Fix documentation generation.

leojklarner · Dec 9, 2023 · ae1eb60 · ae1eb60
1 parent e188803
commit ae1eb60
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Showing 8 changed files with 73 additions and 43 deletions.
diff --git a/.github/workflows/build_documentation.yaml b/.github/workflows/build_documentation.yaml
@@ -0,0 +1,27 @@
+name: documentation
+
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - name: Install dependencies
+        run: |
+          pip install sphinx furo myst_parser
+      - name: Sphinx build
+        run: |
+          sphinx-build doc _build
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true
diff --git a/.requirements/docs.in b/.requirements/docs.in
@@ -1,9 +1,2 @@
 sphinx
-furo
-sphinx-copybutton
-sphinx-inline-tabs
-sphinxcontrib-gtagjs
-sphinxext-opengraph
-m2r2
-nbsphinx
-nvsphinx-link
+furo
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -12,7 +12,8 @@
 #
 # import os
 # import sys
-# sys.path.insert(0, os.path.abspath('.'))
+
+# sys.path.insert(0, os.path.abspath("../../../gauche"))
 
 
 # -- Project information -----------------------------------------------------
@@ -34,13 +35,13 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.intersphinx",
     "sphinx.ext.viewcode",
-    "sphinx_copybutton",
-    "sphinx_inline_tabs",
-    "sphinxcontrib.gtagjs",
-    "sphinxext.opengraph",
-    "m2r2",
-    "nbsphinx",
-    "nbsphinx_link",
+    #"sphinx_copybutton",
+    #"sphinx_inline_tabs",
+    #"sphinxcontrib.gtagjs",
+    #"sphinxext.opengraph",
+    #"m2r2",
+    #"nbsphinx",
+    #"nbsphinx_link",
 ]
 
 # Add any paths that contain templates here, relative to this directory.

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -27,10 +27,11 @@ Welcome to GAUCHE's documentation!
 
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 3
    :caption: API Reference
 
    modules/kernels
+   modules/representations
    modules/dataloader
 
 

diff --git a/docs/source/modules/data_featuriser.rst b/docs/source/modules/data_featuriser.rst
diff --git a/docs/source/modules/dataloader.rst b/docs/source/modules/dataloader.rst
@@ -1,22 +1,23 @@
 gauche.dataloader
-====================
+======================
 
 Dataloader
---------------------
+----------------------
 .. automodule:: gauche.dataloader.dataloader
     :members:
 
 Molecular Properties
---------------------
-.. automodule:: gauche.dataloader.mol_prop
+----------------------
+.. automodule:: gauche.dataloader.mol_prop_loader
+    :members:
+
+Reaction Loader
+----------------------
+.. automodule:: gauche.dataloader.reaction_loader
     :members:
 
 Utils
---------------------
+----------------------
 .. automodule:: gauche.dataloader.data_utils
     :members:
 
-Reaction Loader
-------------------
-.. automodule:: gauche.dataloader.reaction_loader
-    :members:
diff --git a/docs/source/modules/kernels.rst b/docs/source/modules/kernels.rst
@@ -1,10 +1,12 @@
 gauche.kernels
-====================
+=====================
 
 Fingerprint Kernels
---------------------
+---------------------
 .. automodule:: gauche.kernels.fingerprint_kernels.tanimoto_kernel
     :members:
+.. automodule:: gauche.kernels.fingerprint_kernels.braun_blanquet_kernel
+    :members:
 .. automodule:: gauche.kernels.fingerprint_kernels.dice_kernel
     :members:
 .. automodule:: gauche.kernels.fingerprint_kernels.faith_kernel
@@ -30,17 +32,12 @@ Fingerprint Kernels
 .. automodule:: gauche.kernels.fingerprint_kernels.sokal_sneath_kernel
     :members:
 
-GNN Kernels
--------------
-.. automodule:: gauche.kernels.gnn_kernels.pretrained_kernel
-    :members:
-
 Graph Kernels
---------------
-.. automodule:: gauche.gp
+---------------------
+.. automodule:: gauche.kernels.graph_kernels
     :members:
 
 String Kernels
---------------
+---------------------
 .. automodule:: gauche.kernels.string_kernels
     :members:
diff --git a/docs/source/modules/representations.rst b/docs/source/modules/representations.rst
@@ -0,0 +1,17 @@
+gauche.representations
+===========================
+
+Fingerprint Representations
+----------------------------
+.. automodule:: gauche.representations.fingerprints
+    :members:
+
+Graph Representations
+----------------------------
+.. automodule:: gauche.representations.graphs
+    :members:
+
+String Representations
+----------------------------
+.. automodule:: gauche.representations.strings
+    :members: