chore: finalize pre-commit cleanup with spelling suppressions and formatting

Author: kwagoner94

.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]

.codespell/ignore_lines.txt

@@ -1,2 +1,12 @@
 ;; Please include filenames and explanations for each ignored line.
 ;; See https://docs.openverse.org/meta/codespell.html for docs.
+src/diffpy/structure/parsers/p_discus.py:.*DISCUS.*          ;; DISCUS is a valid software/tool name
+src/diffpy/structure/parsers/p_discus.py:.*discus.*          ;; Same reason as above, lowercase version
+src/diffpy/structure/parsers/p_pdb.py:.*CONECT.*             ;; CONECT is a valid PDB record name
+src/diffpy/structure/parsers/p_xcfg.py:.*Te.*                ;; Te is the chemical symbol for Tellurium
+src/diffpy/structure/parsers/p_xcfg.py:.*Nd.*                ;; Nd is the chemical symbol for Neodymium
+src/diffpy/structure/parsers/p_xcfg.py:.*BU.*                ;; BU is used in the file with intended meaning
+src/diffpy/structure/parsers/parser_index_mod.py:.*Discus.*  ;; Capitalized variant
+src/diffpy/structure/parsers/parser_index_mod.py:.*discus.*  ;; lowercase variant
+tests/test_loadstructure.py:.*discus.*                       ;; test file with valid usage
+tests/test_p_discus.py:.*discus.*                            ;; test file with valid usage

.flake8

@@ -1,3 +1,5 @@
+# As of now, flake8 does not natively support configuration via pyproject.toml
+# https://github.com/microsoft/vscode-flake8/issues/135
 [flake8]
 exclude =
     .git,

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -12,7 +12,7 @@ assignees: ""
 - [ ] All the badges on the README are passing.
 - [ ] License information is verified as correct. If you are unsure, please comment below.
 - [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
-  missing), tutorials, and other human written text is up-to-date with any changes in the code.
+      missing), tutorials, and other human written text is up-to-date with any changes in the code.
 - [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) are updated.
 - [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
 - [ ] Grammar and writing quality are checked (no typos).
@@ -31,5 +31,5 @@ version information and details about the pre-release here:
 
 <!-- Before closing this issue, please complete the following: -->
 
-- [ ]  Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
-- [ ]  Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.
+- [ ] Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
+- [ ] Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.

.github/workflows/build-wheel-release-upload.yml

@@ -4,7 +4,7 @@ on:
   workflow_dispatch:
   push:
     tags:
-      - '*'  # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
+      - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 
 jobs:
   release:

.github/workflows/check-news-item.yml

@@ -3,7 +3,7 @@ name: Check for News
 on:
   pull_request_target:
     branches:
-    - main
+      - main
 
 jobs:
   build:

.isort.cfg

@@ -1,4 +1,5 @@
 [settings]
+# Keep import statement below line_length character limit
 line_length = 115
 multi_line_output = 3
 include_trailing_comma = True

.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
@@ -44,3 +44,28 @@ repos:
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        args:
+          - "--ignore-words=.codespell/ignore_words.txt"
+          - "--ignore-regex"
+          - "(?i)\\b(discus|conect|te|nd|bu)\\b"
+        exclude: .*/\.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]

CHANGELOG.rst

@@ -28,7 +28,7 @@ Release Notes
 **Fixed:**
 
 * Add getting started section and re-arrange install success check instructions
-* Added termial script for transtru app in pyproject.toml
+* Added terminal script for transtru app in pyproject.toml
 * Changed requires-python to align with classifiers
 
 

README.rst

@@ -132,7 +132,7 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
 
 Acknowledgement
 ---------------