Separated docstring2argparse into standalone package. #130
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| # Lingfei Wang, 2022, 2024. All rights reserved. | |
| name: Network inference tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| paths: | |
| - 'setup.py' | |
| - 'src/**' | |
| - 'bin/**' | |
| - '.github/workflows/ci-inference.yml' | |
| - '.github/actions/install-bash/**' | |
| - '.github/actions/zenodo-url-translate/**' | |
| - '.github/actions/inference-test-dataset/**' | |
| - '.github/scripts/inference-test-dataset.py' | |
| jobs: | |
| test-skin1: | |
| name: Skin static network end-to-end tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9","3.10"] | |
| nth: ["2"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install | |
| uses: ./.github/actions/install-bash | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Get dataset URL | |
| id: zenodo-url-translate | |
| uses: ./.github/actions/zenodo-url-translate | |
| with: | |
| url: https://zenodo.org/records/6858494/files/inference-skin1.tar.xz?download=1 | |
| - name: Test dataset | |
| uses: ./.github/actions/inference-test-dataset | |
| with: | |
| url: ${{ steps.zenodo-url-translate.outputs.url }} | |
| test-path: ci_testspace | |
| makefile: static.mk | |
| expected-folder: test/tmp_static_expected | |
| actual-folder: tmp_static | |
| expected-h5: test/output/static_expected.h5 | |
| actual-h5: output/static.h5 | |
| makefile-params: '{"ENVMODE": "none", "NTH": "${{ matrix.nth }}", "DEVICE": "cpu", "GENOME_MACS2": "mm", "JOINT": "1", "KPARAMS-NETWORK-RECONSTRUCT+": " --nstep 10 --nstep_report 3"}' | |
| exclusions: 'footprints.bed net_weight.tsv.gz net_covfactor.tsv.gz net_meanvar.tsv.gz net_loss.tsv.gz net_stats.tsv.gz net_nweight.tsv.gz net_iweight.tsv.gz net_inweight.tsv.gz' | |
| test-blood1: | |
| name: Blood static network unit tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9","3.10"] | |
| nth: ["1","2"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install | |
| uses: ./.github/actions/install-bash | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Get dataset URL | |
| id: zenodo-url-translate | |
| uses: ./.github/actions/zenodo-url-translate | |
| with: | |
| url: https://zenodo.org/records/6858494/files/inference-blood1.tar.xz?download=1 | |
| - name: Test dataset | |
| uses: ./.github/actions/inference-test-dataset | |
| with: | |
| url: ${{ steps.zenodo-url-translate.outputs.url }} | |
| test-path: ci_testspace | |
| makefile: test_static.mk | |
| expected-folder: test/tmp_static_expected | |
| actual-folder: test/tmp_static | |
| expected-h5: test/output/static_expected.h5 | |
| actual-h5: test/output/static.h5 | |
| makefile-params: '{"ENVMODE": "none", "NTH": "${{ matrix.nth }}", "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' | |
| test-blood2: | |
| name: Blood dynamic network unit tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9","3.10"] | |
| nth: ["2"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install | |
| uses: ./.github/actions/install-bash | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Get dataset URL | |
| id: zenodo-url-translate | |
| uses: ./.github/actions/zenodo-url-translate | |
| with: | |
| url: https://zenodo.org/records/6858494/files/inference-blood2.tar.xz?download=1 | |
| - name: Test dataset | |
| uses: ./.github/actions/inference-test-dataset | |
| with: | |
| url: ${{ steps.zenodo-url-translate.outputs.url }} | |
| test-path: ci_testspace | |
| makefile: test_dynamic.mk | |
| expected-folder: test/tmp_dynamic_expected | |
| actual-folder: test/tmp_dynamic | |
| expected-h5: test/output/dynamic_expected.h5 | |
| actual-h5: test/output/dynamic.h5 | |
| makefile-params: '{"ENVMODE": "none", "NTH": "${{ matrix.nth }}", "DEVICE": "cpu", "GENOME_MACS2": "hs", "JOINT": "0", "KPARAMS-NETWORK-RECONSTRUCT+": " --nstep 10 --nstep_report 3", "PARAMS-DYNAMIC-SUBSETS_RNA": "1000 10 10"}' | |
| 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' |