MNT moving to pixi for better CI reprodocibility (#451)

* move to pyproject.toml build system

* remove setup.cfg

* config and workflow

* wanna see all runs

* only run new ones

* contributing docs

* pixi versoin

* mypy

* ...

* ...

* ...

* trigger CI

.github/workflows/build-test.yml

@@ -6,7 +6,7 @@ on:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 jobs:
   pytest:
@@ -15,25 +15,17 @@ jobs:
     strategy:
       fail-fast: false # need to see which ones fail
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-        # this is to make the CI run on different sklearn versions
-        include:
-          - python: "3.9"
-            sklearn_version: ">=1.1,<1.2"
-            numpy_version: "numpy<2"
-          - python: "3.10"
-            sklearn_version: ">=1.2,<1.3"
-            numpy_version: "numpy"
-          - python: "3.11"
-            sklearn_version: ">=1.4,<1.5"
-            numpy_version: "numpy"
-          - python: "3.12"
-            sklearn_version: ">=1.5,<1.6"
-            numpy_version: "numpy"
-          - python: "3.13"
-            sklearn_version: "nightly"
-            numpy_version: "numpy"
+        os: [windows-latest, ubuntu-latest, macos-latest]
+        environment: [
+          # ci-min-deps,
+          # ci-sklearn11,
+          # ci-sklearn12,
+          # ci-sklearn13,
+          # ci-sklearn14,
+          ci-sklearn15,
+          ci-sklearn16,
+          ci-sklearn17
+        ]
 
     # Timeout: https://stackoverflow.com/a/59076067/4521646
     timeout-minutes: 15
@@ -52,55 +44,19 @@ jobs:
           echo PR_COMMIT_MESSAGE=$(git log -1 --pretty=format:\"%s\") >> $GITHUB_ENV
         shell: bash
 
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5
+      - uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          python-version: ${{ matrix.python }}
+          pixi-version: v0.39.0
+          environments: ${{ matrix.environment }}
+          # we can freeze the environment and manually bump the dependencies to the
+          # latest version time to time.
+          frozen: true
 
-      - name: Install dependencies
-        run: |
-          set -x
-          python -m pip install -U pip
-          if [ "${{ matrix.os }}" == "macos-latest" ]; then
-            brew install libomp
-          fi
-          pip install "pytest<8"
-          pip install "${{ matrix.numpy_version }}"
-          if [ ${{ matrix.sklearn_version }} == "nightly" ]; then
-            pip install --pre --extra-index https://pypi.anaconda.org/scientific-python-nightly-wheels/simple scikit-learn
-            pip install .[docs,tests]
-          else
-            pip install .[docs,tests] "scikit-learn${{ matrix.sklearn_version }}"
-          fi
-          pip install black=="23.9.1" ruff=="0.0.292" mypy=="1.6.0"
-          if [ ${{ matrix.os }} == "ubuntu-latest" ]; then
-            sudo apt install pandoc && pandoc --version;
-          fi
-          python --version
-          pip --version
-          pip list
-        shell: bash
-
-      - name: Check black
-        run: black --check --diff .
-
-      - name: Check ruff
-        run: ruff check --diff .
-
-      - name: Tests
-        env:
-          SUPER_SECRET: ${{ secrets.HF_HUB_TOKEN }}
-          PYTHONIOENCODING: "utf-8"
-        run: |
-          python -m pytest -s -v --cov-report=xml -m "not inference" skops/
-
-      - name: Mypy
-        run: mypy --config-file pyproject.toml skops
+      - name: Linters
+        run: pixi run -e lint lint
 
-      - name: Inference tests (conditional)
-        if: contains(env.PR_COMMIT_MESSAGE, '[CI inference]')
-        run: |
-          python -l -m pytest -s -v -m "inference" skops/
+      - name: Run tests
+        run: pixi run -e ${{ matrix.environment }} tests
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5

.pixi/config.toml

@@ -0,0 +1,2 @@
+[concurrency]
+downloads = 20

.readthedocs.yml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-lts-latest
   tools:
-    python: "3.10"
+    python: "3.12"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

CONTRIBUTING.rst

@@ -57,29 +57,41 @@ entails. If you don't understand an issue, it's on us, not on you!
 Setting up the dev environment
 ------------------------------
 
-Following these steps you can prepare a dev environment for yourself to
-contribute to `skops`.
+We use `pixi <https://github.com/prefix-dev/pixi>`_ in our CI and development
+workflows and recommend you use it to test the changes you make.
 
-Using conda/mamba
-~~~~~~~~~~~~~~~~~
+Once you have ``pixi`` installed, you can run the tests with:
 
 .. code:: bash
 
-          mamba create -c conda-forge -n skops python=3.10
-          mamba activate skops
-          python -m pip install -e ".[tests,docs]"
-          # add pre-commit hooks
-          mamba install -c conda-forge pre-commit
-          pre-commit install
+   pixi run tests
 
-You can also replace the above `mamba` commands with `conda` if you don't have
-`mamba` installed.
+And you can choose an environment to run the tests with:
 
+.. code:: bash
+
+   pixi run -e ci-sklearn15 tests
+
+In order to setup ``pre-commit`` hooks, you'd need to run the linter once, ignoring
+the outputs:
+
+.. code:: bash
+
+   pixi run -e lint lint
+
+VSCode-like IDEs automatically detect ``pixi`` environments and you can use them as
+your python interpreter.
+
+Running Tests Manually
+~~~~~~~~~~~~~~~~~~~~~~
+
+You can get an interactive shell into an environment with a command like the following:
+
+.. code:: bash
 
-Running Tests
-~~~~~~~~~~~~~
+   pixi shell -e ci-sklearn15
 
-skops uses pytest as its test runner, just run it from the project root:
+``skops`` uses ``pytest`` as its test runner, just run it from the project root:
 
 .. code:: bash
 

docs/requirements.txt

@@ -1 +1,10 @@
--e .[docs]
+matplotlib>=3.3
+pandas>=1
+fairlearn>=0.7.0
+sphinx>=3.2.0
+sphinx-gallery>=0.7.0
+sphinx-rtd-theme>=1
+numpydoc>=1.0.0
+sphinx-prompt>=1.3.0
+sphinx-issues>=1.2.0
+-e .[rich]

examples/plot_model_card.py

@@ -112,7 +112,7 @@
 model_card_authors = "skops_user"
 citation_bibtex = "**BibTeX**\n\n```\n@inproceedings{...,year={2020}}\n```"
 model_card.add(
-    **{
+    **{  # type: ignore
         "Citation": citation_bibtex,
         "Model Card Authors": model_card_authors,
         "Model description": model_description,
@@ -139,7 +139,7 @@
     "The model is evaluated on test data using accuracy and F1-score with "
     "macro average."
 )
-model_card.add(**{"Model description/Evaluation Results": eval_descr})
+model_card.add(**{"Model description/Evaluation Results": eval_descr})  # type: ignore
 
 accuracy = accuracy_score(y_test, y_pred)
 f1 = f1_score(y_test, y_pred, average="micro")