Set Up putior CI/CD

Configure GitHub Actions to automatically regenerate workflow diagrams when source code changes, keeping documentation in sync with code.

When to Use

• Workflow diagrams should always reflect the current state of the code
• The project has CI/CD and wants automated documentation updates
• Multiple contributors may change workflow-affecting code
• Replacing manual diagram regeneration with automated pipeline

Inputs

• Required: GitHub repository with putior annotations in source files
• Required: Target file for diagram output (e.g., README.md, docs/workflow.md)
• Optional: putior theme (default: "github")
• Optional: Source directories to scan (default: "./R/" or "./src/")
• Optional: Branch to trigger on (default: main)

Procedure

Step 1: Create GitHub Actions Workflow

Create the workflow YAML file for automated diagram generation.

# .github/workflows/update-workflow-diagram.yml
name: Update Workflow Diagram

on:
  push:
    branches: [main]
    paths:
      - 'R/**'
      - 'src/**'
      - 'scripts/**'

permissions:
  contents: write

jobs:
  update-diagram:
    if: github.actor != 'github-actions[bot]'
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Install putior
        run: |
          install.packages("putior")
        shell: Rscript {0}

      - name: Generate workflow diagram
        run: |
          Rscript scripts/generate-workflow-diagram.R

      - name: Commit updated diagram
        run: |
          git config --local user.name "github-actions[bot]"
          git config --local user.email "github-actions[bot]@users.noreply.github.com"
          git add README.md docs/workflow.md  # Adjust to match your target files
          git diff --staged --quiet || git commit -m "docs: update workflow diagram [skip ci]"
          git push

Expected: File created at .github/workflows/update-workflow-diagram.yml.

On failure: Ensure the .github/workflows/ directory exists. Adjust the paths filter to match where annotated source files live in the repository.

Step 2: Write Generation Script

Create the R script that generates the diagram and updates target files using sentinel markers.

# scripts/generate-workflow-diagram.R
library(putior)

# Scan source files for annotations (exclude build scripts to avoid circular refs)
workflow <- put_merge("./R/", merge_strategy = "supplement",
  exclude = c("generate-workflow-diagram\\.R$"),
  log_level = NULL)  # Set to "DEBUG" to troubleshoot CI diagram generation

# Generate Mermaid code
mermaid_code <- put_diagram(workflow, output = "raw", theme = "github")

# Read target file (e.g., README.md)
readme <- readLines("README.md")

# Find sentinel markers
start_marker <- "<!-- PUTIOR-WORKFLOW-START -->"
end_marker <- "<!-- PUTIOR-WORKFLOW-END -->"

start_idx <- which(readme == start_marker)
end_idx <- which(readme == end_marker)

if (length(start_idx) == 1 && length(end_idx) == 1 && end_idx > start_idx) {
  # Replace content between sentinels
  new_content <- c(
    readme[1:start_idx],
    "",
    "```mermaid",
    mermaid_code,
    "```",
    "",
    readme[end_idx:length(readme)]
  )
  writeLines(new_content, "README.md")
  cat("Updated README.md workflow diagram\n")
} else {
  warning("Sentinel markers not found in README.md. Add them manually:\n",
          start_marker, "\n", end_marker)
}

# Also write standalone diagram file
writeLines(
  c("# Workflow Diagram", "",
    "```mermaid", mermaid_code, "```"),
  "docs/workflow.md"
)
cat("Updated docs/workflow.md\n")

Expected: Script at scripts/generate-workflow-diagram.R that reads annotations, generates Mermaid code, and replaces content between sentinel markers.

On failure: If put_merge() returns empty, check that source paths match the repository layout. Adjust "./R/" to the actual source directory.

Step 3: Configure Auto-Commit

The workflow must avoid infinite loops where an auto-commit re-triggers the same workflow. Pushes made with the default GITHUB_TOKEN typically do not trigger new workflow runs, but the workflow also includes an explicit if: guard on the job as a safety net.

Key configuration points:

• permissions: contents: write grants push access
• if: github.actor != 'github-actions[bot]' skips the job when the push came from the bot itself
• git diff --staged --quiet || git commit only commits if there are changes
• [skip ci] in the commit message is a convention some CI systems honor (not built into GitHub Actions, but useful as a signal)
• Bot identity used for commits: github-actions[bot]

Expected: The workflow only commits when diagrams actually change. No empty commits, no infinite loops.

On failure: If push fails with permission denied, check repository settings: Settings > Actions > General > Workflow permissions must be set to "Read and write permissions".

Step 4: Add Sentinel Markers to README

Insert sentinel markers in the target file where the diagram should appear.

## Workflow

<!-- PUTIOR-WORKFLOW-START -->
<!-- This section is auto-generated by putior CI. Do not edit manually. -->

```mermaid
flowchart TD
  A["Placeholder — will be replaced on next CI run"]

**Expected:** Sentinel markers in README.md (or other target file). The content between them will be replaced on each CI run.

**On failure:** Ensure markers are on their own lines with no leading/trailing whitespace. The script matches exact line content.

### Step 5: Test the Pipeline

Trigger the workflow and verify the diagram updates.

```bash
# Make a small change to trigger the workflow
echo "# test" >> R/some-file.R
git add R/some-file.R
git commit -m "test: trigger workflow diagram update"
git push

# Monitor the GitHub Actions run
gh run watch

# Verify the diagram was updated
git pull
cat README.md | grep -A 5 "PUTIOR-WORKFLOW-START"

Expected: GitHub Actions run completes successfully. The diagram between sentinel markers in README.md is updated with current workflow data.

On failure: Check the Actions log for errors. Common issues:

• putior package not available: add to DESCRIPTION Suggests or install explicitly in the workflow
• Source path wrong: the R script's put_merge() path must be relative to the repo root
• No sentinel markers: the script warns but doesn't crash; add markers to README.md

Validation

• .github/workflows/update-workflow-diagram.yml exists and is valid YAML
• scripts/generate-workflow-diagram.R runs without errors locally
• README.md contains <!-- PUTIOR-WORKFLOW-START --> and <!-- PUTIOR-WORKFLOW-END --> sentinels
• GitHub Actions workflow triggers on push to the correct branch and paths
• Diagram content between sentinels is updated after a workflow run
• Job-level if: guard prevents infinite commit loops from bot pushes
• No changes = no commit (idempotent)

Common Pitfalls

• Infinite CI loops: Pushes with the default GITHUB_TOKEN typically don't trigger new runs, but always add an explicit if: github.actor != 'github-actions[bot]' guard on the job. The [skip ci] tag in the commit message is a useful convention but is not a built-in GitHub Actions mechanism.
• Permission denied on push: GitHub Actions needs write permission. Set permissions: contents: write in the workflow file, or configure it in repository settings.
• Sentinel marker mismatch: If markers have trailing spaces, leading tabs, or are on the same line as other content, the script won't find them. Keep markers on their own clean lines.
• Source path mismatch: The R script runs from the repo root. Paths like "./R/" or "./src/" must match the actual directory structure.
• Package installation in CI: If the project uses renv, the CI workflow needs renv::restore() before putior is available. Alternatively, install putior explicitly in the workflow.
• Large repos slowing CI: For repos with many source files, limit the paths trigger filter to directories that contain PUT annotations, not the entire repo.

Related Skills

• generate-workflow-diagram — the manual version of what this CI automates
• setup-github-actions-ci — general GitHub Actions CI/CD setup for R packages
• build-ci-cd-pipeline — broader CI/CD pipeline design
• annotate-source-files — annotations must exist before CI can generate diagrams
• commit-changes — understanding auto-commit patterns