diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 0000000..a5bd7fd --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,53 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +# TODO: +# - cache this directory $HOME/.cache/pyensembl/ +# - update coveralls +name: Tests +on: [push, pull_request] + +jobs: + build: + runs-on: ubuntu-latest + strategy: + fail-fast: true + matrix: + python-version: ["3.9", "3.10", "3.11"] + + steps: + - name: Checkout repository + uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + cache: "pip" + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install flake8 pytest pytest-cov coveralls + pip install -r requirements.txt + pip install . + - 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 + - name: Run default linting script + run: | + ./lint.sh + - name: Install Ensembl data + run: | + echo "Before installing Ensembl releases" && df -h + pyensembl install --release 75 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh37.75/ + pyensembl install --release 81 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.81/ + pyensembl install --release 95 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.95/ + pyensembl install --release 95 --species mouse --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.95/ + echo "After installing Ensembl releases" && df -h + - name: Run unit tests + run: | + ./test.sh + - name: Publish coverage to Coveralls + uses: coverallsapp/github-action@v2.2.3 diff --git a/README.md b/README.md index e76d56c..3b38dd9 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,6 @@ + # serializable Base class with serialization methods for user-defined Python objects