From 0deebbcdf3d425085e09bd91e4bd734f06ca0d6a Mon Sep 17 00:00:00 2001
From: Simone Zaccaria <simozacca@gmail.com>
Date: Mon, 13 Jul 2020 23:52:59 -0400
Subject: [PATCH] Packaging CHISEL with setuptools

---
 bin/__init__.py |  1 +
 setup.py        | 55 +++++++++++++++++++++++++++++++++++++++++++++++++
 src/__init__.py |  1 +
 3 files changed, 57 insertions(+)
 create mode 100644 bin/__init__.py
 create mode 100644 setup.py
 create mode 100644 src/__init__.py

diff --git a/bin/__init__.py b/bin/__init__.py
new file mode 100644
index 0000000..11d27f8
--- /dev/null
+++ b/bin/__init__.py
@@ -0,0 +1 @@
+__version__ = '0.1'
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..cc3477c
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,55 @@
+import setuptools
+
+
+setuptools.setup(
+    name='chisel',
+    version='0.1',
+    python_requires='2.7',
+    scripts=['bin/chisel.py', 
+             'bin/chisel-calling.py',
+             'bin/chisel-cloning.py',
+             'bin/chisel-plotting.py',
+             'bin/chisel-pseudonormal.py']
+    author='Simone Zaccaria',
+    author_email='zaccaria@princeton.edu',
+    description='Copy-number Haplotype Inference in Single-cell by Evolutionary Links',
+    long_description='https://github.com/raphael-group/chisel',
+    long_description_content_type='text/markdown',
+    url='https://github.com/ENCODE-DCC/caper',
+    packages=setuptools.find_packages(exclude=['conda',
+                                               'demos', 
+                                               'doc', 
+                                               'demos', 
+                                               'guides', 
+                                               'man']),
+    install_requires=[
+        'numpy==1.16.1',
+        'scipy==1.2.1',
+        'pandas==0.20.1',
+        'matplotlib==2.0.2',
+        'seaborn==0.7.1'
+    ],
+    license='BSD',
+    platforms=["Linux", "MacOs", "Windows"],
+    classifiers=[
+        'Programming Language :: Python :: 2.7',
+        "Intended Audience :: Science/Research",
+        "Natural Language :: English",
+        "Operating System :: MacOS :: MacOS X",
+        "Operating System :: Microsoft :: Windows",
+        "Operating System :: POSIX :: Linux",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+    ],
+    keywords=[
+        'scientific',
+        'sequence analysis',
+        'cancer',
+        'single-cell',
+        'DNA',
+        'copy-number'],
+    entry_points={'console_scripts': ['chisel = bin.chisel:main', 
+                                      'chisel-calling = bin.chisel-calling:main',
+                                      'chisel-cloning = bin.chisel-cloning:main',
+                                      'chisel-plotting = bin.chisel-plotting:main',
+                                      'chisel-pseudonormal = bin.chisel-pseudonormal:main']}
+)
diff --git a/src/__init__.py b/src/__init__.py
new file mode 100644
index 0000000..11d27f8
--- /dev/null
+++ b/src/__init__.py
@@ -0,0 +1 @@
+__version__ = '0.1'