fix(./,.github/workflows/,docs/): fix when CI runs

.github/workflows/docker.yaml

@@ -4,6 +4,7 @@ on:
     branches:
       - main
       - alpha
+
   push:
     branches:
       - main

.github/workflows/package.yaml

@@ -1,20 +1,21 @@
 name: Package
 on:
-  # Building on pull-requests, manual dispatch, and pushes to main; but restricting
-  # publishing only to main pushes and manual dispatch with `if`s in specific steps.
-  workflow_dispatch:
-  workflow_run:
-    workflows: ["Test"]
-    types:
-      - completed
+  push:
+    branches:
+      - main
+      - alpha
+
+  pull_request:
+    branches:
+      - main
+      - alpha
 
 permissions:
   id-token: write
   contents: write
 
 jobs:
   package:
-    if: github.ref_name == 'main' || github.ref_name == 'alpha'
     name: Package
     environment: production
     runs-on: ubuntu-latest

.github/workflows/web-docs.yaml

@@ -2,11 +2,15 @@
 name: Deploy API Documentation
 
 on:
-  # Run after Test
-  workflow_run:
-    workflows: ["Test"]
-    types:
-      - completed
+  pull_request:
+    branches:
+      - main
+      - alpha
+
+  push:
+    branches:
+      - main
+      - alpha
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -26,7 +30,6 @@ concurrency:
 jobs:
   # Single deploy job since we're just deploying
   deploy:
-    if: github.event.workflow_run.conclusion == 'success' && (github.base_ref == 'alpha' || github.base_ref == 'main')
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}

README.md

@@ -260,9 +260,9 @@ You can find all the workflows in the **[.github/workflows directory](https://gi
 | **[Renovate](https://github.com/populationgenomics/cpg-flow/actions/workflows/renovate.yaml)** | Runs Renovate to update dependencies.<br/><br/>[![Renovate](https://github.com/populationgenomics/cpg-flow/actions/workflows/renovate.yaml/badge.svg)](https://github.com/populationgenomics/cpg-flow/actions/workflows/renovate.yaml) | `schedule` and `workflow_dispatch` |
 | **[Update Badges](https://github.com/populationgenomics/cpg-flow/actions/workflows/update-badges.yaml)** | Updates badges.yaml with test results and coverage.<br/><br/>[![Update Badges](https://github.com/populationgenomics/cpg-flow/actions/workflows/update-badges.yaml/badge.svg)](https://github.com/populationgenomics/cpg-flow/actions/workflows/update-badges.yaml) | `workflow_run` (completed) |
 | **[Test](https://github.com/populationgenomics/cpg-flow/actions/workflows/test.yaml)** | Runs unit tests and generates coverage reports.<br/><br/>[![Test](https://github.com/populationgenomics/cpg-flow/actions/workflows/test.yaml/badge.svg)](https://github.com/populationgenomics/cpg-flow/actions/workflows/test.yaml) | `push` |
-| **[Deploy API Documentation](https://github.com/populationgenomics/cpg-flow/actions/workflows/web-docs.yaml)** | Deploys API documentation to GitHub Pages.<br/><br/>[![Deploy API Documentation](https://github.com/populationgenomics/cpg-flow/actions/workflows/web-docs.yaml/badge.svg)](https://github.com/populationgenomics/cpg-flow/actions/workflows/web-docs.yaml) | `workflow_run` (completed) and `workflow_dispatch` |
+| **[Deploy API Documentation](https://github.com/populationgenomics/cpg-flow/actions/workflows/web-docs.yaml)** | Deploys API documentation to GitHub Pages.<br/><br/>[![Deploy API Documentation](https://github.com/populationgenomics/cpg-flow/actions/workflows/web-docs.yaml/badge.svg)](https://github.com/populationgenomics/cpg-flow/actions/workflows/web-docs.yaml) | `pull_request` on `main, alpha` and `push` on `main, alpha` and `workflow_dispatch` |
 | **[Security Checks](https://github.com/populationgenomics/cpg-flow/actions/workflows/security.yaml)** | Performs security checks using pip-audit.<br/><br/>[![Security Checks](https://github.com/populationgenomics/cpg-flow/actions/workflows/security.yaml/badge.svg)](https://github.com/populationgenomics/cpg-flow/actions/workflows/security.yaml) | `workflow_dispatch` and `push` |
-| **[Package](https://github.com/populationgenomics/cpg-flow/actions/workflows/package.yaml)** | Packages the project and publishes it to PyPI and GitHub Releases.<br/><br/>[![Package](https://github.com/populationgenomics/cpg-flow/actions/workflows/package.yaml/badge.svg)](https://github.com/populationgenomics/cpg-flow/actions/workflows/package.yaml) | `workflow_dispatch` and `workflow_run` (completed) |
+| **[Package](https://github.com/populationgenomics/cpg-flow/actions/workflows/package.yaml)** | Packages the project and publishes it to PyPI and GitHub Releases.<br/><br/>[![Package](https://github.com/populationgenomics/cpg-flow/actions/workflows/package.yaml/badge.svg)](https://github.com/populationgenomics/cpg-flow/actions/workflows/package.yaml) | `push` on `main, alpha` and `pull_request` on `main, alpha` |
 | **[Lint](https://github.com/populationgenomics/cpg-flow/actions/workflows/lint.yaml)** | Runs linting checks using pre-commit hooks.<br/><br/>[![Lint](https://github.com/populationgenomics/cpg-flow/actions/workflows/lint.yaml/badge.svg)](https://github.com/populationgenomics/cpg-flow/actions/workflows/lint.yaml) | `push` |
 | **[Docker](https://github.com/populationgenomics/cpg-flow/actions/workflows/docker.yaml)** | Builds and pushes Docker images for the project.<br/><br/>[![Docker](https://github.com/populationgenomics/cpg-flow/actions/workflows/docker.yaml/badge.svg)](https://github.com/populationgenomics/cpg-flow/actions/workflows/docker.yaml) | `pull_request` on `main, alpha` and `push` on `main, alpha` and `workflow_dispatch` |
 

docs/update_readme.py

@@ -1,5 +1,7 @@
 import os
 import re
+import sys
+from copy import deepcopy
 
 import yaml
 
@@ -81,13 +83,19 @@ def update_readme(readme_file):
     with open(readme_file) as file:
         content = file.read()
 
+    previous_content = deepcopy(content)
     content = update_workflow_table(content)
     content = update_readme_links(content)
 
+    if content == previous_content:
+        print('No changes detected in the README.md')
+        sys.exit(0)
+
     with open(readme_file, 'w') as file:
         file.write(content)
 
     print(f'Readme updated: {readme_file}')
+    sys.exit(100)
 
 
 def update_workflow_table(content):