Merge pull request #230 from OSeMOSYS/issue-229

General dependency updates

.pre-commit-config.yaml

@@ -47,13 +47,13 @@ repos:
 #     additional_dependencies: [black]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 4.0.1
+  rev: 7.1.0
   hooks:
   - id: flake8
   ## You can add flake8 plugins via `additional_dependencies`:
   #  additional_dependencies: [flake8-bugbear]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0  # Use the sha / tag you want to point at
+    rev: v1.10.1  # Use the sha / tag you want to point at
     hooks:
     -   id: mypy
         additional_dependencies: ['types-PyYAML']

CONTRIBUTING.rst

@@ -0,0 +1,316 @@
+
+============
+Contributing
+============
+
+Welcome to ``otoole`` contributor's guide!
+
+This document focuses on getting any potential contributor familiarized
+with the development processes, but `other kinds of contributions`_ are also
+appreciated.
+
+If you are new to using git_ or have never collaborated in a project previously,
+please have a look at `contribution-guide.org`_. Other resources are also
+listed in the excellent `guide created by FreeCodeCamp`_.
+
+Please notice, all users and contributors are expected to be **open,
+considerate, reasonable, and respectful**. When in doubt, `Python Software
+Foundation's Code of Conduct`_ is a good reference in terms of behavior
+guidelines.
+
+
+Issue Reports
+=============
+
+If you experience bugs or general issues with ``otoole``, please have a look
+on the `issue tracker`_. If you don't see anything useful there, please feel
+free to fire an issue report.
+
+.. tip::
+   Please don't forget to include the closed issues in your search.
+   Sometimes a solution was already reported, and the problem is considered
+   **solved**.
+
+New issue reports should include information about your programming environment
+(e.g., operating system, Python version) and steps to reproduce the problem.
+Please try also to simplify the reproduction steps to a very minimal example
+that still illustrates the problem you are facing. By removing other factors,
+you help us to identify the root cause of the issue.
+
+
+Documentation Improvements
+==========================
+
+You can help improve ``otoole`` docs by making them more readable and coherent, or
+by adding missing information and correcting mistakes.
+
+``otoole`` documentation uses Sphinx_ as its main documentation compiler.
+This means that the docs are kept in the same repository as the project code, and
+that any documentation update is done in the same way was a code contribution.
+
+Our documentation is written in reStructuredText_.
+
+.. tip::
+    Please notice that the `GitHub web interface`_ provides a quick way of
+    propose changes in ``otoole``'s files. While this mechanism can
+    be tricky for normal code contributions, it works perfectly fine for
+    contributing to the docs, and can be quite handy.
+
+    If you are interested in trying this method out, please navigate to
+    the ``docs`` folder in the source repository_, find which file you
+    would like to propose changes and click in the little pencil icon at the
+    top, to open `GitHub's code editor`_. Once you finish editing the file,
+    please write a message in the form at the bottom of the page describing
+    which changes have you made and what are the motivations behind them and
+    submit your proposal.
+
+When working on documentation changes in your local machine, you can
+compile them using |tox|_::
+
+    tox -e docs
+
+and use Python's built-in web server for a preview in your web browser
+(``http://localhost:8000``)::
+
+    python3 -m http.server --directory 'docs/_build/html'
+
+
+Code Contributions
+==================
+
+``otoole`` is built around a command line tool which is written
+using the Python argparse library. The ``otoole.cli`` module is a useful
+place to start when trying to understand how each command works.
+
+The ``otoole convert`` and ``otoole results`` commands both
+use classes which inherit the ``otoole.Strategy`` class.
+An ``otoole.ReadStrategy`` implements functionality to read in data, while an
+``otoole.WriteStrategy`` writes out the target file format. The internal datastore
+format in ``otool`` is a dictionary of ``pandas.DataFrames``.
+
+Comprehensive unit tests in the ``tests`` folder provide another way to
+understand what each of the components does.
+
+Submit an issue
+---------------
+
+Before you work on any non-trivial code contribution it's best to first create
+a report in the `issue tracker`_ to start a discussion on the subject.
+This often provides additional considerations and avoids unnecessary work.
+
+Create an environment
+---------------------
+
+Before you start coding, we recommend creating an isolated `virtual
+environment`_ to avoid any problems with your installed Python packages.
+This can easily be done via either |virtualenv|_::
+
+    virtualenv <PATH TO VENV>
+    source <PATH TO VENV>/bin/activate
+
+or Miniconda_::
+
+    conda create -n otoole python=3 six virtualenv pytest pytest-cov
+    conda activate otoole
+
+Clone the repository
+--------------------
+
+#. Create an user account on |the repository service| if you do not already have one.
+#. Fork the project repository_: click on the *Fork* button near the top of the
+   page. This creates a copy of the code under your account on |the repository service|.
+#. Clone this copy to your local disk::
+
+    git clone [email protected]:YourLogin/otoole.git
+    cd otoole
+
+#. You should run::
+
+    pip install -U pip setuptools -e .
+
+   to be able to import the package under development in the Python REPL.
+
+#. Install |pre-commit|_::
+
+    pip install pre-commit
+    pre-commit install
+
+   ``otoole`` comes with a lot of hooks configured to automatically help the
+   developer to check the code being written.
+
+Implement your changes
+----------------------
+
+#. Create a branch to hold your changes::
+
+    git checkout -b my-feature
+
+   and start making changes. Never work on the main branch!
+
+#. Start your work on this branch. Don't forget to add docstrings_ to new
+   functions, modules and classes, especially if they are part of public APIs.
+
+#. Add yourself to the list of contributors in ``AUTHORS.rst``.
+
+#. When you’re done editing, do::
+
+    git add <MODIFIED FILES>
+    git commit
+
+   to record your changes in git_.
+
+   Please make sure to see the validation messages from |pre-commit|_ and fix
+   any eventual issues.
+   This should automatically use flake8_/black_ to check/fix the code style
+   in a way that is compatible with the project.
+
+   .. important:: Don't forget to add unit tests and documentation in case your
+      contribution adds an additional feature and is not just a bugfix.
+
+      Moreover, writing a `descriptive commit message`_ is highly recommended.
+      In case of doubt, you can check the commit history with::
+
+         git log --graph --decorate --pretty=oneline --abbrev-commit --all
+
+      to look for recurring communication patterns.
+
+#. Please check that your changes don't break any unit tests with::
+
+    tox
+
+   (after having installed |tox|_ with ``pip install tox`` or ``pipx``).
+
+   You can also use |tox|_ to run several other pre-configured tasks in the
+   repository. Try ``tox -av`` to see a list of the available checks.
+
+Submit your contribution
+------------------------
+
+#. If everything works fine, push your local branch to |the repository service| with::
+
+    git push -u origin my-feature
+
+#. Go to the web page of your fork and click |contribute button|
+   to send your changes for review.
+
+Find more detailed information in `creating a PR`_. You might also want to open
+the PR as a draft first and mark it as ready for review after the feedbacks
+from the continuous integration (CI) system or any required fixes.
+
+We track test coverage using coveralls_. You can check the coverage
+of your PR by clicking on the "details" link in the "Coverage" section of
+the pull request checks.  Try to ensure that your pull requests always increase
+test coverage.
+
+Troubleshooting
+---------------
+
+The following tips can be used when facing problems to build or test the
+package:
+
+#. Make sure to fetch all the tags from the upstream repository_.
+   The command ``git describe --abbrev=0 --tags`` should return the version you
+   are expecting. If you are trying to run CI scripts in a fork repository,
+   make sure to push all the tags.
+   You can also try to remove all the egg files or the complete egg folder, i.e.,
+   ``.eggs``, as well as the ``*.egg-info`` folders in the ``src`` folder or
+   potentially in the root of your project.
+
+#. Sometimes |tox|_ misses out when new dependencies are added, especially to
+   ``setup.cfg`` and ``docs/requirements.txt``. If you find any problems with
+   missing dependencies when running a command with |tox|_, try to recreate the
+   ``tox`` environment using the ``-r`` flag. For example, instead of::
+
+    tox -e docs
+
+   Try running::
+
+    tox -r -e docs
+
+#. Make sure to have a reliable |tox|_ installation that uses the correct
+   Python version (e.g., 3.8+). When in doubt you can run::
+
+    tox --version
+    # OR
+    which tox
+
+   If you have trouble and are seeing weird errors upon running |tox|_, you can
+   also try to create a dedicated `virtual environment`_ with a |tox|_ binary
+   freshly installed. For example::
+
+    virtualenv .venv
+    source .venv/bin/activate
+    .venv/bin/pip install tox
+    .venv/bin/tox -e all
+
+#. `Pytest can drop you`_ in an interactive session in the case an error occurs.
+   In order to do that you need to pass a ``--pdb`` option (for example by
+   running ``tox -- -k <NAME OF THE FALLING TEST> --pdb``).
+   You can also setup breakpoints manually instead of using the ``--pdb`` option.
+
+
+Maintainer tasks
+================
+
+Releases
+--------
+
+If you are part of the group of maintainers and have correct user permissions
+on PyPI_, the following steps can be used to release a new version for
+``otoole``:
+
+#. Make sure all unit tests are successful.
+#. Tag the current commit on the main branch with a release tag, e.g., ``v1.2.3``.
+#. Push the new tag to the upstream repository_, e.g., ``git push upstream v1.2.3``
+#. Clean up the ``dist`` and ``build`` folders with ``tox -e clean``
+   (or ``rm -rf dist build``)
+   to avoid confusion with old builds and Sphinx docs.
+#. Run ``tox -e build`` and check that the files in ``dist`` have
+   the correct version (no ``.dirty`` or git_ hash) according to the git_ tag.
+   Also check the sizes of the distributions, if they are too big (e.g., >
+   500KB), unwanted clutter may have been accidentally included.
+#. Run ``tox -e publish -- --repository pypi`` and check that everything was
+   uploaded to PyPI_ correctly.
+
+.. <-- strart -->
+.. |the repository service| replace:: GitHub
+.. |contribute button| replace:: "Create pull request"
+
+.. _repository: https://github.com/OSeMOSYS/otoole
+.. _issue tracker: https://github.com/OSeMOSYS/otoole/issues
+.. <-- end -->
+
+
+.. |virtualenv| replace:: ``virtualenv``
+.. |pre-commit| replace:: ``pre-commit``
+.. |tox| replace:: ``tox``
+
+
+.. _coveralls: https://coveralls.io/github/OSeMOSYS/otoole
+.. _black: https://pypi.org/project/black/
+.. _CommonMark: https://commonmark.org/
+.. _contribution-guide.org: https://www.contribution-guide.org/
+.. _creating a PR: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request
+.. _descriptive commit message: https://chris.beams.io/posts/git-commit
+.. _docstrings: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+.. _first-contributions tutorial: https://github.com/firstcontributions/first-contributions
+.. _flake8: https://flake8.pycqa.org/en/stable/
+.. _git: https://git-scm.com
+.. _GitHub's fork and pull request workflow: https://guides.github.com/activities/forking/
+.. _guide created by FreeCodeCamp: https://github.com/FreeCodeCamp/how-to-contribute-to-open-source
+.. _Miniconda: https://docs.conda.io/en/latest/miniconda.html
+.. _MyST: https://myst-parser.readthedocs.io/en/latest/syntax/syntax.html
+.. _other kinds of contributions: https://opensource.guide/how-to-contribute
+.. _pre-commit: https://pre-commit.com/
+.. _PyPI: https://pypi.org/
+.. _PyScaffold's contributor's guide: https://pyscaffold.org/en/stable/contributing.html
+.. _Pytest can drop you: https://docs.pytest.org/en/stable/how-to/failures.html#using-python-library-pdb-with-pytest
+.. _Python Software Foundation's Code of Conduct: https://www.python.org/psf/conduct/
+.. _reStructuredText: https://www.sphinx-doc.org/en/master/usage/restructuredtext/
+.. _Sphinx: https://www.sphinx-doc.org/en/master/
+.. _tox: https://tox.wiki/en/stable/
+.. _virtual environment: https://realpython.com/python-virtual-environments-a-primer/
+.. _virtualenv: https://virtualenv.pypa.io/en/stable/
+
+.. _GitHub web interface: https://docs.github.com/en/repositories/working-with-files/managing-files/editing-files
+.. _GitHub's code editor: https://docs.github.com/en/repositories/working-with-files/managing-files/editing-files

docs/conf.py

@@ -88,7 +88,7 @@
 
 # General information about the project.
 project = "otoole"
-copyright = "2022, Will Usher"
+copyright = "2024, Will Usher"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the