diff --git a/.gitignore b/.gitignore index 9b2db68..d4cb5d7 100644 --- 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 new file mode 100644 index 0000000..66b6e30 --- /dev/null +++ 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 \ No newline at end of file diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt index 67e58ee..5a9b1c4 100644 --- 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 index 0caff4a..2c0ca25 100644 --- 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 \ No newline at end of file diff --git a/docs/_sources/tutorial/tutorial_builder_based.ipynb.txt b/docs/_sources/tutorial/tutorial_builder_based.ipynb.txt index 91579e6..811241a 100644 --- 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 index f348527..05bffa8 100644 Binary files a/docs/build/doctrees/environment.pickle and b/docs/build/doctrees/environment.pickle differ diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree index b399f20..f88c867 100644 Binary files a/docs/build/doctrees/index.doctree and b/docs/build/doctrees/index.doctree differ diff --git a/docs/build/doctrees/installation.doctree b/docs/build/doctrees/installation.doctree index d17b128..412ebbe 100644 Binary files a/docs/build/doctrees/installation.doctree and b/docs/build/doctrees/installation.doctree differ diff --git a/docs/build/doctrees/nbsphinx/tutorial/tutorial_builder_based.ipynb b/docs/build/doctrees/nbsphinx/tutorial/tutorial_builder_based.ipynb index 91579e6..811241a 100644 --- 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 index f4d39fc..641e2f8 100644 Binary files a/docs/build/doctrees/tutorial/tutorial_builder_based.doctree and b/docs/build/doctrees/tutorial/tutorial_builder_based.doctree differ diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt index 67e58ee..5a9b1c4 100644 --- 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 index 0caff4a..2c0ca25 100644 --- 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 \ No newline at end of file diff --git a/docs/build/html/_sources/tutorial/tutorial_builder_based.ipynb.txt b/docs/build/html/_sources/tutorial/tutorial_builder_based.ipynb.txt index 91579e6..811241a 100644 --- 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 index 60bfd30..33bb6d7 100644 --- a/docs/build/html/index.html +++ b/docs/build/html/index.html @@ -206,7 +206,11 @@

Installationhttps://scanpy.readthedocs.io/en/stable/installation.html

  • scikit-learn: https://pypi.org/project/scikit-learn/

    • -

    Install from source code:

    +

    Install stagewiseNN with PyPI, run:

    +
    pip install swnn
+
    +
    +

    Alternatively, install from source code:

    git clone https://github.com/zhanglabtools/stagewiseNN.git
 cd stagewiseNN
 python setup.py install
diff --git a/docs/build/html/installation.html b/docs/build/html/installation.html
index 191cd0b..5867e5f 100644
--- a/docs/build/html/installation.html
+++ b/docs/build/html/installation.html
@@ -193,8 +193,8 @@
 
    Installation
    
 
    
 
    PyPI
    
-
    Install stagewiseNN with PyPI, run:
    
-
    pip install stagewisenn
+
    Install StagewiseNN with PyPI, run:
    
+
    pip install swnn
 
    
 
    
 
    
@@ -206,7 +206,6 @@ 
    GitHub
 
    
 
    Tutorial for using stagewiseNN
    
-
    TODO: Add some descriptions
    
+
    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.
    
+
    The sample data used here is a 20%-subsample (29775 cells) of the original scRNA-seq data (~140k cells), which can be download from here.
    
+
    Note that any normalized data-matrix (with stage labels) can be run with StagewiseNN.
    
 
    
 
    [1]:
 
    
diff --git a/docs/build/html/tutorial/tutorial_builder_based.ipynb b/docs/build/html/tutorial/tutorial_builder_based.ipynb
index 91579e6..811241a 100644
--- 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
index 60bfd30..33bb6d7 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -206,7 +206,11 @@ 
    Installationhttps://scanpy.readthedocs.io/en/stable/installation.html
    
 
  • scikit-learn: https://pypi.org/project/scikit-learn/
    • 
 
-
    Install from source code:
    
+
    Install stagewiseNN with PyPI, run:
    
+
    pip install swnn
+
    
+
    
+
    Alternatively, install from source code:
    
 
    git clone https://github.com/zhanglabtools/stagewiseNN.git
 cd stagewiseNN
 python setup.py install
diff --git a/docs/installation.html b/docs/installation.html
index 191cd0b..5867e5f 100644
--- a/docs/installation.html
+++ b/docs/installation.html
@@ -193,8 +193,8 @@
 
    Installation
    
 
    
 
    PyPI
    
-
    Install stagewiseNN with PyPI, run:
    
-
    pip install stagewisenn
+
    Install StagewiseNN with PyPI, run:
    
+
    pip install swnn
 
    
 
    
 
    
@@ -206,7 +206,6 @@ 
    GitHub
 
    
 
    Tutorial for using stagewiseNN
    
-
    TODO: Add some descriptions
    
+
    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.
    
+
    The sample data used here is a 20%-subsample (29775 cells) of the original scRNA-seq data (~140k cells), which can be download from here.
    
+
    Note that any normalized data-matrix (with stage labels) can be run with StagewiseNN.
    
 
    
 
    [1]:
 
    
diff --git a/docs/tutorial/tutorial_builder_based.ipynb b/docs/tutorial/tutorial_builder_based.ipynb
index 91579e6..811241a 100644
--- 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
index 2106ad2..19c64ec 100644
--- a/swnn/__init__.py
+++ b/swnn/__init__.py
@@ -14,4 +14,4 @@
 )
 from .builder import Builder
 
-
+__version__ = '0.1.0'