Merge pull request #27 from ubcbraincircuits/docs/refresh

.github/workflows/docs.yml

@@ -0,0 +1,56 @@
+name: Build & Deploy Sphinx docs
+on:
+  push:
+    branches: [ main, master ]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install system deps (Pandoc)
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+
+      - name: Install Python deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install sphinx furo myst-parser nbsphinx jupyter \
+                      sphinx-copybutton sphinx-autodoc-typehints
+
+      - name: Build Sphinx HTML
+        working-directory: docs
+        run: |
+          sphinx-build -b html . _build/html
+          touch _build/html/.nojekyll
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

README.md

@@ -1,5 +1,5 @@
 # pyDynamo
-![pyDynamo logo](https://ubcbraincircuits.github.io/pyDynamo/tmpLogo.png)
+![pyDynamo logo](img/tmpLogo.png)
 
 Application for the UI and analysis of neurons via **Dyna**mic **Mo**rphometrics.
 

docs/conf.py

@@ -1,50 +1,35 @@
 # Entry point (Sphinx 8+)
 root_doc = "index"
 
-
-# --- Project info ---
 project = "pyDynamo"
 author = "Peter W. Hogg and Patrick Coleman"
-
-# Option A: hardcode a version for now
 release = "dev"
 version = release
 
-# Option B (optional): read from the installed package
-# from importlib.metadata import version as _v, PackageNotFoundError
-# try:
-#     release = _v("pydynamo-brain")
-# except PackageNotFoundError:
-#     release = "dev"
-# version = release
-
-# --- HTML title overrides (removes the “… documentation” suffix) ---
 html_title = "pyDynamo — User & API Guide"
 html_short_title = "pyDynamo"
 
-# Source types
 source_suffix = {".rst": "restructuredtext", ".md": "markdown"}
-
-# Theme + useful extensions
 html_theme = "furo"
+
 extensions = [
     "myst_parser",
-    "sphinx.ext.autodoc",
-    "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
     "sphinx_copybutton",
-    "sphinx_autodoc_typehints",
-    "nbsphinx"
+    "nbsphinx",
 ]
-autosummary_generate = True
-myst_enable_extensions = ["colon_fence", "deflist", "linkify"]
+
+# You can re-enable autosummary/autodoc later if needed.
+# autosummary_generate = True
+
+# MyST: keep only what you need; 'linkify' requires an extra pip package.
+myst_enable_extensions = ["colon_fence", "deflist"]  # remove "linkify" for now
+
 nbsphinx_execute = "never"
-# Mock heavy GUI deps so autodoc never breaks CI
-autodoc_mock_imports = ["PyQt6", "vispy", "pyNeuroTrace", "numpy", "scipy"]
+nbsphinx_requirejs = False
 
-# (Optional) Intersphinx mappings
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
     "numpy": ("https://numpy.org/doc/stable/", None),

docs/fullstate.rst

@@ -46,4 +46,4 @@ Attributes
      - Active channel index (default: ``0``).
    * - ``drawMode``
      - ``DrawMode``
-     - Current drawing mode (``DEFAULT``, ``PUNCTA``, ``RADII``, ``REGISTRA
+     - Current drawing mode (``DEFAULT``, ``PUNCTA``, ``RADII``, ``REGISTRATION``)

pydynamo_brain/requirements.txt

@@ -14,7 +14,7 @@ tqdm
 torchio
 patchify
 tensorflow==2.20.*
-protobuf==5.28.3
+protobuf==5.29.5
 scikit-learn
 monai
 torchvision