Switch test CI from pixi to hatch with dynamic matrix

- Dynamic test matrix extracted from pyproject.toml via hatch env show
- Add hatch-test env config with dependency-groups, scripts, and pre-release matrix
- Add concurrency control, check job (alls-green), and bi-monthly cron schedule
- Switch coverage upload to Codecov OIDC
- Keep visual test artifact upload, MPLBACKEND=agg, and tag triggers

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: timtreis

.github/workflows/test.yaml

@@ -3,73 +3,105 @@ name: Test
 on:
   push:
     branches: [main]
-    tags: ["v*"] # Push events to matching v*, i.e. v1.0, v20.15.10
+    tags: ["v*"]
   pull_request:
-    branches: ["*"]
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  MPLBACKEND: agg
 
 jobs:
-  test:
+  # Dynamically extract the test matrix from hatch so pyproject.toml is the single source of truth.
+  # See [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml.
+  get-environments:
     runs-on: ubuntu-latest
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get test environments
+        id: get-envs
+        run: |
+          ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
+            | map(
+                select(.key | startswith("hatch-test"))
+                | {
+                    name: .key,
+                    label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
+                    python: .value.python
+                  }
+              )')
+          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
+  test:
+    needs: get-environments
+    permissions:
+      id-token: write # for codecov OIDC
+
     strategy:
       fail-fast: false
       matrix:
-        env: ["dev-py311", "dev-py313"]
+        os: [ubuntu-latest]
+        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
 
-    # Configure pytest-xdist
-    env:
-      OMP_NUM_THREADS: "1"
-      OPENBLAS_NUM_THREADS: "1"
-      MKL_NUM_THREADS: "1"
-      NUMEXPR_MAX_THREADS: "1"
-      MPLBACKEND: "agg"
-      DISPLAY: ":42"
-      PYTEST_ADDOPTS: "-n auto --dist=load --durations=10"
+    name: ${{ matrix.env.label }}
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}
 
     steps:
-      - uses: actions/checkout@v4
-
-      # Cache rattler's shared package cache (speeds up downloads)
-      - name: Restore rattler cache
-        uses: actions/cache@v4
+      - uses: actions/checkout@v5
         with:
-          path: ~/.cache/rattler
-          key: rattler-${{ runner.os }}-${{ matrix.env }}-${{ hashFiles('pyproject.toml') }}
-          restore-keys: |
-            rattler-${{ runner.os }}-${{ matrix.env }}-
-            rattler-${{ runner.os }}-
-
-      # Install pixi and the requested environment
-      - uses: prefix-dev/setup-pixi@v0.9.0
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
-          environments: ${{ matrix.env }}
-          # We're not comitting the pixi-lock file
-          locked: false
-          cache: false
-          activate-environment: ${{ matrix.env }}
-
-      - name: Show versions
-        run: |
-          python --version
-          pixi --version
-
+          python-version: ${{ matrix.env.python }}
+      - name: Ensure figure directory exists
+        run: mkdir -p tests/figures
+      - name: Create hatch environment
+        run: uvx hatch env create ${{ matrix.env.name }}
       - name: Run tests
         env:
-          MPLBACKEND: agg
           DISPLAY: ":42"
+        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
+      - name: Generate coverage report
         run: |
-          pytest -v --cov --color=yes --cov-report=xml
-
-      - name: Archive figures generated during testing
+          test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
+          uvx hatch run ${{ matrix.env.name }}:cov-report
+      - name: Archive visual test figures
         if: always()
         uses: actions/upload-artifact@v4
         with:
-          name: visual_test_results_${{ matrix.env }}
-          path: /home/runner/work/spatialdata-plot/spatialdata-plot/tests/figures/*
+          name: visual_test_results_${{ matrix.env.name }}
+          path: tests/figures/*
+      - name: Upload coverage
+        uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: true
+          use_oidc: true
 
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+  # Single required check for branch protection.
+  # See https://github.com/re-actors/alls-green#why
+  check:
+    name: Tests pass in all hatch environments
+    if: always()
+    needs:
+      - get-environments
+      - test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: re-actors/alls-green@release/v1
         with:
-          name: coverage
-          verbose: true
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          jobs: ${{ toJSON(needs) }}

pyproject.toml

@@ -42,10 +42,11 @@ dev = [
   "twine>=4.0.2",
 ]
 test = [
+  "coverage[toml]>=7.4",
   "pooch",
   "pytest",
   "pytest-cov",
-  "pytest-xdist",
+  "pytest-xdist[psutil]",
 ]
 doc = [
   "ipykernel",
@@ -85,9 +86,28 @@ build = "sphinx-build -M html docs docs/_build -W {args}"
 open = "python -m webbrowser -t docs/_build/html/index.html"
 clean = "git clean -fdX -- {args:docs}"
 
+[tool.hatch.envs.hatch-test]
+dependency-groups = [ "test" ]
+
+[tool.hatch.envs.hatch-test.scripts]
+run = "pytest{env:HATCH_TEST_ARGS:} -p no:cov {args}"
+run-cov = "coverage run -m pytest{env:HATCH_TEST_ARGS:} -p no:cov {args}"
+cov-combine = "coverage combine"
+cov-report = [ "coverage report", "coverage xml -o coverage.xml" ]
+
 [[tool.hatch.envs.hatch-test.matrix]]
+deps = [ "stable" ]
 python = [ "3.11", "3.13" ]
 
+[[tool.hatch.envs.hatch-test.matrix]]
+deps = [ "pre" ]
+python = [ "3.13" ]
+
+[tool.hatch.envs.hatch-test.overrides]
+matrix.deps.env-vars = [
+  { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
+]
+
 [tool.ruff]
 line-length = 120
 exclude = [