diff --git a/.github/workflows/cgatcore_python.yml b/.github/workflows/cgatcore_python.yml index 631c4264..00cba1f9 100644 --- a/.github/workflows/cgatcore_python.yml +++ b/.github/workflows/cgatcore_python.yml @@ -19,14 +19,15 @@ jobs: steps: - uses: actions/checkout@v3 + - name: Cache conda uses: actions/cache@v3 env: - # Increase this value to reset cache if conda/environments/cgat-core.yml has not changed CACHE_NUMBER: 0 with: path: ~/conda_pkgs_dir key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda/environments/cgat-core.yml') }} + - name: Set installer URL id: set-installer-url run: | @@ -35,6 +36,7 @@ jobs: elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh" >> $GITHUB_ENV fi + - uses: conda-incubator/setup-miniconda@v2 with: installer-url: ${{ env.installer-url }} @@ -43,28 +45,39 @@ jobs: channel-priority: true activate-environment: cgat-core environment-file: conda/environments/cgat-core.yml + - name: Configure Conda Paths run: echo "/usr/share/miniconda3/condabin" >> $GITHUB_PATH + - name: Show conda run: | conda info conda list + + - name: Debug Python Environment + run: | + python --version + pip list + openssl version + - name: Test run: | pip install . ./all-tests.sh - + + deploy_docs: name: Deploy MkDocs Documentation runs-on: ubuntu-latest needs: build + steps: - uses: actions/checkout@v3 - name: Set up Python uses: actions/setup-python@v4 with: - python-version: '3.x' + python-version: '3.10' - name: Install MkDocs and Dependencies run: | @@ -73,4 +86,4 @@ jobs: - name: Build and Deploy MkDocs Site run: mkdocs gh-deploy --force --clean env: - GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/conda/environments/cgat-core.yml b/conda/environments/cgat-core.yml index f18e3236..3a9f8dbf 100644 --- a/conda/environments/cgat-core.yml +++ b/conda/environments/cgat-core.yml @@ -35,3 +35,4 @@ dependencies: - paramiko - pytest - pytest-pep8 +- pyopenssl>=23.2.0