CI: Test notebooks using pixi

sebp · Jul 6, 2024 · bdf81f0 · bdf81f0
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commit bdf81f0
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Showing 3 changed files with 4 additions and 55 deletions.
diff --git a/.github/workflows/tests-workflow.yaml b/.github/workflows/tests-workflow.yaml
@@ -86,54 +86,3 @@ jobs:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
           coverage-reports: coverage.xml
         if: ${{ steps.coverage.outputs.do == 'true' && github.event_name != 'pull_request' }}
-
-
-  nbval:
-    runs-on: ubuntu-latest
-    name: Build and check notebooks
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          submodules: true
-      - name: Set dependencies
-        id: dependencies
-        env:
-          DEPS_CONFIG: py311
-        run: |
-          source ci/deps/${DEPS_CONFIG}.sh
-          echo "CI_PYTHON_VERSION=${CI_PYTHON_VERSION}" >> $GITHUB_ENV
-          echo "CI_PANDAS_VERSION=${CI_PANDAS_VERSION}" >> $GITHUB_ENV
-          echo "CI_NUMPY_VERSION=${CI_NUMPY_VERSION}" >> $GITHUB_ENV
-          echo "CI_SKLEARN_VERSION=${CI_SKLEARN_VERSION}" >> $GITHUB_ENV
-          echo "CI_NO_SLOW=${CI_NO_SLOW}" >> $GITHUB_ENV
-          echo "CONDA_PKGS_DIRS=${{ runner.temp }}/conda_pkgs_dir" >> $GITHUB_ENV
-          echo "requirements=ci/deps/${DEPS_CONFIG}.sh" >> $GITHUB_OUTPUT
-      - name: Cache downloaded packages
-        uses: actions/cache@v4
-        with:
-          path: ${{ env.CONDA_PKGS_DIRS }}
-          key: ${{ runner.os }}-${{ runner.arch }}-conda-3.11-${{ hashFiles(steps.dependencies.outputs.requirements, 'pyproject.toml', 'ci/deps/requirements.yaml.tmpl') }}
-      - name: Create Conda Environment
-        run: |
-          source ci/setup_conda.sh "${{ runner.os }}" "${{ runner.arch }}" "${{ env.CONDA_PKGS_DIRS }}"
-          ci/setup_env.sh "${{ runner.os }}"
-      - name: Configure matplotlib
-        run: |
-          mkdir -p ${XDG_CONFIG_HOME}/matplotlib
-          echo 'figure.figsize: 6.0, 4.0' > ${XDG_CONFIG_HOME}/matplotlib/matplotlibrc
-          echo 'figure.facecolor: white' >> ${XDG_CONFIG_HOME}/matplotlib/matplotlibrc
-          echo 'figure.edgecolor: white' >> ${XDG_CONFIG_HOME}/matplotlib/matplotlibrc
-          echo 'figure.dpi: 72' >> ${XDG_CONFIG_HOME}/matplotlib/matplotlibrc
-          echo 'font.size: 10' >> ${XDG_CONFIG_HOME}/matplotlib/matplotlibrc
-      - name: Build package
-        run: |
-          source activate sksurv-test
-          python -m build .
-          pip install --exists-action=w --pre --no-index --find-links dist/ scikit-survival
-          rm -fr build dist sksurv
-      - name: Test notebooks
-        run: |
-          source activate sksurv-test
-          pytest --nbval doc/user_guide/*.ipynb --nbval-sanitize-with ci/nb_sanitize.cfg
diff --git a/.github/workflows/tox-workflow.yaml b/.github/workflows/tox-workflow.yaml
@@ -25,14 +25,14 @@ jobs:
           RUFF_OUTPUT_FORMAT: github
         run: |
           eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)"
-          pixi run ${{ matrix.tox_env }}
+          pixi run ${{ matrix.environment }}
       - name: Archive documentation
         uses: actions/upload-artifact@v4
         with:
           name: documentation
           path: doc/_build/html
-        if: ${{ matrix.tox_env == 'build-docs' }}
+        if: ${{ matrix.environment == 'build-docs' }}
     strategy:
       fail-fast: false
       matrix:
-        tox_env: [lint, build-docs]
+        environment: [lint, build-docs, test-nb]
diff --git a/pyproject.toml b/pyproject.toml
@@ -219,6 +219,7 @@ dev = { features = ["dev", "nbval"], solve-group = "default" }
 docs = { features = ["docs"], solve-group = "default" }
 
 [tool.pixi.dependencies]
+# conda dependencies
 "scikit-learn" = "1.5.*"
 
 [tool.pixi.pypi-dependencies]
@@ -237,4 +238,3 @@ spellcheck = "sphinx-build -j auto -E -W -d doc/_build/doctrees -b spelling doc/
 
 [tool.pixi.feature.docs.dependencies]
 pandoc = "*"
-