Expand Pre-Commit Utilities

.gitignore

@@ -1,6 +1,6 @@
 ################################################################################
 # PYTHON GITIGNORE TEMPLATE
-# (https://github.com/github/gitignore/) (2024-10-03)
+# (https://github.com/github/gitignore/blob/main/Python.gitignore) (2024-10-03)
 ################################################################################
 
 # Byte-compiled / optimized / DLL files
@@ -480,6 +480,166 @@ TSWLatexianTemp*
 # Uncomment the next line to have this generated file ignored.
 #*Notes.bib
 
+
+################################################################################
+# R GITIGNORE TEMPLATE
+# (https://github.com/github/gitignore/blob/main/R.gitignore) (2024-12-05)
+################################################################################
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/
+
+
+################################################################################
+# JULIA GITIGNORE TEMPLATE
+# (https://github.com/github/gitignore/blob/main/Julia.gitignore) (2024-12-05)
+################################################################################
+
+# Files generated by invoking Julia with --code-coverage
+*.jl.cov
+*.jl.*.cov
+
+# Files generated by invoking Julia with --track-allocation
+*.jl.mem
+
+# System-specific files and directories generated by the BinaryProvider and BinDeps packages
+# They contain absolute paths specific to the host computer, and so should not be committed
+deps/deps.jl
+deps/build.log
+deps/downloads/
+deps/usr/
+deps/src/
+
+# Build artifacts for creating documentation generated by the Documenter package
+docs/build/
+docs/site/
+
+# File generated by Pkg, the package manager, based on a corresponding Project.toml
+# It records a fixed state of all packages used by the project. As such, it should not be
+# committed for packages, but should be committed for applications that require a static
+# environment.
+Manifest.toml
+
+
+################################################################################
+# GITHUB PAGES GITIGNORE TEMPLATE
+# (https://github.com/github/gitignore/blob/main/GitHubPages.gitignore) (2024-12-05)
+################################################################################
+
+# This .gitignore is appropriate for repositories deployed to GitHub Pages and using
+# a Gemfile as specified at https://github.com/github/pages-gem#conventional
+
+# Basic Jekyll gitignores (synchronize to Jekyll.gitignore)
+_site/
+.sass-cache/
+.jekyll-cache/
+.jekyll-metadata
+
+# Additional Ruby/bundler ignore for when you run: bundle install
+/vendor
+
+# Specific ignore for GitHub Pages
+# GitHub Pages will always use its own deployed version of pages-gem
+# This means GitHub Pages will NOT use your Gemfile.lock and therefore it is
+# counterproductive to check this file into the repository.
+# Details at https://github.com/github/pages-gem/issues/768
+Gemfile.lock
+
+################################################################################
+# SASS GITIGNORE TEMPLATE
+# (https://github.com/github/gitignore/blob/main/Sass.gitignore) (2024-12-05)
+################################################################################
+
+.sass-cache/
+*.css.map
+*.sass.map
+*.scss.map
+
+################################################################################
+# C++ GITIGNORE TEMPLATE
+# (https://github.com/github/gitignore/blob/main/C%2B%2B.gitignore) (2024-12-05)
+################################################################################
+
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
 ################################################################################
 # MISCELLANEOUS
 ################################################################################
@@ -492,3 +652,6 @@ _site
 _freeze
 .DS_Store
 DS_Store
+_book/
+_book
+author_emails.txt

.lintr

@@ -0,0 +1,2 @@
+linters: linters_with_defaults(object_usage_linter = NULL)
+encoding: "UTF-8"

.pre-commit-config.yaml

@@ -1,18 +1,70 @@
+################################################################################
+# OVERVIEW
+################################################################################
+# The following contains the pre-commit hooks for this repository, which are
+# likely a modified version of the author's (AFg6K7h4fhy2) repository template.
+#
+# Links:
+#
+# Pre-commit: https://pre-commit.com/
+# The author's template: https://github.com/AFg6K7h4fhy2/AFg6K7h4fhy2-Template
+# Supported hooks: https://github.com/pre-commit/pre-commit-hooks
 repos:
 ################################################################################
 # GENERAL
 ################################################################################
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
+    # prevent giant files from being committed.
     -   id: check-added-large-files
         args: ["--maxkb=10000"]
+    # simply check whether files parse as valid
+    # python
+    -   id: check-ast
+    # check for files with names that would
+    # conflict on a case-insensitive filesystem
+    # like MacOS HFS+ or Windows FAT.
+    -   id: check-case-conflict
+    # checks for a common error of placing
+    # code before the docstring.
+    -   id: check-docstring-first
+    # attempts to load all yaml files to
+    # verify syntax.
     -   id: check-yaml
+        # allow yaml files which use the
+        # multi-document syntax
         args: ["--allow-multiple-documents"]
+    # attempts to load all TOML files to
+    # verify syntax.
     -   id: check-toml
+    # makes sure files end in a newline and
+    # only a newline.
     -   id: end-of-file-fixer
+    # replaces or checks mixed line ending.
     -   id: mixed-line-ending
+    # verifies that test files are named
+    # correctly.
+    -   id: name-tests-test
+        # ensure tests match test_.*\.py
+        args: ["--pytest-test-first"]
+    # checks that all your JSON files are pretty.
+    # "Pretty" here means that keys are sorted
+    # and indented.
+    -   id: pretty-format-json
+        # automatically format json files;
+        # when autofixing, retain the original
+        # key ordering (instead of sorting
+        # the keys)
+        args: ["--autofix", "--no-sort-keys"]
+    # trims trailing whitespace.
     -   id: trailing-whitespace
+    # checks that non-binary executables have
+    # a proper shebang.
+    -   id: check-executables-have-shebangs
+        files: \.sh$
+    # checks for the existence of private keys.
+    -   id: detect-private-key
 ################################################################################
 # PYTHON
 ################################################################################
@@ -28,10 +80,44 @@ repos:
     -   id: isort
         args: ["--profile", "black", "--line-length", "79"]
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.8.2
     hooks:
       - id: ruff
         args: ["--ignore=E741", "--ignore=E731", "--fix"]
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.13.0
+    hooks:
+      - id: mypy
+################################################################################
+# R
+################################################################################
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.3.9003
+    hooks:
+    -   id: style-files
+    -   id: lintr
+################################################################################
+# MAKE FILES
+################################################################################
+-   repo: https://github.com/mrtazz/checkmake.git
+    rev: 0.2.2
+    hooks:
+    -   id: checkmake
+################################################################################
+# SECURITY
+################################################################################
+# -   repo: https://github.com/gitleaks/gitleaks
+#     rev: v8.19.0
+#     hooks:
+#     -   id: gitleaks
+-   repo: https://github.com/Yelp/detect-secrets
+    rev: v1.5.0
+    hooks:
+    # must first run
+    # detect-secrets scan > .secrets.baseline
+    -   id: detect-secrets
+        args: ["--baseline", ".secrets.baseline"]
+        exclude: package.lock.json
 ################################################################################
 # GITHUB ACTIONS
 ################################################################################
@@ -43,7 +129,7 @@ repos:
 # SPELLING
 ################################################################################
 -   repo: https://github.com/crate-ci/typos
-    rev: v1.28.1
+    rev: typos-dict-v0.11.37
     hooks:
     -   id: typos
         args: ["--force-exclude"]
@@ -54,4 +140,8 @@ repos:
     rev: v4.0.0
     hooks:
     -   id: commitizen
+-   repo: https://github.com/jorisroovers/gitlint
+    rev:  v0.19.1
+    hooks:
+    -   id: gitlint
 ################################################################################