Pixi dependency management

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.github/actions/run-pytest-suite/action.yml

@@ -0,0 +1,74 @@
+name: Run pytest suite
+description: Run a marked pytest suite and publish its reports.
+
+inputs:
+  test-suite-name:
+    description: Test suite name used in coverage, JUnit, and artifact filenames.
+    required: true
+  markers:
+    description: Pytest marker expression to select tests.
+    required: true
+
+runs:
+  using: composite
+  steps:
+    - name: Prepare report names
+      id: report-names
+      shell: bash
+      env:
+        TEST_SUITE_NAME: ${{ inputs.test-suite-name }}
+      run: |
+        echo "coverage-file=.coverage.${TEST_SUITE_NAME}" >> "$GITHUB_OUTPUT"
+        echo "junit-file=test_junit_${TEST_SUITE_NAME}.xml" >> "$GITHUB_OUTPUT"
+        echo "artifact-name=raw_test_reports_${TEST_SUITE_NAME}" >> "$GITHUB_OUTPUT"
+
+    - name: Run pytest
+      id: pytest
+      shell: bash
+      continue-on-error: true
+      env:
+        COVERAGE_FILE: ${{ steps.report-names.outputs.coverage-file }}
+        JUNIT_FILE: ${{ steps.report-names.outputs.junit-file }}
+        PYTEST_MARKERS: ${{ inputs.markers }}
+      run: |
+        pytest_args=(
+          -v
+          -m "${PYTEST_MARKERS}"
+          --cov
+          --cov-report=term
+          --color=yes
+          -o junit_logging=all
+          --junitxml="${JUNIT_FILE}"
+        )
+
+        if [ -n "${TEST_TIMING_OPTION:-}" ]; then
+          read -r -a timing_args <<< "${TEST_TIMING_OPTION}"
+          pytest_args+=("${timing_args[@]}")
+        fi
+
+        pytest "${pytest_args[@]}"
+
+    - name: Publish junit pytest report
+      if: always()
+      uses: mikepenz/action-junit-report@v6
+      with:
+        report_paths: ${{ steps.report-names.outputs.junit-file }}
+        annotate_only: true
+        job_summary: false
+
+    - name: Upload raw test reports
+      if: always()
+      uses: actions/upload-artifact@v7
+      with:
+        name: ${{ steps.report-names.outputs.artifact-name }}
+        include-hidden-files: true
+        path: |
+          ${{ steps.report-names.outputs.coverage-file }}
+          ${{ steps.report-names.outputs.junit-file }}
+        if-no-files-found: error
+        retention-days: 7
+
+    - name: Fail if pytest failed
+      if: steps.pytest.outcome == 'failure'
+      shell: bash
+      run: exit 1

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

@@ -0,0 +1,88 @@
+---
+name: Setup QUEENS pixi environment
+description: >
+  Set up pixi, install QUEENS editable into the selected environment,
+  and optionally ensure rsync is available.
+
+inputs:
+  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"
+  run-install:
+    description: Whether setup-pixi should install the selected pixi environments.
+    required: false
+    default: "true"
+  environments:
+    description: Whitespace-separated list of pixi environments to install.
+    required: false
+    default: default
+  activate-environment:
+    description: Pixi environment to activate and use for the editable install.
+    required: false
+    default: default
+  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"
+  frozen:
+    description: Whether to install with frozen requirements.
+    required: false
+    default: "true"
+
+runs:
+  using: composite
+  steps:
+    - name: Read pixi version
+      id: pixi-version
+      shell: bash
+      run: |
+        pixi_version="$(tr -d '[:space:]' < "${GITHUB_WORKSPACE}/.pixi-version")"
+        echo "version=${pixi_version}" >> "$GITHUB_OUTPUT"
+
+    - uses: prefix-dev/setup-pixi@v0.9.5
+      with:
+        pixi-version: ${{ steps.pixi-version.outputs.version }}
+        cache: ${{ inputs.cache }}
+        cache-write: ${{ inputs.cache-write }}
+        run-install: ${{ inputs.run-install }}
+        environments: ${{ inputs.environments }}
+        frozen: ${{ inputs.frozen }}
+        activate-environment: ${{ inputs.activate-environment }}
+
+    - name: Install QUEENS in workspace
+      if: ${{ inputs.install-editable != 'false' }}
+      shell: bash
+      run: |
+        pixi run --locked -e "${{ inputs.activate-environment }}" install-editable
+
+    - name: Mark repo as safe for git
+      shell: bash
+      run: |
+        git config --global --add safe.directory "${GITHUB_WORKSPACE}"
+
+    - name: Ensure rsync is available
+      if: ${{ inputs.ensure-rsync != 'false' }}
+      shell: bash
+      run: |
+        if command -v rsync >/dev/null 2>&1; then
+          rsync --version
+        elif [ "${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/dependabot.yml

@@ -0,0 +1,15 @@
+---
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directories:
+      - /
+      - /.github/actions/setup-queens-pixi
+    schedule:
+      interval: monthly
+    groups:
+      github-actions:
+        patterns:
+          - "*"
+    cooldown:
+      default-days: 7

.github/workflows/build_documentation.yml

@@ -1,7 +1,6 @@
-# yamllint disable
-name: build_documentation
+name: Build documentation
 
-on:
+"on":
   pull_request:
   push:
     branches:
@@ -15,56 +14,48 @@ permissions:
 
 jobs:
   build-documentation:
+    name: Build documentation
     runs-on: ubuntu-latest
     container:
       image: ghcr.io/4c-multiphysics/4c-minimal:main
       options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -l -eo pipefail {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: dev
+          activate-environment: 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
+          set -x
           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 +65,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v5