Merge pull request #13 from XingyanLiu/dev

debug-docs
XingyanLiu · Jul 13, 2022 · d846444 · d846444
2 parents 8035a2f + 7e1342e
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diff --git a/.gitmodules → docs/.nojekyll b/.gitmodules → docs/.nojekyll
diff --git a/docs/_config.yml b/docs/_config.yml
@@ -0,0 +1,2 @@
+remote_theme: jekyll-theme-cayman
+theme: jekyll-theme-cayman
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diff --git a/...getting_started_pipeline_aligned_16_1.png → ...getting_started_pipeline_aligned_16_1.png b/...getting_started_pipeline_aligned_16_1.png → ...getting_started_pipeline_aligned_16_1.png
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diff --git a/...ooks_getting_started_pipeline_un_38_0.png → ...ooks_getting_started_pipeline_un_39_0.png b/...ooks_getting_started_pipeline_un_38_0.png → ...ooks_getting_started_pipeline_un_39_0.png
diff --git a/...ooks_getting_started_pipeline_un_40_0.png → ...ooks_getting_started_pipeline_un_40_0.png b/...ooks_getting_started_pipeline_un_40_0.png → ...ooks_getting_started_pipeline_un_40_0.png
diff --git a/...ooks_getting_started_pipeline_un_42_1.png → ...ooks_getting_started_pipeline_un_43_1.png b/...ooks_getting_started_pipeline_un_42_1.png → ...ooks_getting_started_pipeline_un_43_1.png
diff --git a/docs/_sources/generated/came.make_abstracted_graph.rst.txt b/docs/_sources/generated/came.make_abstracted_graph.rst.txt
diff --git a/docs/_sources/generated/came.utils.preprocess.change_names.rst.txt b/docs/_sources/generated/came.utils.preprocess.change_names.rst.txt
diff --git a/docs/_sources/generated/came.utils.preprocess.get_homologues.rst.txt b/docs/_sources/generated/came.utils.preprocess.get_homologues.rst.txt
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
@@ -10,8 +10,8 @@ CAME is a tool for Cell-type Assignment and Module Extraction,
 based on a heterogeneous graph neural network.
 
 To get started with CAME's pipeline, browse the tutorials below:
-  * :doc:`_notebooks/getting_started_pipeline_un`
-  * :doc:`_notebooks/getting_started_pipeline_aligned`
+  * :doc:`tut_notebooks/getting_started_pipeline_un`
+  * :doc:`tut_notebooks/getting_started_pipeline_aligned`
 
 
 .. image:: _static/Fig1ABC.png

diff --git a/...etting_started_pipeline_aligned.ipynb.txt → ...etting_started_pipeline_aligned.ipynb.txt b/...etting_started_pipeline_aligned.ipynb.txt → ...etting_started_pipeline_aligned.ipynb.txt
diff --git a/...oks/getting_started_pipeline_un.ipynb.txt → ...oks/getting_started_pipeline_un.ipynb.txt b/...oks/getting_started_pipeline_un.ipynb.txt → ...oks/getting_started_pipeline_un.ipynb.txt
diff --git a/...sources/_notebooks/load_results.ipynb.txt → ...rces/tut_notebooks/load_results.ipynb.txt b/...sources/_notebooks/load_results.ipynb.txt → ...rces/tut_notebooks/load_results.ipynb.txt
diff --git a/docs/_sources/tutorials.rst.txt b/docs/_sources/tutorials.rst.txt
@@ -39,6 +39,6 @@ Getting started
 .. toctree::
    :maxdepth: 1
 
-   _notebooks/getting_started_pipeline_un
-   _notebooks/getting_started_pipeline_aligned
-   _notebooks/load_results
+   tut_notebooks/getting_started_pipeline_un
+   tut_notebooks/getting_started_pipeline_aligned
+   tut_notebooks/load_results
diff --git a/docs/_static/came_pipeline.png b/docs/_static/came_pipeline.png
diff --git a/docs/_static/rrgcn_structure0.png b/docs/_static/rrgcn_structure0.png
diff --git a/docs/api.html b/docs/api.html
@@ -43,7 +43,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="came.load_example_data" href="generated/came.load_example_data.html" />
-    <link rel="prev" title="Load pre-computed results" href="_notebooks/load_results.html" /> 
+    <link rel="prev" title="Load pre-computed results" href="tut_notebooks/load_results.html" /> 
 </head>
 
 <body class="wy-body-for-nav">
@@ -502,7 +502,7 @@ <h2>I/O Functions<a class="headerlink" href="#i-o-functions" title="Permalink to
           <footer>
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
         <a href="generated/came.load_example_data.html" class="btn btn-neutral float-right" title="came.load_example_data" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-        <a href="_notebooks/load_results.html" class="btn btn-neutral float-left" title="Load pre-computed results" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="tut_notebooks/load_results.html" class="btn btn-neutral float-left" title="Load pre-computed results" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
     </div>
 
   <hr/>

diff --git a/docs/build/doctrees/_notebooks/getting_started_pipeline_aligned.doctree b/docs/build/doctrees/_notebooks/getting_started_pipeline_aligned.doctree
diff --git a/docs/build/doctrees/_notebooks/getting_started_pipeline_un.doctree b/docs/build/doctrees/_notebooks/getting_started_pipeline_un.doctree
diff --git a/docs/build/doctrees/_notebooks/load_results.doctree b/docs/build/doctrees/_notebooks/load_results.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/tutorials.doctree b/docs/build/doctrees/tutorials.doctree