Changes in [1622:3d2f34a594e5:1654:61fbdcb67aab] in orange-bioinformatics


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Files:
203 added
200 deleted
4 edited

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  • .hgtags

    r1586 r1624  
    1 412f9d1e1da135dade3c563112ff6f8af36da077 1.1a 
    21973f84dca0f2488aa4ddd587e07fae26ae4fb9da 1.1a 
  • MANIFEST.in

    r1420 r1650  
    1 include *.py *.txt addon.xml 
    2 recursive-include widgets * 
    3 recursive-include doc * 
     1recursive-include _bioinformatics *.png 
     2recursive-include scripts * 
     3recursive-include tests * 
     4include COPYING 
     5include LICENSE 
     6include *.py *.txt *.rst 
  • setup.py

    r1596 r1653  
    11#!/usr/bin/env python 
    2 """\ 
    3 Orange Bioinformatics 
    4 ===================== 
    52 
    6 Orange Bioinformatics is an add-on for Orange data mining  
    7 software package. It extends Orange by providing common functionality 
    8 for basic tasks in bioinformatics. 
    9 """ 
     3import distribute_setup 
     4distribute_setup.use_setuptools() 
    105 
    11 DOCLINES = __doc__.split("\n") 
     6import os 
    127 
    13 try: 
    14     from setuptools import setup 
    15     have_setuptools = True 
    16 except ImportError: 
    17     from distutils.core import setup 
    18     have_setuptools = False 
     8from setuptools import setup, find_packages 
    199 
    20 import os, glob 
     10NAME = 'Orange-Bioinformatics' 
    2111 
    22 CLASSIFIERS = """\ 
    23 Development Status :: 4 - Beta 
    24 Programming Language :: Python 
    25 License :: OSI Approved :: GNU General Public License (GPL) 
    26 Operating System :: POSIX 
    27 Operating System :: Microsoft :: Windows 
    28 Topic :: Scientific/Engineering :: Visualization 
    29 Topic :: Scientific/Engineering :: Bio-Informatics 
    30 Intended Audience :: Education 
    31 Intended Audience :: Science/Research 
    32 """ 
     12VERSION = '1.1a' 
    3313 
    34 KEYWORDS = """\ 
    35 data mining  
    36 machine learning, 
    37 artificial intelligence 
    38 bioinformatics, 
    39 gene ontology 
    40 KEGG 
    41 expression profiles 
    42 """                       
     14DESCRIPTION = 'Orange Bioinformatics add-on for Orange data mining software package.' 
     15LONG_DESCRIPTION = open(os.path.join(os.path.dirname(__file__), 'README.rst')).read() 
     16AUTHOR = 'Bioinformatics Laboratory, FRI UL' 
     17AUTHOR_EMAIL = 'contact@orange.biolab.si' 
     18URL = 'http://orange.biolab.si/addons/' 
     19DOWNLOAD_URL = 'https://bitbucket.org/biolab/orange-bioinformatics/downloads' 
     20LICENSE = 'GPLv3' 
    4321 
    44 NAME                = "Orange-Bioinformatics" 
    45 DESCRIPTION         = DOCLINES[0] 
    46 LONG_DESCRIPTION    = "\n".join(DOCLINES[3:]) 
    47 URL                 = "http://www.biolab.si/obi/" 
    48 DOWNLOAD_URL        = "https://bitbucket.org/biolab/orange-addon-bioinformatics/downloads" 
    49 LICENSE             = "GNU General Public License (GPL)" 
    50 CLASSIFIERS         = filter(None, CLASSIFIERS.split("\n")) 
    51 AUTHOR              = "Bioinformatics Laboratory, FRI UL" 
    52 AUTHOR_EMAIL        = "orange@fri.uni-lj.si" 
    53 KEYWORDS            = filter(None, KEYWORDS.split('\n')) 
     22KEYWORDS = ( 
     23    'data mining', 
     24    'machine learning', 
     25    'artificial intelligence', 
     26    'bioinformatics', 
     27    'gene ontology', 
     28    'KEGG', 
     29    'expression profiles', 
     30    'microarray', 
     31    'genomics', 
     32) 
    5433 
    55 MAYOR = 1 
    56 MINOR = 1 
    57 MICRO = 0 
    58 ISRELEASED = False 
     34CLASSIFIERS = ( 
     35    'Development Status :: 4 - Beta', 
     36    'Environment :: X11 Applications :: Qt', 
     37    'Environment :: Console', 
     38    'Environment :: Plugins', 
     39    'Programming Language :: Python', 
     40    'Framework :: Orange', 
     41    'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)', 
     42    'Operating System :: OS Independent', 
     43    'Topic :: Scientific/Engineering :: Artificial Intelligence', 
     44    'Topic :: Scientific/Engineering :: Visualization', 
     45    'Topic :: Scientific/Engineering :: Bio-Informatics', 
     46    'Topic :: Software Development :: Libraries :: Python Modules', 
     47    'Intended Audience :: Education', 
     48    'Intended Audience :: Science/Research', 
     49    'Intended Audience :: Developers', 
     50) 
    5951 
    60 VERSION = "%i.%ia.%i" % (MAYOR, MINOR, MICRO) 
     52PACKAGES = find_packages( 
     53    exclude = ('*.tests', '*.tests.*', 'tests.*', 'tests'), 
     54) 
     55  
     56PACKAGE_DATA = { 
     57} 
    6158 
     59SETUP_REQUIRES = ( 
     60    'distribute', 
     61) 
    6262 
    63 # list all documentation files that need to be included 
    64 docFiles = [] 
    65 for (dirp, dirns, n) in os.walk('doc'): 
    66     nr = [n1.replace('\\', '/') for n1 in n] 
    67     dirn = dirp.replace('\\', '/')[4:] 
    68     if len(dirn): 
    69         dirn = dirn + '/' 
    70     docFiles.extend( [dirn + n1r for n1r in nr if '.svn' not in dirp + '/' + n1r] ) 
     63INSTALL_REQUIRES = ( 
     64    'Orange', 
     65    'distribute', 
     66    'suds', 
     67    'numpy', 
     68    'requests', 
     69    'oasa', 
     70    'bkchem', 
     71    'PIL', 
     72    'networkx', 
     73    'pygraphviz', 
     74    # Dependencies which are problematic to install automatically 
     75    #'openbabel-python', # You get bindings together with the openbabel library and not stand-alone 
     76    #'scipy', # Requires Fortran compiler 
     77    #'matplotlib', # Requires that numpy is installed first 
     78), 
    7179 
    72 DEST_DIR="Orange/add-ons/Bioinformatics" 
     80EXTRAS_REQUIRE = { 
     81    'GUI': ( 
     82        # Dependencies which are problematic to install automatically 
     83        #'PyQt', # No setup.py 
     84    ), 
     85} 
    7386 
     87DEPENDENCY_LINKS = ( 
     88    'http://bkchem.zirael.org/download/bkchem-0.13.0.tar.gz', 
     89    'http://orange.biolab.si/download/bkchem-0.13.0.tar.gz', 
     90    'http://bkchem.zirael.org/download/oasa-0.13.1.tar.gz', 
     91    'http://orange.biolab.si/download/oasa-0.13.1.tar.gz', 
     92) 
    7493 
    75 if os.path.exists("VERSION.txt"): 
    76     VERSION = open("VERSION.txt", "rb").read() 
     94ENTRY_POINTS = { 
     95    'orange.addons': ( 
     96        'bioinformatics = _bioinformatics', 
     97    ), 
     98    'orange.widgets': ( 
     99        'Bioinformatics = _bioinformatics.widgets', 
     100        # This should be unneeded, because module given should load (register) 
     101        # all wanted widgets and prototypes should just have a flag, but for now ... 
     102        'Prototypes = _bioinformatics.widgets.prototypes', 
     103    ), 
     104} 
    77105 
    78 if have_setuptools: 
    79     setuptool_args = {"install_requires": ["Orange", "suds"], 
    80                       "zip_safe": False, 
    81                      } 
    82 else: 
    83     setuptool_args = {} 
    84      
    85 PACKAGES = [ 'widgets', 'widgets.prototypes', 'doc', '', 
    86              'obiKEGG2', 'obiKEGG2.entry' ] 
    87      
    88 PACKAGE_DATA = {'widgets': ['icons/*.png'], 
    89                 'doc': docFiles, 
    90                 '':["addon.xml"] 
    91                 } 
    92                            
    93 if __name__ == "__main__": 
    94     setup(name = NAME, 
    95           version = VERSION, 
    96           description = DESCRIPTION, 
    97           long_description = LONG_DESCRIPTION, 
    98           author = AUTHOR, 
    99           author_email = AUTHOR_EMAIL, 
    100           url = URL, 
    101           download_url = DOWNLOAD_URL, 
    102           license = LICENSE, 
    103           keywords = KEYWORDS, 
    104           classifiers = CLASSIFIERS, 
    105           package_dir = {"": "."}, 
    106           packages = PACKAGES, 
    107           package_data = PACKAGE_DATA, 
    108           extra_path=("orange-bioinformatics", DEST_DIR), 
    109            
    110           **setuptool_args) 
     106if __name__ == '__main__': 
     107    setup( 
     108        name = NAME, 
     109        version = VERSION, 
     110        description = DESCRIPTION, 
     111        long_description = LONG_DESCRIPTION, 
     112        author = AUTHOR, 
     113        author_email = AUTHOR_EMAIL, 
     114        url = URL, 
     115        download_url = DOWNLOAD_URL, 
     116        license = LICENSE, 
     117        keywords = KEYWORDS, 
     118        classifiers = CLASSIFIERS, 
     119        packages = PACKAGES, 
     120        package_data = PACKAGE_DATA, 
     121        setup_requires = SETUP_REQUIRES, 
     122        install_requires = INSTALL_REQUIRES, 
     123        extras_require = EXTRAS_REQUIRE, 
     124        dependency_links = DEPENDENCY_LINKS, 
     125        entry_points = ENTRY_POINTS, 
     126        include_package_data = True, 
     127        zip_safe = False, 
     128    ) 
  • tests/test_kegg.py

    r1548 r1632  
    11import unittest 
    2 import obiKEGG2 as kegg 
     2 
     3from Orange.bioinformatics import obiKEGG2 as kegg 
    34 
    45#from obiKEGGservices import  
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