Merge pull request #83 from sib-swiss/auto-create-collection

Auto create collection

.github/workflows/generate_readme.yml

@@ -0,0 +1,29 @@
+
+name: generate readme
+on:
+  schedule:
+    - cron: "0 0 * * SUN"
+  push:
+    branches: 
+      - 'main'
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v3
+      - name: setup python 
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - name: recreate readme
+        run: |
+          pip install requests
+          python scripts/create_collection_from_rest_api.py
+      - name: Commit and push changes
+        run: |
+          git config --global user.name "geertvangeest"
+          git add -A
+          git commit -m "auto-generated readme" || exit 0
+          git push

scripts/collection_header.md

@@ -0,0 +1,20 @@
+[![DOI](https://zenodo.org/badge/437832906.svg)](https://zenodo.org/badge/latestdoi/437832906)
+
+# Bioinformatics training materials
+
+Do you like this collection? You're going to love [glittr.org](https://glittr.org)! The collection below is still maintained but updated by glittr.org. So, if you have anything to add or to ask, see you there!
+
+[![](assets/logo-vertical.svg)](https://glittr.org)
+
+If you haven't stopped reading, you're one of the few that still prefer the old school `README` :neckbeard:. Nice !
+
+Below you'll find a curated list of **bioinformatics training material**. All material is:
+
+- In a GitHub or GitLab repository
+- Free to use
+- Written in markdown or similar
+
+**NOTE:** This list of courses is selected *only* based on the above criteria. There are *no* checks on quality.
+
+## Contents
+

scripts/create_collection_from_rest_api.py

@@ -0,0 +1,41 @@
+import requests
+
+def get_repos():
+    r = requests.get("https://glittr.org/api/list")
+    collection_list = r.json()
+    return(collection_list)
+
+def write_toc(collection_list, outfile):
+    for category in collection_list:
+        category_name = category['name']
+        outfile.write(f"- [{category_name}](#{category_name.lower().replace(' ', '-')})\n")
+        for topic in category['topics']:
+            topic_name = topic['name']
+            outfile.write(f"  - [{topic_name}](#{topic_name.lower().replace(' ', '-')})\n")
+
+
+def write_collection(collection_list, outfile):
+    for category in collection_list:
+        category_name = category['name']
+        outfile.write("\n## " + category_name + '\n\n')
+        for topic in category['topics']:
+            topic_name = topic['name']
+            outfile.write("\n### " + topic_name + '\n\n')
+            repo_list = topic['repositories']
+            for repo in repo_list:
+                if repo['website'] == '':
+                    outfile.write(f"- [**{repo['author']['display_name'].strip()}** {repo['name']}]({repo['url']})\n")
+                else:
+                    outfile.write(f"- [**{repo['author']['display_name'].strip()}** {repo['name']}]({repo['url']}) | [website]({repo['website']})\n")
+
+if __name__ == '__main__':
+    collection_list = get_repos()
+
+    output_file = 'README.md'
+
+    with open(output_file, 'w') as outfile:
+        with open('scripts/collection_header.md') as infile:
+            for line in infile:
+                outfile.write(line)
+            write_toc(collection_list, outfile)
+            write_collection(collection_list, outfile)