few fixes #1051
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| name: Continuous Integration | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| schedule: | |
| # run this every week at 12 noon on Monday | |
| - cron: '0 12 * * 1' | |
| env: | |
| EXAMPLE_DATA_FILE_VERSION: v5 | |
| # Setting this did not appear to work. Instead will need to | |
| # find/replace when changing it. | |
| # CONTAINER_IMAGE: ghcr.io/lsstdesc/txpipe:latest | |
| jobs: | |
| # Run a download step first so that it is in | |
| # the cache, because all the other jobs will be running | |
| # at the same time and so might miss it. | |
| Download_Data: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Cache example data | |
| id: cache-example | |
| uses: actions/cache@v4 | |
| env: | |
| cache-name: cache-example-data | |
| with: | |
| path: example.tar.gz | |
| # update this when we change package contents and want | |
| # to force an update | |
| key: example-data-${{ env.EXAMPLE_DATA_FILE_VERSION }} | |
| - name: Download test data | |
| if: steps.cache-example.outputs.cache-hit != 'true' | |
| run: | | |
| wget -O example.tar.gz "https://portal.nersc.gov/cfs/lsst/txpipe/data/example.tar.gz" | |
| Run_Installer: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-14] | |
| include: | |
| - os: ubuntu-latest | |
| INSTALL_DEPS: sudo apt-get update && sudo apt-get -y install wget | |
| - os: macos-14 | |
| INSTALL_DEPS: echo nothing to do | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Install wget | |
| run: | | |
| ${{ matrix.INSTALL_DEPS }} | |
| - name: Cache conda environment | |
| id: cache-conda | |
| uses: actions/cache@v4 | |
| env: | |
| cache-name: cache-conda-environment | |
| with: | |
| path: ./conda | |
| key: ${{ matrix.os }}-conda-${{ hashFiles('bin/install.sh','environment*.yml' ) }} | |
| fail-on-cache-miss: false | |
| - name: Run installer | |
| if: steps.cache-conda.outputs.cache-hit != 'true' | |
| run: | | |
| ./bin/install.sh | |
| Unit_Tests: | |
| runs-on: ${{ matrix.os }} | |
| needs: Run_Installer | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-14] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Restore conda environment | |
| id: restore-conda | |
| uses: actions/cache@v4 | |
| env: | |
| cache-name: cache-conda-environment | |
| with: | |
| path: ./conda | |
| key: ${{ matrix.os }}-conda-${{ hashFiles('bin/install.sh','environment*.yml' ) }} | |
| fail-on-cache-miss: true | |
| - name: Test with pytest | |
| run: | | |
| source conda/bin/activate | |
| ceci --version | |
| pytest txpipe | |
| Pipelines: | |
| runs-on: ${{ matrix.os }} | |
| needs: [Run_Installer, Download_Data] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-14] | |
| pipeline: [metadetect, metacal, redmagic, lensfit, metadetect_source_only, mock_shear] | |
| include: | |
| - os: ubuntu-latest | |
| INSTALL_DEPS: echo nothing to do | |
| - os: macos-14 | |
| INSTALL_DEPS: brew update-reset && brew install --cask basictex && eval "$(/usr/libexec/path_helper)" && pdflatex --version | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Install dependencies | |
| run: | | |
| ${{ matrix.INSTALL_DEPS }} | |
| - name: Restore conda environment | |
| id: restore-conda | |
| uses: actions/cache@v4 | |
| env: | |
| cache-name: cache-conda-environment | |
| with: | |
| path: ./conda | |
| key: ${{ matrix.os }}-conda-${{ hashFiles('bin/install.sh','environment*.yml' ) }} | |
| fail-on-cache-miss: true | |
| - name: Restore example data | |
| uses: actions/cache@v4 | |
| with: | |
| path: example.tar.gz | |
| key: example-data-${{ env.EXAMPLE_DATA_FILE_VERSION }} | |
| fail-on-cache-miss: true | |
| - name: Extract test data | |
| run: | | |
| tar -zxvf example.tar.gz | |
| - name: Run pipeline | |
| run: | | |
| mkdir -p cache/workspaces | |
| source ./conda/bin/activate | |
| # Just for the metadetect source pipeline | |
| # we activate the debug mode with an env var | |
| if [ "${{ matrix.pipeline }}" == "metadetect_source_only" ]; then | |
| export TX_DASK_DEBUG=1 | |
| fi | |
| ceci examples/${{ matrix.pipeline }}/pipeline.yml | |
| if [ "${{ matrix.pipeline }}" == "mock_shear" ]; then | |
| test -f data/example/outputs_mock_shear/binned_shear_catalog.hdf5 | |
| else | |
| test -f data/example/outputs_${{ matrix.pipeline }}/shear_xi_plus.png | |
| fi | |
| - name: Show logs | |
| if: always() | |
| run: | | |
| # always run | |
| cat data/example/logs_${{ matrix.pipeline }}/* | |
| - name: Create output report | |
| if: matrix.os == 'macos-14' | |
| run: | | |
| source ./conda/bin/activate | |
| eval "$(/usr/libexec/path_helper)" | |
| python bin/make_output_report.py data/example/outputs_${{ matrix.pipeline }} ${{ matrix.pipeline }}-report.md | |
| pandoc ${{ matrix.pipeline }}-report.md -o ${{ matrix.pipeline }}-report.pdf | |
| - name: Upload output report | |
| if: matrix.os == 'macos-14' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.pipeline }}-report | |
| path: ${{ matrix.pipeline }}-report.pdf |