Merge branch 'main' into add-yamllint

.git-blame-ignore-revs

@@ -2,3 +2,5 @@
 b42067f6776dcd763827000d585a88e071b78af3
 # applied prettier - https://github.com/glass-dev/glass/pull/227
 f9bac62f497a7288aa71fd4dbd948945c37f854e
+# applied ruff-linting - https://github.com/glass-dev/glass/pull/232
+e58d8616c03b8447aba90996905a98b42f18ba0a

.github/test-constraints.txt

@@ -1,2 +1,2 @@
---prefer-binary
 --only-binary numpy,scipy,healpy,healpix
+--prefer-binary

.github/workflows/examples.yml

@@ -0,0 +1,31 @@
+name: Test examples
+
+on:
+  push:
+    paths:
+      - "glass/**"
+    branches:
+      - main
+  pull_request:
+    paths:
+      - "glass/**"
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  test-examples:
+    name: Test examples
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+          cache: pip
+      - run: pipx run --spec '.[examples]' jupyter execute examples/**/*.ipynb

.github/workflows/pull_request.yml

@@ -11,6 +11,7 @@ on:
 
 jobs:
   check-pr-title:
+    if: ${{ github.actor != 'pre-commit-ci[bot]' }}
     runs-on: ubuntu-latest
     steps:
       - uses: thehanimo/[email protected]

.github/workflows/release.yml

@@ -2,20 +2,58 @@
 name: Release
 
 on:
+  workflow_dispatch:
+    inputs:
+      target:
+        description: 'Deployment target. Can be "pypi" or "testpypi"'
+        default: "testpypi"
   release:
     types:
       - published
 
 jobs:
+  dist:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build SDist and wheel
+        run: pipx run build
+
+      - name: Check metadata
+        run: pipx run twine check dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          path: dist/*
+
   publish:
-    name: Publish on PyPI
+    needs: [dist]
     runs-on: ubuntu-latest
     environment:
       name: publish
       url: https://pypi.org/p/glass
     permissions:
       id-token: write
+
     steps:
-      - uses: actions/checkout@v4
-      - run: pipx run build
-      - uses: pypa/[email protected]
+      - uses: actions/download-artifact@v4
+        with:
+          name: artifact
+          path: dist
+
+      - name: List distributions to be deployed
+        run: ls -l dist/
+
+      - if:
+          github.event.inputs.target == 'pypi' || (github.event_name ==
+          'release' && github.event.action == 'published')
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - if: github.event.inputs.target == 'testpypi'
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

.github/workflows/test.yml

@@ -6,8 +6,6 @@ on:
     branches:
       - main
   pull_request:
-    branches:
-      - main
 
 concurrency:
   # Skip intermediate builds: always.
@@ -68,16 +66,3 @@ jobs:
           sudo apt-get update
           sudo apt-get install pandoc
       - run: pipx run --spec '.[docs]' sphinx-build -W -b html docs _build/html
-
-  examples:
-    name: Examples
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-          cache: pip
-      - run: pipx run --spec '.[examples]' jupyter execute examples/**/*.ipynb

.pre-commit-config.yaml

@@ -1,4 +1,7 @@
----
+ci:
+  autoupdate_commit_msg: "MNT: update pre-commit hooks"
+  autofix_commit_msg: "STY: pre-commit fixes"
+
 repos:
   - repo: https://github.com/adrienverge/yamllint
     rev: v1.35.1
@@ -46,9 +49,32 @@ repos:
               }
             }
           - --strict
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args:
+          - --fix=lf
+      - id: trailing-whitespace
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-check-blanket-type-ignore
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.6.3
     hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
       - id: ruff-format
   - repo: https://github.com/pappasam/toml-sort
     rev: v0.23.1
@@ -59,8 +85,8 @@ repos:
           - --in-place
           - --spaces-indent-inline-array=4
           - --trailing-comma-inline-array
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.1.0
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.3.3
     hooks:
       - id: prettier
         args:

docs/conf.py

@@ -12,7 +12,7 @@
 
 project = "GLASS"
 author = "GLASS developers"
-copyright = f"2022-{datetime.date.today().year} {author}"
+copyright = f"2022-{datetime.date.today().year} {author}"  # noqa: A001, DTZ011
 version = metadata.version("glass")
 release = version
 

docs/examples.rst

@@ -13,7 +13,7 @@ and for the cosmological background.  Make sure you have CAMB installed:
     $ python -c 'import camb'  # should not give an error
 
 If you want to compute the angular matter power spectra in the examples, you
-need the `glass.ext.camb` package:
+need the ``glass.ext.camb`` package:
 
 .. code-block:: console
 

docs/make.bat

@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/manual/releases.rst

@@ -75,7 +75,7 @@ These notes document the changes between individual *GLASS* releases.
   power spectra by index from a list using GLASS ordering.
 
 * The :func:`~glass.galaxies.gaussian_phz()` function now accepts bounds using
-  `lower=` and `upper=` keyword parameters.
+  ``lower=`` and ``upper=`` keyword parameters.
 
 
 2023.6 (30 Jun 2023)
@@ -157,7 +157,7 @@ These notes document the changes between individual *GLASS* releases.
     by window functions using :func:`glass.shells.restrict` and
     :func:`glass.shells.partition`.
 
-  - The ``zmin`` and ``zmax`` parameters of `glass.galaxies.redshifts_from_nz`
+  - The ``zmin`` and ``zmax`` parameters of ``glass.galaxies.redshifts_from_nz``
     have been removed for the same reason.
 
   - The ``glass.lensing.multi_plane_weights`` function, which computed all

docs/user/how-glass-works.rst

@@ -20,11 +20,11 @@ Radial discretisation
 The discretisation in the radial (line of sight) direction is done in *GLASS*
 using the concept of a :term:`radial window`, which consists of a window
 function :math:`W` that assigns a weight :math:`W(z)` to each redshift
-:math:`z`.  In the *GLASS* code, the :class:`~glass.shells.RadialWindow` named
+:math:`z`.  In the *GLASS* code, the :class:`~glass.RadialWindow` named
 tuple is used to define radial windows.
 
 A sequence :math:`W_1, W_2, \ldots` of such window functions defines the shells
-of the simulation.  For example, the :func:`~glass.shells.tophat_windows`
+of the simulation.  For example, the :func:`~glass.tophat_windows`
 function takes redshift boundaries and returns a sequence of top hat windows,
 which are flat and non-overlapping.
 
@@ -169,7 +169,7 @@ shells:
 
 In short, the requirements say that each shell has an effective redshift which
 partitions the window functions of all other shells. In *GLASS*, it is stored
-as the ``zeff`` attribute of :class:`~glass.shells.RadialWindow`.  Functions
+as the ``zeff`` attribute of :class:`~glass.RadialWindow`.  Functions
 that construct a list of windows for shells should ensure these requirements
 are met.