From 3a494736a5d4209f07c95fd6fc3e1f56c42f7038 Mon Sep 17 00:00:00 2001
From: Zachary Susswein <utb2@cdc.gov>
Date: Tue, 6 Aug 2024 20:46:27 +0000
Subject: [PATCH] Use R specific pre-commit

---
 .pre-commit-config.yaml | 61 ++++++++++++++++++++++++++++-------------
 1 file changed, 42 insertions(+), 19 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 05457317..237d474c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,45 +1,66 @@
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
-#####
-# Basic file cleanliness
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+# R
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.2
     hooks:
+    -   id: style-files
+        args: [--style_pkg=styler, --style_fun=tidyverse_style]    
+    -   id: roxygenize
+    -   id: use-tidy-description
+    -   id: lintr
+    -   id: readme-rmd-rendered
+    -   id: parsable-R
+    -   id: no-browser-statement
+    -   id: no-print-statement
+    -   id: no-debug-statement
+    -   id: deps-in-desc
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks: 
     -   id: check-added-large-files
-    -   id: check-yaml
-    -   id: check-toml
+        args: ['--maxkb=200']
+    -   id: file-contents-sorter
+        files: '^\.Rbuildignore$'
     -   id: end-of-file-fixer
-    -   id: mixed-line-ending
-    -   id: trailing-whitespace
+        exclude: '\.Rd'
+-   repo: https://github.com/pre-commit-ci/pre-commit-ci-config
+    rev: v1.6.1
+    hooks:
+    # Only required when https://pre-commit.ci is used for config validation
+    -   id: check-pre-commit-ci-config
+-   repo: local
+    hooks:
+    -   id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
+        language: fail
+        files: '\.(Rhistory|RData|Rds|rds)$'
+        # `exclude: <regex>` to allow committing specific files
 #####
 # Python
 -   repo: https://github.com/psf/black
-    rev: 23.10.0
+    rev: 24.4.2
     hooks:
         # if you have ipython notebooks, consider using
         # `black-jupyter` hook instead
     -   id: black
         args: ['--line-length', '79']
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
     -   id: isort
         args: ['--profile', 'black',
                '--line-length', '79']
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.0
+  rev: v0.4.2
   hooks:
     - id: ruff
 #####
-# R
--   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.2
-    hooks:
-    -   id: style-files
-    -   id: lintr
-#####
 # Java
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.11.0
+  rev: v2.13.0
   hooks:
   - id: pretty-format-java
     args: [--aosp,--autofix]
@@ -59,3 +80,5 @@ repos:
     -   id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
         exclude: package.lock.json
+ci:
+    autoupdate_schedule: monthly