Modernise packaging and tooling to match the MetEOR template

.github/workflows/publish.yml

@@ -0,0 +1,97 @@
+name: Publish to PyPI
+
+# Triggered by pushing a v* tag, or manually via the "Run workflow" button.
+on:
+  push:
+    tags: ["v*"]
+  workflow_dispatch:
+    inputs:
+      confirm:
+        description: "Type 'publish' to confirm release"
+        required: true
+
+jobs:
+  # -----------------------------------------------------------------------
+  # Guard: manual runs require the confirmation input.
+  # -----------------------------------------------------------------------
+  check:
+    name: Check confirmation
+    runs-on: ubuntu-latest
+    if: >
+      github.event_name == 'push' ||
+      github.event.inputs.confirm == 'publish'
+    steps:
+      - run: echo "Confirmed — proceeding with release."
+
+  # -----------------------------------------------------------------------
+  # Test gate: don't publish if tests fail.
+  # -----------------------------------------------------------------------
+  test:
+    name: Tests (Python 3.13)
+    needs: check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          cache: pip
+      - run: pip install -e ".[dev]"
+      - run: pytest --cov=obsarray
+
+  # -----------------------------------------------------------------------
+  # Build source distribution and wheel.
+  # -----------------------------------------------------------------------
+  build:
+    name: Build distribution
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          fetch-depth: 0  # full history so setuptools_scm picks up the tag
+
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+
+      - name: Build
+        run: |
+          pip install build
+          python -m build
+
+      - name: Store distribution packages
+        uses: actions/upload-artifact@v7
+        with:
+          name: dist
+          path: dist/
+
+  # -----------------------------------------------------------------------
+  # Publish to PyPI via trusted publisher (OIDC — no API token needed).
+  #
+  # One-time setup required in the PyPI project settings:
+  #   Publisher:   GitHub Actions
+  #   Owner:       comet-toolkit
+  #   Repository:  obsarray
+  #   Workflow:    publish.yml
+  #   Environment: pypi
+  # -----------------------------------------------------------------------
+  publish:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/obsarray
+    permissions:
+      id-token: write  # required for OIDC trusted publishing
+
+    steps:
+      - name: Download distribution packages
+        uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yml

@@ -0,0 +1,72 @@
+name: Tests
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: "Python ${{ matrix.python-version }}"
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install dependencies
+        run: pip install -e ".[dev]"
+
+      - name: Run tests
+        run: |
+          mkdir -p test_report
+          pytest \
+            --html=test_report/report.html \
+            --cov-report html:test_report/cov_report \
+            --cov-report xml:test_report/coverage.xml \
+            --junitxml=test_report/junit.xml \
+            --cov=obsarray
+
+      - name: Upload test report
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: test-report-py${{ matrix.python-version }}
+          path: test_report/
+          retention-days: 7
+
+      - name: Upload coverage to Codecov
+        if: matrix.python-version == '3.13'
+        uses: codecov/codecov-action@v7
+        with:
+          files: test_report/coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
+
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          cache: pip
+      - run: pip install -e ".[dev]"
+      - name: ruff format
+        run: ruff format --check obsarray
+      - name: ruff lint
+        run: ruff check obsarray
+      - name: mypy
+        run: mypy obsarray

.gitignore

@@ -1,6 +1,12 @@
+# macOS
+.DS_Store
+
 # Mypy cache
 .mypy_cache
 
+# Ruff cache
+.ruff_cache
+
 # Compiles docs for gitlab pages
 public
 latex
@@ -59,6 +65,7 @@ coverage.xml
 *.cover
 .hypothesis/
 .pytest_cache/
+test_report/
 
 # Translations
 *.mo
@@ -117,4 +124,5 @@ ENV/
 
 # IDE settings
 .vscode/.git.old
+
 CLAUDE.md

.pre-commit-config.yaml

@@ -1,5 +1,21 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: stable
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
     hooks:
-      - id: black
+      - id: check-added-large-files
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.13
+    hooks:
+      - id: ruff-check
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v2.1.0
+    hooks:
+      - id: mypy
+        # Match the CI lint job: check the package only, with numpy/xarray
+        # type information available (CI installs the package).
+        files: ^obsarray/
+        additional_dependencies: [numpy, xarray]

.readthedocs.yaml

@@ -6,15 +6,23 @@ version: 2
 
 # Set the OS, Python version and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.10"
+    python: "3.13"
+  jobs:
+    # Read the Docs clones shallowly; setuptools_scm needs the tags to
+    # derive the version shown in the docs.
+    post_checkout:
+      - git fetch --unshallow || true
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# Declare the Python requirements required to build docs
+# Install the package with its docs extras from pyproject.toml
 python:
   install:
-    - requirements: requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

MANIFEST.in

@@ -1,2 +1,2 @@
-include versioneer.py
-include obsarray/_version.py
+include README.md
+include LICENSE