ci: update gha workflows from template repo (#6)

* refactor: load local MOSuite

* Squashed 'code/MOSuite/' content from commit c09ee39

git-subtree-dir: code/MOSuite
git-subtree-split: c09ee39f9b282237f13d88dcf4cdfed965209c68

* ci: update workflows from template

Author: kelly-sovacool

.github/WORDLIST.txt

@@ -3,44 +3,45 @@ name: auto-format
 on:
   workflow_dispatch:
   pull_request:
+    branches: [dev, main]
 
-env:
-  GH_TOKEN: ${{ github.token }}
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 permissions:
   contents: write
   pull-requests: write
 
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
 jobs:
   auto-format:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
-        if: github.event_name == 'pull_request'
+      - name: Generate a token
+        id: generate-token
+        uses: actions/create-github-app-token@v2
         with:
-          fetch-depth: 0
-          ref: ${{ github.head_ref }}
-      - uses: actions/checkout@v4
-        if: github.event_name != 'pull_request'
+          app-id: ${{ vars.CCBR_BOT_APP_ID }}
+          private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
+          owner: ${{ github.repository_owner }}
+
+      - uses: actions/checkout@v7
         with:
-          fetch-depth: 0
-          ref: ${{ github.ref_name }}
+          token: ${{ steps.generate-token.outputs.token }}
+          ref: ${{ github.event_name == 'pull_request' && github.head_ref || github.ref_name }}
 
       - name: git config
         run: |
-          git config --global user.name "github-actions[bot]"
-          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
-
-      - name: Format R code with air
-        uses: rstudio/shiny-workflows/format-r-code@v1
+          git config --global user.name "CCBR-bot"
+          git config --global user.email "258092125+ccbr-bot@users.noreply.github.com"
 
+      - name: format
+        uses: pre-commit/action@v3.0.1
+        continue-on-error: true
       - name: commit & push
+        if: ${{ github.event_name == 'pull_request' }}
         run: |
           git add .
-          git commit -m "ci: 🤖 auto-format" || echo "nothing to commit"
+          git commit -m "ci: 🤖 auto-format with pre-commit" || echo "nothing to commit"
           git push || echo "nothing to push"

.github/workflows/auto-format.yml

@@ -2,15 +2,19 @@ name: tests
 
 on:
   push:
-    branches: [ main, dev ]
+    branches: [main, dev]
   pull_request:
-    branches: [ main, dev ]
+    branches: [main, dev]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   tests:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v7
 
       - name: Parse environment.json and set Docker image
         id: docker_image

.github/workflows/tests.yml

@@ -0,0 +1,52 @@
+default_install_hook_types: [pre-commit, commit-msg]
+default_stages: [pre-commit]
+exclude: |
+  (?x)(
+      ^.codeocean/|
+      ^environment/|
+      ^metadata/|
+      ^code/MOSuite|
+      ^code/SCWorkflow|
+      ^code/OMIX*
+   )
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-added-large-files
+        args: ["--maxkb=10240"]
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-json
+  # spell check
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.2
+    hooks:
+      - id: codespell
+        args:
+          [ -I, .github/WORDLIST.txt ]
+  # R formatting
+  - repo: https://github.com/posit-dev/air-pre-commit
+    rev: 0.10.0
+    hooks:
+      - id: air-format
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.3.9028
+    hooks:
+      - id: parsable-R
+  # Python formatting
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.16
+    hooks:
+      - id: ruff-check
+        args: [--fix]
+      - id: ruff-format
+
+  # enforce conventional commit format
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v4.4.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: []

.pre-commit-config.yaml

@@ -0,0 +1 @@
+any::ggplot2@3.5.2

code/MOSuite/.github/package-versions.txt

@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "Posit.air-vscode"
+    ]
+}

code/MOSuite/.vscode/extensions.json

@@ -0,0 +1,13 @@
+{
+    "[r]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "Posit.air-vscode"
+    },
+    "[quarto]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "quarto.quarto"
+    },
+    "chat.tools.terminal.autoApprove": {
+        "timeout": true
+    }
+}