Merge pull request #7 from quadbio/feature/pixi-modernization

Modernize template: pixi environment + copilot instructions

Author: Marius1311

.github/copilot-instructions.md

@@ -0,0 +1,28 @@
+# Copilot Instructions for Analysis Template
+
+## Project context (fill these in!)
+- **Project name:** <fill>
+- **One-liner goal:** <fill>
+- **Primary datasets / locations:** <fill>
+
+## Critical rules
+- **Don't update Jupyter notebooks** — I manage them myself
+- Use `pixi run <command>` or `pixi shell` for all commands
+- Summarize in chat, don't create markdown summary files
+
+## Quick reference
+
+| Task | Command |
+|------|---------|
+| Run Python | `pixi run python script.py` |
+| Run tests | `pixi run test` |
+| Add conda package | `pixi add <package>` |
+| Add PyPI package | `pixi add --pypi <package>` |
+
+## Project structure
+- **Notebooks**: `analysis/[INITIALS]-[YYYY]-[MM]-[DD]_description.ipynb`
+- **Data**: `data/<dataset>/{raw,processed,resources,results}/`
+- **Paths**: Use `from myanalysis import FilePaths` (edit `_constants.py` for datasets)
+- **Deps**: All in `pixi.toml` (not pyproject.toml)
+- pyproject.toml exists mainly for package metadata and testing
+- Run `pixi install` after pulling changes that update `pixi.toml`

.github/workflows/build.yaml

@@ -0,0 +1,27 @@
+name: Code Quality
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Lint & Format
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: prefix-dev/setup-pixi@v0.8.0
+        with:
+          pixi-version: v0.40.0
+          cache: true
+      - name: Run pre-commit checks
+        run: pixi run pre-commit run --all-files

.github/workflows/lint.yaml

@@ -1,102 +1,27 @@
-name: Test
+name: Tests
 
 on:
   push:
     branches: [main]
   pull_request:
     branches: [main]
-  schedule:
-    - cron: "0 5 1,15 * *"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-defaults:
-  run:
-    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
-    shell: bash -euo pipefail {0}
-
 jobs:
-  # Get the test environment from hatch as defined in pyproject.toml.
-  # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
-  # run locally and on continuous integration.
-  # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
-  # more details.
-  get-environments:
-    runs-on: ubuntu-latest
-    outputs:
-      envs: ${{ steps.get-envs.outputs.envs }}
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          filter: blob:none
-          fetch-depth: 0
-      - name: Install uv
-        uses: astral-sh/setup-uv@v5
-      - name: Get test environments
-        id: get-envs
-        run: |
-          ENVS_JSON=$(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
-
-  # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
   test:
-    needs: get-environments
-
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest]
-        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
-
-    name: ${{ matrix.env.label }}
-    runs-on: ${{ matrix.os }}
-
+    name: Run pytest
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
           filter: blob:none
           fetch-depth: 0
-      - name: Install uv
-        uses: astral-sh/setup-uv@v5
+      - uses: prefix-dev/setup-pixi@v0.8.0
         with:
-          python-version: ${{ matrix.env.python }}
-          cache-dependency-glob: pyproject.toml
-      - name: create hatch environment
-        run: uvx hatch env create ${{ matrix.env.name }}
-      - name: run tests using hatch
-        env:
-          MPLBACKEND: agg
-          PLATFORM: ${{ matrix.os }}
-          DISPLAY: :42
-        run: |
-          uvx hatch run ${{ matrix.env.name }}:coverage run -m pytest -v --color=yes
-      - name: generate coverage report
-        run: uvx hatch run ${{ matrix.env.name }}:coverage xml
-      - name: Upload coverage
-        uses: codecov/codecov-action@v4
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-
-  # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
-  # protection instead of having to update it frequently. 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:
-            jobs: ${{ toJSON(needs) }}
+          pixi-version: v0.40.0
+          cache: true
+      - name: Run tests
+        run: pixi run test

.github/workflows/test.yaml

@@ -109,6 +109,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+.pixi/
 
 # Spyder project settings
 .spyderproject