Update pre-commit

To use the local and GHA version in cdcgov/cfa-gam-rt. These use the
cache to run much faster. They also auto-commit changes when running,
allowing for auto-formatting when accepting suggestions in PRs.

.github/workflows/pre-commit.yaml

@@ -1,14 +1,37 @@
 name: pre-commit
-
 on:
   pull_request:
   push:
-    branches: [main]
-
+    branches: [main, prod]
 jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
-    - uses: ./.github/actions/pre-commit
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/R/renv
+        key: r-precommit-cache|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
+    - name: Run pre-commit
+      uses: pre-commit/[email protected]
+    - name: Commit files
+      if: failure() && startsWith(github.ref, 'refs/heads')
+      run: |
+          if [[ `git status --porcelain --untracked-files=no` ]]; then
+            git config --local user.email "github-actions[bot]@users.noreply.github.com"
+            git config --local user.name "github-actions[bot]"
+            git checkout -- .github/workflows
+            git commit -m "pre-commit" -a
+          fi
+    - name: Push changes
+      if: failure() && startsWith(github.ref, 'refs/heads')
+      uses: ad-m/github-push-action@master
+      with:
+         github_token: ${{ secrets.GITHUB_TOKEN }}
+         branch: ${{ github.ref }}
+    env:
+      RENV_CONFIG_CACHE_ENABLED: FALSE

.pre-commit-config.yaml

@@ -3,27 +3,36 @@
 repos:
 # R
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3
+    rev: v0.4.2
     hooks:
     -   id: style-files
-        args: [--style_pkg=styler, --style_fun=tidyverse_style]    
+        args: [--style_pkg=styler, --style_fun=tidyverse_style,
+               --cache-root=styler-perm]
+    -   id: roxygenize
     -   id: use-tidy-description
     -   id: lintr
     -   id: readme-rmd-rendered
     -   id: parsable-R
     -   id: no-browser-statement
     -   id: no-print-statement
+        exclude: '^tests/testthat/test-print\.R$'
     -   id: no-debug-statement
     -   id: deps-in-desc
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
-    hooks: 
+    hooks:
     -   id: check-added-large-files
         args: ['--maxkb=200']
     -   id: file-contents-sorter
         files: '^\.Rbuildignore$'
     -   id: end-of-file-fixer
-        exclude: '\.Rd'
+        exclude: '(\.Rd)|(tests/testthat/_snaps/)'
+    -   id: check-yaml
+    -   id: check-toml
+    -   id: mixed-line-ending
+        args: ['--fix=lf']
+    -   id: trailing-whitespace
+        exclude: 'tests/testthat/_snaps/'
 -   repo: https://github.com/pre-commit-ci/pre-commit-ci-config
     rev: v1.6.1
     hooks:
@@ -38,6 +47,40 @@ repos:
         files: '\.(Rhistory|RData|Rds|rds)$'
         # `exclude: <regex>` to allow committing specific files
 #####
+# Python
+-   repo: https://github.com/psf/black
+    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: 5.13.2
+    hooks:
+    -   id: isort
+        args: ['--profile', 'black',
+               '--line-length', '79']
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.2
+  hooks:
+    - id: ruff
+#####
+# Java
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.13.0
+  hooks:
+  - id: pretty-format-java
+    args: [--aosp,--autofix]
+#####
+# Julia
+# Due to lack of first-class Julia support, this needs Julia local install
+#   and JuliaFormatter.jl installed in the library
+# - repo: https://github.com/domluna/JuliaFormatter.jl
+#   rev: v1.0.39
+#   hooks:
+#   - id: julia-formatter
+#####
 # Secrets
 -   repo: https://github.com/Yelp/detect-secrets
     rev: v1.4.0