docstring #225
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: test_NoTramp | |
| on: | |
| push: | |
| branches: [ "**" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| release: | |
| types: [ "created" ] | |
| permissions: | |
| contents: read | |
| jobs: | |
| get-python-versions: | |
| runs-on: ubuntu-22.04 # ubuntu-latest | |
| outputs: | |
| python-versions: ${{ steps.set-python-versions.outputs.versions }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: get-python-versions | |
| uses: snok/latest-python-versions@v1 | |
| id: get-python-versions | |
| with: | |
| min-version: "3.7" | |
| - name: set-python-versions | |
| id: set-python-versions | |
| run: | | |
| pinned_versions='["3.7", "3.10"]' | |
| # Get all versions and extract the penultimate one | |
| all_versions=$(echo '${{ steps.get-python-versions.outputs.latest-python-versions }}' | jq -r '.[]') | |
| sorted_versions=$(echo "$all_versions" | sort -V) | |
| penultimate=$(echo "$sorted_versions" | tail -n 2 | head -n 1) | |
| combined_versions=$(echo $pinned_versions | jq '. + ["'"$penultimate"'"]' | jq -c .) | |
| echo "Current penultimate major python version is $penultimate" | |
| echo "versions=${combined_versions}" >> $GITHUB_OUTPUT | |
| echo "Combined versions: $combined_versions" | |
| build: | |
| needs: get-python-versions | |
| runs-on: ubuntu-22.04 # ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ${{ fromJson(needs.get-python-versions.outputs.python-versions) }} | |
| minimap2-version: ["2.16", "latest"] # "2.28" | |
| fail-fast: false # do not cancel other jobs if one fails | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| # auto-update-conda: true | |
| # channels: bioconda, conda-forge | |
| # channel-priority: strict | |
| # activate-environment: env_name | |
| miniforge-version: latest | |
| # python-version: "3.10" | |
| # python-version: 3.* | |
| python-version: ${{ matrix.python-version == '3.x' && '3.*' || matrix.python-version }} | |
| auto-activate-base: true | |
| conda-remove-defaults: true | |
| use-mamba: true | |
| - name: create dedicated conda env | |
| shell: bash -el {0} | |
| run: | | |
| conda create -n tests python=${{ matrix.python-version == '3.x' && '3.*' || matrix.python-version }} | |
| - name: Install required and recommended dependencies | |
| shell: bash -el {0} | |
| run: | | |
| conda activate tests | |
| python -m pip install --upgrade pip | |
| pip install psutil | |
| if [ "${{ matrix.minimap2-version }}" = "latest" ]; then | |
| conda install -c bioconda -c conda-forge minimap2 | |
| else | |
| conda install -c bioconda -c conda-forge minimap2=${{ matrix.minimap2-version }} | |
| fi | |
| # conda install -c bioconda -c conda-forge minimap2=${{ matrix.minimap2-version }} | |
| - name: Run NoTramp all mode with single amplicons as reads | |
| shell: bash -el {0} | |
| run: | | |
| pwd | |
| ls -al | |
| python -c "import sys; print(sys.path)" | |
| conda activate tests | |
| conda list | |
| # python notramp/notramp_main.py -a -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| python -m notramp -a -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| echo "Showing contents of logfile:" | |
| cat /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| rm /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| - name: Run NoTramp all mode with single amplicons as reads and include primers | |
| shell: bash -el {0} | |
| run: | | |
| pwd | |
| conda activate tests | |
| conda list | |
| # python notramp/notramp_main.py -a --incl_prim -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| python -m notramp -a --incl_prim -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| echo "Showing contents of logfile:" | |
| cat /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| rm /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| - name: Run NoTramp all mode with fasta input and request fastq output | |
| shell: bash -el {0} | |
| run: | | |
| pwd | |
| conda activate tests | |
| conda list | |
| # python notramp/notramp_main.py -a --fastq -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| python -m notramp -a --fastq -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| echo "Showing contents of logfile:" | |
| cat /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| rm /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| - name: Run NoTramp all mode with empty reads-file | |
| shell: bash -el {0} | |
| run: | | |
| pwd | |
| conda activate tests | |
| conda list | |
| # python notramp/notramp_main.py -a -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/reads_file_empty.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| python -m notramp -a -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/reads_file_empty.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| echo "Showing contents of logfile:" | |
| cat /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| rm /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| - name: Run NoTramp trimming mode only | |
| shell: bash -el {0} | |
| run: | | |
| pwd | |
| conda activate tests | |
| conda list | |
| # python notramp/notramp_main.py -t -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| python -m notramp -t -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| echo "Showing contents of logfile:" | |
| cat /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| rm /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| - name: Run NoTramp coverage capping mode only | |
| shell: bash -el {0} | |
| run: | | |
| pwd | |
| conda activate tests | |
| conda list | |
| # python notramp/notramp_main.py -c -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| python -m notramp -c -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| echo "Showing contents of logfile:" | |
| cat /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| rm /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| - name: Run NoTramp all with short-read fastq input | |
| shell: bash -el {0} | |
| run: | | |
| pwd | |
| conda activate tests | |
| conda list | |
| # python notramp/notramp_main.py --set_min_len 100 -a -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v4.1_nCoV-2019.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/reads_file_regular.fq -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta -n /home/runner/work/NoTrAmp/NoTrAmp/notramp/resources/artic_nCoV_scheme_v1-v4.json | |
| python -m notramp --set_min_len 100 -a -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v4.1_nCoV-2019.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/reads_file_regular.fq -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta -n /home/runner/work/NoTrAmp/NoTrAmp/notramp/resources/artic_nCoV_scheme_v1-v4.json | |
| echo "Showing contents of logfile:" | |
| cat /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| rm /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| - name: Run NoTramp all with fastq short-read input and fastq output | |
| shell: bash -el {0} | |
| run: | | |
| pwd | |
| conda activate tests | |
| conda list | |
| # python notramp/notramp_main.py -a --set_min_len 100 --fastq -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v4.1_nCoV-2019.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/reads_file_regular.fq -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta -n /home/runner/work/NoTrAmp/NoTrAmp/notramp/resources/artic_nCoV_scheme_v1-v4.json | |
| python -m notramp -a --set_min_len 100 --fastq -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v4.1_nCoV-2019.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/reads_file_regular.fq -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta -n /home/runner/work/NoTrAmp/NoTrAmp/notramp/resources/artic_nCoV_scheme_v1-v4.json | |
| echo "Showing contents of logfile:" | |
| cat /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| rm /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| - name: Install optional dependencies | |
| shell: bash -el {0} | |
| run: | | |
| conda activate tests | |
| pip install matplotlib | |
| - name: Run NoTramp all mode with single amplicons as reads with figures | |
| shell: bash -el {0} | |
| run: | | |
| pwd | |
| conda activate tests | |
| conda list | |
| # python notramp/notramp_main.py -a --figures -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| python -m notramp -a --figures -p /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_SARS-CoV-2_v5.3.2_400.primer.bed -r /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/ARTIC_v5.3.2_Amplicons_Wuhan1_reference.fasta -g /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/MN908947.3_SARS-CoV2_Wuhan-reference.fasta | |
| echo "Showing contents of logfile:" | |
| cat /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| rm /home/runner/work/NoTrAmp/NoTrAmp/notramp/test/notramp.log | |
| - name: Install linter | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics |