Merge branch 'master' of github.com:SystemsGenetics/GSForge

SystemsGenetics · Jan 7, 2020 · 341ed7e · 341ed7e
2 parents 4ac2f6b + 872bb0f
commit 341ed7e
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diff --git a/README.md b/README.md
@@ -1,4 +1,5 @@
 [![Build Status](https://travis-ci.com/SystemsGenetics/GSForge.svg?branch=master)](https://travis-ci.com/SystemsGenetics/GSForge)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/SystemsGenetics/GSForge/master?filepath=examples%2Fuser_guide.ipynb)
 
 # GSForge
 

diff --git a/binder/environment.yml b/binder/environment.yml
@@ -0,0 +1,28 @@
+name: GSForge
+channels:
+  - conda-forge
+dependencies:
+  - python=3.7
+  - boruta_py
+  - bokeh
+  - click
+  - datashader
+  - h5py
+  - holoviews
+  - jupyter
+  - matplotlib
+  - netcdf4
+  - numpy
+  - pandas
+  - panel
+  - param
+  - scikit-learn
+  - scipy
+  - seaborn
+  - statsmodels
+  - tqdm
+  - umap-learn
+  - pip
+  - pip:
+      - methodtools
+      - git+https://github.com/SystemsGenetics/GSForge
diff --git a/binder/postBuild b/binder/postBuild
@@ -0,0 +1,4 @@
+#!/bin/bash
+GSFORGE_DEMO_DATA="${HOME}/GSForge_demo_data"
+pip install osfclient
+osf -p rbhfz clone "$GSFORGE_DEMO_DATA"
diff --git a/doc/user_guide/index.rst b/doc/user_guide/index.rst
@@ -2,9 +2,6 @@
 User Guide
 **********
 
-*Under Construction...*
-
-
 Getting Started
 ---------------
 

diff --git a/examples/user_guide/R_integration_guide/DESeq2_GeneSets.ipynb b/examples/user_guide/R_integration_guide/DESeq2_GeneSets.ipynb
@@ -4,8 +4,6 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# DESeq2 Integration\n",
-    "\n",
     "*This notebook covers how to run and load a basic `DESeq2` DEG result as a `GSForge.GeneSet`.*\n",
     "\n",
     "---"
@@ -393,8 +391,17 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.7.3"
+  },
+  "pycharm": {
+   "stem_cell": {
+    "cell_type": "raw",
+    "source": [],
+    "metadata": {
+     "collapsed": false
+    }
+   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/examples/user_guide/R_integration_guide/EdgeR_GeneSets.ipynb b/examples/user_guide/R_integration_guide/EdgeR_GeneSets.ipynb
@@ -1,11 +1,15 @@
 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
+   "cell_type": "markdown",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "Coming soon..."
+   ]
   }
  ],
  "metadata": {
@@ -25,8 +29,17 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.7.3"
+  },
+  "pycharm": {
+   "stem_cell": {
+    "cell_type": "raw",
+    "source": [],
+    "metadata": {
+     "collapsed": false
+    }
+   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/examples/user_guide/R_integration_guide/R_GEM_normalizations.ipynb b/examples/user_guide/R_integration_guide/R_GEM_normalizations.ipynb
@@ -1,11 +1,15 @@
 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
+   "cell_type": "markdown",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "Coming soon...\n"
+   ]
   }
  ],
  "metadata": {
@@ -25,8 +29,17 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.7.3"
+  },
+  "pycharm": {
+   "stem_cell": {
+    "cell_type": "raw",
+    "source": [],
+    "metadata": {
+     "collapsed": false
+    }
+   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/setup.py b/setup.py
@@ -1,15 +1,6 @@
 from setuptools import setup, find_packages
 
-setup(
-    name='GSForge',
-    version='0.2',
-    packages=find_packages(),
-    url='https://systemsgenetics.github.io/GSForge/',
-    license='LICENSE.txt',
-    author='Tyler Biggs',
-    author_email='tyler.biggs@wsu.edu',
-    description='Feature (gene) selection package for gene expression data.',
-    install_requires="""\
+requirements = """\
 Boruta
 bokeh
 click
@@ -30,11 +21,17 @@
 statsmodels
 tqdm
 umap_learn
-xarray""".split(),
-    #
-    # ['boruta', 'umap_learn', 'h5py', 'netcdf4',
-    #                   'xarray', 'pandas', 'numpy', 'lightgbm',
-    #                   'param', 'scipy', 'scikit-learn', 'click',
-    #                   'methodtools', 'datashader', 'seaborn'],
-)
+xarray""".split()
 
+setup(
+    name='GSForge',
+    version='0.2',
+    packages=find_packages(),
+    url='https://systemsgenetics.github.io/GSForge/',
+    license='LICENSE.txt',
+    author='Tyler Biggs',
+    author_email='tyler.biggs@wsu.edu',
+    description='Feature (gene) selection package for gene expression data.',
+    python_requires='>3.7',
+    install_requires=requirements,
+)