Initial commit to google code svn.

The svn on sysbio.engin.umich.edu has about 25 revisions worth of old history but most of that is useless.

Author: abhik

README.txt

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+README file for PEBL. Just a place holder for now.

ez_setup.py

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+#!python
+"""Bootstrap setuptools 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 ez_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 sys
+DEFAULT_VERSION = "0.6c5"
+DEFAULT_URL     = "http://cheeseshop.python.org/packages/%s/s/setuptools/" % sys.version[:3]
+
+md5_data = {
+    'setuptools-0.6b1-py2.3.egg': '8822caf901250d848b996b7f25c6e6ca',
+    'setuptools-0.6b1-py2.4.egg': 'b79a8a403e4502fbb85ee3f1941735cb',
+    'setuptools-0.6b2-py2.3.egg': '5657759d8a6d8fc44070a9d07272d99b',
+    'setuptools-0.6b2-py2.4.egg': '4996a8d169d2be661fa32a6e52e4f82a',
+    'setuptools-0.6b3-py2.3.egg': 'bb31c0fc7399a63579975cad9f5a0618',
+    'setuptools-0.6b3-py2.4.egg': '38a8c6b3d6ecd22247f179f7da669fac',
+    'setuptools-0.6b4-py2.3.egg': '62045a24ed4e1ebc77fe039aa4e6f7e5',
+    'setuptools-0.6b4-py2.4.egg': '4cb2a185d228dacffb2d17f103b3b1c4',
+    'setuptools-0.6c1-py2.3.egg': 'b3f2b5539d65cb7f74ad79127f1a908c',
+    'setuptools-0.6c1-py2.4.egg': 'b45adeda0667d2d2ffe14009364f2a4b',
+    'setuptools-0.6c2-py2.3.egg': 'f0064bf6aa2b7d0f3ba0b43f20817c27',
+    'setuptools-0.6c2-py2.4.egg': '616192eec35f47e8ea16cd6a122b7277',
+    'setuptools-0.6c3-py2.3.egg': 'f181fa125dfe85a259c9cd6f1d7b78fa',
+    'setuptools-0.6c3-py2.4.egg': 'e0ed74682c998bfb73bf803a50e7b71e',
+    'setuptools-0.6c3-py2.5.egg': 'abef16fdd61955514841c7c6bd98965e',
+    'setuptools-0.6c4-py2.3.egg': 'b0b9131acab32022bfac7f44c5d7971f',
+    'setuptools-0.6c4-py2.4.egg': '2a1f9656d4fbf3c97bf946c0a124e6e2',
+    'setuptools-0.6c4-py2.5.egg': '8f5a052e32cdb9c72bcf4b5526f28afc',
+    'setuptools-0.6c5-py2.3.egg': 'ee9fd80965da04f2f3e6b3576e9d8167',
+    'setuptools-0.6c5-py2.4.egg': 'afe2adf1c01701ee841761f5bcd8aa64',
+    'setuptools-0.6c5-py2.5.egg': 'a8d3f61494ccaa8714dfed37bccd3d5d',
+}
+
+import sys, os
+
+def _validate_md5(egg_name, data):
+    if egg_name in md5_data:
+        from md5 import md5
+        digest = md5(data).hexdigest()
+        if digest != md5_data[egg_name]:
+            print >>sys.stderr, (
+                "md5 validation of %s failed!  (Possible download problem?)"
+                % egg_name
+            )
+            sys.exit(2)
+    return data
+
+
+def use_setuptools(
+    version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir,
+    download_delay=15
+):
+    """Automatically find/download setuptools and make it available on sys.path
+
+    `version` should be a valid setuptools 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 setuptools will be downloaded, if
+    it is not already available.  If `download_delay` is specified, it should
+    be the number of seconds that will be paused before initiating a download,
+    should one be required.  If an older version of setuptools is installed,
+    this routine will print a message to ``sys.stderr`` and raise SystemExit in
+    an attempt to abort the calling script.
+    """
+    try:
+        import setuptools
+        if setuptools.__version__ == '0.0.1':
+            print >>sys.stderr, (
+            "You have an obsolete version of setuptools installed.  Please\n"
+            "remove it from your system entirely before rerunning this script."
+            )
+            sys.exit(2)
+    except ImportError:
+        egg = download_setuptools(version, download_base, to_dir, download_delay)
+        sys.path.insert(0, egg)
+        import setuptools; setuptools.bootstrap_install_from = egg
+
+    import pkg_resources
+    try:
+        pkg_resources.require("setuptools>="+version)
+
+    except pkg_resources.VersionConflict, e:
+        # XXX could we install in a subprocess here?
+        print >>sys.stderr, (
+            "The required version of setuptools (>=%s) is not available, and\n"
+            "can't be installed while this script is running. Please install\n"
+            " a more recent version first.\n\n(Currently using %r)"
+        ) % (version, e.args[0])
+        sys.exit(2)
+
+def download_setuptools(
+    version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir,
+    delay = 15
+):
+    """Download setuptools from a specified location and return its filename
+
+    `version` should be a valid setuptools 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.
+    """
+    import urllib2, shutil
+    egg_name = "setuptools-%s-py%s.egg" % (version,sys.version[:3])
+    url = download_base + egg_name
+    saveto = os.path.join(to_dir, egg_name)
+    src = dst = None
+    if not os.path.exists(saveto):  # Avoid repeated downloads
+        try:
+            from distutils import log
+            if delay:
+                log.warn("""
+---------------------------------------------------------------------------
+This script requires setuptools version %s to run (even to display
+help).  I will attempt to download it for you (from
+%s), but
+you may need to enable firewall access for this script first.
+I will start the download in %d seconds.
+
+(Note: if this machine does not have network access, please obtain the file
+
+   %s
+
+and place it in this directory before rerunning this script.)
+---------------------------------------------------------------------------""",
+                    version, download_base, delay, url
+                ); from time import sleep; sleep(delay)
+            log.warn("Downloading %s", url)
+            src = urllib2.urlopen(url)
+            # Read/write all in one block, so we don't create a corrupt file
+            # if the download is interrupted.
+            data = _validate_md5(egg_name, src.read())
+            dst = open(saveto,"wb"); dst.write(data)
+        finally:
+            if src: src.close()
+            if dst: dst.close()
+    return os.path.realpath(saveto)
+
+def main(argv, version=DEFAULT_VERSION):
+    """Install or upgrade setuptools and EasyInstall"""
+
+    try:
+        import setuptools
+    except ImportError:
+        egg = None
+        try:
+            egg = download_setuptools(version, delay=0)
+            sys.path.insert(0,egg)
+            from setuptools.command.easy_install import main
+            return main(list(argv)+[egg])   # we're done here
+        finally:
+            if egg and os.path.exists(egg):
+                os.unlink(egg)
+    else:
+        if setuptools.__version__ == '0.0.1':
+            # tell the user to uninstall obsolete version
+            use_setuptools(version)
+
+    req = "setuptools>="+version
+    import pkg_resources
+    try:
+        pkg_resources.require(req)
+    except pkg_resources.VersionConflict:
+        try:
+            from setuptools.command.easy_install import main
+        except ImportError:
+            from easy_install import main
+        main(list(argv)+[download_setuptools(delay=0)])
+        sys.exit(0) # try to force an exit
+    else:
+        if argv:
+            from setuptools.command.easy_install import main
+            main(argv)
+        else:
+            print "Setuptools version",version,"or greater has been installed."
+            print '(Run "ez_setup.py -U setuptools" to reinstall or upgrade.)'
+
+
+
+def update_md5(filenames):
+    """Update our built-in md5 registry"""
+
+    import re
+    from md5 import md5
+
+    for name in filenames:
+        base = os.path.basename(name)
+        f = open(name,'rb')
+        md5_data[base] = md5(f.read()).hexdigest()
+        f.close()
+
+    data = ["    %r: %r,\n" % it for it in md5_data.items()]
+    data.sort()
+    repl = "".join(data)
+
+    import inspect
+    srcfile = inspect.getsourcefile(sys.modules[__name__])
+    f = open(srcfile, 'rb'); src = f.read(); f.close()
+
+    match = re.search("\nmd5_data = {\n([^}]+)}", src)
+    if not match:
+        print >>sys.stderr, "Internal error!"
+        sys.exit(2)
+
+    src = src[:match.start(1)] + repl + src[match.end(1):]
+    f = open(srcfile,'w')
+    f.write(src)
+    f.close()
+
+
+if __name__=='__main__':
+    if len(sys.argv)>2 and sys.argv[1]=='--md5update':
+        update_md5(sys.argv[2:])
+    else:
+        main(sys.argv[1:])
+
+
+
+
+

setup.py

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+# download setuptools if needed
+import ez_setup
+ez_setup.use_setuptools()
+
+from setuptools import setup, find_packages
+
+setup(
+    name='Pebl',
+    version='0.2.1',
+    description='Python Environment for Bayesian Learning',
+    package_dir={'': 'src'},
+    packages=find_packages('src'),
+
+    ## Package metadata.. for upload to PyPI
+    author='Abhik Shah',
+    author_email='[email protected]',
+    url='http://sysbio.engin.umich.edu/Pebl/',
+
+    # required dependencies
+    install_requires=['numpy >= 0.9', 'nose >= 0.9', 'pydot'],
+    
+    # data files (mostly just the test data for unit tests)
+    include_package_data = True,
+)