add checks and exceptions

Author: HGWright

.flake8

@@ -23,6 +23,6 @@ ignore =
     W503,
     # W504: line break after binary operator
     W504
-exclude = 
+exclude =
     .eggs
     build

.github/ISSUE_TEMPLATE/bug-report.md

@@ -13,17 +13,17 @@ assignees: ''
 ## How To Reproduce
 Steps to reproduce the behaviour:
 
-1. 
-2. 
-3. 
+1.
+2.
+3.
 
 ## Expected behaviour
 <!-- A clear and concise description of what you expected to happen -->
 
 ## Screenshots
 <!-- If applicable, add screenshots to help explain your problem -->
 
-## Environment 
+## Environment
  - OS & Version: [e.g., Ubuntu 20.04 LTS]
  - Stratify Version
 

.github/workflows/ci-wheels.yml

@@ -76,7 +76,7 @@ jobs:
     - name: "Building sdist"
       shell: bash
       run: |
-        pipx run build --sdist 
+        pipx run build --sdist
 
     - uses: actions/upload-artifact@v4
       with:

.github/workflows/stale.yml

@@ -38,7 +38,7 @@ jobs:
             Otherwise this issue will be automatically closed in ${{ env.DAYS_BEFORE_CLOSE }} days time.
 
           # Comment on the staled prs.
-          stale-pr-message: | 
+          stale-pr-message: |
             In order to maintain a backlog of relevant PRs, we automatically label them as stale after ${{ env.DAYS_BEFORE_STALE }} days of inactivity.
 
             If this PR is still important to you, then please comment on this PR and the stale label will be removed.
@@ -48,15 +48,15 @@ jobs:
           # Comment on the staled issues while closed.
           close-issue-message: |
             This stale issue has been automatically closed due to a lack of community activity.
-            
+
             If you still care about this issue, then please either:
               * Re-open this issue, if you have sufficient permissions, or
               * Add a comment pinging `@SciTools/stratify-maintainers` who will re-open on your behalf.
 
           # Comment on the staled prs while closed.
           close-pr-message: |
             This stale PR has been automatically closed due to a lack of community activity.
-            
+
             If you still care about this PR, then please either:
               * Re-open this PR, if you have sufficient permissions, or
               * Add a comment pinging `@SciTools/stratify-maintainers` who will re-open on your behalf.
@@ -85,4 +85,4 @@ jobs:
           ascending: true
 
           # Exempt all issues/prs with milestones from stale.
-          exempt-all-milestones: true
+          exempt-all-milestones: true

.gitignore

@@ -133,4 +133,4 @@ dmypy.json
 .pyre/
 
 # PyCharm
-.idea
+.idea

.pre-commit-config.yaml

@@ -2,7 +2,8 @@
 # See https://pre-commit.com/hooks.html for more hooks
 
 ci:
-  autoupdate_commit_msg: "chore: update pre-commit hooks"
+    autofix_prs: false
+    autoupdate_commit_msg: "chore: update pre-commit hooks"
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
@@ -18,27 +19,43 @@ repos:
     -   id: check-merge-conflict
         # Check for debugger imports and py37+ `breakpoint()` calls in Python source.
     -   id: debug-statements
+        # Check TOML file syntax.
+    - id: check-toml
+        # Check YAML file syntax.
+    - id: check-yaml
+        # Makes sure files end in a newline and only a newline.
+        # Duplicates Ruff W292 but also works on non-Python files.
+    - id: end-of-file-fixer
+        # Replaces or checks mixed line ending.
+    - id: mixed-line-ending
         # Don't commit to master branch.
     -   id: no-commit-to-branch
--   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: '24.10.0'
+      # Trims trailing whitespace.
+      # Duplicates Ruff W291 but also works on non-Python files.
+    -   id: trailing-whitespace
+
+
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.7.3"
     hooks:
-    -   id: black
+    -   id: ruff
+        types: [file, python]
+        args: [--fix, --show-fixes]
+    -   id: ruff-format
         types: [file, python]
-        args: [--config=./pyproject.toml, .]
--   repo: https://github.com/PyCQA/flake8
-    rev: '7.1.1'
+
+-   repo: https://github.com/codespell-project/codespell
+    rev: "v2.3.0"
     hooks:
-        # Run flake8.
-    -   id: flake8
-        args: [--config=./.flake8]
+    -   id: codespell
+        types_or: [asciidoc, python, markdown, rst]
+        additional_dependencies: [tomli]
+
+
+
 -   repo: https://github.com/pycqa/isort
     rev: '5.13.2'
     hooks:
-    -   id: isort
-        name: isort (python)
-        types: [file, python]
-        args: [--filter-files]
     -   id: isort
         name: isort (cython)
         types: [file, cython]
@@ -49,3 +66,28 @@ repos:
     hooks:
     - id: sort-all
       types: [file, python]
+
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.13.0'
+    hooks:
+    -   id: mypy
+        exclude: 'noxfile\.py|docs/conf\.py'
+
+-   repo: https://github.com/abravalheri/validate-pyproject
+    # More exhaustive than Ruff RUF200.
+    rev: "v0.23"
+    hooks:
+    - id: validate-pyproject
+
+-   repo: https://github.com/scientific-python/cookie
+    rev: 2024.08.19
+    hooks:
+    - id: sp-repo-review
+      additional_dependencies: ["repo-review[cli]"]
+      args: ["--show=errskip"]
+
+-   repo: https://github.com/numpy/numpydoc
+    rev: v1.8.0
+    hooks:
+      - id: numpydoc-validation
+        types: [file, python]

LICENSE

@@ -1,5 +1,5 @@
 BSD 3-Clause License
-Copyright (c) 2015 - 2017, Met Office. 
+Copyright (c) 2015 - 2017, Met Office.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -26,4 +26,3 @@ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-

README.md

@@ -33,4 +33,3 @@ pip install stratify
 
 ## License
 Stratify is licenced under a [BSD 3-Clause License](LICENSE).
-

pyproject.toml

@@ -68,10 +68,10 @@ where = ["src"]
 write_to = "src/stratify/_version.py"
 local_scheme = "dirty-tag"
 
-[tool.black]
-target-version = ["py310", "py311", "py312"]
-line-length = 88
-include = '\.pyi?$'
+#[tool.black]
+#target-version = ["py310", "py311", "py312"]
+#line-length = 88
+#include = '\.pyi?$'
 
 [tool.isort]
 profile = "black"
@@ -88,3 +88,169 @@ ignore = [
 [tool.pytest.ini_options]
 addopts = "-ra -v --doctest-modules"
 testpaths = ["src/stratify"]
+
+[tool.mypy]
+disable_error_code = ["call-arg", "no-untyped-def", "no-untyped-call", "attr-defined", "misc", "index", "var-annotated", "assignment"]
+enable_error_code = ["ignore-without-code", "truthy-bool", "redundant-expr"]
+warn_unreachable = true
+strict = true
+# exclude = [
+    # No common agreement yet
+    # NOTE: these exclusions must also appear in pre-commit-config.yaml.
+    #  https://stackoverflow.com/questions/77350979/running-pre-commits-excluding-a-directory-for-multiples-hooks/77352664#77352664
+# ]
+# NOTE: Non-permanent disabling should be done via the ".mypy.ini" file.
+# disable_error_code = No common agreement yet
+
+[tool.numpydoc_validation]
+checks = [
+    "all",  # Enable all numpydoc validation rules, apart from the following:
+
+    # -> Docstring text (summary) should start in the line immediately
+    #    after the opening quotes (not in the same line, or leaving a
+    #    blank line in between)
+    "GL01",  # Permit summary line on same line as docstring opening quotes.
+
+    # -> Closing quotes should be placed in the line after the last text
+    #    in the docstring (do not close the quotes in the same line as
+    #    the text, or leave a blank line between the last text and the
+    #    quotes)
+    "GL02",  # Permit a blank line before docstring closing quotes.
+
+    # -> Double line break found; please use only one blank line to
+    #    separate sections or paragraphs, and do not leave blank lines
+    #    at the end of docstrings
+    "GL03",  # Ignoring.
+
+    "GL08",
+
+    "PR01",
+    "PR02",
+    "PR10",
+    "RT04",
+    "SS06",
+
+
+    # -> See Also section not found
+    "SA01",  # Not all docstrings require a "See Also" section.
+
+    # -> No extended summary found
+    "ES01",  # Not all docstrings require an "Extended Summary" section.
+
+    # -> No examples section found
+    "EX01",  # Not all docstrings require an "Examples" section.
+
+    # -> No Yields section found
+    "YD01",  # Not all docstrings require a "Yields" section.
+
+    # Record temporarily ignored checks below; will be reviewed at a later date:
+
+]
+exclude = [
+    '\.__eq__$',
+    '\.__ne__$',
+    '\.__repr__$',
+]
+
+[tool.ruff]
+line-length = 88
+
+[tool.ruff.format]
+preview = false
+
+[tool.ruff.lint]
+ignore = [
+    # NOTE: Non-permanent exclusions should be added to the ".ruff.toml" file.
+    "ERA001",
+    "RUF005",
+    "D100",
+    "B028",
+    "D101",
+    "RUF012",
+    "ANN201",
+    "D102",
+    "T201",
+    "C419",
+    "D104",
+    "D106",
+    "ANN202",
+    "SLF001",
+    "N801",
+    "D205",
+    "PT009",
+    "PT027",
+    "ANN001",
+    "ARG002",
+    "ARG003",
+    "ANN002",
+    "ANN204",
+    "D103",
+    "FBT002",
+    "ANN003",
+    "RET504",
+    "C405",
+    "PLR2004",
+
+
+    # flake8-commas (COM)
+    # https://docs.astral.sh/ruff/rules/#flake8-commas-com
+    "COM812",  # Trailing comma missing.
+    "COM819",  # Trailing comma prohibited.
+
+    # flake8-implicit-str-concat (ISC)
+    # https://docs.astral.sh/ruff/rules/single-line-implicit-string-concatenation/
+    # NOTE: This rule may cause conflicts when used with "ruff format".
+    "ISC001",  # Implicitly concatenate string literals on one line.
+    ]
+    preview = false
+    select = [
+        "ALL",
+        # list specific rules to include that is skipped using numpy convention.
+        "D212",  # Multi-line docstring summary should start at the first line
+    ]
+
+[tool.ruff.lint.isort]
+force-sort-within-sections = true
+# Change to match specific package name:
+known-first-party = ["iris"]
+
+[tool.ruff.lint.per-file-ignores]
+# All test scripts
+
+# Change to match specific package path:
+"lib/iris/tests/*.py" = [
+    # https://docs.astral.sh/ruff/rules/undocumented-public-module/
+    "D100",  # Missing docstring in public module
+    "D205",  # 1 blank line required between summary line and description
+    "D401",  # 1 First line of docstring should be in imperative mood
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.codespell]
+ignore-words-list = "ND,Nd"
+
+[tool.repo-review]
+# These are a list of the currently failing tests to be fixed later:
+ignore = [
+    "PY004", # Has docs folder
+    "PP302", # Sets a minimum pytest to at least 6
+    "PP304", # Sets the log level in pytest
+    "PP305", # Specifies xfail_strict
+    "PP306", # Specifies strict config
+    "PP307", # Specifies strict markers
+    "PP308",
+    "PP309", # Filter warnings specified
+    "PY007", # Supports an easy task runner (nox or tox)
+    "PP003", # Does not list wheel as a build-dep
+    "PC111", # Uses blacken-docs
+    "PC140", # Uses a type checker
+    "PC160", # Uses a spell checker
+    "PC170", # Uses PyGrep hooks (only needed if rST present)
+    "PC180", # Uses a markdown formatter
+    "PC190", # Uses Ruff
+    "MY100", # Uses MyPy (pyproject config)
+    "RF001", # Has Ruff config
+    "RTD100" # Uses ReadTheDocs (pyproject config)
+]

requirements/pypi-core.txt

@@ -1,3 +1,3 @@
 Cython
 dask[array]
-numpy==1.26.4
+numpy==1.26.4