Accepting Ruff, MyPy, NumPydoc pre-commit checks (#288)

* add checks and exceptions

* remove .flake8 file

* add citations to ignored checks

* review comments and rerun repo review

* add extra links

Author: HGWright

.flake8

@@ -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/ISSUE_TEMPLATE/bug-report.md

@@ -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/ci-wheels.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

.github/workflows/stale.yml

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

.gitignore

@@ -1,8 +1,11 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+# See https://pre-commit.ci/#configuration
+# See https://github.com/scientific-python/cookie#sp-repo-review
 
 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 +21,43 @@ 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 +68,28 @@ 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]

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 BSD 3-Clause License
-Copyright (c) 2015 - 2017, Met Office. 
+Copyright (c) 2015 - 2024, 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.
-

LICENSE

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