Move from mamba to pixi (#594)

After #589, #381 and countless TeamCity troubles, it is time to try something new
Deltares · Sep 14, 2023 · c48a479 · c48a479
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diff --git a/.github/workflows/core_tests.yml b/.github/workflows/core_tests.yml
@@ -13,9 +13,6 @@ jobs:
   test:
     name: Julia ${{ matrix.julia_version }} - ${{ matrix.os }} - ${{ matrix.arch }}
     runs-on: ${{ matrix.os }}
-    defaults:
-      run:
-        shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
@@ -29,18 +26,17 @@ jobs:
           - x64
     steps:
       - uses: actions/checkout@v4
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/[email protected]
         with:
-          cache-downloads: true
-          cache-environment: true
-          environment-file: ./environment.yml
-      - name: Install ribasim
-        run: pip install --editable python/ribasim
-      - name: Install ribasim_testmodels
-        run: pip install --editable python/ribasim_testmodels
+          pixi-version: latest
+          cache: true
+      - name: Prepare pixi
+        run: |
+          pixi install
+          pixi run post-install
       - name: Prepare model input
-        run: python python/ribasim/tests/conftest.py
+        run: |
+          pixi run generate-testmodels
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia_version }}

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -14,9 +14,6 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: write
-    defaults:
-      run:
-        shell: bash -l {0}
     strategy:
       matrix:
         julia_version:
@@ -40,37 +37,23 @@ jobs:
           cache-compiled: "true"
           cache-registries: "true"
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/[email protected]
         with:
-          cache-downloads: true
-          cache-environment: true
-          environment-file: ./environment.yml
-
-      - name: Install ribasim-python
-        run: pip install --editable python/ribasim
-
-      - name: Set up Quarto
-        uses: quarto-dev/quarto-actions/setup@v2
+          pixi-version: latest
+          cache: true
+      - name: Prepare pixi
+        run: |
+          pixi install
+          pixi run post-install
 
       - name: Check Quarto installation and all engines
-        run: quarto check all
-
-      - name: Generate API pages
-        working-directory: docs
-        # objects.json: https://github.com/machow/quartodoc/issues/63
-        run: |
-          quartodoc build
-          rm objects.json
+        run: pixi run quarto-check
 
       - name: Generate Julia docs
-        working-directory: docs
-        run: |
-          julia --project -e "using Pkg; Pkg.instantiate()"
-          julia --project make.jl
+        run: pixi run build-julia-docs
 
       - name: Render Quarto Project
-        run: "quarto render docs --to html --execute"
+        run: pixi run quarto-render
 
       - name: Publish Quarto Project
         if: github.ref == 'refs/heads/main'

diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml
@@ -14,28 +14,22 @@ jobs:
     name: Mypy
     runs-on: ubuntu-latest
     continue-on-error: true
-    defaults:
-      run:
-        shell: bash -l {0}
     steps:
       - uses: actions/checkout@v4
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/[email protected]
         with:
-          cache-downloads: true
-          cache-environment: true
-          environment-file: ./environment.yml
-      - name: Install python packages
+          pixi-version: "latest"
+          cache: true
+      - name: Prepare pixi
         run: |
-          pip install python/ribasim
-          pip install python/ribasim_testmodels
-          pip install python/ribasim_api
+          pixi install
+          pixi run post-install
       - name: Run mypy on python/ribasim
         run: |
-          mypy --ignore-missing-imports python/ribasim/ribasim
+          pixi run mypy-ribasim-python
       - name: Run mypy on python/ribasim_testmodels
         run: |
-          mypy --ignore-missing-imports python/ribasim_testmodels/ribasim_testmodels
+          pixi run mypy-ribasim-testmodels
       - name: Run mypy on python/ribasim_api
         run: |
-          mypy --ignore-missing-imports python/ribasim_api/ribasim_api
+          pixi run mypy-ribasim-api
diff --git a/.github/workflows/python_tests.yml b/.github/workflows/python_tests.yml
@@ -13,9 +13,6 @@ jobs:
   test:
     name: Python ${{ matrix.python_version }} - ${{ matrix.os }} - ${{ matrix.arch }}
     runs-on: ${{ matrix.os }}
-    defaults:
-      run:
-        shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
@@ -32,23 +29,17 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/[email protected]
         with:
-          cache-downloads: true
-          cache-environment: true
-          environment-file: ./environment.yml
-          create-args: >-
-            python=${{ matrix.python_version }}
-
-      - name: Install ribasim
-        run: pip install --editable python/ribasim
-
-      - name: Install ribasim_testmodels
-        run: pip install --editable python/ribasim_testmodels
+          pixi-version: latest
+          cache: true
+      - name: Prepare pixi
+        run: |
+          pixi install
+          pixi run post-install
 
       - name: Run tests
-        run: pytest --cov=ribasim --cov-report=xml python/ribasim/tests
+        run: pixi run test-ribasim-python-cov
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
diff --git a/.gitignore b/.gitignore
@@ -155,3 +155,5 @@ dmypy.json
 .vscode/settings.json
 
 /.luarc.json
+build/ribasim_cli/tests/temp/
+report.xml
diff --git a/docs/contribute/addnode.qmd b/docs/contribute/addnode.qmd
@@ -258,8 +258,5 @@ To generate the Python module `models.py` from the JSON Schemas, run:
 datamodel-codegen --use-title-as-name --input docs/schema/root.schema.json --output python/ribasim/ribasim/models.py
 ```
 
-Run [Black](python.qmd#sec-black) to format the generated code.
-To catch possible Python issues run [Ruff](python.qmd#sec-ruff).
-
 Since adding a node type touches both the Python and Julia code,
 it is a good idea to run both the [Python test suite](python.qmd#test) and [Julia test suite](core.qmd#test) locally before creating a pull request.
diff --git a/docs/contribute/core.qmd b/docs/contribute/core.qmd
@@ -24,11 +24,6 @@ pkg> add Revise TestEnv
 Revise.jl is a library that allows you to modify code and use the changes without restarting Julia.
 You can let it start automatically by following these [instructions](https://timholy.github.io/Revise.jl/stable/config/#Using-Revise-by-default-1).
 
-## Install Quarto
-
-Quarto is the publishing system that builds our documentation.
-The installation instructions can be found on their [web page](https://quarto.org/docs/get-started/).
-
 ## Clone Ribasim
 
 In order to have the Ribasim repository locally available, you can clone it with Git.
@@ -107,32 +102,18 @@ That way you don't have to type `activate core` every time you open the REPL.
 ## Render documentation
 
 Example models are created and simulated as part of the rendering of the documentation.
-Therefore you need to have both the `ribasim` Python package and the Julia `Ribasim` package
-installed. Furthermore you need these 3 Python packages installed: `jupyter quartodoc xarray`.
-
-The Python API reference is created using quartodoc by running this command from the `docs/`
-folder:
-
-```bash
-quartodoc build
-```
-
-You typically only have to run this once, or if you want to check out how it looks after
-changing Python docstrings.
-
-The Julia API reference is created using Documenter.jl by running this command from the `docs/` folder:
+The Julia API reference is created using Documenter.jl by running this command:
 
 ```bash
-julia --project -e "using Pkg; Pkg.instantiate()"  # needed once
-julia --project make.jl  # after changing the Julia docstrings
+pixi run build-julia-docs
 ```
 
 In order to preview documentation you can run the following command from the `docs/` folder.
 Afterwards, a browser tab will open with the rendered documentation, updating it as you
 make changes.
 
 ```bash
-quarto preview
+pixi run quarto-preview
 ```
 
 The documentation also includes [Jupyter notebooks](https://jupyter.org/).

diff --git a/docs/contribute/python.qmd b/docs/contribute/python.qmd
@@ -4,89 +4,26 @@ title: "Python tooling development"
 
 # Set up the developer environment
 
-## Setting up conda
+## Setting up pixi
 
-In order to develop on `ribasim` locally, please follow the following steps:
+First, set up pixi as described on their getting started [page](https://prefix.dev/docs/pixi/overview).
 
-- Download and install [miniconda](https://docs.conda.io/en/latest/miniconda.html).
+Then set up the environment by running the following commands:
 
-- Initialize `conda` by running the following in the `Miniconda prompt`:
-
-```
-conda init
-```
-
-- Depending on your company settings, you might also have to run the following in a Powershell terminal as administrator:
-
-```
-Set-ExecutionPolicy -ExecutionPolicy RemoteSigned
 ```
-
-## Creating (or updating) the environment
-
-- Create (or update) the environment by executing the following in your terminal:
-
-```
-conda env create --file=environment.yml --force
-```
-
-## Installing Python packages
-
-- Activate the environment
-
-```
-conda activate ribasim
-```
-
-In order to develop on `ribasim` locally, execute the following line inside your virtual environment with the repo root as your working directory:
-
-```bash
-pip install --editable python/ribasim
-pip install --editable python/ribasim_testmodels
-pip install --editable python/ribasim_api
-```
-
-## Install the pre-commit hook {#sec-precommit}
-
-If not already done, activate the environment:
-
-```
-conda activate ribasim
-```
-
-Pre-commit ensures that all linters are happy with your code before you commit your files.
-In order to install the pre-commit hook run:
-
-```bash
-pre-commit install
+pixi install
+pixi run post-install
 ```
 
 
 ## Running the tests {#sec-test}
 
-If not already done, activate the environment:
-
-```
-conda activate ribasim
-```
-
-To run the tests call `pytest` with the path to the Python package.
-Here the the root of the repository is the working directory:
+In order to run tests on Ribasim Python execute
 
 ```bash
-pytest python/ribasim
-```
-
-## Building the documentation
-
-Run in the docs folder:
-
-```
-quartodoc build
+pixi run test-ribasim-python
 ```
 
-This will generate the `.qmd` files in `docs/python/reference` for inspection.
-
 ## Updating example notebooks
 
 Make sure to run `Clear All Outputs` on the notebook before committing.
@@ -136,42 +73,26 @@ twine check dist/*
 twine upload dist/*
 ```
 
-## Automatic code formatting with Black {#sec-black}
-
-We use the [Black](https://black.readthedocs.io/en/stable/) code formatter.
-Code only passes the continuous integration checks if it is fully formatted according to the Black code style.
-When working in VS Code the settings suggested in @sec-vscode run Black automatically when saving Python files.
-
-If you want to run Black manually, you can run it from the command line.
-To run it on the entire repository, use the command below.
-Here the repository root is the working directory.
-
-```
-black .
-```
-
-## Code linting with Ruff {#sec-ruff}
-
-We use the [Ruff](https://github.com/charliermarsh/ruff) linter to help finding issues with Python code.
-Code only passes the continuous integration checks if Ruff does not find any issues.
+## Linting
 
-To run Ruff on the entire repository, use the command below.
-Here the repository root is the working directory.
+To run our linting suite locally, execute:
 
 ```
-ruff .
+pixi run lint
 ```
 
 # Code maintenance {#sec-codecov}
 
 For new features new tests have to be added. To monitor how much of the code is covered by the tests we use [Codecov](https://about.codecov.io/).
 For a simple overview of the local code coverage run
 ```
+pixi shell
 pytest --cov=ribasim tests/
 ```
 from  `python/ribasim`. For an extensive overview in `html` format use
 ```
-ytest --cov=ribasim --cov-report=html tests/
+pixi shell
+pytest --cov=ribasim --cov-report=html tests/
 ```
 which creates a folder `htmlcov` in the working directory. To see te contents open `htmlcov/index.html` in a browser.