aristoteleo · Starlitnightly · Oct 4, 2024 · Oct 4, 2024 · Oct 4, 2024 · Oct 4, 2024
diff --git a/.gitignore b/.gitignore
@@ -53,6 +53,10 @@ docs/build
 docs/source/dynamo*
 docs/source/_autosummary
 
+docs/generated/
+docs/_build/
+docs/api/reference/*rst
+
 # always-ignore directories
 /build/
 /dist/

diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "docs/tutorials/notebooks"]
+	path = docs/tutorials/notebooks
+	url = https://github.com/aristoteleo/dynamo-tutorials.git
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -9,7 +9,7 @@ build:
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/source/conf.py
+  configuration: docs/conf.py
 
 # python:
 #     version: 3.7
@@ -23,4 +23,9 @@ python:
       extra_requirements:
         - docs
     # - method: setuptools
-    #   path: package
+    #   path: package
+
+submodules:
+  include:
+    - "docs/tutorials/notebooks"
+  recursive: true
diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/docs/Makefile b/docs/Makefile
@@ -1,11 +1,12 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -16,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_static/Preprocessor_tutorial_files/output_20_1.png b/docs/_static/Preprocessor_tutorial_files/output_20_1.png
diff --git a/docs/_static/Preprocessor_tutorial_files/output_23_1.png b/docs/_static/Preprocessor_tutorial_files/output_23_1.png
diff --git a/docs/_static/Preprocessor_tutorial_files/output_26_1.png b/docs/_static/Preprocessor_tutorial_files/output_26_1.png
diff --git a/docs/_static/Preprocessor_tutorial_files/output_29_1.png b/docs/_static/Preprocessor_tutorial_files/output_29_1.png
diff --git a/docs/_static/Preprocessor_tutorial_files/output_38_0.png b/docs/_static/Preprocessor_tutorial_files/output_38_0.png
diff --git a/docs/_static/Preprocessor_tutorial_files/output_40_1.png b/docs/_static/Preprocessor_tutorial_files/output_40_1.png
diff --git a/docs/_static/Preprocessor_tutorial_files/output_42_0.png b/docs/_static/Preprocessor_tutorial_files/output_42_0.png
diff --git a/docs/_static/Preprocessor_tutorial_files/output_49_1.png b/docs/_static/Preprocessor_tutorial_files/output_49_1.png
diff --git a/docs/_static/Preprocessor_tutorial_files/output_54_1.png b/docs/_static/Preprocessor_tutorial_files/output_54_1.png
diff --git a/docs/_static/Preprocessor_tutorial_files/output_67_1.png b/docs/_static/Preprocessor_tutorial_files/output_67_1.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/1_1.png b/docs/_static/Shiny_tutorial_files/lap/1_1.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/1_2.png b/docs/_static/Shiny_tutorial_files/lap/1_2.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/2_1.jpg b/docs/_static/Shiny_tutorial_files/lap/2_1.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/2_2.jpg b/docs/_static/Shiny_tutorial_files/lap/2_2.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/2_3.jpg b/docs/_static/Shiny_tutorial_files/lap/2_3.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/2_4.png b/docs/_static/Shiny_tutorial_files/lap/2_4.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/2_5.jpg b/docs/_static/Shiny_tutorial_files/lap/2_5.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/2_6.jpg b/docs/_static/Shiny_tutorial_files/lap/2_6.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/3_1.jpg b/docs/_static/Shiny_tutorial_files/lap/3_1.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/3_2.png b/docs/_static/Shiny_tutorial_files/lap/3_2.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/4_1.jpg b/docs/_static/Shiny_tutorial_files/lap/4_1.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/4_2.png b/docs/_static/Shiny_tutorial_files/lap/4_2.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/5_1.jpg b/docs/_static/Shiny_tutorial_files/lap/5_1.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/5_2.jpg b/docs/_static/Shiny_tutorial_files/lap/5_2.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/6.png b/docs/_static/Shiny_tutorial_files/lap/6.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/7_1.png b/docs/_static/Shiny_tutorial_files/lap/7_1.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/7_2.jpg b/docs/_static/Shiny_tutorial_files/lap/7_2.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/8_1.jpg b/docs/_static/Shiny_tutorial_files/lap/8_1.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/8_2.png b/docs/_static/Shiny_tutorial_files/lap/8_2.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/9_1.png b/docs/_static/Shiny_tutorial_files/lap/9_1.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/9_2.jpg b/docs/_static/Shiny_tutorial_files/lap/9_2.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/9_3.jpg b/docs/_static/Shiny_tutorial_files/lap/9_3.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/9_4.jpg b/docs/_static/Shiny_tutorial_files/lap/9_4.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/9_5.png b/docs/_static/Shiny_tutorial_files/lap/9_5.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/9_6.jpg b/docs/_static/Shiny_tutorial_files/lap/9_6.jpg
diff --git a/docs/_static/Shiny_tutorial_files/lap/9_7.png b/docs/_static/Shiny_tutorial_files/lap/9_7.png
diff --git a/docs/_static/Shiny_tutorial_files/lap/9_8.png b/docs/_static/Shiny_tutorial_files/lap/9_8.png
diff --git a/docs/_static/Shiny_tutorial_files/perturbation/1.png b/docs/_static/Shiny_tutorial_files/perturbation/1.png
diff --git a/docs/_static/Shiny_tutorial_files/perturbation/1_1.jpg b/docs/_static/Shiny_tutorial_files/perturbation/1_1.jpg
diff --git a/docs/_static/Shiny_tutorial_files/perturbation/2_1.jpg b/docs/_static/Shiny_tutorial_files/perturbation/2_1.jpg
diff --git a/docs/_static/Shiny_tutorial_files/perturbation/2_2.jpg b/docs/_static/Shiny_tutorial_files/perturbation/2_2.jpg
diff --git a/docs/_static/Shiny_tutorial_files/perturbation/2_3.jpg b/docs/_static/Shiny_tutorial_files/perturbation/2_3.jpg
diff --git a/docs/_static/Shiny_tutorial_files/perturbation/3_1.jpg b/docs/_static/Shiny_tutorial_files/perturbation/3_1.jpg
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
@@ -0,0 +1,37 @@
+.caption-text{
+   padding: 0px;
+}
+
+.rst-content .output_area img {
+   max-width: unset;
+   width: 100% !important;
+   height: auto !important;
+}
+
+
+/* sidebar */
+.rst-content .sidebar {
+    /* margin: 0px 0px 0px 12px; */
+    padding-bottom: 0px;
+}
+.rst-content .sidebar p {
+    margin-bottom: 12px;
+}
+.rst-content .sidebar p,
+.rst-content .sidebar ul,
+.rst-content .sidebar dl {
+    font-size: 13px;
+}
+
+.scrollit {
+    overflow-x:auto;
+}
+
+/* Sidebar header (and topbar for mobile) */
+.wy-side-nav-search, .wy-nav-top {
+    background: #1b1b1b;
+}
+/* Sidebar */
+.wy-nav-side {
+background: #373737;
+}
diff --git a/docs/_static/css/override.css b/docs/_static/css/override.css
diff --git a/docs/_static/dynamo-horizontal.svg b/docs/_static/dynamo-horizontal.svg
diff --git a/docs/_static/img/anndata_manager_schematic.svg b/docs/_static/img/anndata_manager_schematic.svg
diff --git a/docs/_static/img/setup_anndata_before_after.svg b/docs/_static/img/setup_anndata_before_after.svg
diff --git a/docs/_static/logo.png b/docs/_static/logo.png