Merge pull request #26 from pinellolab/update_readthedocs

Update readthedocs
pinellolab · Aug 23, 2023 · 7810a73 · 7810a73
2 parents 43ac398 + 42c6426
commit 7810a73
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Showing 5 changed files with 38 additions and 847 deletions.
diff --git a/docs/source/Introduction.rst b/docs/source/Introduction.rst
diff --git a/docs/source/Tutorials.rst b/docs/source/Tutorials.rst
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -24,26 +24,48 @@
 # The full version, including alpha/beta/rc tags
 release = "v0.1.0"
 
+# -- Retrieve notebooks -------------------------------
+
+from urllib.request import urlretrieve  # noqa: E402
+
+notebooks_url = "https://github.com/pinellolab/STREAM2_tutorials/raw/main/tutorial_notebooks/"  # noqa
+notebooks_v1_0 = [
+    "complex_structure.ipynb",
+    "supervision_ordinal.ipynb",
+    "supervision_categorical.ipynb",
+    "multiomics.ipynb",
+    "stream_plots.ipynb",
+]
+
+for nb in notebooks_v1_0:
+    try:
+        urlretrieve(notebooks_url + nb, nb)
+    except Exception:
+        pass
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    "sphinx.ext.intersphinx",
     "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    'sphinx.ext.napoleon',
+    "sphinx.ext.intersphinx",
     "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
+    "nbsphinx",
 ]
+autosummary_generate = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
+exclude_patterns = ['_build']
 
 
 # -- Options for HTML output -------------------------------------------------
@@ -53,6 +75,9 @@
 #
 html_theme = "sphinx_rtd_theme"
 
+github_repo = 'stream2'
+github_nb_repo = 'stream2_tutorials'
+
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -14,14 +14,17 @@ Contents
    :maxdepth: 2
    :caption: Contents:
 
-   Introduction
+   About STREAM2
    Installation
-   Tutorials
+   API
 
 
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+.. toctree::
+   :maxdepth: 1
+   :caption: Tutorials
+
+   complex_structure
+   supervision_ordinal
+   supervision_categorical
+   multiomics
+   stream_plots
diff --git a/docs/tutorial/stream_plots.ipynb b/docs/tutorial/stream_plots.ipynb