Linters refresh

.github/workflows/docs.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: ['*']
+    branches: ["*"]
 
 defaults:
   run:
@@ -20,7 +20,6 @@ jobs:
       - name: Setup Conda Environment
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           miniforge-version: latest
           use-mamba: true
           environment-file: ci/requirements-docs.yml

.github/workflows/pre-commit.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: ['*']
+    branches: ["*"]
 
 jobs:
   checks:

.github/workflows/pytest.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: ['*']
+    branches: ["*"]
   workflow_dispatch: # allows you to trigger manually
 
 # When this workflow is queued, automatically cancel any previous running
@@ -19,41 +19,42 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.os }} ${{ matrix.python-version }} ${{ matrix.requirements }}
+    name:
+      ${{ matrix.os }} ${{ matrix.python-version }} ${{ matrix.requirements }}
     runs-on: ${{ matrix.os }}-latest
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         requirements: [latest]
         include:
           # Test on macos and windows (first and last version of python only)
           - os: macos
-            python-version: '3.8'
+            python-version: "3.8"
             requirements: latest
           - os: macos
-            python-version: '3.12'
+            python-version: "3.12"
             requirements: latest
           - os: windows
-            python-version: '3.8'
+            python-version: "3.8"
             requirements: latest
           - os: windows
-            python-version: '3.12'
+            python-version: "3.12"
             requirements: latest
           # Test on minimal requirements
           - os: ubuntu
-            python-version: '3.8'
+            python-version: "3.8"
             requirements: minimal
           - os: macos
-            python-version: '3.8'
+            python-version: "3.8"
             requirements: minimal
           - os: windows
-            python-version: '3.8'
+            python-version: "3.8"
             requirements: minimal
           # Test on nightly builds of requirements
           - os: ubuntu
-            python-version: '3.12'
+            python-version: "3.12"
             requirements: upstream
 
     steps:
@@ -65,7 +66,6 @@ jobs:
       - name: Setup Conda Environment
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           miniforge-version: latest
           use-mamba: true
           python-version: ${{ matrix.python-version }}
@@ -85,7 +85,7 @@ jobs:
         run: |
           # Pick up https://github.com/mamba-org/mamba/pull/2903
           mamba install -n base 'mamba>=1.5.2'
-      
+
           mamba uninstall --force numpy pandas scipy pyarrow
           python -m pip install --no-deps --pre --prefer-binary \
               --extra-index-url https://pypi.fury.io/arrow-nightlies/ \

.pre-commit-config.yaml

@@ -1,23 +1,66 @@
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    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
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.4.2
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
   - repo: https://github.com/MarcoGorelli/absolufy-imports
     rev: v0.3.1
     hooks:
       - id: absolufy-imports
         name: absolufy-imports
-  - repo: https://github.com/psf/black
-    rev: 23.12.1
-    hooks:
-      - id: black
-        language_version: python3
-        args:
-          - --target-version=py38
+
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.14
+    rev: v0.8.4
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.10.0.1"
+    hooks:
+      - id: shellcheck
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.23
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.30.0"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.14.0
     hooks:
       - id: mypy
         additional_dependencies:

.readthedocs.yaml

@@ -9,9 +9,9 @@ conda:
   environment: ci/requirements-docs.yml
 
 python:
-   install:
-      - method: pip
-        path: .
+  install:
+    - method: pip
+      path: .
 
 sphinx:
   builder: html

README.md

@@ -1,5 +1,5 @@
-xarray_extras
-=============
+# xarray_extras
+
 [![doc-badge](https://github.com/crusaderky/xarray_extras/actions/workflows/docs.yml/badge.svg)](https://github.com/crusaderky/xarray_extras/actions)
 [![pre-commit-badge](https://github.com/crusaderky/xarray_extras/actions/workflows/pre-commit.yml/badge.svg)](https://github.com/crusaderky/xarray_extras/actions)
 [![pytest-badge](https://github.com/crusaderky/xarray_extras/actions/workflows/pytest.yml/badge.svg)](https://github.com/crusaderky/xarray_extras/actions)

doc/_static/style.css

@@ -1,15 +1,15 @@
 @import url("theme.css");
 
-.wy-side-nav-search>a img.logo,
-.wy-side-nav-search .wy-dropdown>a img.logo {
-  width: 12rem
+.wy-side-nav-search > a img.logo,
+.wy-side-nav-search .wy-dropdown > a img.logo {
+  width: 12rem;
 }
 
 .wy-side-nav-search {
   background-color: #eee;
 }
 
-.wy-side-nav-search>div.version {
+.wy-side-nav-search > div.version {
   display: none;
 }
 

doc/_templates/layout.html

@@ -1,2 +1,2 @@
-{% extends "!layout.html" %}
-{% set css_files = css_files + ["_static/style.css"] %}
+{% extends "!layout.html" %} {% set css_files = css_files +
+["_static/style.css"] %}

doc/api/sort.rst

@@ -9,7 +9,7 @@ sort
 
 An example that uses all of the above functions is *source attribution*.
 Given a generic function :math:`y = f(x_{0}, x_{1}, ..., x_{i})`, which is
-embarassingly parallel along a given dimension, one wants to find:
+embarrassingly parallel along a given dimension, one wants to find:
 
 - the top k elements of y along the dimension
 - the elements of all x's that generated the top k elements of y
@@ -20,7 +20,7 @@ embarassingly parallel along a given dimension, one wants to find:
     >>> from xarray_extras.sort import *
     >>> x = DataArray([[5, 3, 2, 8, 1],
     >>>                [0, 7, 1, 3, 2]], dims=['x', 's'])
-    >>> y = x.sum('x')  # y = f(x), embarassingly parallel among dimension 's'
+    >>> y = x.sum('x')  # y = f(x), embarrassingly parallel among dimension 's'
     >>> y
     <xarray.DataArray (s: 5)>
     array([ 5, 10,  3, 11,  3])

doc/conf.py

@@ -61,7 +61,7 @@
 
 # General information about the project.
 project = "xarray_extras"
-copyright = "2018-%s, xarray_extras Developers" % datetime.datetime.now().year
+copyright = f"2018-{datetime.datetime.now().year}, xarray_extras Developers"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/index.rst

@@ -64,4 +64,4 @@ License
 
 xarray-extras is available under the open source `Apache License`__.
 
-__ http://www.apache.org/licenses/LICENSE-2.0.html
+__ http://www.apache.org/licenses/LICENSE-2.0.html

pyproject.toml

@@ -31,14 +31,16 @@ dynamic = ["version"]
 
 [project.urls]
 Homepage = "https://github.com/crusaderky/xarray_extras"
+"Bug Tracker" = "https://github.com/crusaderky/xarray_extras/issues"
+Changelog = "https://xarray-extras.readthedocs.io/en/latest/whats-new.html"
 
 [project.readme]
 text = "Advanced / experimental algorithms for xarray"
 content-type = "text/x-rst"
 
 [tool.setuptools]
 packages = ["xarray_extras"]
-zip-safe = false  # https://mypy.readthedocs.io/en/latest/installed_packages.html
+zip-safe = false # https://mypy.readthedocs.io/en/latest/installed_packages.html
 include-package-data = true
 
 [tool.setuptools_scm]
@@ -72,6 +74,8 @@ filterwarnings = [
     # FIXME these need to be looked at
     'ignore:.*will no longer be implicitly promoted:FutureWarning',
     'ignore:.*updating coordinate .* with a PandasMultiIndex would leave the multi-index level coordinates .* in an inconsistent state:FutureWarning',
+    # xarray vs. pandas upstream
+    'ignore:Converting non-nanosecond precision datetime:UserWarning',
 ]
 
 [tool.coverage.report]
@@ -88,27 +92,52 @@ exclude_lines = [
     '@(numba\.)?guvectorize',
 ]
 
+[tool.codespell]
+ignore-words-list = ["ND"]
+
 [tool.ruff]
-builtins = ["ellipsis"]
 exclude = [".eggs"]
 target-version = "py38"
 
 [tool.ruff.lint]
 ignore = [
-  "E402",  # module level import not at top of file
-  "SIM108",  # use ternary operator instead of if-else block
+  "EM101",    # Exception must not use a string literal, assign to variable first
+  "EM102",    # Exception must not use an f-string literal, assign to variable first
+  "N802",     # Function name should be lowercase
+  "N803",     # Argument name should be lowercase
+  "N806",     # Variable should be lowercase
+  "N816",     # Variable in global scope should not be mixedCase
+  "PD901",    # Avoid using the generic variable name `df` for DataFrames
+  "PT006",    # Wrong type passed to first argument of `pytest.mark.parametrize`; expected `tuple`
+  "PLC0414",  # Import alias does not rename original package
+  "PLR0912",  # Too many branches
+  "PLR0913",  # Too many arguments in function definition
+  "PLR2004",  # Magic value used in comparison, consider replacing `123` with a constant variable
+  "PLW2901",  # for loop variable overwritten by assignment target
+  "SIM108",   # Use ternary operator instead of if-else block
 ]
 select = [
-  "F",    # Pyflakes
+  "YTT",  # flake8-2020
   "B",    # flake8-bugbear
   "C4",   # flake8-comprehensions
-  "ISC",  # flake8-implicit-str-concat
+  "EM",   # flake8-errmsg
+  "EXE",  # flake8-executable
+  "ICN",  # flake8-import-conventions
+  "G",    # flake8-logging-format
+  "PIE",  # flake8-pie
+  "PT",   # flake8-pytest-style
+  "RET",  # flake8-return
   "SIM",  # flake8-simplify
-  "E",    # Pycodestyle
-  "W",    # Pycodestyle
+  "ARG",  # flake8-unused-arguments
   "I",    # isort
+  "NPY",  # NumPy specific rules
   "N",    # pep8-naming
-  "UP",   # Pyupgrade
+  "E",    # Pycodestyle
+  "W",    # Pycodestyle
+  "PGH",  # pygrep-hooks
+  "F",    # Pyflakes
+  "PL",   # pylint
+  "UP",   # pyupgrade
   "RUF",  # unused-noqa
   "EXE001",  #  Shebang is present but file is not executable
 ]
@@ -117,9 +146,9 @@ select = [
 known-first-party = ["xarray_extras"]
 
 [tool.mypy]
-allow_incomplete_defs = false
-allow_untyped_decorators = false
-allow_untyped_defs = false
+disallow_incomplete_defs = true
+disallow_untyped_decorators = true
+disallow_untyped_defs = true
 ignore_missing_imports = true
 no_implicit_optional = true
 show_error_codes = true
@@ -129,4 +158,4 @@ warn_unreachable = true
 
 [[tool.mypy.overrides]]
 module = ["*.tests.*"]
-allow_untyped_defs = true
+disallow_untyped_defs = false