Drop requirement for id column and experiment identifiers to be set, … #2
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| on: [push, pull_request] | |
| env: | |
| # Python minimum version is used for testing full libtbx-bootstrap | |
| PYTHON_MINIMUM_VERSION: "3.9" | |
| # Testing version is used for everything else | |
| PYTHON_TESTING_VERSION: "3.12" | |
| jobs: | |
| build_test: | |
| name: Build/Test | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu, macOS, windows] | |
| defaults: | |
| run: | |
| shell: bash | |
| runs-on: ${{ matrix.os }}-latest | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modules/dials | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PYTHON_MINIMUM_VERSION }} | |
| - name: Prepare for Base Environment | |
| run: | | |
| OS="$(python -c "print('${{ runner.os }}'.lower())")" | |
| echo "ninja | |
| pytest-md | |
| dials-data | |
| pytest-cov | |
| pytest-timeout" >> modules/dials/.conda-envs/${OS}.txt | |
| echo "$(pwd)/conda_base/bin" >> $GITHUB_PATH | |
| # These needed by windows | |
| echo "$(pwd)/conda_base/Scripts" >> $GITHUB_PATH | |
| echo "$(pwd)/conda_base/Library/bin" >> $GITHUB_PATH | |
| echo "$(pwd)/conda_base/" >> $GITHUB_PATH | |
| - name: Install Base Environment | |
| run: | | |
| python modules/dials/installer/bootstrap.py update base \ | |
| --python "${{ env.PYTHON_TESTING_VERSION }}" | |
| - if: runner.os != 'Windows' | |
| run: echo "CMAKE_GENERATOR=Ninja" >> $GITHUB_ENV | |
| - name: Build | |
| run: python modules/dials/installer/bootstrap.py build --config-flags='-DCMAKE_UNITY_BUILD=true' | |
| - name: Prepare for cache restoration | |
| run: | | |
| set -x | |
| find . -name "dials.data*" | |
| echo "DIALS_DATA_VERSION_FULL=$(dials.data info -v | grep version.full)" >> $GITHUB_ENV | |
| echo "DIALS_DATA_VERSION=$(dials.data info -v | grep version.major_minor)" >> $GITHUB_ENV | |
| echo "DIALS_DATA=${PWD}/data" >> $GITHUB_ENV | |
| echo "CURRENT_WEEK=$(date +W%W)" >> $GITHUB_ENV | |
| echo "TODAY_ISO=$(date +%Y%m%d)" >> $GITHUB_ENV | |
| - name: Restore Cache | |
| uses: actions/cache@v4 | |
| with: | |
| key: "${{ env.CURRENT_WEEK }}-${{ env.DIALS_DATA_VERSION }}-${{ env.TODAY_ISO }}-${{ env.DIALS_DATA_VERSION_FULL }}" | |
| restore-keys: | | |
| ${{ env.CURRENT_WEEK }}-${{ env.DIALS_DATA_VERSION }}-${{ env.TODAY_ISO }}- | |
| ${{ env.CURRENT_WEEK }}-${{ env.DIALS_DATA_VERSION }}- | |
| path: ${{ github.workspace }}/data | |
| - name: Run pytest | |
| uses: pavelzw/pytest-action@510c5e90c360a185039bea56ce8b3e7e51a16507 # v2.2.0 | |
| with: | |
| verbose: true | |
| emoji: false | |
| job-summary: true | |
| custom-arguments: modules/dials --regression | |
| click-to-expand: true | |
| - name: "Set to Use HDF5" | |
| run: | | |
| echo "DIALS_USE_H5=1" >> $GITHUB_ENV | |
| - name: Run pytest | |
| uses: pavelzw/pytest-action@510c5e90c360a185039bea56ce8b3e7e51a16507 # v2.2.0 | |
| with: | |
| verbose: true | |
| emoji: false | |
| job-summary: true | |
| custom-arguments: modules/dials --regression | |
| click-to-expand: true | |
| report-title: DIALS_USE_H5 Pytest | |
| build_libtbx: | |
| name: libtbx build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modules/dials | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PYTHON_MINIMUM_VERSION }} | |
| - name: Install Base Environment | |
| run: | | |
| echo "pytest-md | |
| dials-data | |
| pytest-cov | |
| pytest-timeout" >> modules/dials/.conda-envs/linux.txt | |
| python modules/dials/installer/bootstrap.py update base \ | |
| --python "${{ env.PYTHON_MINIMUM_VERSION }}" \ | |
| --libtbx | |
| echo "$(pwd)/conda_base/bin" >> $GITHUB_PATH | |
| - name: Build | |
| run: python modules/dials/installer/bootstrap.py build --libtbx | |
| - name: Create Installer | |
| run: | | |
| mamba install -yp ./conda_base conda-pack | |
| pip3 uninstall dxtbx xia2 | |
| build/bin/libtbx.python modules/cctbx_project/libtbx/auto_build/create_installer.py \ | |
| --install_script modules/dials/installer/dials_installer.py \ | |
| --version dev$(date +"%Y%m%d") \ | |
| --license modules/dials/LICENSE \ | |
| --readme modules/dials/LICENSE \ | |
| --binary tmp/dials-installer-dev | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: dials-installer | |
| path: dist/dials-installer-dev.tar.gz | |
| if-no-files-found: error | |
| compression-level: 0 | |
| test_libtbx: | |
| name: Test libtbx build | |
| runs-on: ubuntu-latest | |
| needs: build_libtbx | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: dials-installer | |
| - name: Install DIALS | |
| run: | | |
| tar -xf dials-installer-dev.tar.gz | |
| cd dials-installer-dev | |
| echo "CI" > VERSION # To ensure we know the exact install path | |
| ./install --prefix=.. | |
| cd .. | |
| rm -rf ./dials-installer* | |
| echo "$(pwd)/dials-CI/conda_base/bin" >> $GITHUB_PATH | |
| echo "$(pwd)/dials-CI/build/bin" >> $GITHUB_PATH | |
| - name: Prepare for cache restoration | |
| run: | | |
| set -x | |
| find . -name "dials.data*" | |
| echo "DIALS_DATA_VERSION_FULL=$(dials.data info -v | grep version.full)" >> $GITHUB_ENV | |
| echo "DIALS_DATA_VERSION=$(dials.data info -v | grep version.major_minor)" >> $GITHUB_ENV | |
| echo "DIALS_DATA=${PWD}/data" >> $GITHUB_ENV | |
| echo "CURRENT_WEEK=$(date +W%W)" >> $GITHUB_ENV | |
| echo "TODAY_ISO=$(date +%Y%m%d)" >> $GITHUB_ENV | |
| - name: Restore Cache | |
| uses: actions/cache@v4 | |
| with: | |
| key: "${{ env.CURRENT_WEEK }}-${{ env.DIALS_DATA_VERSION }}-${{ env.TODAY_ISO }}-${{ env.DIALS_DATA_VERSION_FULL }}" | |
| restore-keys: | | |
| ${{ env.CURRENT_WEEK }}-${{ env.DIALS_DATA_VERSION }}-${{ env.TODAY_ISO }}- | |
| ${{ env.CURRENT_WEEK }}-${{ env.DIALS_DATA_VERSION }}- | |
| path: ${{ github.workspace }}/data | |
| - name: Run pytest | |
| uses: pavelzw/pytest-action@510c5e90c360a185039bea56ce8b3e7e51a16507 # v2.2.0 | |
| with: | |
| verbose: true | |
| emoji: false | |
| job-summary: true | |
| custom-arguments: dials-CI/modules/dials --regression | |
| click-to-expand: true | |
| custom-pytest: dials-CI/build/bin/libtbx.python -mpytest | |
| test_xfel: | |
| name: Test XFEL | |
| runs-on: ubuntu-latest | |
| needs: build_libtbx | |
| if: ${{ github.event_name == 'pull_request' }} | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: dials-installer | |
| - name: Install DIALS | |
| run: | | |
| set -x | |
| tar -xf dials-installer-dev.tar.gz | |
| cd dials-installer-dev | |
| echo "CI" > VERSION # To ensure we know the exact install path | |
| ./install --prefix=.. | |
| cd .. | |
| rm -rf ./dials-installer* | |
| echo "$(pwd)/dials-CI/conda_base/bin" >> $GITHUB_PATH | |
| echo "$(pwd)/dials-CI/build/bin" >> $GITHUB_PATH | |
| - name: Install XFEL-regression | |
| working-directory: ./dials-CI | |
| run: | | |
| source dials_env.sh | |
| set -x | |
| conda install -yp ./conda_base bash distro git-lfs mpi4py openmpi pandas | |
| GIT_LFS_SKIP_SMUDGE=1 git clone https://gitlab.com/cctbx/xfel_regression.git modules/xfel_regression | |
| libtbx.configure xfel_regression | |
| # Patch for this ubuntu so that we can run without arbitrary failure | |
| cd modules/xfel_regression | |
| # PATCH: This tests tests _explicitly_ for ubuntu 20.04 | |
| DISTRO=$(python3 -c "import distro; print(distro.version())") | |
| sed -i'' "s/20.04/${DISTRO}/" test/command_line/tst_xfel_merge.py | |
| # Patching done, show what we did | |
| git diff | |
| - name: Restore Cache | |
| uses: actions/cache@v4 | |
| with: | |
| key: "xfel-regression" | |
| path: | | |
| ${{ github.workspace }}/data | |
| ${{ github.workspace }}/dials-CI/modules/xfel_regression/.git/lfs | |
| - name: Update Regression Data | |
| run: | | |
| cd dials-CI/modules/xfel_regression | |
| git lfs install --local | |
| echo "DIALS_DATA=${{ github.workspace }}/data" >> $GITHUB_ENV | |
| set -x | |
| git lfs pull | |
| dials.data get 4fluoro_cxi | |
| - name: Run xfel_regression tests | |
| working-directory: ./dials-CI | |
| run: | | |
| source dials_env.sh | |
| mkdir tests | |
| cd tests | |
| libtbx.run_tests_parallel module=xfel_regression nproc=auto |