diff --git a/MANIFEST.in b/MANIFEST.in index 3856bf4..1d87613 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,3 +1,3 @@ include README.md include cancerscope/resources/* - +include requirements.txt diff --git a/README.md b/README.md index 620da78..36c823d 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ [![build_status](https://travis-ci.org/jasgrewal/cancerscope.svg?branch=master)](https://travis-ci.org/jasgrewal/cancerscope) [![Documentation Status](https://readthedocs.org/projects/cancerscope/badge/?version=latest)](http://cancerscope.readthedocs.io/?badge=latest) [![license](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) +[![downloads](https://img.shields.io/pypi/dw/cancerscope)](https://img.shields.io/pypi/dw/cancerscope) [![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/) [![PyPI pyversions](https://img.shields.io/pypi/pyversions/ansicolortags.svg)](https://pypi.python.org/pypi/cancerscope/) @@ -15,7 +16,7 @@ Since SCOPE is an ensemble-based approach, it is possible to train additional mo ## Installation ### Using theano and lasagne backend -Version 0.41 is the last compatible version (py2.7-py3.7 supported) +All releases pre-Version 1.00 are theano and lasagne compatible (py2.7-py3.7 supported) Before installing **cancerscope**, you will need to install the correct version of the packages [lasagne](https://lasagne.readthedocs.io/en/latest/) and [theano](https://pypi.org/project/Theano/). `pip install --upgrade https://github.com/Theano/Theano/archive/master.zip` diff --git a/cancerscope/__init__.py b/cancerscope/__init__.py index 8ed04ef..5ce121f 100644 --- a/cancerscope/__init__.py +++ b/cancerscope/__init__.py @@ -22,6 +22,6 @@ if sys.version_info < (2, 7): raise ImportError("Cancerscope module requires Python 2.7*") -__version__ = '0.41' +__version__ = '0.42' diff --git a/cancerscope/requirements.txt b/cancerscope/requirements.txt new file mode 100644 index 0000000..5516215 --- /dev/null +++ b/cancerscope/requirements.txt @@ -0,0 +1,9 @@ +coverage +numpy +scikit-learn>=0.18 +scipy +requests +pandas +pyyaml +matplotlib>=2.2.2 +pysocks==1.6.8 diff --git a/setup.py b/setup.py index 76d90a8..71220a7 100755 --- a/setup.py +++ b/setup.py @@ -4,7 +4,7 @@ from setuptools import setup, find_packages import os, sys import re -from tests import * +#from tests import * """Identify basic variables needd for setup""" pckg_dir = os.path.abspath(os.path.dirname(__file__)) @@ -42,7 +42,7 @@ install_requires=requirements, include_package_data=True, zip_safe=False, test_suite='nose.collector', tests_require=['nose'], - classifiers = ['Programming Language :: Python :: 2.7', 'Topic :: Scientific/Engineering :: Artificial Intelligence', 'Development Status :: 5 - Production/Stable', 'Intended Audience :: Healthcare Industry', 'Topic :: Scientific/Engineering :: Medical Science Apps.', 'Topic :: Scientific/Engineering :: Bio-Informatics'], + classifiers = ['Programming Language :: Python :: 2.7', 'Programming Language :: Python :: 3', 'Topic :: Scientific/Engineering :: Artificial Intelligence', 'Development Status :: 5 - Production/Stable', 'Intended Audience :: Healthcare Industry', 'Topic :: Scientific/Engineering :: Medical Science Apps.', 'Topic :: Scientific/Engineering :: Bio-Informatics'], package_data = {'cancerscope': ['resources/*.txt', '*.rst']} ) diff --git a/tests/__init__.py b/tests/__init__.py index 8b13789..e69de29 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -1 +0,0 @@ - diff --git a/tox.ini b/tox.ini index 9727d5b..6c6040c 100644 --- a/tox.ini +++ b/tox.ini @@ -1,8 +1,13 @@ [tox] -envlist = py27,py36 +envlist = py36 +requires = tox-conda [testenv] -deps = pytest commands = + pip install --upgrade https://github.com/Theano/Theano/archive/master.zip + pip install --upgrade https://github.com/Lasagne/Lasagne/archive/master.zip pytest - +deps = + -rrequirements.txt + pytest +passenv = PYTHONPATH diff --git a/~/.cache/pip/http/9/f/3/4/9/9f349e7ef9cbd8b6fc33427ac5bc4b50286d1f573805bb012cd3f0b9 b/~/.cache/pip/http/9/f/3/4/9/9f349e7ef9cbd8b6fc33427ac5bc4b50286d1f573805bb012cd3f0b9 new file mode 100644 index 0000000..0a48190 Binary files /dev/null and b/~/.cache/pip/http/9/f/3/4/9/9f349e7ef9cbd8b6fc33427ac5bc4b50286d1f573805bb012cd3f0b9 differ diff --git a/~/.cache/pip/http/a/1/9/5/3/a19537d3cf37c122db841d6fe4cd322bc10d1a558bb00d146b85cb9a b/~/.cache/pip/http/a/1/9/5/3/a19537d3cf37c122db841d6fe4cd322bc10d1a558bb00d146b85cb9a new file mode 100644 index 0000000..de0699c Binary files /dev/null and b/~/.cache/pip/http/a/1/9/5/3/a19537d3cf37c122db841d6fe4cd322bc10d1a558bb00d146b85cb9a differ diff --git a/~/.cache/pip/http/d/7/0/c/b/d70cb55d2599562ea67c809f3f8e3e30332633b34e60d8cbcba7f877 b/~/.cache/pip/http/d/7/0/c/b/d70cb55d2599562ea67c809f3f8e3e30332633b34e60d8cbcba7f877 new file mode 100644 index 0000000..879a503 Binary files /dev/null and b/~/.cache/pip/http/d/7/0/c/b/d70cb55d2599562ea67c809f3f8e3e30332633b34e60d8cbcba7f877 differ diff --git a/~/.cache/pip/selfcheck/2637447f5adc6e2b39d42b1fd617d542070cbd886c4e0a79691243fd b/~/.cache/pip/selfcheck/2637447f5adc6e2b39d42b1fd617d542070cbd886c4e0a79691243fd new file mode 100644 index 0000000..7a9e4fb --- /dev/null +++ b/~/.cache/pip/selfcheck/2637447f5adc6e2b39d42b1fd617d542070cbd886c4e0a79691243fd @@ -0,0 +1 @@ +{"key":"/projects/jgrewal_prj/mygits/cancerscope/.tox/py37","last_check":"2020-03-18T18:30:55Z","pypi_version":"20.0.2"} \ No newline at end of file