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

weiji14 · seisman · web-flow · commit b5242be7cd84 · 2024-06-11T16:25:48.000+12:00
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 &lt;seisman.info@gmail.com&gt;
diff --git a/.github/workflows/format-command.yml b/.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 '58130806+actions-bot@users.noreply.github.com'
diff --git a/.github/workflows/style_checks.yaml b/.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: |
diff --git a/.pre-commit-config.yaml b/.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']
diff --git a/CODE_OF_CONDUCT.md b/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).
diff --git a/MANIFEST.in b/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
diff --git a/Makefile b/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)
diff --git a/doc/_templates/autosummary/class.rst b/doc/_templates/autosummary/class.rst
@@ -30,4 +30,3 @@
 .. raw:: html
 
      <div style='clear:both'></div>
-
diff --git a/doc/_templates/autosummary/exception.rst b/doc/_templates/autosummary/exception.rst
@@ -8,4 +8,3 @@
 .. raw:: html
 
      <div style='clear:both'></div>
-
diff --git a/doc/_templates/autosummary/function.rst b/doc/_templates/autosummary/function.rst
@@ -10,4 +10,3 @@
 .. raw:: html
 
      <div style='clear:both'></div>
-
diff --git a/doc/changes.md b/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
 
diff --git a/doc/contributing.md b/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
diff --git a/doc/team.md b/doc/team.md
@@ -116,4 +116,3 @@ year will be moved to Distinguished Contributors.
 ::::
 
 :::::
-
diff --git a/environment.yml b/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
diff --git a/examples/projections/README.txt b/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.
diff --git a/pygmt/tests/data/contours.txt b/pygmt/tests/data/contours.txt
@@ -5,4 +5,4 @@
 600 A
 700 C
 800 A
-900 C
+900 C

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`All participants in the PyGMT community must abide by`
`2`		`-the [Generic Mapping Tools organization Code of Conduct](https://github.com/GenericMappingTools/.github/blob/main/CODE_OF_CONDUCT.md).`
	`2`	`+the [Generic Mapping Tools organization Code of Conduct](https://github.com/GenericMappingTools/.github/blob/main/CODE_OF_CONDUCT.md).`
Original file line number	Diff line number	Diff line change
`@@ -30,4 +30,3 @@`
`30`	`30`	`.. raw:: html`
`31`	`31`
`32`	`32`	`<div style='clear:both'></div>`
`33`		`-`
Original file line number	Diff line number	Diff line change
`@@ -8,4 +8,3 @@`
`8`	`8`	`.. raw:: html`
`9`	`9`
`10`	`10`	`<div style='clear:both'></div>`
`11`		`-`
Original file line number	Diff line number	Diff line change
`@@ -10,4 +10,3 @@`
`10`	`10`	`.. raw:: html`
`11`	`11`
`12`	`12`	`<div style='clear:both'></div>`
`13`		`-`