Merge pull request #13 from phuse-org/tidy

Update website with Dinakar's new content

.github/workflows/publish.yml

@@ -12,8 +12,12 @@ on:
       - '**.scss'
 
 jobs:
+  links:
+    name: Links
+    uses: phuse-org/devops-toolkit/.github/workflows/urlchecker.yml@main
   publish:
     name: Build & Deploy Site
+    needs: links
     runs-on: ubuntu-latest
     container:
       image: rocker/tidyverse:latest

content/cicdworkflows-minimum/posts/code-coverage.qmd

@@ -13,7 +13,7 @@ toc: true
 :::{.callout-note style="margin-top: 0rem;" collapse="false"}
 ## About the gh-action
 
-**Example of use:** [admiral R package](https://github.com/pharmaverse/admiralci#code-coverage)
+**Example of use:** [falcon R package](https://github.com/pharmaverse/falcon/blob/use-phuse-cicd/.github/workflows/phuse-basics.yml)
 
 **Expected output:** Badge (![Code
 Coverage](https://github.com/pharmaverse/admiralci/actions/workflows/code-coverage.yml/badge.svg)) or change pipeline depending on reported code coverage.
@@ -39,10 +39,29 @@ setting up tests with test that.
 You can call this action via adding a call to this job in a github action. A minimal example 
 that runs this on commits to master is:
 
-> ..... Have a 'recomended' yaml like admiral does with common? 
-Then can link to that line of code in that gh-action file?
+```bash
+name: Code coverage
+# sourced from phuse-org/devops-toolkit
 
-> ....... How do the badges work with this one? The docs seem to contradict what is present in the admiral R package.
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  coverage:
+    name: Code Coverage
+    uses: phuse-org/devops-toolkit/.github/workflows/test-coverage.yml@main
+```
 
 ## The deets
 

content/cicdworkflows-minimum/posts/pkgdown.qmd

@@ -13,7 +13,7 @@ toc: true
 :::{.callout-note style="margin-top: 0rem;" collapse="false"}
 ## About the gh-action
 
-**Example of use:** [teal R package](https://github.com/insightsengineering/teal/blob/main/.github/workflows/docs.yaml)
+**Example of use:** [falcon R package](https://github.com/pharmaverse/falcon/blob/use-phuse-cicd/.github/workflows/phuse-basics.yml)
 
 **Expected output:** Generate and deploy to gh-pages versioned documentation, and upload copy of documentation to release.
 :::
@@ -47,11 +47,9 @@ on:
 jobs:
   docs:
     name: Pkgdown Docs 📚
-    uses: insightsengineering/r.pkg.template/.github/workflows/pkgdown.yaml@main
+    uses: phuse-org/devops-toolkit/.github/workflows/pkgdown.yml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
-    with:
-      default-landing-page: latest-tag
 ```
 
 ## The deets
@@ -60,4 +58,3 @@ If you have built docs locally in the past, you are probably aware that your git
 of each piece version of every plot and image you have used in your documentation. This `gh-action` will help you avoid that, by 
 placing the versioned documentation into an orphan branch. Helping to keep your docs (a built artefact) seperate from your source code.
 
-The `gh-action` is well documented in-line, [and stored at this location](https://github.com/insightsengineering/r.pkg.template/blob/main/.github/workflows/pkgdown.yaml).

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

@@ -12,9 +12,7 @@ toc: true
 :::{.callout-note style="margin-top: 0rem;" collapse="false"}
 ## About the gh-action
 
-[**Link to `gh-action`**](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/r-cmd-check.yml)
-
-**Example of use:** ADD
+**Example of use:** [falcon R package](https://github.com/pharmaverse/falcon/blob/use-phuse-cicd/.github/workflows/phuse-basics.yml)
 
 **Expected output:** Fail the pipeline if `R CMD Check` fails.
 :::
@@ -34,28 +32,33 @@ Below is an example of using this `gh-action` whenever someone tries to make PR
 
 
 ```bash
----
-name: R CMD Check
+name: Run R-CMD-check
+# sourced from phuse-org/devops-toolkit
 
 on:
-  push:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
     branches:
       - main
-      - devel
-  pull_request:
+  push:
     branches:
       - main
-      - devel
+  workflow_dispatch:
 
 jobs:
-  check:
-    name: Check
-    uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
-    if: github.event_name == 'pull_request'
+  links:
+    name: Links
+    uses: phuse-org/devops-toolkit/.github/workflows/R-CMD-check.yml@main
 ```
 
 ## The deets
 
+
+
 ## Advanced use
 
 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

@@ -13,15 +13,15 @@ toc: true
 :::{.callout-note style="margin-top: 0rem;" collapse="false"}
 ## About the gh-action
 
-**Example of use:** [admiral R package](https://github.com/pharmaverse/admiralci#links)
+**Example of use:** [falcon R package](https://github.com/pharmaverse/falcon/blob/use-phuse-cicd/.github/workflows/phuse-basics.yml)
 
-**Expected output:** Fail the pipeline if a link is broken in your repo.
+**Expected output:** Fail the pipeline if a link is broken in your repo (**CHECK IT DOES THIS**)
 :::
 
 ## 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.
+These links can stop working over time - and often you won't know till a user flags your links are broken.
 
 This `gh-action` lets you stay on top of broken links, by actively scanning for them.
 
@@ -31,24 +31,27 @@ Below is an example of using this `gh-action` whenever someone tries to make PR
 
 
 ```bash
----
-name: Docs 📚
+name: Check URLs in docs 📚
+# sourced from phuse-org/devops-toolkit
 
 on:
-  push:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
     branches:
       - main
-      - devel
-  pull_request:
+  push:
     branches:
       - main
-      - devel
+  workflow_dispatch:
 
 jobs:
   links:
     name: Links
-    uses: pharmaverse/admiralci/.github/workflows/links.yml@main
-    if: github.event_name == 'pull_request'
+    uses: phuse-org/devops-toolkit/.github/workflows/urlchecker.yml@main
 ```
 
 ## The deets

index.qmd

@@ -89,7 +89,6 @@ A recomended plan for success in implenting CICD on your project is to:
 
 - [Read this post](post/posts/gh-actions.html) on the general anatomy of a `gh-action`
 - Browse our recomended `gh-action`'s below
-- Review this case study of CICD is used in `admiral`
 - Implement CICD on your git repo!
 
 We've also collected togther [this list of external learning resources](post/posts/external-resources.html).