style: using new pcmt

Author: Tieqiong

.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]

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -12,33 +12,34 @@ 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).
 
 Please mention @sbillinge here when you are ready for PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
 
-### PyPI/GitHub  full-release preparation checklist:
+### PyPI/GitHub full-release preparation checklist:
+
 - [ ] Create a new conda environment and install the rc from pypi (`pip install <package-name>=??`)
 - [ ] License information at Pypi is verified as correct.
 - [ ] Docs deployed successfully to `<package-name>.github.io`
 - [ ] Successfully run all tests, tutorial examples or do functional testing
 
-Please let  @sbillinge know that all checks are done and package is ready for full release.
+Please let @sbillinge know that all checks are done and package is ready for full release.
 
 ### conda-forge release preparation checklist:
 
 <!-- After @sbillinge releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
 
 - [ ] Ensure that the full release has appeared on Pypi successfully
 - [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock.
-- [ ] Close any open issues on the feedstock.  Reach out to @bobleesj if you have questions
+- [ ] Close any open issues on the feedstock. Reach out to @bobleesj if you have questions
 - [ ] let @sbillinge and @bobleesj when this is ready
 
 ### Post-release checklist
 
 <!-- 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:
   check-news-item:

.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]

doc/source/examples/Ni_calculation.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+"""Calculate PDF of FCC nickel.
 
-"""Calculate PDF of FCC nickel. Save data to Ni_calculation.cgr and plot it using matplotlib.
+Save data to Ni_calculation.cgr and plot it using matplotlib.
 """
 
 import matplotlib.pyplot as plt

doc/source/examples/Ni_refinement.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-
 """Perform simple refinement of Ni structure to the experimental x-ray PDF.
+
 Save fitted curve, refined structure and results summary.
 """
 

setup.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 # Extensions script for diffpy.pdffit2
-
 """PDFfit2 - real space structure refinement engine
 
 Packages:   diffpy.pdffit2

src/diffpy/__init__.py

@@ -14,7 +14,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """diffpy - tools for structure analysis by diffraction.
 
 Blank namespace package for module diffpy."""

src/diffpy/pdffit2/__init__.py

@@ -14,7 +14,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """PDFfit2 - real space structure refinement program."""
 
 # WARNING: Do NOT remove the isort: off/on comments in this file.