add dev env and linting #3
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| # .github/workflows/build-conda.yml | |
| name: Build and Upload Conda Package | |
| on: | |
| push: | |
| branches: [integrate-conda] | |
| workflow_dispatch: | |
| jobs: | |
| build-and-upload: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Cache conda build cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: /home/runner/miniconda3/conda-bld | |
| key: ${{ runner.os }}-conda-bld-${{ hashFiles('recipe/meta.yaml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-conda-bld- | |
| - name: Setup Miniforge and mamba | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-variant: Miniforge3 | |
| miniforge-version: latest | |
| mamba-version: '*' | |
| use-mamba: true | |
| conda-solver: libmamba | |
| auto-activate-base: true | |
| - name: Install dependencies | |
| run: | | |
| mamba install -y -c conda-forge conda-build anaconda-client boa | |
| - name: Get latest commit SHA from integrate-conda branch | |
| id: get_sha | |
| run: | | |
| echo "Fetching latest commit on integrate-conda branch..." | |
| COMMIT_SHA=$(git ls-remote origin refs/heads/integrate-conda | cut -f1) | |
| echo "COMMIT_SHA=$COMMIT_SHA" >> $GITHUB_ENV | |
| - name: Update meta.yaml with latest ref and sha256 | |
| run: | | |
| echo "Updating meta.yaml with commit: $COMMIT_SHA" | |
| # 1) Update the Jinja-set 'ref' (this is fine) | |
| sed -i "s|^{% set ref = \".*\" %}|{% set ref = \"$COMMIT_SHA\" %}|" ./recipe/meta.yaml | |
| # 2) Download the tarball and compute the checksum | |
| curl -L -o source.tar.gz \ | |
| https://github.com/khanlab/labelmerge/archive/${COMMIT_SHA}.tar.gz | |
| SHA256_SUM=$(sha256sum source.tar.gz | awk '{print $1}') | |
| echo "New sha256: $SHA256_SUM" | |
| # 3) Replace the literal 'sha256:' line under source: | |
| sed -i "s|^\(\s*sha256:\s*\).*|\1$SHA256_SUM|" ./recipe/meta.yaml | |
| - name: Build & capture path | |
| id: build | |
| run: | | |
| cd recipe | |
| OUT=$(conda build . -c conda-forge -c bioconda --output 2>/dev/null) | |
| echo "PACKAGE_PATH=$OUT" >> $GITHUB_ENV | |
| conda mambabuild . -c conda-forge -c bioconda | |
| - name: Upload package to Khanlab channel | |
| shell: bash -l {0} | |
| run: |- | |
| conda activate base | |
| anaconda login \ | |
| --username ${{ secrets.ANACONDA_USERNAME }} \ | |
| --password ${{ secrets.ANACONDA_PASSWORD }} | |
| anaconda upload "$PACKAGE_PATH" \ | |
| --label main \ | |
| --force \ |