Discussion :

[bioinfornatics]

Bonjour,
Je souhaite généré un fichier .ini durant l'install stokant les informations relatives au chemin d'installation des données.
En effet si un utilisateur ne stocke pas a un endroit prévue notamment en utilisant --home-dir .... le programme n'a aucun moyen post installation de connaitre la localisation
Donc l'idée était de stocker ces chemin dans un fichier, voilà ce que ça donne:

Code :

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from distutils.command.build        import build        as _build
from distutils.command.build_py     import build_py     as _build_py
from distutils.command.install_data import install_data as _install_data
from distutils.command.install_lib  import install_lib  as _install_lib
from distutils.command.install      import install      as _install
from distutils.core                 import setup, Command
from distutils.errors               import DistutilsFileError
import subprocess, shutil, os, fileinput, sys, re, glob
from os.path import *
sys.path.insert(0, join(dirname(__file__), "src"))
 
class package_ini(Command):
    """
    Locate "package.ini" in all installed packages and patch it as requested
    by wildcard references to install process.
    """
 
    user_options    = []
 
 
    def initialize_options(self):
        pass
 
    def finalize_options(self):
        pass
 
    def visit(self, dirname, names):
        packages = self.distribution.get_command_obj(_build_py.__name__).packages
        if basename(dirname) in packages:
            if "package.ini" in names:
                self.patch(join(dirname, "package.ini"))
 
    def patch(self, ini_file):
        print "patching file" + ini_file
        with open(ini_file,"r") as infile:
            file_data = infile.readlines()
        with open(ini_file,"w") as outfile:
            for line in file_data:
                _line = self.patch_line(line)
                if _line:
                    line = _line
                outfile.write(line)
 
    def patch_line(self, line):
        """
        Patch an installed package.ini with setup"s variables
        """
        match = re.match("(?P<identifier>\w+)\s*=.*##SETUP_PATCH\\((?P<command>.*)\.(?P<variable>.*)\\)", line)
        if not match:
            return line
        print "Replacing:"+line
        line = match.group("identifier")
        line += " = "
        data = "(self).distribution.get_command_obj(\""+\
                match.group("command")+"\")"+"."+\
                match.group("variable")
        line += "\""+ eval(data)+ "\"" + "\n"
        print "With:" + line
        return line
 
    def run(self):
        """
        Patch package.ini files in distribution package with variables from setup
        """
        walk(
            self.distribution.get_command_obj(install.__name__).install_lib,
            package_ini.visit,
            self
        )
 
class install(_install):
    sub_commands = _install.sub_commands + [ (package_ini.__name__, None) ]
 
setup(
        cmdclass        =   {
                                "build_py"      : _build_py     ,
                                "install_data"  : _install_data ,
                                "install_lib"   : _install_lib  ,
                                "install"       : install       ,
                                "package_ini"   : package_ini
                            },
        name            =   "libbbcf",
        version         =   "1.9rc1",
        description     =   "Utility modules for deploying workflows in the BBCF",
        long_description=   open("README").read(),
        keywords        =   "bioinformatic genomic chipseq",
        author          =   "EPFL BBCF,Jonathan Mercier, Fred Ross, Jacques Rougemont",
        author_email    =   "webmaster.bbcf@epfl.ch",
        license         =   "GPLv3",
        packages        =   ["bbcf", "bbcf.core", "bbcf.binding"],
        package_dir     =   {"bbcf": "src/bbcf"},
        package_data    =   {"bbcf":["package.ini"]},
        data_files      =   [
                                ( "share/bbcf/", glob.glob("data/bbcf.sql") ),
                                ( "share/bbcf/", ["README"]                 ),
                                ( "share/bbcf/", ["LICENSE"]                )
                            ],
        install_requires=   ["bein", "pysqlite"],
        classifiers     =   [
                                "Topic :: Scientific/Engineering :: Bio-Informatics",
                                "Intended Audience :: Developers"                   ,
                                "Programming Language :: Python"                    ,
                                "Environment :: Console"                            ,
                                "License :: OSI Approved :: GNU GPLv3"              ,
                                "Operating System :: MacOS :: MacOS X"              ,
                                "Operating System :: Microsoft :: Windows"          ,
                                "Operating System :: POSIX"
                            ]
      )

et la sortie

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# python setup.py -v install --record files.txt
/usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
  warnings.warn(msg)
running install
running build
running build_py
copying src/bbcf/__init__.py -> build/lib/bbcf
copying src/bbcf/core/matrix.py -> build/lib/bbcf/core
copying src/bbcf/core/pattern.py -> build/lib/bbcf/core
copying src/bbcf/core/generic.py -> build/lib/bbcf/core
copying src/bbcf/core/exception.py -> build/lib/bbcf/core
copying src/bbcf/core/format.py -> build/lib/bbcf/core
copying src/bbcf/core/sequence.py -> build/lib/bbcf/core
copying src/bbcf/core/data.py -> build/lib/bbcf/core
copying src/bbcf/core/common.py -> build/lib/bbcf/core
copying src/bbcf/core/__init__.py -> build/lib/bbcf/core
copying src/bbcf/binding/genrep.py -> build/lib/bbcf/binding
copying src/bbcf/binding/__init__.py -> build/lib/bbcf/binding
copying src/bbcf/binding/database.py -> build/lib/bbcf/binding
copying src/bbcf/binding/gdv.py -> build/lib/bbcf/binding
copying src/bbcf/binding/meme.py -> build/lib/bbcf/binding
copying src/bbcf/binding/hts.py -> build/lib/bbcf/binding
running install_lib
not copying build/lib/bbcf/__init__.py (output up-to-date)
not copying build/lib/bbcf/binding/genrep.py (output up-to-date)
not copying build/lib/bbcf/binding/__init__.py (output up-to-date)
not copying build/lib/bbcf/binding/database.py (output up-to-date)
not copying build/lib/bbcf/binding/gdv.py (output up-to-date)
not copying build/lib/bbcf/binding/meme.py (output up-to-date)
not copying build/lib/bbcf/binding/hts.py (output up-to-date)
not copying build/lib/bbcf/core/matrix.py (output up-to-date)
not copying build/lib/bbcf/core/pattern.py (output up-to-date)
not copying build/lib/bbcf/core/generic.py (output up-to-date)
not copying build/lib/bbcf/core/exception.py (output up-to-date)
not copying build/lib/bbcf/core/format.py (output up-to-date)
not copying build/lib/bbcf/core/sequence.py (output up-to-date)
not copying build/lib/bbcf/core/data.py (output up-to-date)
not copying build/lib/bbcf/core/common.py (output up-to-date)
not copying build/lib/bbcf/core/__init__.py (output up-to-date)
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/__init__.py to __init__.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/binding/genrep.py to genrep.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/binding/__init__.py to __init__.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/binding/database.py to database.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/binding/gdv.py to gdv.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/binding/meme.py to meme.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/binding/hts.py to hts.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/core/matrix.py to matrix.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/core/pattern.py to pattern.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/core/generic.py to generic.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/core/exception.py to exception.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/core/format.py to format.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/core/sequence.py to sequence.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/core/data.py to data.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/core/common.py to common.pyc
skipping byte-compilation of /usr/lib/python2.7/site-packages/bbcf/core/__init__.py to __init__.pyc
running install_data
copying data/bbcf.sql -> /usr/share/bbcf/
copying README -> /usr/share/bbcf/
copying LICENSE -> /usr/share/bbcf/
running install_egg_info
Removing /usr/lib/python2.7/site-packages/libbbcf-1.9rc1-py2.7.egg-info
Writing /usr/lib/python2.7/site-packages/libbbcf-1.9rc1-py2.7.egg-info
running package_ini
Traceback (most recent call last):
  File "setup.py", line 107, in <module>
    "Operating System :: POSIX"
  File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/usr/lib64/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/usr/lib64/python2.7/distutils/command/install.py", line 582, in run
    outputs = self.get_outputs()
  File "/usr/lib64/python2.7/distutils/command/install.py", line 625, in get_outputs
    for filename in cmd.get_outputs():
  File "/usr/lib64/python2.7/distutils/cmd.py", line 105, in __getattr__
    raise AttributeError, attr
AttributeError: get_outputs

Merci par avance de toute aide