Update pre-commit

.github/workflows/pr-commands.yaml

@@ -8,7 +8,7 @@ name: Commands
 
 jobs:
   document:
-    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') || github.event.comment.author_association == 'CONTRIBUTOR') && startsWith(github.event.comment.body, '/document') }}
     name: document
     runs-on: ubuntu-latest
     env:
@@ -45,7 +45,7 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
   style:
-    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') || github.event.comment.author_association == 'CONTRIBUTOR') && startsWith(github.event.comment.body, '/style') }}
     name: style
     runs-on: ubuntu-latest
     env:

.pre-commit-config.yaml

@@ -6,24 +6,33 @@ repos:
     rev: v0.4.3
     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
@@ -46,4 +89,13 @@ repos:
         args: ['--baseline', '.secrets.baseline']
         exclude: package.lock.json
 ci:
-    autoupdate_schedule: monthly
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+        for more information, see https://pre-commit.ci
+    autofix_prs: true
+    autoupdate_branch: ''
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: weekly
+    skip: [roxygenize]
+    submodules: false

DESCRIPTION

@@ -17,12 +17,12 @@ Description: Add logging, metadata handling, and data handling
 License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.1
 Suggests:
     testthat (>= 3.0.0),
     withr
 Config/testthat/edition: 3
-Imports: 
+Imports:
     AzureRMR,
     AzureStor,
     cli,

NEWS.md

@@ -1,5 +1,6 @@
 # CFAEpiNow2Pipeline (development version)
 
+* Updated, faster pre-commit checks
 * Azure Blob file download utilities
 * CI running on Ubuntu only & working pkgdown deploy to Github Pages
 * Initial R package with checks running in CI

R/add.R

@@ -1,5 +1,7 @@
 #' A temp function
 #'
+#' Adding some meaningless text to test rendering via PR command.
+#'
 #' @param x A number
 #' @param y Another number
 #' @return Their sum

README.md

@@ -3,7 +3,7 @@
 ## Overview
 
 A lightweight wrapper around [{EpiNow2}](https://github.com/epiforecasts/EpiNow2) to add functionality for deployment in Azure Batch.
-It holds some helper functions to interface with Azure services, convert input data to EpiNow2's expected input format, and save expected outputs. 
+It holds some helper functions to interface with Azure services, convert input data to EpiNow2's expected input format, and save expected outputs.
 It also adds metadata and logging.
 
 This package is meant to enhance the `{EpiNow2}` package to support deployment in CFA's computational environment.