Setup using requirements.txt and cython code compiled on setup

.gitignore

@@ -23,6 +23,11 @@ example/output
 *.egg-info/
 dist/
 
+# Cython compiled code
+build/*
+*.so
+*.c
+
 *.pickle.gz
 example/cds
 example/cdsOriginal

MANIFEST.in

@@ -0,0 +1,5 @@
+# Files to be included in the distribution
+include MANIFEST.in
+include requirements.txt
+include optional-requirements.txt
+global-exclude *.c *.so

README.rst

@@ -1,12 +1,18 @@
+.. _readme:
+
 OncodriveFML
 ============
 
 Recent years saw the development of methods to detect signals of positive selection in the pattern of somatic mutations in genes across cohorts of tumors, and the discovery of hundreds of driver genes. The next major challenge in tumor genomics is the identification of non-coding regions which may also drive tumorigenesis. We present OncodriveFML, a method that estimates the accumulated functional impact bias of somatic mutations in any genomic region of interest based on a local simulation of the mutational process affecting it. It may be applied to all genomic elements to detect likely drivers amongst them. OncodriveFML can discover signals of positive selection when only a small fraction of the genome, like a panel of genes, has been sequenced.
 
+.. _readme license:
+
 License
 -------
 OncodriveFML is made available to the general public subject to certain conditions described in its `LICENSE <LICENSE>`_. For the avoidance of doubt, you may use the software and any data accessed through UPF software for academic, non-commercial and personal use only, and you may not copy, distribute, transmit, duplicate, reduce or alter in any way for commercial purposes, or for the purpose of redistribution, without a license from the Universitat Pompeu Fabra (UPF). Requests for information regarding a license for commercial use or redistribution of OncodriveFML may be sent via e-mail to [email protected].
 
+.. _readme install:
+
 Installation
 ------------
 
@@ -25,9 +31,30 @@ Finally, you can get the latest code from the repository and install with ``pip`
         $ cd oncodrivefml
         $ pip install .
 
+.. note::
+
+   OncodriveFML has a set up dependency with `Cython <http://cython.org/>`_,
+   which is required to compile the :file:`*.pyx` files.
+
+
 The first time that you run OncodriveFML it will download the genome reference from our servers.
 By default the downloaded datasets go to ``~/.bgdata`` if you want to move this datasets to another folder you have to define the system environment variable BGDATA_LOCAL with an export command.
 
 The following command will show you the command help::
 
 	$ oncodrivefml --help 
+
+.. _readme docs:
+
+Documentation
+-------------
+
+Find OncodriveFML documentation in ReadTheDocs.
+.. TODO link
+
+You can also compile the documentation yourself using `Sphinx <http://www.sphinx-doc.org/en/stable/>`_.
+To do so, intall the optional packages in :file:`optional-requirements.txt` and build the
+documentation in the docs folder::
+
+    $ cd docs
+    $ make html

oncodrivefml/__init__.py

@@ -1,2 +1,2 @@
 __logger_name__ = 'oncodrivefml'
-__version__ = "1.2.1"
+__version__ = "2.0.0"

oncodrivefml/walker.py

@@ -1,9 +1,6 @@
 import numpy as np
-import pyximport
 
 from oncodrivefml.stats import STATISTIC_TESTS
-
-pyximport.install()
 from oncodrivefml.walker_cython import walker_sampling
 
 
@@ -103,4 +100,4 @@ def compute_sampling_cython(samples, muts, obs_val, scores, probs):
 
     s = time.time()
     obs, neg_obs = compute_sampling_cython(samples, muts, obs_val, scores, probs)
-    print("Cython time: {} Obs:{} Neg_obs:{}".format(time.time() - s, obs, neg_obs))
+    print("Cython time: {} Obs:{} Neg_obs:{}".format(time.time() - s, obs, neg_obs))

optional-requirements.txt

@@ -0,0 +1,3 @@
+# This packages are required to build the documentation
+sphinx>=1.5.1
+sphinx_rtd_theme>=0.1.9

requirements.txt

@@ -0,0 +1,17 @@
+bgconfig>=0.5
+numpy>=1.11.2
+scipy>=0.18
+statsmodels>=0.8
+pytabix>=0.1
+bokeh>=0.12
+pandas>=0.19
+matplotlib>=1.5.3
+intervaltree>=2.1
+bgqmap>=1.0
+bgdata>=1.0
+itab>=0.9
+bgreference>=0.1
+click>=6.7
+bgparsers>=0.1
+#bgcache>=0.1
+cython>=0.25.2

setup.py

@@ -1,10 +1,14 @@
-import sys
-from setuptools import setup, find_packages
 
+from os import path
+
+from setuptools import Extension
+from setuptools import setup, find_packages
 from oncodrivefml import __version__
 
-if sys.hexversion < 0x03000000:
-    raise RuntimeError('This package requires Python 3.0 or later.')
+
+directory = path.dirname(path.abspath(__file__))
+with open(path.join(directory, 'requirements.txt')) as f:
+    required = f.read().splitlines()
 
 setup(
     name='oncodrivefml',
@@ -14,28 +18,14 @@
     url="https://bitbucket.org/bbglab/oncodrivefml",
     download_url="https://bitbucket.org/bbglab/oncodrivefml/get/"+__version__+".tar.gz",
     license='UPF Free Source Code',
-    author='Biomedical Genomics Group',
-    author_email='[email protected]',
+    author='BBGLab (Barcelona Biomedical Genomics Lab)',
+    author_email='[email protected]',
     description='',
-    install_requires=[
-        'bgconfig >= 0.5.0',
-        'numpy >= 1.9.0',
-        'scipy >= 0.14.0',
-        'statsmodels >= 0.6.1',
-        'pytabix >= 0.1',
-        'bokeh >= 0.12',
-        'pandas >= 0.15.2',
-        'matplotlib >= 1.4.0',
-        'intervaltree >= 2.1.0',
-        'bgqmap >= 1.0.0',
-        'bgdata >= 0.6.0',
-        'itab >= 0.3.0',
-        'bgreference >= 0.1.1',
-        'click >= 5.0',
-        'bgparsers>=0.1',
-        'bgcache>=0.1'
+    setup_requires=[
+        'cython',
     ],
-
+    install_requires=required,
+    ext_modules=[Extension('oncodrivefml.walker_cython', ['oncodrivefml/walker_cython.pyx'])],
     entry_points={
         'console_scripts': [
             'oncodrivefml = oncodrivefml.main:cmdline'