Pin torch version and add debug for conda-build channels #19
Workflow file for this run
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| name: Python Package using Conda | |
| on: | |
| push: | |
| branches: | |
| - main | |
| tags: | |
| - 'v*' # Trigger on tags like v0.1.0 | |
| jobs: | |
| build-and-test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Conda with Python 3.10 | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: '3.10' | |
| auto-update-conda: true | |
| environment-file: environment.yml | |
| activate-environment: deeptaxa_env | |
| channels: pytorch,conda-forge,defaults | |
| - name: Install DeepTaxa and test dependencies | |
| shell: bash -l {0} | |
| run: | | |
| pip install . # Install DeepTaxa from source | |
| conda install flake8 pytest -y | |
| - name: Lint with flake8 | |
| shell: bash -l {0} | |
| run: | | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| shell: bash -l {0} | |
| run: | | |
| pytest tests/ -v | |
| build-and-release: | |
| runs-on: ubuntu-latest | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| needs: build-and-test | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Conda with Python 3.10 | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: '3.10' | |
| auto-update-conda: true | |
| channels: pytorch,conda-forge,defaults | |
| activate-environment: build_env | |
| - name: Install Conda Build Tools | |
| shell: bash -l {0} | |
| run: | | |
| conda install conda-build anaconda-client -c conda-forge -y | |
| - name: Debug Channel Configuration | |
| shell: bash -l {0} | |
| run: | | |
| conda config --show channels | |
| conda config --add channels pytorch | |
| conda config --add channels conda-forge | |
| conda config --add channels defaults | |
| conda config --show channels # Verify channels | |
| - name: Build Conda Package | |
| shell: bash -l {0} | |
| run: | | |
| conda-build conda-recipe/ --output-folder ./conda-bld --channel pytorch --channel conda-forge --channel defaults --override-channels | |
| ls -l ./conda-bld/noarch/ || ls -l ./conda-bld/linux-64/ # Debug: Show built files | |
| - name: Upload to Anaconda.org | |
| shell: bash -l {0} | |
| run: | | |
| echo "Uploading files:" | |
| ls -l ./conda-bld/noarch/ || ls -l ./conda-bld/linux-64/ # Debug: List files | |
| anaconda upload --user systems-genomics-lab ./conda-bld/noarch/deeptaxa-*.tar.bz2 || anaconda upload --user systems-genomics-lab ./conda-bld/linux-64/deeptaxa-*.tar.bz2 | |
| echo "Upload completed" | |
| env: | |
| ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |