Fix out links from docs collections section, generate collection repo…

…rt automatically.

Fixes #126

.github/workflows/documentation.yml

@@ -1,10 +1,17 @@
-name: mkdocs-generation
+name: Deploy documentation
+
 on:
   push:
     branches:
       - main
+
 permissions:
   contents: write
+
+env:
+  # Path to directory that contains the cohorts, one cohort per folder.
+  NOTEBOOK_DIR: notebooks
+
 jobs:
   deploy:
     runs-on: ubuntu-latest
@@ -17,9 +24,16 @@ jobs:
         with:
           key: ${{ github.ref }}
           path: .cache
-      - run: pip install mkdocs-material
-      - run: pip install mkdocs-material[imaging]
-      - run: pip install pillow cairosvg
-      - run: pip install mkdocs-material-extensions
-      - run: pip install mkdocstrings[python]
-      - run: mkdocs gh-deploy --force
+
+      - name: Install docs dependencies
+        run: |
+          python3 -m pip install .[docs]
+
+      - name: Generate reports
+        run: |
+          python3 -m ppktstore report collections --notebook-dir ${NOTEBOOK_DIR} --output docs/collections.md
+
+      - name: Deploy docs
+        run: |
+          mkdocs gh-deploy --force
+  

GetPhenopackets.ipynb

@@ -735,7 +735,10 @@
     "import os\n",
     "from ppktstore.stats import generate_phenopacket_store_report\n",
     "\n",
-    "report = generate_phenopacket_store_report(notebook_dir)\n",
+    "report = generate_phenopacket_store_report(\n",
+    "    notebook_dir=\"notebooks\", \n",
+    "    notebook_dir_url='https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks'\n",
+    ")\n",
     "\n",
     "outfile = os.path.join('docs', 'collections.md')\n",
     "with open(outfile, 'w') as fh:\n",