Merge pull request #43 from pnnl/ci-fixes

Update continuous integration to use rattler-build

.github/workflows/actions.yml

@@ -34,7 +34,7 @@ jobs:
       - name: Setup environment
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
+          miniforge-variant: miniforge3
           miniforge-version: latest
           use-mamba: true
           environment-file: envs/linux.yml
@@ -65,7 +65,7 @@ jobs:
       - name: Setup environment
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
+          miniforge-variant: miniforge3
           miniforge-version: latest
           use-mamba: true
           environment-file: envs/osx.yml
@@ -82,46 +82,44 @@ jobs:
           # pytest
 
   Deploy:
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     needs:
       - Test_Linux
       - Test_Mac
-    runs-on: ubuntu-latest
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            target-platform: linux-64
+          - os: macos-latest
+            target-platform: osx-arm64
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
-
-      - name: Setup environment
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          use-mamba: true
-          python-version: 3.12
-          channels: conda-forge,bioconda,smcolby
-          use-only-tar-bz2: false
-          auto-activate-base: true
-
-      - name: Install dependencies
-        run: |
-          mamba install boa anaconda-client conda-verify conda-build
-
+
       - name: Build conda package
-        run: |
-          mkdir build/
-          conda mambabuild conda-recipe/ --output-folder build/
-          conda index build/
-        
-      - name: Convert to osx-arm64
-        run: conda convert -p osx-arm64 build/linux-64/*.tar.bz2 -o build/
-
-      - name: Upload packages
+        uses: prefix-dev/rattler-build-action@v0.2.24
+        with:
+          # Needs to be unique for each matrix entry
+          artifact-name: isicle-${{ matrix.target-platform }}
+          build-args: |
+            --target-platform ${{ matrix.target-platform }}
+            --recipe rattler-recipe/recipe.yaml
+            --variant-config rattler-recipe/variants.yaml
+            --output-dir build/
+            -c conda-forge
+            -c bioconda
+      
+      - name: Upload conda package
         env:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         run: |
-          anaconda upload build/linux-64/*.tar.bz2
-          anaconda upload build/osx-arm64/*.tar.bz2
+          for pkg in $(find build/ -type f \( -name "*.conda" -o -name "*.tar.bz2" \) ); do
+            echo "Uploading ${pkg}"
+            rattler-build upload anaconda --owner smcolby "${pkg}"
+          done

conda-recipe/meta.yaml → rattler-recipe/recipe.yaml

@@ -1,9 +1,9 @@
-{% set data = load_setup_py_data(setup_file="../setup.py",
-                                 from_recipe_dir=True) %}
+context:
+  version: "2.0.0" # TODO: obtain this from package directly
 
 package:
   name: isicle
-  version: {{ data.get("version") }}
+  version: ${{ version }}
 
 source:
   path: ..
@@ -17,7 +17,8 @@ extra:
 
 build:
   number: 0
-  script: "{{ PYTHON }} -m pip install -vv --no-deps ."
+  script:
+    - python -m pip install -vv --no-deps .
 
 requirements:
   host:
@@ -37,7 +38,3 @@ requirements:
     - snakemake >=6.3.0
     - statsmodels >=0.11.1
     - xtb >=6.5.1
-
-test:
-  imports:
-    - isicle

rattler-recipe/variants.yaml

@@ -0,0 +1,6 @@
+
+python:
+    - "3.12"
+    - "3.11"
+    - "3.10"
+    - "3.9"