Merge branch 'main' of github.com:phuse-org/devops

.github/workflows/publish.yml

@@ -12,12 +12,8 @@ on:
       - '**.scss'
 
 jobs:
-  links:
-    name: Links
-    uses: filiph/[email protected]
   publish:
     name: Build & Deploy Site
-    needs: links
     runs-on: ubuntu-latest
     container:
       image: rocker/tidyverse:latest
@@ -37,3 +33,21 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./_site
           keep_files: true
+
+  broken_link_checker_job:
+    runs-on: ubuntu-latest
+    needs: publish
+    name: Check for broken links
+    steps:
+      - name: Check for broken links
+        id: link-report
+        uses: celinekurpershoek/[email protected]
+        with:
+          # Required:
+          url: "https://phuse-org.github.io/devops/"
+          # optional:
+          honorRobotExclusions: false
+          ignorePatterns: "github,google"
+          recursiveLinks: false # Check all URLs on all reachable pages (could take a while)
+      - name: Get the result
+        run: echo "${{steps.link-report.outputs.result}}"

content/cicdworkflows-enhanced/posts/validate/validate.qmd

@@ -21,39 +21,62 @@ toc: true
 
 ## Why should I use this?
 
-As a codebase grows, it becomes more likely you will end up with a number of links in your documentation. 
-These links can over time stop working - and often you won't know till a user flags your links or broken.
+Validation is not a fixed term, and it is strongly recommended to make yourself aware of the work of the R Validation Hub (https://www.pharmar.org/), including the 
+regulatory repo project.
 
-This `gh-action` lets you stay on top of broken links, by actively scanning for them.
+When using an R package, it is important to know that what the documentation claims the package does is tested, and these tests pass on the 
+environment you will be using. This gh-action generates a generic report, that takes the documentation and links it to the 
+unit tests, and records how the the tests performed against a specific R environment. 
+
+The aim here is to who in a pan-company way to document the relationship between documentation and tests. Before 
+using internally, you would need to 1) confirm the documentation is well written, 2) the unit tests are sufficient to 
+test that documentation and 3) you are assessing against the actual environments you use internally.
 
 ## How do I set it up?
 
-Below is an example of using this `gh-action` whenever someone tries to make PR into your `main` or `devel` branch.
+Below is an example of using this `gh-action` when a release is made.
 
 
 ```bash
 ---
-name: Docs 📚
-
-on:
-  push:
-    branches:
-      - main
-      - devel
-  pull_request:
-    branches:
-      - main
-      - devel
+name: R Package Validation report
+
+on: # Run this action when a release is published
+  release:
+    types: [published]
 
 jobs:
-  links:
-    name: Links
-    uses: pharmaverse/admiralci/.github/workflows/links.yml@main
-    if: github.event_name == 'pull_request'
+  r-pkg-validation:
+    name: Create report 📃
+    runs-on: ubuntu-latest
+    container:
+      image: rocker/verse:4.1.1
+    # Set Github token permissions
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+      packages: write
+      deployments: write
+    steps:
+      - name: Checkout repo 🛎
+        uses: actions/checkout@v3
+
+      - name: Build report 🏗
+        id: validation
+        uses: insightsengineering/thevalidatoR@main
+        # see parameters above for custom templates and other formats
+
+      # Upload the validation report to the release
+      - name: Upload report to release 🔼
+        if: success()
+        uses: svenstaro/upload-release-action@v2
+        with:
+          file: ${{ steps.validation.outputs.report_output_filename }}
+          asset_name: ${{ steps.validation.outputs.report_output_filename }}
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          tag: ${{ github.ref }}
+          overwrite: false
 ```
 
-## The deets
 
-This gh-action uses lychee. If you need to prevent false positive deadlinks stopping the 
-process, you can use a `.lycheeignore` file. There is an example of this file [from 
-admiral here](https://github.com/pharmaverse/admiral/blob/devel/.lycheeignore).

content/cicdworkflows-minimum/posts/pkgdown.qmd

@@ -48,8 +48,6 @@ jobs:
   docs:
     name: Pkgdown Docs 📚
     uses: phuse-org/devops-toolkit/.github/workflows/pkgdown.yml@main
-    secrets:
-      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
 ```
 
 ## The deets

content/cicdworkflows-minimum/posts/r-cmd-check/r-cmd-check.qmd

@@ -50,8 +50,8 @@ on:
   workflow_dispatch:
 
 jobs:
-  links:
-    name: Links
+  check:
+    name: Check
     uses: phuse-org/devops-toolkit/.github/workflows/R-CMD-check.yml@main
 ```
 
@@ -61,4 +61,4 @@ jobs:
 
 ## Advanced use
 
-TODO: Add here how to also run against pharmaverse's r-universe latest & the latest release of PPM packages.
+TODO: Add here how to also run against pharmaverse's r-universe latest & the latest release of PPM packages.

content/cicdworkflows-recommend/posts/check-links/check-links.qmd

@@ -56,6 +56,4 @@ jobs:
 
 ## The deets
 
-This gh-action uses lychee. If you need to prevent false positive deadlinks stopping the 
-process, you can use a `.lycheeignore` file. There is an example of this file [from 
-admiral here](https://github.com/pharmaverse/admiral/blob/devel/.lycheeignore).
+This `gh-action` is using https://urlchecker.r-lib.org/, so is specific to R packages.