Bug correction for h5 file output when some static GRN inference fails. #129
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| # Lingfei Wang, 2022. All rights reserved. | |
| name: "Conda package" | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| paths: | |
| - 'setup.py' | |
| - 'src/**' | |
| - 'bin/**' | |
| - 'utils/conda/**' | |
| - '.github/actions/conda-build-publish/**' | |
| - '.github/actions/install-conda/**' | |
| - '.github/workflows/ci-conda.yml' | |
| - '.github/actions/zenodo-url-translate/**' | |
| - '.github/actions/inference-test-dataset/**' | |
| - '.github/scripts/inference-test-dataset.py' | |
| jobs: | |
| build: | |
| name: Build and publish conda package with pretest suffix | |
| if: github.repository == 'pinellolab/dictys' | |
| runs-on: ubuntu-latest | |
| outputs: | |
| package: ${{ steps.publish-pretest.outputs.name }} | |
| version: ${{ steps.publish-pretest.outputs.version }} | |
| buildstr: ${{ steps.publish-pretest.outputs.buildstr }} | |
| steps: | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Mask token | |
| shell: bash | |
| run: echo "::add-mask::${{ secrets.ANACONDA_TOKEN }}" | |
| - name: Build and publish pretest version | |
| uses: ./.github/actions/conda-build-publish | |
| id: publish-pretest | |
| with: | |
| base-dir: utils/conda | |
| user: lingfeiwang | |
| token: ${{ secrets.ANACONDA_TOKEN }} | |
| preproc: "sed -i 's/ name: dictys/ name: dictys-pretest/' meta.yaml" | |
| options: "--force" | |
| test-blood1: | |
| name: Blood static network unit tests | |
| needs: build | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9","3.10"] | |
| steps: | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Add conda to system path | |
| shell: bash | |
| run: | | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - uses: actions/checkout@v3 | |
| - name: Install package | |
| uses: ./.github/actions/install-conda | |
| with: | |
| package: ${{ needs.build.outputs.package }}=${{ needs.build.outputs.version }}=${{ needs.build.outputs.buildstr }} | |
| python-version: ${{ matrix.python-version }} | |
| - name: Get dataset URL | |
| id: zenodo-url-translate | |
| uses: ./.github/actions/zenodo-url-translate | |
| with: | |
| url: https://zenodo.org/record/6858494/files/inference-blood1.tar.xz?download=1 | |
| - name: Test dataset | |
| uses: ./.github/actions/inference-test-dataset | |
| with: | |
| url: ${{ steps.zenodo-url-translate.outputs.url }} | |
| test-path: ci_testspace | |
| makefile: test_static.mk | |
| expected-folder: test/tmp_static_expected | |
| actual-folder: test/tmp_static | |
| expected-h5: test/output/static_expected.h5 | |
| actual-h5: test/output/static.h5 | |
| makefile-params: '{"ENVMODE": "none", "NTH": "2", "DEVICE": "cpu", "GENOME_MACS2": "hs", "JOINT": "0", "KPARAMS-NETWORK-RECONSTRUCT+": " --nstep 10 --nstep_report 3"}' | |
| exclusions: 'reads.bam reads.bai net_weight.tsv.gz net_covfactor.tsv.gz net_meanvar.tsv.gz net_loss.tsv.gz net_stats.tsv.gz' | |
| build-publish: | |
| name: Build and publish conda package | |
| needs: [ build, test-blood1 ] | |
| if: ( github.ref_name == 'master' ) && ( github.repository == 'pinellolab/dictys' ) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Mask token | |
| shell: bash | |
| run: echo "::add-mask::${{ secrets.ANACONDA_TOKEN }}" | |
| - name: Get serial ID | |
| id: serialid | |
| shell: bash | |
| run: | | |
| version='${{ needs.build.outputs.version }}' | |
| version="${version//./[.]}" | |
| serialid=$( (conda search -c lingfeiwang --override-channels -q dictys | grep '^dictys[[:blank:]]*'"$version"'[[:blank:]]' || true ) | wc -l) | |
| echo "serialid=$serialid" >> $GITHUB_OUTPUT | |
| - name: Build and publish release version | |
| uses: ./.github/actions/conda-build-publish | |
| id: publish | |
| with: | |
| base-dir: utils/conda | |
| user: lingfeiwang | |
| serialid: ${{ steps.serialid.outputs.serialid }} | |
| token: ${{ secrets.ANACONDA_TOKEN }} |