Add pre-commit config with pre-commit-hooks (#3283)

Adding a .pre-commit-config.yaml file with some pre-commit hooks
(check-added-large-files, check-yaml, end-of-file-fixer, trailing-whitespace,
forbid-crlf, remove-crlf, chmod).

* Add .pre-commit-config.yaml to MAINIFEST.in
* Add forbid-crlf, remove-crlf and chmod hooks, remove from GitHub Actions
* Add `pre-commit run --all-files` to `make format`
* Add pre-commit to Style Checks and format-command workflows
* Update note on style_checks.yaml to mention ruff+pre-commit is ran
* Mention that pre-commit is used to enforce LF ending and 644 permissions

---------

Co-authored-by: Dongdong Tian <[email protected]>

.github/workflows/format-command.yml

@@ -32,16 +32,13 @@ jobs:
  # Install formatting tools
  - name: Install formatting tools
  run: |
- python -m pip install ruff
+ python -m pip install ruff pre-commit
  python -m pip list
- sudo apt-get install dos2unix
 
  # Run "make format" and commit the change to the PR branch
  - name: Commit to the PR branch if any changes
  run: |
  make format
- git ls-files -z | xargs -0 dos2unix --quiet
- git ls-files -z | xargs -0 chmod 644
  if [[ $(git ls-files -m) ]]; then
  git config --global user.name 'actions-bot'
  git config --global user.email '[email protected]'

.github/workflows/style_checks.yaml

@@ -34,18 +34,13 @@ jobs:
 
  - name: Install packages
  run: |
- python -m pip install ruff
+ python -m pip install ruff pre-commit
  python -m pip list
- sudo apt-get install dos2unix
 
- - name: Formatting check (ruff)
- run: make check
-
- - name: Ensure files use UNIX line breaks and have 644 permission
+ - name: Formatting check (ruff + pre-commit)
  run: |
- git ls-files -z | xargs -0 dos2unix --quiet
- git ls-files -z | xargs -0 chmod 644
- if [[ $(git ls-files -m) ]]; then git --no-pager diff HEAD; exit 1; fi
+ make check
+ pre-commit run --all-files
 
  - name: Ensure example scripts have at least one code block separator
  run: |

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.6.0
+ hooks:
+ - id: check-added-large-files
+ - id: check-yaml
+ - id: end-of-file-fixer
+ - id: trailing-whitespace
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+ rev: v1.5.5
+ hooks:
+ - id: forbid-crlf
+ - id: remove-crlf
+ - id: chmod
+ args: ['644']

CODE_OF_CONDUCT.md

@@ -1,2 +1,2 @@
 All participants in the PyGMT community must abide by
-the [Generic Mapping Tools organization Code of Conduct](https://github.com/GenericMappingTools/.github/blob/main/CODE_OF_CONDUCT.md).
+the [Generic Mapping Tools organization Code of Conduct](https://github.com/GenericMappingTools/.github/blob/main/CODE_OF_CONDUCT.md).

MANIFEST.in

@@ -6,6 +6,7 @@ prune examples*
 prune pygmt/tests*
 exclude .dvcignore
 exclude .gitignore
+exclude .pre-commit-config.yaml
 exclude .readthedocs.yaml
 exclude AUTHORSHIP.md
 exclude CODE_OF_CONDUCT.md

Makefile

@@ -61,6 +61,7 @@ test_no_images: _runtest
 format:
  ruff check --fix --exit-zero $(FORMAT_FILES)
  ruff format $(FORMAT_FILES)
+ pre-commit run --all-files
 
 check:
  ruff check $(FORMAT_FILES)

doc/_templates/autosummary/class.rst

@@ -30,4 +30,3 @@
 .. raw:: html
 
  <div style='clear:both'></div>
-

doc/_templates/autosummary/exception.rst

@@ -8,4 +8,3 @@
 .. raw:: html
 
  <div style='clear:both'></div>
-

doc/_templates/autosummary/function.rst

@@ -10,4 +10,3 @@
 .. raw:: html
 
  <div style='clear:both'></div>
-

doc/changes.md

@@ -7,9 +7,9 @@
 ### Highlights
 
 * 🎉 **Twelfth minor release of PyGMT** 🎉
-* 🚀 Almost all module wrappers (with a few exceptions) now use in-memory GMT *virtual files* instead of intermediate temporary files to improve performance ([#2730](https://github.com/GenericMappingTools/pygmt/issues/2730)) 
+* 🚀 Almost all module wrappers (with a few exceptions) now use in-memory GMT *virtual files* instead of intermediate temporary files to improve performance ([#2730](https://github.com/GenericMappingTools/pygmt/issues/2730))
 * Almost all module wrappers (with a few exceptions) now have consistent behavior for table-like output ([#1318](https://github.com/GenericMappingTools/pygmt/issues/1318))
-* Adopt [SPEC 0](https://scientific-python.org/specs/spec-0000/) policy for minimum supported versions of GMT, Python, and other core dependencies 
+* Adopt [SPEC 0](https://scientific-python.org/specs/spec-0000/) policy for minimum supported versions of GMT, Python, and other core dependencies
 
 ### Enhancements
 

doc/contributing.md

@@ -481,8 +481,8 @@ the code yourself. Before committing, run it to automatically format your code:
 make format
 ```
 
-For consistency, we also use UNIX-style line endings (`\n`) and file permission
-644 (`-rw-r--r--`) throughout the whole project.
+For consistency, we also use `pre-commit` hooks to enforce UNIX-style line endings
+(`\n`) and file permission 644 (`-rw-r--r--`) throughout the whole project.
 Don't worry if you forget to do it. Our continuous integration systems will
 warn us and you can make a new commit with the formatted code.
 Even better, you can just write `/format` in the first line of any comment in a

doc/team.md

@@ -116,4 +116,3 @@ year will be moved to Distinguished Contributors.
 ::::
 
 :::::
-

environment.yml

@@ -25,6 +25,7 @@ dependencies:
  - pip
  # Dev dependencies (style checks)
  - codespell
+ - pre-commit
  - ruff>=0.3.0
  # Dev dependencies (unit testing)
  - matplotlib-base

examples/projections/README.txt

@@ -2,7 +2,7 @@ Projections
 ===========
 
 PyGMT supports many map projections. Use the ``projection`` parameter to specify which
-one you want to use in all plotting methods. The projection is specified by a one-letter 
+one you want to use in all plotting methods. The projection is specified by a one-letter
 code along with (sometimes optional) reference longitude and latitude and the
 width of the map (for example, **A**\ *lon0/lat0*\ [*/horizon*\ ]\ */width*). The map
 height is determined based on the region and projection.

pygmt/tests/data/contours.txt

@@ -5,4 +5,4 @@
 600 A
 700 C
 800 A
-900 C
+900 C