Changeset 45

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Timestamp:
08/26/09 19:38:41 (2 years ago)
Author:
mauro
Message:

* refactoring

Location:
plone4bio.base/trunk
Files:
184 added
1 removed
5 modified

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  • plone4bio.base/trunk

    • Property svn:ignore set to

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  • plone4bio.base/trunk/README.txt

    r14 r45  
    1 plone4bio 
    2 ========= 
    3  
    4 Overview 
    5 -------- 
    6  
    7 The *plone4bio* package provides the possibility to add a new content 
    8 type, called `sequence', than can be either written by hand or imported 
    9 from a FASTA file, and to apply to that sequence a program, called 
    10 `predictor', that gives a back a plot of predicted probabilites for the 
    11 sequence to have a given property (the property that the predictor tries 
    12 to determine).  
    13  
    14 A predictor can try to assess if a protein sequence is trans-membrane, 
    15 whether a signal peptide exists, and so on.  
    16  
    17 The *plone4bio.base* is a package that defines a skeleton 
    18 predictor: deriving from that it is possible to integrate any other 
    19 application and visualize all the results together.  A predictor can be 
    20 a pure Python program or another application wrapped to be usable by the 
    21 interface defined in the *plone4bio.base* package. 
    22  
    23 Developer Notes 
    24 --------------- 
    25  
    26 The plone4bio* plone products are mainly developed on Debian Stable, so 
    27 they are mainly tested in that environment. Usually there should be no 
    28 problem in installing the products in GNU/Linux Zope/Plone environments. 
    29  
    30 This product is produced independently from the product Plone, and carries no 
    31 guarantee from the Plone Foundation about quality, suitability or anything 
    32 else. The supplier of this product assumes all responsibility for it. 
    33  
    34 Maintainer 
    35 ---------- 
    36  
    37 Mauro Amico (amico AT biodec DOT com) is the active maintainer of the 
    38 *plone4bio.base* framework. 
     1see: ./src/plone4bio/base/README.txt 

  • plone4bio.base/trunk/docs/COPYRIGHT.txt

    r8 r45  
    22plone4bio.base is a software to predict properties of biosequences, 
    33meant to be used in a bioinformatics content management system. 
    4 plone4bio.base is Copyright (C) 2008 BioDec S.r.l. 
     4plone4bio.base is Copyright (C) 2008-2009 BioDec S.r.l. 

  • plone4bio.base/trunk/docs/LICENSE.txt

    r8 r45  
    2424 
    2525BioDec S.r.l. is an Italian company: 
    26         * Address: BioDec S.r.l.; via Calzavecchio 20/2; I-40033 
    27         Casalecchio di Reno (BO), Italy 
     26        * Address: BioDec S.r.l. 
     27                via Calzavecchio 20/2  
     28                I-40033 Casalecchio di Reno (BO)  
     29                Italy 
    2830 
    2931This General Public License does not permit incorporating your program 

  • plone4bio.base/trunk/setup.py

    r8 r45  
    11from setuptools import setup, find_packages 
    22 
    3 version = '0.9' 
    4 readme = open('README.txt') 
     3version = '1.0.1' 
     4readme = open('./src/plone4bio/base/README.txt') 
    55long_description = readme.read() 
    66readme.close() 
    … …  
    88setup(name='plone4bio.base', 
    99      version=version, 
    10       description="", 
    11       long_description="""\ 
    12 """, 
     10      description="Plone4Bio base package", 
     11      long_description=long_description, 
    1312      # Get more strings from http://www.python.org/pypi?%3Aaction=list_classifiers 
    1413      classifiers=[ 
    … …  
    1615        "Framework :: Zope2", 
    1716        "Framework :: Zope3", 
     17        "Framework :: Bio", 
    1818        "Programming Language :: Python", 
    1919        "Topic :: Software Development :: Libraries :: Python Modules", 
    2020        ], 
    2121      keywords='', 
    22       author='BioDec Srl', 
    23       author_email='', 
    24       url='http://www.biodec.com', 
     22      author='Mauro Amico', 
     23      author_email='mauro@biodec.com', 
     24      url='http://www.plone4bio.org', 
    2525      license='GPL', 
    26       packages=find_packages(exclude=['ez_setup']), 
     26      packages=find_packages('src', exclude=['ez_setup']), 
     27      package_dir = {'':'src'}, 
    2728      namespace_packages=['plone4bio'], 
    2829      include_package_data=True, 
    … …  
    3132          'setuptools', 
    3233          # -*- Extra requirements: -*- 
     34          'biopython', 
    3335      ], 
    3436      entry_points="""