diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..1d90c29 --- /dev/null +++ b/.flake8 @@ -0,0 +1,3 @@ +[flake8] + +extend-ignore = E221,E211,E222,E202,F541,E201,E203,E501 diff --git a/.github/workflows/testsuite.yml b/.github/workflows/testsuite.yml new file mode 100644 index 0000000..0eb043d --- /dev/null +++ b/.github/workflows/testsuite.yml @@ -0,0 +1,101 @@ +name: Test suite + +on: + + workflow_dispatch: + + pull_request: + + branches: + - develop + - master + + paths: + - .github/workflows/testsuite.yml + - giatools/*.py + - setup.py + - tests/*.py + - tests/data/** + - requirements.txt + + push: + + branches: + - master + +permissions: + contents: read + issues: write + pull-requests: write + +jobs: + + python_lint: + + name: Linting + runs-on: ubuntu-latest + + steps: + + - name: Checkout + uses: actions/checkout@v4 + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install flake8 isort + + - name: Run flake8 + shell: bash + run: | + flake8 giatools + flake8 tests + + - name: Run isort + shell: bash + run: | + isort giatools --check-only + isort tests --check-only + + run_testsuite: + + name: Tests + runs-on: ubuntu-latest + + strategy: + matrix: + python-version: + - "3.8" + - "3.9" + - "3.10" + - "3.11" + - "3.12" + + steps: + + - name: Checkout + uses: actions/checkout@v4 + + - name: Install system dependencies + shell: bash + run: | + sudo apt install -y libopenblas-dev + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r requirements.txt + + - name: Run tests + uses: kostrykin/report-test-coverage-action@v1.0.0 + with: + report: ${{ strategy.job-index == 0 }} + gist-id: 07509ac0c0aa1d5a65ca03806bd3600b + github-auth: ${{ secrets.GITHUB_TOKEN }} + gist-auth: ${{ secrets.GIST_SECRET }} + gist-filename: giatools.json diff --git a/README.md b/README.md deleted file mode 100644 index 0944a7e..0000000 --- a/README.md +++ /dev/null @@ -1,5 +0,0 @@ -# giatools - -Tools required for Galaxy Image Analysis - -Use ``python -m unittest`` in the root directory of the repository to run the test suite. diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..14f1783 --- /dev/null +++ b/README.rst @@ -0,0 +1,15 @@ +.. raw:: html + +