Update setup. Version bump.

LICENSE.txt

@@ -0,0 +1,23 @@
+Copyright (c) 2011-2015 Marinka Zitnik and Blaz Zupan.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.rst

@@ -1,9 +1,9 @@
 Nimfa
 -----
 
-Nimfa is a Python library that implements a number of nonnegative matrix factorization algorithms.
+Nimfa is a Python module that implements many algorithms for nonnegative matrix factorization.
 
-Documentation and examples on real-world data are at `Nimfa website`_.
+Documentation and examples are at `Nimfa website`_.
 
 .. _Nimfa website: http://nimfa.biolab.si
 

nimfa/__init__.py

@@ -1,10 +1,10 @@
 
 """
-###########
+#################
 Nimfa (``nimfa``)
-###########
+#################
 
-Nimfa is a Python library which includes a number of published matrix
+Nimfa is a Python module which includes a number of published matrix
 factorization algorithms, initialization methods, quality and performance
 measures and facilitates the combination of these to produce new strategies.
 The library represents a unified and efficient interface to matrix
@@ -20,3 +20,5 @@
 
 from nimfa import examples
 from nimfa.methods.factorization import *
+from .version import \
+    short_version as __version__, git_revision as __git_version__

requirements.txt

@@ -0,0 +1,2 @@
+numpy>=1.7.0
+scipy>=0.12.0

setup.cfg

@@ -0,0 +1,2 @@
+[bdist_wheel]
+universal=1

setup.py

@@ -1,21 +1,39 @@
 import os
 from glob import glob
 from setuptools import setup, find_packages
+import subprocess
+import imp
 
-NAME = "nimfa"
 
-def read(fname):
-    return open(os.path.join(os.path.dirname(__file__), fname)).read()
+DISTNAME = 'nimfa'
+MAINTAINER = 'Marinka Zitnik'
+MAINTAINER_EMAIL = '[email protected]'
+DESCRIPTION = 'A Python module for nonnegative matrix factorization'
+LONG_DESCRIPTION = open('README.rst').read()
+URL = 'http://nimfa.biolab.si'
+DOWNLOAD_URL = 'http://github.com/marinkaz/nimfa'
+KEYWORDS = ['matrix factorization', 'nonnegative matrix factorization',
+            'bioinformatics', 'data mining']
+LICENSE = 'GPLv3'
+VERSION = '1.2.2'
+ISRELEASED = True
+
+INSTALL_REQUIRES = (
+    'numpy>=1.7.0',
+    'scipy>=0.12.0',
+)
+
 
 def get_package_data(topdir, excluded=set()):
     retval = []
-    for dirname, subdirs, files in os.walk(os.path.join(NAME, topdir)):
+    for dirname, subdirs, files in os.walk(os.path.join(DISTNAME, topdir)):
         for x in excluded:
             if x in subdirs:
                 subdirs.remove(x)
-        retval.append(os.path.join(dirname[len(NAME)+1:], '*.*'))
+        retval.append(os.path.join(dirname[len(DISTNAME)+1:], '*.*'))
     return retval
 
+
 def get_data_files(dest, source):
     retval = []
     for dirname, subdirs, files in os.walk(source):
@@ -25,23 +43,103 @@ def get_data_files(dest, source):
     return retval
 
 
-setup(
-    name = NAME,
-    version = "1.2.1",
-    author = "Marinka Zitnik",
-    author_email = "[email protected]",
-    description = "A Python Library for Nonnegative Matrix Factorization Techniques",
-    url = "http://nimfa.biolab.si",
-    download_url = "https://github.com/marinkaz/MF",
-    packages = find_packages(),
-    package_dir = {NAME: "./nimfa"},
-    package_data = {NAME: get_package_data("datasets")},
-    license = "OSI Approved :: GNU General Public License (GPL)",
-    long_description = read("README.rst"),
-    classifiers = [
-        "License :: OSI Approved :: GNU General Public License (GPL)",
-        "Natural Language :: English",
-        "Programming Language :: Python",
-        "Topic :: Scientific/Engineering"
-        ]
-    )
+# Return the git revision as a string
+def git_version():
+    """Return the git revision as a string.
+
+    Copied from numpy setup.py
+    """
+    def _minimal_ext_cmd(cmd):
+        # construct minimal environment
+        env = {}
+        for k in ['SYSTEMROOT', 'PATH']:
+            v = os.environ.get(k)
+            if v is not None:
+                env[k] = v
+        # LANGUAGE is used on win32
+        env['LANGUAGE'] = 'C'
+        env['LANG'] = 'C'
+        env['LC_ALL'] = 'C'
+        out = subprocess.Popen(cmd, stdout = subprocess.PIPE, env=env).communicate()[0]
+        return out
+
+    try:
+        out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
+        GIT_REVISION = out.strip().decode('ascii')
+    except OSError:
+        GIT_REVISION = "Unknown"
+    return GIT_REVISION
+
+
+def write_version_py(filename='nimfa/version.py'):
+    # Copied from numpy setup.py
+    cnt = """
+# THIS FILE IS GENERATED FROM NIMFA SETUP.PY
+short_version = '%(version)s'
+version = '%(version)s'
+full_version = '%(full_version)s'
+git_revision = '%(git_revision)s'
+release = %(isrelease)s
+
+if not release:
+    version = full_version
+    short_version += ".dev"
+"""
+    FULLVERSION = VERSION
+    if os.path.exists('.git'):
+        GIT_REVISION = git_version()
+    elif os.path.exists('nimfa/version.py'):
+        # must be a source distribution, use existing version file
+        version = imp.load_source("nimfa.version", "nimfa/version.py")
+        GIT_REVISION = version.git_revision
+    else:
+        GIT_REVISION = "Unknown"
+
+    if not ISRELEASED:
+        FULLVERSION += '.dev0+' + GIT_REVISION[:7]
+
+    a = open(filename, 'w')
+    try:
+        a.write(cnt % {'version': VERSION,
+                       'full_version': FULLVERSION,
+                       'git_revision': GIT_REVISION,
+                       'isrelease': str(ISRELEASED)})
+    finally:
+        a.close()
+
+
+
+def setup_package():
+    write_version_py()
+    setup(
+        name=DISTNAME,
+        version=VERSION,
+        author=MAINTAINER,
+        author_email=MAINTAINER_EMAIL,
+        maintainer=MAINTAINER,
+        maintainer_email=MAINTAINER_EMAIL,
+        description=DESCRIPTION,
+        url=URL,
+        download_url=DOWNLOAD_URL,
+        keywords=KEYWORDS,
+        install_requires=INSTALL_REQUIRES,
+        packages=find_packages(),
+        package_dir={DISTNAME: "./nimfa"},
+        package_data={DISTNAME: get_package_data("datasets")},
+        license=LICENSE,
+        long_description=LONG_DESCRIPTION,
+        classifiers=['Intended Audience :: Science/Research',
+                     'Intended Audience :: Developers',
+                     'License :: OSI Approved',
+                     'Programming Language :: Python',
+                     'Topic :: Software Development',
+                     'Topic :: Scientific/Engineering',
+                     'Topic :: Scientific/Engineering :: Artificial Intelligence',
+                     'Topic :: Scientific/Engineering :: Bio-Informatics',
+                     'Programming Language :: Python :: 2',
+                     'Programming Language :: Python :: 3',],
+        )
+
+
+if __name__ == "__main__":
+    setup_package()