Modularization and use of miniconda and mamba

kalininalab · Apr 5, 2024 · 29647da · 29647da
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Showing 2 changed files with 50 additions and 6 deletions.
diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
@@ -10,13 +10,35 @@ jobs:
     runs-on: 'ubuntu-latest'
     steps:
     - uses: actions/checkout@v4
-    - name: Publish DataSAIL to Conda
-      env:
-        ANACONDA_TOKEN: ${{ secrets.DATASAIL_ANACONDA_TOKEN }}
+
+    - name: Setup Mamba
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: '3.10'
+        miniforge-variant: Mambaforge
+        miniforge-version: latest
+        activate-environment: MPP
+        use-mamba: true
+
+    - name: Install environment
       shell: bash -l {0}
       run: |
         conda install -y anaconda-client conda-build git
+
+    - name: Build DataSAIL for linux-64
+      shell: bash -l {0}
+      run: |
         conda-build -q --variants "{python: [3.8, 3.9, 3.10, 3.11, 3.12]}" -c conda-forge -c bioconda --output-folder . --no-test recipe
+
+    - name: Convert DataSAIL to osx-64
+      shell: bash -l {0}
+      run: |
         conda convert -p osx-64 linux-64/*.tar.bz2
+
+    - name: Publish DataSAIL to Conda
+      env:
+        ANACONDA_TOKEN: ${{ secrets.DATASAIL_ANACONDA_TOKEN }}
+      shell: bash -l {0}
+      run: |
         anaconda -t "$ANACONDA_TOKEN" upload linux-64/*.tar.bz2
         anaconda -t "$ANACONDA_TOKEN" upload osx-64/*.tar.bz2
diff --git a/.github/workflows/publish_lite.yaml b/.github/workflows/publish_lite.yaml
@@ -10,16 +10,38 @@ jobs:
     runs-on: 'ubuntu-latest'
     steps:
     - uses: actions/checkout@v4
-    - name: Publish DataSAIL-lite to Conda
-      env:
-        ANACONDA_TOKEN: ${{ secrets.DATASAIL_ANACONDA_TOKEN }}
+
+    - name: Setup Mamba
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: '3.10'
+        miniforge-variant: Mambaforge
+        miniforge-version: latest
+        activate-environment: MPP
+        use-mamba: true
+
+    - name: Install environment
       shell: bash -l {0}
       run: |
         conda install -y anaconda-client conda-build git
+
+    - name: Build DataSAIL for linux-64
+      shell: bash -l {0}
+      run: |
         conda-build -q --variants "{python: [3.8, 3.9, 3.10, 3.11, 3.12]}" -c conda-forge -c bioconda --output-folder . --no-test recipe_lite
+
+    - name: Convert DataSAIL to osx-64, osx-arm64, win-64
+      shell: bash -l {0}
+      run: |
         conda convert -p osx-64 linux-64/*.tar.bz2
         conda convert -p osx-arm64 linux-64/*.tar.bz2
         conda convert -p win-64 linux-64/*.tar.bz2
+
+    - name: Publish DataSAIL-lite to Conda
+      env:
+        ANACONDA_TOKEN: ${{ secrets.DATASAIL_ANACONDA_TOKEN }}
+      shell: bash -l {0}
+      run: |
         anaconda -t "$ANACONDA_TOKEN" upload linux-64/*.tar.bz2
         anaconda -t "$ANACONDA_TOKEN" upload osx-64/*.tar.bz2
         anaconda -t "$ANACONDA_TOKEN" upload osx-arm64/*.tar.bz2