Updated to match new zenodo URLs. #72
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Lingfei Wang, 2022, 2023. All rights reserved. | |
| name: "Container image" | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| paths: | |
| - 'setup.py' | |
| - 'src/**' | |
| - 'bin/**' | |
| - 'utils/docker/**' | |
| - 'doc/scripts/install.sh' | |
| - '.github/workflows/ci-container.yml' | |
| - '.github/actions/dockerhub-build-publish/**' | |
| jobs: | |
| build-cpu: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: local | |
| - name: Log in to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USER }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and publish pretest version | |
| uses: ./local/.github/actions/dockerhub-build-publish | |
| id: publish-pretest | |
| with: | |
| registry: lfwa | |
| image: dictys-cpu-dev | |
| test-blood1-cpu: | |
| name: Blood static network unit tests | |
| needs: build-cpu | |
| runs-on: ubuntu-latest | |
| container: | |
| image: lfwa/dictys-cpu-dev | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - 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": "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-cpu: | |
| needs: test-blood1-cpu | |
| if: ( github.ref_name == 'master' ) && ( github.repository == 'pinellolab/dictys' ) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: local | |
| - name: Log in to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USER }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and publish | |
| uses: ./local/.github/actions/dockerhub-build-publish | |
| id: publish | |
| with: | |
| registry: lfwa | |
| image: dictys-cpu | |
| build-publish-cuda: | |
| needs: test-blood1-cpu | |
| if: false && ( github.ref_name == 'master' ) && ( github.repository == 'pinellolab/dictys' ) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| cuda: [11.3,11.6,11.7] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: local | |
| - name: Log in to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USER }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and publish | |
| uses: ./local/.github/actions/dockerhub-build-publish | |
| id: publish | |
| with: | |
| registry: lfwa | |
| cuda: ${{ matrix.cuda }} | |
| image: dictys-cuda{{ matrix.cuda }} |