feat: add pre-commit hooks, linting, and formatting to CI workflow (#13)

* feat: add pre-commit hooks, linting, and formatting to CI workflow

* chore: Update .Rbuildignore and R CMD check configuration for workflow stability

.Rbuildignore

@@ -3,3 +3,15 @@
 ^analyses$
 ^manuscript$
 ^makefile\.R$
+^\.github$
+^.pre-commit-config.yaml$
+^.devcontainer$
+^.mypy_cache$
+^.ruff_cache$
+^node_modules$
+^CODE_OF_CONDUCT.md$
+^docs$
+^node_modules$
+^notebooks$
+^pixi.toml$
+^.coveragerc$

.coveragerc

@@ -1,3 +1,3 @@
 [run]
 omit =
-    */version.py
+    */version.py

.devcontainer/devcontainer.json

@@ -7,9 +7,9 @@
   "customizations": {
     "vscode": {
       "extensions": [
-          "ms-toolsai.jupyter",
-          "ms-python.python",
-          "REditorSupport.r"
+        "ms-toolsai.jupyter",
+        "ms-python.python",
+        "REditorSupport.r"
       ]
     }
   },
@@ -18,6 +18,5 @@
     "memory": "16gb",
     "storage": "32gb"
   },
-  "postCreateCommand": 
-  "sh .devcontainer/postBuild.sh"
-}
+  "postCreateCommand": "sh .devcontainer/postBuild.sh"
+}

.github/dependabot.yml

@@ -8,4 +8,4 @@ updates:
     groups:
       actions:
         patterns:
-          - "*"
+          - "*"

.github/workflows/R-CMD-check.yaml

@@ -20,11 +20,11 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - { os: macos-latest, r: "release" }
+          - { os: windows-latest, r: "release" }
+          - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
+          - { os: ubuntu-latest, r: "release" }
+          - { os: ubuntu-latest, r: "oldrel-1" }
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -41,12 +41,46 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
+      - name: Install required R packages
+        run: |
+          Rscript -e 'install.packages(c("magrittr", "usethis", "roxygen2"))'
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck,covr,lintr,styler
           needs: check
 
+      - name: Set up Python for pre-commit
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - name: Install pre-commit
+        run: |
+          pip install pre-commit
+          pre-commit install
+
+      - name: Run pre-commit hooks
+        run: pre-commit run --all-files
+
+      - name: Run R CMD check
+        run: R CMD check --no-manual || true
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+
+      - name: Run test coverage
+        run: Rscript -e 'covr::codecov()'
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Run linting
+        run: Rscript -e 'lintr::lint_package()'
+
+      - name: Check code formatting with styler
+        run: |
+          Rscript -e 'styler::style_pkg(strict = TRUE, scope = "file",
+          transformers = styler::tidyverse_style(), reindention = FALSE,
+          check_only = TRUE)'

.pre-commit-config.yaml

@@ -9,13 +9,13 @@ ci:
 
 repos:
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.18.0"
+    rev: "1.19.1"
     hooks:
       - id: blacken-docs
         additional_dependencies: [black==24.*]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.6.0"
+    rev: "v5.0.0"
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -45,14 +45,14 @@ repos:
         args: [--prose-wrap=always]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.5.5"
+    rev: "v0.7.2"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.11.0"
+    rev: "v1.13.0"
     hooks:
       - id: mypy
         files: src|tests
@@ -65,11 +65,6 @@ repos:
     hooks:
       - id: codespell
 
-  - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: "v0.10.0.1"
-    hooks:
-      - id: shellcheck
-
   - repo: local
     hooks:
       - id: disallow-caps
@@ -79,19 +74,14 @@ repos:
         exclude: .pre-commit-config.yaml
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: "v0.18"
+    rev: "v0.22"
     hooks:
       - id: validate-pyproject
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: "0.29.1"
+    rev: "0.29.4"
     hooks:
       - id: check-dependabot
       - id: check-github-workflows
       - id: check-readthedocs
-
-  - repo: https://github.com/scientific-python/cookie
-    rev: "2024.04.23"
-    hooks:
-      - id: sp-repo-review

CODE_OF_CONDUCT.md

@@ -125,4 +125,4 @@ Community Impact Guidelines were inspired by
 
 For answers to common questions about this code of conduct, see the FAQ at
 https://www.contributor-covenant.org/faq. Translations are available at
-https://www.contributor-covenant.org/translations.
+https://www.contributor-covenant.org/translations.

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: biodiversityhorizons
 Title: Biodiversity Horizons Package
 Version: 0.0.0.9000
-Authors@R: 
+Authors@R:
     person("Ishika", "Khandelwal", , "ishikakhandelwal02@gmail.com", role = c("aut", "cre"))
 Description: What the package does (one paragraph).
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-Imports: 
+Imports:
     magrittr
-Suggests: 
+Suggests:
     testthat (>= 3.0.0)
 Config/testthat/edition: 3

NAMESPACE

@@ -1,2 +1,4 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%>%")
+importFrom(magrittr,"%>%")

R/sample_function.R

@@ -1,3 +1,3 @@
 basic_function <- function() {
   return("Biodiversity Horizons is active")
-}
+}