1. Miha Stajdohar
  2. orange-modelmaps


Miha Stajdohar  committed d0b1937

Wrapped to Orange add-on.

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+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read


View file
+Copyright (C) 2010-2012 Miha Stajdohar, FRI UL
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+This program is distributed in the hope that it will be useful, but WITHOUT ANY
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.
+Together with the source code this program may contain also additional content.
+Unless specified otherwise, this content is available under Creative Commons
+Attribution-ShareAlike license, either version 3.0 of the license, or (at your
+option) any later version.  You are free to copy, distribute, transmit, adapt
+and/or commercially use this content or part(s) of it, provided you publicly,
+clearly and visibly attribute wlan slovenija, open wireless network of
+Slovenia, and provide a link to its website <http://wlan-si.net/>, if
+applicable.  If you alter, transform, or build upon this content or part(s) of
+it, you may distribute the results only under the same or similar license to
+this one.
+For more information about Creative Commons Attribution-ShareAlike license see
+This program may contain, use, link to and/or distribute also parts under third
+party copyright with possibly different licensing conditions. Make sure you
+check and respect also those conditions.


View file
+recursive-include Orange *.png
+recursive-include tests *
+include COPYING
+include LICENSE
+include *.py *.txt *.rst

File README.rst

View file
-Add mm to the PYTHONPATH for examples to work.
+Orange Model Maps
+Orange Model Maps is an add-on for Orange_ data mining software package. It extends Orange by providing modules for building model maps. It also provides widgets for Orange Canvas to enable users explore model maps.
+.. _Orange: http://orange.biolab.si/
+To install Model Maps add-on for Orange run::
+    python setup.py install
+To build Python egg run::
+    python setup.py bdist_egg

File distribute_setup.py

View file
+"""Bootstrap distribute installation
+If you want to use setuptools in your package's setup.py, just include this
+file in the same directory with it, and add this to the top of your setup.py::
+    from distribute_setup import use_setuptools
+    use_setuptools()
+If you want to require a specific version of setuptools, set a download
+mirror, or use an alternate download directory, you can do so by supplying
+the appropriate options to ``use_setuptools()``.
+This file can also be run as a script to install or upgrade setuptools.
+import os
+import sys
+import time
+import fnmatch
+import tempfile
+import tarfile
+from distutils import log
+    from site import USER_SITE
+except ImportError:
+    USER_SITE = None
+    import subprocess
+    def _python_cmd(*args):
+        args = (sys.executable,) + args
+        return subprocess.call(args) == 0
+except ImportError:
+    # will be used for python 2.3
+    def _python_cmd(*args):
+        args = (sys.executable,) + args
+        # quoting arguments if windows
+        if sys.platform == 'win32':
+            def quote(arg):
+                if ' ' in arg:
+                    return '"%s"' % arg
+                return arg
+            args = [quote(arg) for arg in args]
+        return os.spawnl(os.P_WAIT, sys.executable, *args) == 0
+DEFAULT_URL = "http://pypi.python.org/packages/source/d/distribute/"
+Metadata-Version: 1.0
+Name: setuptools
+Version: %s
+Summary: xxxx
+Home-page: xxx
+Author: xxx
+Author-email: xxx
+License: xxx
+Description: xxx
+def _install(tarball, install_args=()):
+    # extracting the tarball
+    tmpdir = tempfile.mkdtemp()
+    log.warn('Extracting in %s', tmpdir)
+    old_wd = os.getcwd()
+    try:
+        os.chdir(tmpdir)
+        tar = tarfile.open(tarball)
+        _extractall(tar)
+        tar.close()
+        # going in the directory
+        subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
+        os.chdir(subdir)
+        log.warn('Now working in %s', subdir)
+        # installing
+        log.warn('Installing Distribute')
+        if not _python_cmd('setup.py', 'install', *install_args):
+            log.warn('Something went wrong during the installation.')
+            log.warn('See the error message above.')
+    finally:
+        os.chdir(old_wd)
+def _build_egg(egg, tarball, to_dir):
+    # extracting the tarball
+    tmpdir = tempfile.mkdtemp()
+    log.warn('Extracting in %s', tmpdir)
+    old_wd = os.getcwd()
+    try:
+        os.chdir(tmpdir)
+        tar = tarfile.open(tarball)
+        _extractall(tar)
+        tar.close()
+        # going in the directory
+        subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
+        os.chdir(subdir)
+        log.warn('Now working in %s', subdir)
+        # building an egg
+        log.warn('Building a Distribute egg in %s', to_dir)
+        _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
+    finally:
+        os.chdir(old_wd)
+    # returning the result
+    log.warn(egg)
+    if not os.path.exists(egg):
+        raise IOError('Could not build the egg.')
+def _do_download(version, download_base, to_dir, download_delay):
+    egg = os.path.join(to_dir, 'distribute-%s-py%d.%d.egg'
+                       % (version, sys.version_info[0], sys.version_info[1]))
+    if not os.path.exists(egg):
+        tarball = download_setuptools(version, download_base,
+                                      to_dir, download_delay)
+        _build_egg(egg, tarball, to_dir)
+    sys.path.insert(0, egg)
+    import setuptools
+    setuptools.bootstrap_install_from = egg
+def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+                   to_dir=os.curdir, download_delay=15, no_fake=True):
+    # making sure we use the absolute path
+    to_dir = os.path.abspath(to_dir)
+    was_imported = 'pkg_resources' in sys.modules or \
+        'setuptools' in sys.modules
+    try:
+        try:
+            import pkg_resources
+            if not hasattr(pkg_resources, '_distribute'):
+                if not no_fake:
+                    _fake_setuptools()
+                raise ImportError
+        except ImportError:
+            return _do_download(version, download_base, to_dir, download_delay)
+        try:
+            pkg_resources.require("distribute>="+version)
+            return
+        except pkg_resources.VersionConflict:
+            e = sys.exc_info()[1]
+            if was_imported:
+                sys.stderr.write(
+                "The required version of distribute (>=%s) is not available,\n"
+                "and can't be installed while this script is running. Please\n"
+                "install a more recent version first, using\n"
+                "'easy_install -U distribute'."
+                "\n\n(Currently using %r)\n" % (version, e.args[0]))
+                sys.exit(2)
+            else:
+                del pkg_resources, sys.modules['pkg_resources']    # reload ok
+                return _do_download(version, download_base, to_dir,
+                                    download_delay)
+        except pkg_resources.DistributionNotFound:
+            return _do_download(version, download_base, to_dir,
+                                download_delay)
+    finally:
+        if not no_fake:
+            _create_fake_setuptools_pkg_info(to_dir)
+def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+                        to_dir=os.curdir, delay=15):
+    """Download distribute from a specified location and return its filename
+    `version` should be a valid distribute version number that is available
+    as an egg for download under the `download_base` URL (which should end
+    with a '/'). `to_dir` is the directory where the egg will be downloaded.
+    `delay` is the number of seconds to pause before an actual download
+    attempt.
+    """
+    # making sure we use the absolute path
+    to_dir = os.path.abspath(to_dir)
+    try:
+        from urllib.request import urlopen
+    except ImportError:
+        from urllib2 import urlopen
+    tgz_name = "distribute-%s.tar.gz" % version
+    url = download_base + tgz_name
+    saveto = os.path.join(to_dir, tgz_name)
+    src = dst = None
+    if not os.path.exists(saveto):  # Avoid repeated downloads
+        try:
+            log.warn("Downloading %s", url)
+            src = urlopen(url)
+            # Read/write all in one block, so we don't create a corrupt file
+            # if the download is interrupted.
+            data = src.read()
+            dst = open(saveto, "wb")
+            dst.write(data)
+        finally:
+            if src:
+                src.close()
+            if dst:
+                dst.close()
+    return os.path.realpath(saveto)
+def _no_sandbox(function):
+    def __no_sandbox(*args, **kw):
+        try:
+            from setuptools.sandbox import DirectorySandbox
+            if not hasattr(DirectorySandbox, '_old'):
+                def violation(*args):
+                    pass
+                DirectorySandbox._old = DirectorySandbox._violation
+                DirectorySandbox._violation = violation
+                patched = True
+            else:
+                patched = False
+        except ImportError:
+            patched = False
+        try:
+            return function(*args, **kw)
+        finally:
+            if patched:
+                DirectorySandbox._violation = DirectorySandbox._old
+                del DirectorySandbox._old
+    return __no_sandbox
+def _patch_file(path, content):
+    """Will backup the file then patch it"""
+    existing_content = open(path).read()
+    if existing_content == content:
+        # already patched
+        log.warn('Already patched.')
+        return False
+    log.warn('Patching...')
+    _rename_path(path)
+    f = open(path, 'w')
+    try:
+        f.write(content)
+    finally:
+        f.close()
+    return True
+_patch_file = _no_sandbox(_patch_file)
+def _same_content(path, content):
+    return open(path).read() == content
+def _rename_path(path):
+    new_name = path + '.OLD.%s' % time.time()
+    log.warn('Renaming %s into %s', path, new_name)
+    os.rename(path, new_name)
+    return new_name
+def _remove_flat_installation(placeholder):
+    if not os.path.isdir(placeholder):
+        log.warn('Unkown installation at %s', placeholder)
+        return False
+    found = False
+    for file in os.listdir(placeholder):
+        if fnmatch.fnmatch(file, 'setuptools*.egg-info'):
+            found = True
+            break
+    if not found:
+        log.warn('Could not locate setuptools*.egg-info')
+        return
+    log.warn('Removing elements out of the way...')
+    pkg_info = os.path.join(placeholder, file)
+    if os.path.isdir(pkg_info):
+        patched = _patch_egg_dir(pkg_info)
+    else:
+        patched = _patch_file(pkg_info, SETUPTOOLS_PKG_INFO)
+    if not patched:
+        log.warn('%s already patched.', pkg_info)
+        return False
+    # now let's move the files out of the way
+    for element in ('setuptools', 'pkg_resources.py', 'site.py'):
+        element = os.path.join(placeholder, element)
+        if os.path.exists(element):
+            _rename_path(element)
+        else:
+            log.warn('Could not find the %s element of the '
+                     'Setuptools distribution', element)
+    return True
+_remove_flat_installation = _no_sandbox(_remove_flat_installation)
+def _after_install(dist):
+    log.warn('After install bootstrap.')
+    placeholder = dist.get_command_obj('install').install_purelib
+    _create_fake_setuptools_pkg_info(placeholder)
+def _create_fake_setuptools_pkg_info(placeholder):
+    if not placeholder or not os.path.exists(placeholder):
+        log.warn('Could not find the install location')
+        return
+    pyver = '%s.%s' % (sys.version_info[0], sys.version_info[1])
+    setuptools_file = 'setuptools-%s-py%s.egg-info' % \
+            (SETUPTOOLS_FAKED_VERSION, pyver)
+    pkg_info = os.path.join(placeholder, setuptools_file)
+    if os.path.exists(pkg_info):
+        log.warn('%s already exists', pkg_info)
+        return
+    log.warn('Creating %s', pkg_info)
+    f = open(pkg_info, 'w')
+    try:
+        f.write(SETUPTOOLS_PKG_INFO)
+    finally:
+        f.close()
+    pth_file = os.path.join(placeholder, 'setuptools.pth')
+    log.warn('Creating %s', pth_file)
+    f = open(pth_file, 'w')
+    try:
+        f.write(os.path.join(os.curdir, setuptools_file))
+    finally:
+        f.close()
+_create_fake_setuptools_pkg_info = _no_sandbox(_create_fake_setuptools_pkg_info)
+def _patch_egg_dir(path):
+    # let's check if it's already patched
+    pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO')
+    if os.path.exists(pkg_info):
+        if _same_content(pkg_info, SETUPTOOLS_PKG_INFO):
+            log.warn('%s already patched.', pkg_info)
+            return False
+    _rename_path(path)
+    os.mkdir(path)
+    os.mkdir(os.path.join(path, 'EGG-INFO'))
+    pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO')
+    f = open(pkg_info, 'w')
+    try:
+        f.write(SETUPTOOLS_PKG_INFO)
+    finally:
+        f.close()
+    return True
+_patch_egg_dir = _no_sandbox(_patch_egg_dir)
+def _before_install():
+    log.warn('Before install bootstrap.')
+    _fake_setuptools()
+def _under_prefix(location):
+    if 'install' not in sys.argv:
+        return True
+    args = sys.argv[sys.argv.index('install')+1:]
+    for index, arg in enumerate(args):
+        for option in ('--root', '--prefix'):
+            if arg.startswith('%s=' % option):
+                top_dir = arg.split('root=')[-1]
+                return location.startswith(top_dir)
+            elif arg == option:
+                if len(args) > index:
+                    top_dir = args[index+1]
+                    return location.startswith(top_dir)
+        if arg == '--user' and USER_SITE is not None:
+            return location.startswith(USER_SITE)
+    return True
+def _fake_setuptools():
+    log.warn('Scanning installed packages')
+    try:
+        import pkg_resources
+    except ImportError:
+        # we're cool
+        log.warn('Setuptools or Distribute does not seem to be installed.')
+        return
+    ws = pkg_resources.working_set
+    try:
+        setuptools_dist = ws.find(pkg_resources.Requirement.parse('setuptools',
+                                  replacement=False))
+    except TypeError:
+        # old distribute API
+        setuptools_dist = ws.find(pkg_resources.Requirement.parse('setuptools'))
+    if setuptools_dist is None:
+        log.warn('No setuptools distribution found')
+        return
+    # detecting if it was already faked
+    setuptools_location = setuptools_dist.location
+    log.warn('Setuptools installation detected at %s', setuptools_location)
+    # if --root or --preix was provided, and if
+    # setuptools is not located in them, we don't patch it
+    if not _under_prefix(setuptools_location):
+        log.warn('Not patching, --root or --prefix is installing Distribute'
+                 ' in another location')
+        return
+    # let's see if its an egg
+    if not setuptools_location.endswith('.egg'):
+        log.warn('Non-egg installation')
+        res = _remove_flat_installation(setuptools_location)
+        if not res:
+            return
+    else:
+        log.warn('Egg installation')
+        pkg_info = os.path.join(setuptools_location, 'EGG-INFO', 'PKG-INFO')
+        if (os.path.exists(pkg_info) and
+            _same_content(pkg_info, SETUPTOOLS_PKG_INFO)):
+            log.warn('Already patched.')
+            return
+        log.warn('Patching...')
+        # let's create a fake egg replacing setuptools one
+        res = _patch_egg_dir(setuptools_location)
+        if not res:
+            return
+    log.warn('Patched done.')
+    _relaunch()
+def _relaunch():
+    log.warn('Relaunching...')
+    # we have to relaunch the process
+    # pip marker to avoid a relaunch bug
+    if sys.argv[:3] == ['-c', 'install', '--single-version-externally-managed']:
+        sys.argv[0] = 'setup.py'
+    args = [sys.executable] + sys.argv
+    sys.exit(subprocess.call(args))
+def _extractall(self, path=".", members=None):
+    """Extract all members from the archive to the current working
+       directory and set owner, modification time and permissions on
+       directories afterwards. `path' specifies a different directory
+       to extract to. `members' is optional and must be a subset of the
+       list returned by getmembers().
+    """
+    import copy
+    import operator
+    from tarfile import ExtractError
+    directories = []
+    if members is None:
+        members = self
+    for tarinfo in members:
+        if tarinfo.isdir():
+            # Extract directories with a safe mode.
+            directories.append(tarinfo)
+            tarinfo = copy.copy(tarinfo)
+            tarinfo.mode = 448 # decimal for oct 0700
+        self.extract(tarinfo, path)
+    # Reverse sort directories.
+    if sys.version_info < (2, 4):
+        def sorter(dir1, dir2):
+            return cmp(dir1.name, dir2.name)
+        directories.sort(sorter)
+        directories.reverse()
+    else:
+        directories.sort(key=operator.attrgetter('name'), reverse=True)
+    # Set correct owner, mtime and filemode on directories.
+    for tarinfo in directories:
+        dirpath = os.path.join(path, tarinfo.name)
+        try:
+            self.chown(tarinfo, dirpath)
+            self.utime(tarinfo, dirpath)
+            self.chmod(tarinfo, dirpath)
+        except ExtractError:
+            e = sys.exc_info()[1]
+            if self.errorlevel > 1:
+                raise
+            else:
+                self._dbg(1, "tarfile: %s" % e)
+def _build_install_args(argv):
+    install_args = []
+    user_install = '--user' in argv
+    if user_install and sys.version_info < (2,6):
+        log.warn("--user requires Python 2.6 or later")
+        raise SystemExit(1)
+    if user_install:
+        install_args.append('--user')
+    return install_args
+def main(argv, version=DEFAULT_VERSION):
+    """Install or upgrade setuptools and EasyInstall"""
+    tarball = download_setuptools()
+    _install(tarball, _build_install_args(argv))
+if __name__ == '__main__':
+    main(sys.argv[1:])

File setup.py

View file
+#!/usr/bin/env python
+import distribute_setup
+import os
+from setuptools import setup, find_packages
+NAME = 'Model-Maps'
+VERSION = '0.1a'
+DESCRIPTION = 'Model Maps is an add-on for Orange data mining software package.'
+LONG_DESCRIPTION = open(os.path.join(os.path.dirname(__file__), 'README.rst')).read()
+AUTHOR = 'Miha Stajdohar, FRI UL'
+AUTHOR_EMAIL = 'miha.stajdohar@gmail.com'
+URL = ''
+DOWNLOAD_URL = 'https://bitbucket.org/mstajdohar/orange-modelmaps/downloads'
+    'data mining',
+    'machine learning',
+    'artificial intelligence',
+    'meta learning',
+    'Development Status :: 1 - Beta',
+    'Environment :: X11 Applications :: Qt',
+    'Environment :: Console',
+    'Environment :: Plugins',
+    'Programming Language :: Python',
+    'Framework :: Orange',
+    'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
+    'Operating System :: POSIX',
+    'Operating System :: Microsoft :: Windows',
+    'Topic :: Scientific/Engineering :: Artificial Intelligence',
+    'Topic :: Scientific/Engineering :: Visualization',
+    'Topic :: Software Development :: Libraries :: Python Modules',
+    'Intended Audience :: Education',
+    'Intended Audience :: Science/Research',
+    'Intended Audience :: Developers',
+PACKAGES = find_packages(
+    exclude = ('*.tests', '*.tests.*', 'tests.*', 'tests'),
+    'Orange',
+    'suds',
+    'numpy',
+    'requests',
+    'oasa',
+    'bkchem',
+    'PIL',
+    'networkx',
+    'pygraphviz',
+    # Dependencies which are problematic to install automatically
+    #'PyQt', # No setup.py
+    #'openbabel-python', # You get bindings together with the openbabel library and not stand-alone
+    #'scipy', # Requires Fortran compiler
+    #'matplotlib', # Requires that numpy is installed first
+    'http://bkchem.zirael.org/download/bkchem-0.13.0.tar.gz',
+    'http://bkchem.zirael.org/download/oasa-0.13.1.tar.gz',
+    'orange.addons': (
+        'modelmaps = _modelmaps',
+    ),
+    'orange.widgets': (
+        'ModelMaps = _modelmaps.widgets',
+        # This should be unneeded, because module given should load (register)
+        # all wanted widgets and prototypes should just have a flag, but for now ...
+        #'Prototypes = _modelmaps.widgets.prototypes',
+    ),
+if __name__ == '__main__':
+    setup(
+        name = NAME,
+        version = VERSION,
+        description = DESCRIPTION,
+        long_description = LONG_DESCRIPTION,
+        author = AUTHOR,
+        author_email = AUTHOR_EMAIL,
+        url = URL,
+        download_url = DOWNLOAD_URL,
+        license = LICENSE,
+        keywords = KEYWORDS,
+        classifiers = CLASSIFIERS,
+        packages = PACKAGES,
+        package_data = PACKAGE_DATA,
+        setup_requires = SETUP_REQUIRES,
+        install_requires = INSTALL_REQUIRES,
+        extras_require = EXTRAS_REQUIRE,
+        dependency_links = DEPENDENCY_LINKS,
+        entry_points = ENTRY_POINTS,
+        include_package_data = True,
+        zip_safe = False,
+    )

File tests/__init__.py

Empty file added.