Track RAVEN develop3 and render NumPy-style API docs

.github/workflows/update-submodules.yml

@@ -0,0 +1,41 @@
+name: Update submodules
+
+on:
+  schedule:
+    - cron: '0 4 * * *'       # daily at 04:00 UTC
+  workflow_dispatch: {}       # adds a "Run workflow" button for manual runs
+
+permissions:
+  contents: write             # needed to push the pointer commit
+
+concurrency:                  # avoid overlapping runs racing on a commit
+  group: update-submodules
+  cancel-in-progress: false
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout raven-docs
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+          fetch-depth: 1
+
+      - name: Bump submodules to their tracked branches
+        run: |
+          # Pulls each submodule to the tip of the branch in .gitmodules
+          # (RAVEN -> develop3, raven-python -> develop, hanpo-GEM -> main)
+          git submodule update --remote --recursive
+
+      - name: Commit & push if anything changed
+        run: |
+          git config user.name  "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          if git diff --quiet; then
+            echo "No submodule updates."
+          else
+            git add -A
+            git commit -m "chore: update submodules to latest tracked branches"
+            git push
+          fi

.gitmodules

@@ -1,12 +1,12 @@
 [submodule "RAVEN"]
 	path = RAVEN
 	url = https://github.com/SysBioChalmers/RAVEN.git
-	branch = main
+	branch = develop3
 	shallow = true
 [submodule "raven-python"]
 	path = raven-python
 	url = https://github.com/SysBioChalmers/raven-python.git
-	branch = main
+	branch = develop
 	shallow = true
 [submodule "hanpo-GEM"]
 	path = hanpo-GEM

mkdocs.yml

@@ -37,16 +37,27 @@ plugins:
         # (legacy/ and external/ are intentionally excluded).
         matlab:
           paths:
-            - RAVEN/core
+            - RAVEN/reconstruction
+            - RAVEN/manipulation
+            - RAVEN/analysis
+            - RAVEN/gapfilling
+            - RAVEN/annotation
+            - RAVEN/biomass
+            - RAVEN/curation
+            - RAVEN/conversion
+            - RAVEN/conditions
+            - RAVEN/comparison
+            - RAVEN/omics
+            - RAVEN/localization
+            - RAVEN/queries
             - RAVEN/io
             - RAVEN/solver
-            - RAVEN/pathway
-            - RAVEN/plotting
-            - RAVEN/hpa
-            - RAVEN/struct_conversion
+            - RAVEN/tasks
+            - RAVEN/visualization
             - RAVEN/utils
           paths_recursive: true
           options:
+            docstring_style: numpy
             show_root_heading: false
             show_root_toc_entry: false
             show_source: false

scripts/gen_api_pages.py

@@ -35,13 +35,23 @@
 # Mirrors the matlab handler `paths:` in mkdocs.yml. legacy/ and external/ are
 # intentionally excluded (deprecated / third-party).
 MATLAB_CATEGORIES = [
-    ("core", "Core"),
+    ("reconstruction", "Reconstruction"),
+    ("manipulation", "Manipulation"),
+    ("analysis", "Analysis"),
+    ("gapfilling", "Gap-filling"),
+    ("annotation", "Annotation"),
+    ("biomass", "Biomass"),
+    ("curation", "Curation"),
+    ("conversion", "Format conversion"),
+    ("conditions", "Conditions"),
+    ("comparison", "Comparison"),
+    ("omics", "Omics integration"),
+    ("localization", "Localization"),
+    ("queries", "Queries"),
     ("io", "Input / output"),
     ("solver", "Solvers"),
-    ("pathway", "Pathways"),
-    ("plotting", "Plotting"),
-    ("hpa", "Human Protein Atlas"),
-    ("struct_conversion", "Model structure conversion"),
+    ("tasks", "Metabolic tasks"),
+    ("visualization", "Visualization"),
     ("utils", "Utilities"),
 ]