From c623ad9dbbf80d49a64c54f498fa683c8ce50769 Mon Sep 17 00:00:00 2001
From: Allen Lynch <alynch@dsalynchmacport.local>
Date: Thu, 3 Sep 2020 14:39:49 -0400
Subject: [PATCH] ready to publish

---
 .../README-checkpoint.ipynb                   |  57 ++++++++
 docs/README.ipynb                             | 125 ------------------
 setup.py                                      |   1 +
 3 files changed, 58 insertions(+), 125 deletions(-)
 create mode 100644 docs/.ipynb_checkpoints/README-checkpoint.ipynb
 delete mode 100644 docs/README.ipynb

diff --git a/docs/.ipynb_checkpoints/README-checkpoint.ipynb b/docs/.ipynb_checkpoints/README-checkpoint.ipynb
new file mode 100644
index 0000000..1c152d4
--- /dev/null
+++ b/docs/.ipynb_checkpoints/README-checkpoint.ipynb
@@ -0,0 +1,57 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# LISA: Landscape In-Silico deletion Analysis\n",
+    "<hr>\n",
+    "\n",
+    "## About\n",
+    "\n",
+    "LISA predicts which TFs regulate a set of genes using integrative modeling of chromatin accessiblity and ChIP-seq binding. Particularly, LISA models the effects of deleting the influence of a TF on the expression of the genes-of-interest. For more information, see <a href=https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1934-6>https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1934-6</a>. This implementation extends the original, running 30x faster, reducing dependencies, and adding useful CLI functions for pipeline integration. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Requirements\n",
+    "\n",
+    "* python >= 3.6\n",
+    "* numpy, scipy, scikit-learn, and h5py\n",
+    "* ~15GB of storage space"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Installation\n",
+    "\n",
+    "LISA is available for install from PyPI. It is recommended that you set up a virtual environment using ```venv```, then run:"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "lisa_test",
+   "language": "python",
+   "name": "lisa_test"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/docs/README.ipynb b/docs/README.ipynb
deleted file mode 100644
index 5dc94d5..0000000
--- a/docs/README.ipynb
+++ /dev/null
@@ -1,125 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!source /Users/alynch/projects/.venvs/lisa_test/bin/activate"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import lisa"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import pandas as pd"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 9,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "c = pd.read_csv('/Users/alynch/projects/.venvs/lisa_test/lib/python3.7/site-packages/lisa/data/hg38/metadata/Motifs.tsv',\n",
-    "               sep = '\\t', encoding = 'latin')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 11,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "0       ATF2::JUN\n",
-       "1            IRF1\n",
-       "2           TFCP2\n",
-       "3           RUNX1\n",
-       "4           ZBTB6\n",
-       "          ...    \n",
-       "1056         ELF2\n",
-       "1057         Etv5\n",
-       "1058         Elf4\n",
-       "1059         Etv6\n",
-       "1060       Gm5454\n",
-       "Name: symbol, Length: 1061, dtype: object"
-      ]
-     },
-     "execution_count": 11,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "c.symbol"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 13,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Index(['id', 'edition', 'source', 'sourcefile', 'status', 'numseqs', 'pmid',\n",
-       "       'dbd', 'family', 'description', 'species', 'cellline', 'entrez',\n",
-       "       'symbol', 'synonym', 'refseq', 'cluster', 'comment2', 'comment2.1',\n",
-       "       'comment3', 'comment4', 'comment5', 'datasetid', 'zscore', 'seqfactors',\n",
-       "       'seqdbds', 'seqdatasetid', 'nmotifs', 'pssm'],\n",
-       "      dtype='object')"
-      ]
-     },
-     "execution_count": 13,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "c.columns"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "bioenv",
-   "language": "python",
-   "name": "bioenv"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.6.10"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
diff --git a/setup.py b/setup.py
index a33503a..8c1ed99 100644
--- a/setup.py
+++ b/setup.py
@@ -23,4 +23,5 @@
         'scikit-learn'
     ],
     include_package_data=True,
+    python_requires='>=3.6',
 )
\ No newline at end of file