CI, packaging and doc maintenance

codecov.yml → .github/codecov.yml

@@ -1,9 +1,12 @@
+codecov:
+  notify:
+    after_n_builds: 3
 coverage:
   status:
     project:
       default:
         target: auto
-        threshold: 2%
+        threshold: 5%
     patch: false
     changes: false
 

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/release.yml

@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci

.github/workflows/pypipublish.yaml

@@ -1,26 +1,46 @@
 name: Upload Python Package
 
 on:
+  workflow_dispatch:
   release:
-    types: [created]
+    types: [published]
+  pull_request:
+    paths:
+      - ".github/workflows/pypipublish.yml"
+      - "pyproject.toml"
 
 jobs:
-  deploy:
+  dist:
+    name: Build & inspect package
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2.3.4
-      - name: Set up Python
-        uses: actions/setup-python@v2.1.4
+      - uses: actions/checkout@v4
         with:
-          python-version: "3.x"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install setuptools setuptools-scm wheel twine
-      - name: Build and publish
-        env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: |
-          python setup.py sdist bdist_wheel
-          twine upload dist/*
+          fetch-depth: 0
+
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  publish:
+    name: Upload package to PyPI
+    needs: [dist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+      attestations: write
+      contents: read
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - name: Get dist files
+        uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+
+      - name: Generate artifact attestation for sdist and wheel
+        uses: actions/attest-build-provenance@v2
+        with:
+          subject-path: "dist/*"
+
+      - name: Publish on PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yaml

@@ -1,4 +1,4 @@
-name: test
+name: Tests
 
 on:
   push:
@@ -12,41 +12,36 @@ jobs:
   test:
     name: pytest (${{ matrix.os }}, ${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
     strategy:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.10", "3.13"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
-      - name: Install miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: actions/checkout@v5
         with:
-          python-version: ${{ matrix.python-version }}
-          mamba-version: "*"
-          channels: conda-forge,defaults
-          channel-priority: true
-          auto-activate-base: false
-      - name: Conda info
-        shell: bash -l {0}
-        run: |
-          conda info
-          conda list
-          conda config --show-sources
-          conda config --show
-          printenv | sort
-      - name: Install dependencies
-        shell: bash -l {0}
-        run: mamba install xarray dask numpy scipy scikit-learn pys2index pytest pytest-cov
-      - name: Build and install xoak
-        shell: bash -l {0}
+          fetch-depth: 0
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: ci/environment.yml
+          cache-environment: true
+          cache-downloads: false
+          create-args: >-
+            python=${{ matrix.python-version }}
+
+      - name: Install xoak
         run: |
-          python -m pip install . --no-deps -v
-          python -OO -c "import xoak"
+          python -m pip install .
+
       - name: Run tests
-        shell: bash -l {0}
-        run: pytest . --verbose --color=yes
-      - name: Codecov
-        if: matrix.os == 'macos-latest' && matrix.python-version == '3.8'
-        uses: codecov/codecov-action@v1
+        run: |
+          python -m pytest -vv --cov=xoak --color=yes src/xoak/tests
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v5

.pre-commit-config.yaml

@@ -1,25 +1,21 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.3.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-docstring-first
       - id: check-yaml
-      - id: double-quote-string-fixer
 
-  - repo: https://github.com/ambv/black
-    rev: 20.8b1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.5
     hooks:
-      - id: black
-        args: ["--line-length", "100", "--skip-string-normalization"]
+      - id: ruff-format
+        types_or: [ python, pyi ]
+      - id: ruff
+        args: [--fix]
+        types_or: [ python, pyi ]
 
-  - repo: https://gitlab.com/PyCQA/flake8
-    rev: 3.8.4
-    hooks:
-      - id: flake8
-
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.6.4
-    hooks:
-      - id: isort
+ci:
+  autofix_prs: false
+  autoupdate_schedule: quarterly

.readthedocs.yml

@@ -1,15 +1,20 @@
 # Required
 version: 2
 
-# Build documentation in the doc/ directory with Sphinx
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "mambaforge-4.10"
+
 sphinx:
   configuration: doc/conf.py
 
 conda:
-    environment: environment_doc.yml
+    environment: doc/environment.yml
 
 python:
-  version: 3.8
   install:
     - method: pip
       path: .
+
+formats: []

ci/environment.yml

@@ -0,0 +1,15 @@
+name: xoak
+channels:
+  - conda-forge
+dependencies:
+  - python
+  - numpy
+  - xarray
+  - dask
+  - scipy
+  - scikit-learn
+  - pys2index
+  - pytest
+  - pytest-cov
+  - pydata-sphinx-theme=0.15.4
+  - sphinx-book-theme=1.1.4

doc/_static/style.css

@@ -0,0 +1,55 @@
+
+code.literal {
+  background-color: unset;
+  border: unset;
+}
+
+.xr-wrap {
+  /* workaround when (ipy)widgets are present in output cells
+   * https://github.com/xarray-contrib/xarray-indexes/issues/14
+   * only rely on pydata-sphinx-theme variables here!
+  */
+  --xr-font-color0: var(--pst-color-text-base);
+  --xr-font-color2: var(--pst-color-text-base);
+  --xr-font-color3: var(--pst-color-text-base);
+  --xr-border-color: hsl(from var(--pst-color-text-base) h s calc(l + 40));
+  --xr-disabled-color: hsl(from var(--pst-color-text-base) h s calc(l + 40));
+  --xr-background-color: var(--pst-color-on-background);
+  --xr-background-color-row-even: hsl(
+    from var(--pst-color-on-background) h s calc(l - 5)
+  );
+  --xr-background-color-row-odd: hsl(
+    from var(--pst-color-on-background) h s calc(l - 15)
+  );
+
+  font-size: 0.9em;
+  margin-left: 1.25em;
+}
+
+html[data-theme="dark"] .xr-wrap {
+  --xr-border-color: hsl(from var(--pst-color-text-base) h s calc(l - 40));
+  --xr-disabled-color: hsl(from var(--pst-color-text-base) h s calc(l - 40));
+  --xr-background-color-row-even: hsl(
+    from var(--pst-color-on-background) h s calc(l + 5)
+  );
+  --xr-background-color-row-odd: hsl(
+    from var(--pst-color-on-background) h s calc(l + 15)
+  );
+}
+
+.xr-array-wrap,
+.xr-var-data,
+.xr-var-preview {
+  /* font-size: 0.9em; */
+}
+.gp {
+  color: darkorange;
+}
+
+/* workaround Pydata Sphinx theme using light colors for widget cell outputs in dark-mode */
+/* works for many widgets but not for Xarray html reprs */
+/* https://github.com/pydata/pydata-sphinx-theme/issues/2189 */
+html[data-theme="dark"] .output_area.rendered_html:has(div.xr-wrap) {
+  background-color: var(--pst-color-on-background) !important;
+  color: var(--pst-color-text-base) !important;
+}