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XingyanLiu · Mar 16, 2022 · f9bad49 · f9bad49
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diff --git a/.gitignore b/.gitignore
@@ -16,6 +16,6 @@ __pycache__
 
 _tmp*
 
-#dist/
-#build/
-#*.egg-info
+dist/
+build/
+*.egg-info
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,4 @@
+include ./sample_data/subsampled_B-L0-0.2.h5ad.rar
+include ./sample_data/hvg_frequencies.csv
+include ./sample_data/lineage_colors.csv
+include README.md
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
@@ -37,8 +37,14 @@ Requirements:
 - scanpy: https://scanpy.readthedocs.io/en/stable/installation.html
 - scikit-learn: https://pypi.org/project/scikit-learn/
 
+Install stagewiseNN with PyPI, run:
 
-Install from source code:
+.. code-block:: PowerShell
+
+   pip install swnn
+
+
+Alternatively, install from source code:
 
 .. code:: shell
 

diff --git a/docs/_sources/installation.rst.txt b/docs/_sources/installation.rst.txt
@@ -4,11 +4,11 @@ Installation
 PyPI
 ~~~~
 
-Install stagewiseNN with PyPI, run:
+Install StagewiseNN with PyPI, run:
 
 .. code-block:: PowerShell
 
-   pip install stagewisenn
+   pip install swnn
 
 
 GitHub
@@ -22,4 +22,3 @@ Or fetch from GitHub and manually install:
     cd stagewiseNN
     python setup.py install
 
-END
diff --git a/docs/_sources/tutorial/tutorial_builder_based.ipynb.txt b/docs/_sources/tutorial/tutorial_builder_based.ipynb.txt
@@ -7,8 +7,13 @@
    "source": [
     "# Tutorial for using stagewiseNN\n",
     "\n",
-    "TODO:\n",
-    "    Add some descriptions"
+    "Here is a tutorial of using StagewiseNN to build the single-cell graph and \n",
+    "developmental tree from scratch, i.e., using the raw count data. \n",
+    "\n",
+    "The sample data used here is a **20%-subsample** (29775 cells) of the original scRNA-seq data (~140k cells),\n",
+    "which can be download from [here](https://github.com/XingyanLiu/stagewiseNN/tree/main/sample_data).\n",
+    "\n",
+    "Note that any normalized data-matrix (with stage labels) can be run with StagewiseNN."
    ]
   },
   {

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/installation.doctree b/docs/build/doctrees/installation.doctree
diff --git a/docs/build/doctrees/nbsphinx/tutorial/tutorial_builder_based.ipynb b/docs/build/doctrees/nbsphinx/tutorial/tutorial_builder_based.ipynb
@@ -7,8 +7,13 @@
    "source": [
     "# Tutorial for using stagewiseNN\n",
     "\n",
-    "TODO:\n",
-    "    Add some descriptions"
+    "Here is a tutorial of using StagewiseNN to build the single-cell graph and \n",
+    "developmental tree from scratch, i.e., using the raw count data. \n",
+    "\n",
+    "The sample data used here is a **20%-subsample** (29775 cells) of the original scRNA-seq data (~140k cells),\n",
+    "which can be download from [here](https://github.com/XingyanLiu/stagewiseNN/tree/main/sample_data).\n",
+    "\n",
+    "Note that any normalized data-matrix (with stage labels) can be run with StagewiseNN."
    ]
   },
   {

diff --git a/docs/build/doctrees/tutorial/tutorial_builder_based.doctree b/docs/build/doctrees/tutorial/tutorial_builder_based.doctree
diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
@@ -37,8 +37,14 @@ Requirements:
 - scanpy: https://scanpy.readthedocs.io/en/stable/installation.html
 - scikit-learn: https://pypi.org/project/scikit-learn/
 
+Install stagewiseNN with PyPI, run:
 
-Install from source code:
+.. code-block:: PowerShell
+
+   pip install swnn
+
+
+Alternatively, install from source code:
 
 .. code:: shell
 

diff --git a/docs/build/html/_sources/installation.rst.txt b/docs/build/html/_sources/installation.rst.txt
@@ -4,11 +4,11 @@ Installation
 PyPI
 ~~~~
 
-Install stagewiseNN with PyPI, run:
+Install StagewiseNN with PyPI, run:
 
 .. code-block:: PowerShell
 
-   pip install stagewisenn
+   pip install swnn
 
 
 GitHub
@@ -22,4 +22,3 @@ Or fetch from GitHub and manually install:
     cd stagewiseNN
     python setup.py install
 
-END
diff --git a/docs/build/html/_sources/tutorial/tutorial_builder_based.ipynb.txt b/docs/build/html/_sources/tutorial/tutorial_builder_based.ipynb.txt
@@ -7,8 +7,13 @@
    "source": [
     "# Tutorial for using stagewiseNN\n",
     "\n",
-    "TODO:\n",
-    "    Add some descriptions"
+    "Here is a tutorial of using StagewiseNN to build the single-cell graph and \n",
+    "developmental tree from scratch, i.e., using the raw count data. \n",
+    "\n",
+    "The sample data used here is a **20%-subsample** (29775 cells) of the original scRNA-seq data (~140k cells),\n",
+    "which can be download from [here](https://github.com/XingyanLiu/stagewiseNN/tree/main/sample_data).\n",
+    "\n",
+    "Note that any normalized data-matrix (with stage labels) can be run with StagewiseNN."
    ]
   },
   {

diff --git a/docs/build/html/index.html b/docs/build/html/index.html
@@ -206,7 +206,11 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <li><p>scanpy: <a class="reference external" href="https://scanpy.readthedocs.io/en/stable/installation.html">https://scanpy.readthedocs.io/en/stable/installation.html</a></p></li>
 <li><p>scikit-learn: <a class="reference external" href="https://pypi.org/project/scikit-learn/">https://pypi.org/project/scikit-learn/</a></p></li>
 </ul>
-<p>Install from source code:</p>
+<p>Install stagewiseNN with PyPI, run:</p>
+<div class="highlight-PowerShell notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">swnn</span>
+</pre></div>
+</div>
+<p>Alternatively, install from source code:</p>
 <div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>git clone https://github.com/zhanglabtools/stagewiseNN.git
 <span class="nb">cd</span> stagewiseNN
 python setup.py install

diff --git a/docs/build/html/installation.html b/docs/build/html/installation.html
@@ -193,8 +193,8 @@
 <h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="pypi">
 <h2>PyPI<a class="headerlink" href="#pypi" title="Permalink to this headline">¶</a></h2>
-<p>Install stagewiseNN with PyPI, run:</p>
-<div class="highlight-PowerShell notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">stagewisenn</span>
+<p>Install StagewiseNN with PyPI, run:</p>
+<div class="highlight-PowerShell notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">swnn</span>
 </pre></div>
 </div>
 </div>
@@ -206,7 +206,6 @@ <h2>GitHub<a class="headerlink" href="#github" title="Permalink to this headline
 python setup.py install
 </pre></div>
 </div>
-<p>END</p>
 </div>
 </div>
 

diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
diff --git a/docs/build/html/tutorial/tutorial_builder_based.html b/docs/build/html/tutorial/tutorial_builder_based.html
@@ -455,7 +455,9 @@
 </style>
 <div class="section" id="Tutorial-for-using-stagewiseNN">
 <h1>Tutorial for using stagewiseNN<a class="headerlink" href="#Tutorial-for-using-stagewiseNN" title="Permalink to this headline">¶</a></h1>
-<p>TODO: Add some descriptions</p>
+<p>Here is a tutorial of using StagewiseNN to build the single-cell graph and developmental tree from scratch, i.e., using the raw count data.</p>
+<p>The sample data used here is a <strong>20%-subsample</strong> (29775 cells) of the original scRNA-seq data (~140k cells), which can be download from <a class="reference external" href="https://github.com/XingyanLiu/stagewiseNN/tree/main/sample_data">here</a>.</p>
+<p>Note that any normalized data-matrix (with stage labels) can be run with StagewiseNN.</p>
 <div class="nbinput nblast docutils container">
 <div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
 </pre></div>

diff --git a/docs/build/html/tutorial/tutorial_builder_based.ipynb b/docs/build/html/tutorial/tutorial_builder_based.ipynb
@@ -7,8 +7,13 @@
    "source": [
     "# Tutorial for using stagewiseNN\n",
     "\n",
-    "TODO:\n",
-    "    Add some descriptions"
+    "Here is a tutorial of using StagewiseNN to build the single-cell graph and \n",
+    "developmental tree from scratch, i.e., using the raw count data. \n",
+    "\n",
+    "The sample data used here is a **20%-subsample** (29775 cells) of the original scRNA-seq data (~140k cells),\n",
+    "which can be download from [here](https://github.com/XingyanLiu/stagewiseNN/tree/main/sample_data).\n",
+    "\n",
+    "Note that any normalized data-matrix (with stage labels) can be run with StagewiseNN."
    ]
   },
   {

diff --git a/docs/index.html b/docs/index.html
@@ -206,7 +206,11 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <li><p>scanpy: <a class="reference external" href="https://scanpy.readthedocs.io/en/stable/installation.html">https://scanpy.readthedocs.io/en/stable/installation.html</a></p></li>
 <li><p>scikit-learn: <a class="reference external" href="https://pypi.org/project/scikit-learn/">https://pypi.org/project/scikit-learn/</a></p></li>
 </ul>
-<p>Install from source code:</p>
+<p>Install stagewiseNN with PyPI, run:</p>
+<div class="highlight-PowerShell notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">swnn</span>
+</pre></div>
+</div>
+<p>Alternatively, install from source code:</p>
 <div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>git clone https://github.com/zhanglabtools/stagewiseNN.git
 <span class="nb">cd</span> stagewiseNN
 python setup.py install

diff --git a/docs/installation.html b/docs/installation.html
@@ -193,8 +193,8 @@
 <h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="pypi">
 <h2>PyPI<a class="headerlink" href="#pypi" title="Permalink to this headline">¶</a></h2>
-<p>Install stagewiseNN with PyPI, run:</p>
-<div class="highlight-PowerShell notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">stagewisenn</span>
+<p>Install StagewiseNN with PyPI, run:</p>
+<div class="highlight-PowerShell notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">swnn</span>
 </pre></div>
 </div>
 </div>
@@ -206,7 +206,6 @@ <h2>GitHub<a class="headerlink" href="#github" title="Permalink to this headline
 python setup.py install
 </pre></div>
 </div>
-<p>END</p>
 </div>
 </div>
 

diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -37,8 +37,14 @@ Requirements:
 - scanpy: https://scanpy.readthedocs.io/en/stable/installation.html
 - scikit-learn: https://pypi.org/project/scikit-learn/
 
+Install stagewiseNN with PyPI, run:
 
-Install from source code:
+.. code-block:: PowerShell
+
+   pip install swnn
+
+
+Alternatively, install from source code:
 
 .. code:: shell
 

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -4,11 +4,11 @@ Installation
 PyPI
 ~~~~
 
-Install stagewiseNN with PyPI, run:
+Install StagewiseNN with PyPI, run:
 
 .. code-block:: PowerShell
 
-   pip install stagewisenn
+   pip install swnn
 
 
 GitHub
@@ -22,4 +22,3 @@ Or fetch from GitHub and manually install:
     cd stagewiseNN
     python setup.py install
 
-END
diff --git a/docs/source/tutorial/tutorial_builder_based.ipynb b/docs/source/tutorial/tutorial_builder_based.ipynb
@@ -7,8 +7,13 @@
    "source": [
     "# Tutorial for using stagewiseNN\n",
     "\n",
-    "TODO:\n",
-    "    Add some descriptions"
+    "Here is a tutorial of using StagewiseNN to build the single-cell graph and \n",
+    "developmental tree from scratch, i.e., using the raw count data. \n",
+    "\n",
+    "The sample data used here is a **20%-subsample** (29775 cells) of the original scRNA-seq data (~140k cells),\n",
+    "which can be download from [here](https://github.com/XingyanLiu/stagewiseNN/tree/main/sample_data).\n",
+    "\n",
+    "Note that any normalized data-matrix (with stage labels) can be run with StagewiseNN."
    ]
   },
   {

diff --git a/docs/tutorial/tutorial_builder_based.html b/docs/tutorial/tutorial_builder_based.html
@@ -455,7 +455,9 @@
 </style>
 <div class="section" id="Tutorial-for-using-stagewiseNN">
 <h1>Tutorial for using stagewiseNN<a class="headerlink" href="#Tutorial-for-using-stagewiseNN" title="Permalink to this headline">¶</a></h1>
-<p>TODO: Add some descriptions</p>
+<p>Here is a tutorial of using StagewiseNN to build the single-cell graph and developmental tree from scratch, i.e., using the raw count data.</p>
+<p>The sample data used here is a <strong>20%-subsample</strong> (29775 cells) of the original scRNA-seq data (~140k cells), which can be download from <a class="reference external" href="https://github.com/XingyanLiu/stagewiseNN/tree/main/sample_data">here</a>.</p>
+<p>Note that any normalized data-matrix (with stage labels) can be run with StagewiseNN.</p>
 <div class="nbinput nblast docutils container">
 <div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
 </pre></div>

diff --git a/docs/tutorial/tutorial_builder_based.ipynb b/docs/tutorial/tutorial_builder_based.ipynb
@@ -7,8 +7,13 @@
    "source": [
     "# Tutorial for using stagewiseNN\n",
     "\n",
-    "TODO:\n",
-    "    Add some descriptions"
+    "Here is a tutorial of using StagewiseNN to build the single-cell graph and \n",
+    "developmental tree from scratch, i.e., using the raw count data. \n",
+    "\n",
+    "The sample data used here is a **20%-subsample** (29775 cells) of the original scRNA-seq data (~140k cells),\n",
+    "which can be download from [here](https://github.com/XingyanLiu/stagewiseNN/tree/main/sample_data).\n",
+    "\n",
+    "Note that any normalized data-matrix (with stage labels) can be run with StagewiseNN."
    ]
   },
   {

diff --git a/swnn/__init__.py b/swnn/__init__.py
@@ -14,4 +14,4 @@
 )
 from .builder import Builder
 
-
+__version__ = '0.1.0'
-Original file line number
+Diff line change
@@ Expand Up / @@ -16,6 +16,6 @@ __pycache__ @@
     _tmp*
-    #dist/
-    #build/
-    #*.egg-info
+    dist/
+    build/
+    *.egg-info
Original file line number	Diff line number	Diff line change
Expand Up		@@ -14,4 +14,4 @@
		)
		from .builder import Builder


		__version__ = '0.1.0'