) and [Getting started](#getting-started)), you'll need to specify a configuration file and an output directory. -Create an output directory using: +Define an output directory: ```bash dest=test_output/ ``` -Note: The directory will be automatically created if it doesn't already exist. +Note: The directory will be created on run time if it doesn't already exist. -There are several default config files available under ```src/pyflexplot/data/presets/opr```. Furthermore, there are already several default config files available in the directory ```src/pyflexplot/data/presets/opr```. To run the program for all presets in the PDF graphics format with the default input data, use: ```bash @@ -111,7 +81,46 @@ After selecting a preset, run pyflexplot interactively: pyflexplot --preset "$preset" --merge-pdfs --dest=$dest ``` -## Developer Notes +## The Developer's Guide through the Project + +### Getting Started + +Once you created or cloned this repository, make sure the installation is running properly. Install the package dependencies with the provided script `setup_env.sh`. +Check available options with +```bash +tools/setup_env.sh -h +``` +We distinguish pinned installations based on exported (reproducible) environments and free installations where the installation +is based on top-level dependencies listed in `requirements/requirements.yml`. If you start developing, you might want to do an unpinned installation and export the environment: + +```bash +tools/setup_env.sh -u -e -n +``` +*Hint*: If you are the package administrator, it is a good idea to understand what this script does, you can do everything manually with `conda` instructions. + +*Hint*: Use the flag `-m` to speed up the installation using mamba. Of course you will have to install mamba first (we recommend to install mamba into your base +environment `conda install -c conda-forge mamba`. If you install mamba in another (maybe dedicated) environment, environments installed with mamba will be located +in `/envs/mamba/envs`, which is not very practical. + +The package itself is installed with `pip`. For development, install in editable mode: + +```bash +conda activate +pip install --editable . +``` + +*Warning:* Make sure you use the right pip, i.e. the one from the installed conda environment (`which pip` should point to something like `path/to/miniconda/envs//bin/pip`). + +Once your package is installed, navigate to the root directory and run the tests by typing: + +```bash +cd +conda activate +pytest +``` + +If the tests pass, you are good to go. Make sure to update your requirement files and export your environments after installation +every time you add new imports while developing. Check the next section to find some guidance on the development process if you are new to Python and/or SEN. As this package was created with the SEN Python blueprint, it comes with a stack of development tools, which are described in more detail on the [Website](https://meteoswiss-apn.github.io/mch-python-blueprint/). Here, we give a brief overview on what is implemented. @@ -130,8 +139,8 @@ Here are some of the key debugging features: ### Roadmap to your first Contribution -Generally, the source code of your library is located in `src/`. The blueprint will generate some example code in `mutable_number.py`, `utils.py` and `cli.py`. `cli.py` thereby serves as an entry -point for functionalities you want to execute from the command line, it is based on the Click library. If you do not need interactions with the command line, you should remove `cli.py`. Moreover, of course there exist other options for command line interfaces, +Generally, the source code of your library is located in `src/`. `cli.py` thereby serves as an entry +point for functionalities you want to execute from the command line and it is based on the Click library. If you do not need interactions with the command line, you should remove `cli.py`. Moreover, of course there exist other options for command line interfaces, a good overview may be found [here](https://realpython.com/comparing-python-command-line-parsing-libraries-argparse-docopt-click/), we recommend however to use click. The provided example code should provide some guidance on how the individual source code files interact within the library. In addition to the example code in `src/`, there are examples for unit tests in `tests//`, which can be triggered with `pytest` from the command line. Once you implemented a feature (and of course you also