Bump scipy from 1.11.4 to 1.12.0 #303
Workflow file for this run
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| --- | |
| # MegaLinter GitHub Action configuration file | |
| # More info at https://megalinter.io | |
| name: MegaLinter | |
| permissions: | |
| checks: write | |
| pull-requests: write | |
| contents: write | |
| on: # yamllint disable-line rule:truthy | |
| # Trigger mega-linter at every push. Action will also be visible from Pull Requests to main | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| env: # Comment env block if you do not want to apply fixes | |
| # Apply linter fixes configuration | |
| APPLY_FIXES: all # When active, APPLY_FIXES must also be defined as environment variable (in github/workflows/mega-linter.yml or other CI tool) | |
| APPLY_FIXES_EVENT: push # Decide which event triggers application of fixes in a commit or a PR (pull_request, push, all) | |
| # I tried around a lot to make the test workflow run on pull_request events, | |
| # but it it only worked when creating a new PR. By default, this would target the branch of the PR | |
| # and not the main branch. Instead of trying around to cherry-pick the commits from the PR | |
| # etc. I decided to just run the workflow on push events to the main branch and then create | |
| # a PR targeting the main branch. | |
| APPLY_FIXES_MODE: pull_request # If APPLY_FIXES is used, defines if the fixes are directly committed (commit) or posted in a PR (pull_request) | |
| concurrency: | |
| group: ${{ github.ref }}-${{ github.workflow }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| name: MegaLinter | |
| runs-on: ubuntu-latest | |
| permissions: | |
| # Give the default GITHUB_TOKEN write permission to commit and push, comment issues & post new PR | |
| # Remove the ones you do not need | |
| contents: write | |
| issues: write | |
| pull-requests: write | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.head_ref }} | |
| fetch-depth: 0 | |
| - name: Create alpine-wheels folder | |
| run: mkdir alpine-wheels | |
| - name: Cache wheel directory | |
| id: cache-wheels | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ github.workspace }}/alpine-wheels | |
| key: ${{ runner.os }}-alpine-wheels-${{ hashFiles('requirements-dev.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-alpine-wheels-${{ hashFiles('requirements-dev.txt') }} | |
| - name: Set up Alpine Linux | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| uses: jirutka/setup-alpine@v1 | |
| with: # cfitsio, py3-pkgconfig, curl-dev, and zlib for healpy | |
| packages: > | |
| build-base | |
| python3-dev | |
| py3-pip | |
| gfortran | |
| fftw-dev | |
| git | |
| openblas-dev | |
| cmake | |
| geos-dev | |
| cfitsio | |
| py3-pkgconfig | |
| curl-dev | |
| zlib-dev | |
| - name: List workspace | |
| run: ls -l . | |
| - name: Create Python virtual environment | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: | | |
| python -m venv "${{ github.workspace }}/venv" | |
| echo "VENV_PATH=${{ github.workspace }}/venv" >> "$GITHUB_ENV" | |
| shell: alpine.sh {0} | |
| - name: Upgrade pip and install requirements for building | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: | | |
| source "$VENV_PATH/bin/activate" | |
| python -m ensurepip | |
| python -m pip install --upgrade pip | |
| python -m pip install --upgrade meson-python meson ninja wheel build | |
| shell: alpine.sh {0} | |
| - name: Remove version settings | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: | | |
| sed 's/==.*//' requirements-dev.txt > requirements-dev_no_version.txt | |
| - name: Remove torch, triton, jax, and nvidia entries (unsupported by alpine) | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: | | |
| sed -i '/^torch/d' requirements-dev_no_version.txt | |
| sed -i '/^nvidia/d' requirements-dev_no_version.txt | |
| sed -i '/^triton/d' requirements-dev_no_version.txt | |
| sed -i '/^jax/d' requirements-dev_no_version.txt | |
| - name: Run CMake to find LAPACK | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: | | |
| echo "find_package(LAPACK)" > CMakeLists.txt | |
| echo "if(LAPACK_FOUND)" >> CMakeLists.txt | |
| echo ' message("LAPACK found")' >> CMakeLists.txt | |
| echo ' message("LAPACK include dirs: ${LAPACK_INCLUDE_DIRS}")' >> CMakeLists.txt | |
| echo ' message("LAPACK libraries: ${LAPACK_LIBRARIES}")' >> CMakeLists.txt | |
| echo "else()" >> CMakeLists.txt | |
| echo ' message(FATAL_ERROR "LAPACK not found")' >> CMakeLists.txt | |
| echo "endif()" >> CMakeLists.txt | |
| cmake . | |
| shell: alpine.sh {0} | |
| - name: Run pkg-config to find LAPACK | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: | | |
| pkg-config --libs --cflags lapack || true | |
| shell: alpine.sh {0} | |
| - name: Build wheel for pyshtools | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: | | |
| git clone https://github.com/FlorianPfaff/SHTOOLS.git | |
| cd SHTOOLS | |
| git checkout meson | |
| source "$VENV_PATH/bin/activate" | |
| python -m build | |
| cd .. | |
| mv SHTOOLS/dist/*.whl ./alpine-wheels/ | |
| rm -rf SHTOOLS | |
| shell: alpine.sh {0} | |
| - name: Install Packages Sequentially | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: | | |
| source "$VENV_PATH/bin/activate" | |
| cat requirements-dev_no_version.txt | |
| while read requirement; do | |
| echo "Installing $requirement..." | |
| pip install "$requirement" --find-links=./alpine-wheels | |
| done < requirements-dev_no_version.txt | |
| shell: alpine.sh {0} | |
| - name: Freeze requirements | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: | | |
| source "$VENV_PATH/bin/activate" | |
| python -m pip freeze > requirements-tmp.txt | |
| shell: alpine.sh {0} | |
| - name: Download compatible packages | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: | | |
| source "$VENV_PATH/bin/activate" | |
| python -m pip download --find-links=./alpine-wheels -r requirements-tmp.txt -d ./alpine-wheels | |
| shell: alpine.sh {0} | |
| - name: Build wheels | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: | | |
| source "$VENV_PATH/bin/activate" | |
| cd ./alpine-wheels | |
| # Set a flag to indicate if any .tar.gz files are found | |
| found=0 | |
| # Loop through all .tar.gz files | |
| for src in *.tar.gz; do | |
| # Check if the glob gets expanded to existing files. | |
| # If not, src will be exactly '*.tar.gz'. | |
| [ -e "$src" ] || continue | |
| # If we reach this point, at least one file exists | |
| found=1 | |
| python -m pip wheel "$src" --no-deps --wheel-dir=./ | |
| rm "$src" | |
| done | |
| # Check if no files were found | |
| if [ "$found" -eq 0 ]; then | |
| echo "No .tar.gz files found." | |
| fi | |
| cd .. | |
| shell: alpine.sh {0} | |
| - name: Clean up temporary files (in case they are generated) | |
| if: steps.cache-wheels.outputs.cache-hit != 'true' | |
| run: rm -r venv CMakeFiles CMakeCache.txt cmake_install.cmake Makefile | |
| - name: List available wheels | |
| run: ls -l ./alpine-wheels | |
| # MegaLinter | |
| - name: MegaLinter | |
| id: ml | |
| # You can override MegaLinter flavor used to have faster performances | |
| # More info at https://megalinter.io/latest/configuration/#shared-variables | |
| uses: oxsecurity/megalinter/flavors/[email protected] | |
| env: | |
| # All available variables are described in documentation | |
| # https://megalinter.io/latest/configuration/#shared-variables | |
| # ADD YOUR CUSTOM ENV VARIABLES HERE OR DEFINE THEM IN A FILE .mega-linter.yml AT THE ROOT OF YOUR REPOSITORY | |
| VALIDATE_ALL_CODEBASE: true # ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} # Validates all source when push on main, else just the git diff with main. Override with true if you always want to lint all sources | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| EMAIL_REPORTER_SMTP_PASSWORD: ${{ secrets.SMTP_PASSWORD }} | |
| # Upload MegaLinter artifacts | |
| - name: Archive production artifacts | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: MegaLinter reports | |
| path: | | |
| megalinter-reports | |
| mega-linter.log | |
| # Create Pull Request step | |
| - name: Create Pull Request with applied fixes | |
| id: cpr | |
| if: github.ref == 'refs/heads/main' && steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'pull_request' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository) && !contains(github.event.head_commit.message, 'skip fix') | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| token: ${{ secrets.PAT || secrets.GITHUB_TOKEN }} | |
| commit-message: "[MegaLinter] Apply linters automatic fixes" | |
| title: "[MegaLinter] Apply linters automatic fixes" | |
| branch: megalinter-fixes | |
| labels: bot | |
| base: main | |
| # Output PR details | |
| - name: Create PR output | |
| if: github.ref == 'refs/heads/main' && steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'pull_request' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository) && !contains(github.event.head_commit.message, 'skip fix') | |
| run: | | |
| echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}" | |
| echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}" | |
| # Push new commit if applicable (for now works only on PR from same repository, not from forks) | |
| - name: Prepare commit | |
| if: steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'commit' && github.ref != 'refs/heads/main' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository) && !contains(github.event.head_commit.message, 'skip fix') | |
| run: sudo chown -Rc $UID .git/ | |
| - name: Commit and push applied linter fixes | |
| if: steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'commit' && github.ref != 'refs/heads/main' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository) && !contains(github.event.head_commit.message, 'skip fix') | |
| uses: stefanzweifel/git-auto-commit-action@v4 | |
| with: | |
| branch: ${{ github.event.pull_request.head.ref || github.head_ref || github.ref }} | |
| commit_message: "[MegaLinter] Apply linters fixes" | |
| commit_user_name: megalinter-bot | |
| commit_user_email: [email protected] |