style: update pre-commit and auto fix (#246)

* update pre-commit with autofix

* add news

* conflicts to be reverted

---------

Co-authored-by: Simon Billinge <[email protected]>

Author: Tieqiong

Diff for: .codecov.yml

@@ -1,14 +1,14 @@
 coverage:
   status:
-    project:  # more options at https://docs.codecov.com/docs/commit-status
+    project: # more options at https://docs.codecov.com/docs/commit-status
       default:
         target: auto # use the coverage from the base commit, fail if coverage is lower
-        threshold: 0%  # allow the coverage to drop by
+        threshold: 0% # allow the coverage to drop by
 
 comment:
   layout: " diff, flags, files"
   behavior: default
   require_changes: false
-  require_base: false  # [true :: must have a base report to post]
-  require_head: false  # [true :: must have a head report to post]
+  require_base: false # [true :: must have a base report to post]
+  require_head: false # [true :: must have a head report to post]
   hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage]

Diff for: .pre-commit-config.yaml

@@ -1,14 +1,14 @@
 default_language_version:
-    python: python3
+  python: python3
 ci:
-    autofix_commit_msg: |
-        [pre-commit.ci] auto fixes from pre-commit hooks
-    autofix_prs: true
-    autoupdate_branch: 'pre-commit-autoupdate'
-    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-    autoupdate_schedule: monthly
-    skip: [no-commit-to-branch]
-    submodules: false
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit hooks
+  autofix_prs: true
+  autoupdate_branch: "pre-commit-autoupdate"
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
+  autoupdate_schedule: monthly
+  skip: [no-commit-to-branch]
+  submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
@@ -47,6 +47,20 @@ repos:
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
-    - id: codespell
-      additional_dependencies:
-        - tomli
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  # prettier - multi formatter for .json, .yml, and .md files
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - "prettier@^3.2.4"
+  # docformatter - PEP 257 compliant docstring formatter
+  - repo: https://github.com/s-weigand/docformatter
+    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]

Diff for: doc/manual/extractEquations.py

@@ -37,6 +37,7 @@
 
 def loadEquations():
     """Search for equation codes preceded by @EquationMark macro.
+
     Store equation codes in rc['eqns'].
     """
     lines = []
@@ -116,6 +117,7 @@ def convertToPNG(texfile):
 
 def getBoundingBox(psfilename):
     """Run ghostscript to obtain effective bounding box of psfilename.
+
     Return a list of bounding box coordinates.
     """
     cmd = "gs -dNOPAUSE -dBATCH -q -sDEVICE=bbox %r" % psfilename
@@ -132,6 +134,7 @@ def getBoundingBox(psfilename):
 
 def getPageBoundingBox(psfilename):
     """Obtain bounding box value defined in psfilename.
+
     Return a list of bounding box coordinates.
     """
     import re

Diff for: doc/manual/fixHTMLCode.py

@@ -25,7 +25,7 @@
 
 
 def eqreplace(mx):
-    """helper function to replace equation marks.
+    """Helper function to replace equation marks.
 
     mx -- regular expression match object
 
@@ -41,6 +41,7 @@ def eqreplace(mx):
 
 def replaceEquationMarks(s):
     """Replace equation marks in given string.
+
     Return modified string.
     """
     s1 = re.sub(eqmark, eqreplace, s)