fix: pin mikado python dependencies to fix issues with installation #… #643
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Mikado | |
| on: | |
| [ push, pull_request ] | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| python-version: [ 3.7, 3.8, 3.9 ] | |
| os: [ubuntu-latest, macos-latest] | |
| steps: | |
| - name: Install system development tools | |
| if: startsWith(runner.os, 'Linux') | |
| run: | | |
| export DEBIAN_FRONTEND=noninteractive | |
| sudo apt update | |
| sudo apt install -y build-essential zlib1g-dev zlib1g | |
| - uses: actions/checkout@v2 | |
| - uses: actions/cache@v2 | |
| if: startsWith(runner.os, 'Linux') | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - uses: actions/cache@v2 | |
| if: startsWith(runner.os, 'macOS') | |
| with: | |
| path: ~/Library/Caches/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Cache conda | |
| id: cache-miniconda | |
| uses: actions/cache@v2 | |
| env: | |
| CACHE_NUMBER: 1 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| path: ~/conda_pkgs_dir | |
| key: | |
| ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('./environment.yml') }} | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| miniconda-version: "latest" | |
| environment-file: ./environment.yml | |
| mamba-version: "*" | |
| use-mamba: true | |
| channels: conda-forge, defaults | |
| use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | |
| # auto-update-conda: false | |
| activate-environment: "mikado2" | |
| # auto-activate-base: false | |
| - name: Install dependencies | |
| run: | | |
| gcc --help | |
| pip install -r requirements.txt | |
| python -c "import pysam; print(pysam.__version__)" | |
| pip install Cython pytest-cov | |
| python setup.py develop | |
| - name: Test light | |
| run: | | |
| pytest -m slow Mikado/tests/test_light.py::LightTest::test_subprocess_multi_empty_orfs | |
| - name: Test full with coverage | |
| if: startsWith(runner.os, 'Linux') | |
| run: | | |
| pytest --cov=Mikado --cov-report=xml --cov-config=.coveragerc -m 'not triage'; | |
| - name: Test full without coverage | |
| if: startsWith(runner.os, 'macOS') | |
| run: | | |
| pytest -m 'not triage'; | |
| - name: Upload coverage to Codecov | |
| if: startsWith(runner.os, 'Linux') | |
| uses: codecov/codecov-action@v1 | |
| - name: Test daijin | |
| if: startsWith(runner.os, 'Linux') | |
| run: | | |
| mamba install -c bioconda -c conda-forge -y bioconda::portcullis stringtie scallop "gmap!=2021.02.22" \ | |
| star hisat2 prodigal blast diamond transdecoder conda-forge::gnuplot kallisto samtools gffread; | |
| cd sample_data; snakemake --latency-wait 60 --jobs 5 --cores 5 | |
| - name: Test daijin mikado | |
| if: startsWith(runner.os, 'macOS') | |
| run: | | |
| mamba install -c bioconda -c conda-forge -y prodigal blast diamond transdecoder kallisto samtools gffread; | |
| cd sample_data; snakemake --latency-wait 60 --jobs 5 --cores 5 complete_no_assemble | |
| - name: Test fast | |
| run: | | |
| python -c "import Mikado; Mikado.test(label='fast')"; | |
| - name: Test seed | |
| run: | | |
| # Check that the seed is set properly | |
| mikado serialise --junctions sample_data/junctions.bed --genome Mikado/tests/chr5.fas.gz \ | |
| --transcripts Mikado/tests/check_seed.fa --configuration Mikado/tests/check_seed.yaml; | |
| mikado pick --log $(pwd)/pick.20a.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz \ | |
| --configuration Mikado/tests/check_seed.yaml -od 20a Mikado/tests/check_seed.gtf; | |
| mikado pick --log $(pwd)/pick.20b.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz \ | |
| --configuration Mikado/tests/check_seed.yaml -od 20b Mikado/tests/check_seed.gtf; | |
| mikado pick --log $(pwd)/pick.20c.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz \ | |
| --json-conf Mikado/tests/check_seed.yaml -od 20c Mikado/tests/check_seed.gtf; | |
| mikado pick --log $(pwd)/pick.20d.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz \ | |
| --json-conf Mikado/tests/check_seed.yaml -od 20d Mikado/tests/check_seed.gtf; | |
| mikado pick --log $(pwd)/pick.10.log --procs 2 --seed 1000 --genome Mikado/tests/chr5.fas.gz \ | |
| --json-conf Mikado/tests/check_seed.yaml -od 1000 Mikado/tests/check_seed.gtf; | |
| if [[ $(diff -q 20a 20b) || $(diff -q 20a 20c) || $(diff -q 20a 20d) ]]; then exit 1; fi | |
| if [[ ! $(diff -q 20a 1000) ]]; then exit 1; fi |