Pixi dependency management

.github/actions/create_python_environment/action.yml

@@ -10,16 +10,18 @@ runs:
   using: composite
   steps:
     - uses: conda-incubator/setup-miniconda@v3
-    - name: Create environment and install QUEENS
+      with:
+        miniforge-version: "latest"
+    - name: Create conda-lock environment and install QUEENS
       id: environment
       shell: bash -l {0}
       env:
         PYTHON_PACKAGE_MANAGER: conda
       run: |
-        $PYTHON_PACKAGE_MANAGER env create -f environment.yml
+        $PYTHON_PACKAGE_MANAGER install -c conda-forge conda-lock -y
+        conda-lock install --conda mamba -n queens composed.conda-lock.yml
         $PYTHON_PACKAGE_MANAGER activate queens
-        pip install torch==2.5.1 --index-url https://download.pytorch.org/whl/cpu
-        pip install -e .[safe_develop,fourc]
+        pip install --no-deps -e .
         $PYTHON_PACKAGE_MANAGER env export > pipeline_conda_environment.yml
         $PYTHON_PACKAGE_MANAGER list
         echo "ppm=$PYTHON_PACKAGE_MANAGER" >> $GITHUB_OUTPUT

.github/actions/setup-queens-pixi/action.yml

@@ -0,0 +1,77 @@
+name: Setup QUEENS pixi environment
+description: Set up pixi, install QUEENS editable into the selected environment, and optionally ensure rsync is available.
+
+inputs:
+  pixi-version:
+    description: Pixi version to install.
+    required: false
+    default: v0.67.0
+  cache:
+    description: Whether setup-pixi should enable caching.
+    required: false
+    default: "true"
+  cache-write:
+    description: Whether setup-pixi should write to the cache.
+    required: false
+    default: "false"
+  environments:
+    description: Whitespace-separated list of pixi environments to install.
+    required: false
+    default: queens-dev
+  activate-environment:
+    description: Pixi environment to activate and use for the editable install.
+    required: false
+    default: queens-dev
+  install-editable:
+    description: Whether to install QUEENS editable into the selected pixi environment.
+    required: false
+    default: "true"
+  ensure-rsync:
+    description: Whether to verify that rsync is available, installing it if necessary.
+    required: false
+    default: "true"
+
+runs:
+  using: composite
+  steps:
+    - uses: prefix-dev/setup-pixi@v0.9.4
+      with:
+        pixi-version: ${{ inputs.pixi-version }}
+        cache: ${{ inputs.cache }}
+        cache-write: ${{ inputs.cache-write }}
+        environments: ${{ inputs.environments }}
+        frozen: true
+        activate-environment: ${{ inputs.activate-environment }}
+
+    - name: Install QUEENS in workspace
+      if: ${{ inputs.install-editable != 'false' }}
+      shell: bash
+      run: |
+        set -euo pipefail
+        pixi run --locked -e "${{ inputs.activate-environment }}" python -m pip install --no-deps -e .
+
+    - name: Mark repo as safe for git
+      shell: bash
+      run: |
+        set -euo pipefail
+        git config --global --add safe.directory "${GITHUB_WORKSPACE}"
+
+    - name: Ensure rsync is available
+      if: ${{ inputs.ensure-rsync != 'false' }}
+      shell: bash
+      run: |
+        set -euo pipefail
+
+        if command -v rsync >/dev/null 2>&1; then
+          rsync --version
+        elif [ "${RUNNER_OS}" = "Linux" ]; then
+          sudo apt-get update
+          sudo apt-get install -y rsync
+          rsync --version
+        elif [ "${RUNNER_OS}" = "macOS" ]; then
+          brew install rsync
+          rsync --version
+        else
+          echo "Unsupported runner OS for rsync setup: ${RUNNER_OS}"
+          exit 1
+        fi

.github/workflows/build_documentation.yml

@@ -1,5 +1,5 @@
 # yamllint disable
-name: build_documentation
+name: Build documentation
 
 on:
   pull_request:
@@ -15,6 +15,7 @@ permissions:
 
 jobs:
   build-documentation:
+    name: Build documentation
     runs-on: ubuntu-latest
     container:
       image: ghcr.io/4c-multiphysics/4c-minimal:main
@@ -23,48 +24,39 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v4
-      - name: Mark repo as safe for git
-        run: |
-          git config --global --add safe.directory "$GITHUB_WORKSPACE"
-      - name: Install rsync
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y rsync
+      - uses: actions/checkout@v6
+      - uses: ./.github/actions/setup-queens-pixi
+        with:
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+          environments: queens-dev
+          activate-environment: queens-dev
       - name: Create links to 4C
         run: |
           ln -s /home/user/4C/bin/ config/4C_build
-      - name: Create Python environment
-        id: environment
-        uses: ./.github/actions/create_python_environment
-      - name: Add tutorial dependencies
-        env:
-          PYTHON_PACKAGE_MANAGER: ${{steps.environment.outputs.ppm}}
+      - name: Register Jupyter kernel
         run: |
-          $PYTHON_PACKAGE_MANAGER activate queens
-          pip install -e .[tutorial]
           python -m ipykernel install --user --name queens --display-name "Python (queens)"
       - name: Install xvfb
         run: |
           apt-get update
           apt-get install -y xvfb
       - name: Sphinx build
         env:
-          PYTHON_PACKAGE_MANAGER: ${{steps.environment.outputs.ppm}}
           PYTHONPATH: ${{ github.workspace }}
         run: |
           set -euxo pipefail
-          $PYTHON_PACKAGE_MANAGER activate queens
           sphinx-apidoc -o doc/source src/ -fMT
           cd doc
           xvfb-run -a sphinx-build -b html -d build/doctrees source build/html -W
       - name: Upload html
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@v5
         with:
           path: doc/build/html
           retention-days: 1
 
   deploy-documentation:
+    name: Deploy documentation
     needs: build-documentation
     if: ${{github.ref == 'refs/heads/main'}}
     environment:
@@ -74,4 +66,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v5