fix: remove requirement for ID in match_part/exon lines for extrinsic… #85
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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: Python package | |
| on: | |
| [ push, pull_request ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| python-version: [ 3.8, 3.7 ] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - name: Cache conda | |
| id: cache-miniconda | |
| uses: actions/cache@v1 | |
| env: | |
| CACHE_NUMBER: 0 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| path: ~/conda_pkgs_dir | |
| key: | |
| ${{ runner.os }}-conda-${{ hashFiles('./environment.yml') }} | |
| - name: Install system development tools | |
| run: | | |
| export DEBIAN_FRONTEND=noninteractive | |
| sudo apt update | |
| sudo apt install -y build-essential zlib1g-dev zlib1g git | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| miniconda-version: "latest" | |
| environment-file: ./environment.yml | |
| mamba-version: "*" | |
| use-mamba: true | |
| channels: bioconda, conda-forge, defaults | |
| use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | |
| auto-update-conda: true | |
| activate-environment: "minos" | |
| auto-activate-base: false | |
| - name: Install dependencies | |
| run: | | |
| python setup.py bdist_wheel | |
| pip install dist/minos*.whl; | |
| python -c "import numpy" | |
| - name: Install CPC2 | |
| run: | | |
| git clone --depth=1 https://github.com/EI-CoreBioinformatics/CPC2 | |
| cd CPC2 | |
| python setup.py develop | |
| CPC2 -h | |
| - name: Miscellaneous tests | |
| run: | | |
| which minos | |
| minos_folder=$(dirname $(python -c "import pkg_resources; print(pkg_resources.resource_filename(\"minos\", \"__init__.py\"))")) | |
| version=$(python -c "import sys; print(sys.version_info.major, '.', sys.version_info.minor, sep='')") | |
| ls ${minos_folder} | |
| ls ${minos_folder}/etc | |
| python -c "from minos import __version__; print(__version__);" | |
| minos -h |