Dev #2
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
| name: Main Branch | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: xpresspipe | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda clean --all | |
| conda env update --file requirements.yml --name xpresspipe | |
| conda activate xpresspipe | |
| pip install . | |
| pip install codecov | |
| - name: Run test_arguments.py | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_arguments.py | |
| - name: Run test_utils.py | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_utils.py | |
| - name: Run test_bam.py | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_bam.py | |
| - name: Run test_modifyGTF.py | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_modifyGTF.py | |
| - name: Run test_truncateGTF.py | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_truncateGTF.py | |
| - name: Run test_metagene.py | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_metagene.py | |
| - name: Run test_periodicity.py | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_periodicity.py | |
| - name: Run test_complexity.py | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_complexity.py | |
| - name: Run test_rrnaProbe.py | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_rrnaProbe.py | |
| - name: Run test_help.py | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_help.py | |
| - name: Run test_pipelines.py | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_pipelines.py | |
| - name: Generate coverage report | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage report | |
| bash <(curl -s https://codecov.io/bash) -cF python | |
| - name: Generate conda version report | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| conda list --explicit > conda-spec-file.txt | |
| cat conda-spec-file.txt | |
| - name: Generate R packages version report | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| Rscript -e 'installed.packages() %>% as.data.frame() %>% write.table("R-packages-version-report.txt", sep="\t")' | |
| cat R-packages-version-report.txt | |