merge

.hgignore

 syntax: glob
-*.pyo
+
 *~
 \#*\#
-doc/indexes/oplist.txt
-doc/indexes/typelist.txt
-doc/.build/
+build
 compiled/*.cpp
+core.*
 cutils_ext.cpp
+dist
+doc/.build/
+doc/indexes/oplist.txt
+doc/indexes/typelist.txt
 html
 *.o
+*.orig
 pdf
 pull.sh
 *.pyc
+*.pyo
 *.so
 *.sw?
-core.*
-*.orig
+Theano.egg-info

doc/introduction.txt

@@ -5,19 +5,19 @@
 Introduction
 ============
 
-Theano is a Python library that allows you to definite, optimize, and
+Theano is a Python library that allows you to define, optimize, and
 efficiently evaluate mathematical expressions involving multi-dimensional
-arrays. It can be extended to support other types. Theano melds some
-aspects of a computer algebra system (CAS) with aspects of an optimizing
-compiler. It can even transform some or all of the expression into C code
-and compile it into native machine instructions. This combination of CAS
-with optimizing compilation is particularly useful for computational
-fields in which complicated mathematical expressions are evaluated
-numerous times over large data sets.
-
-Theano was written at the LISA_ lab to support the development of
-efficient machine learning algorithms while minimizing human
-time. We use it especially in gradient-based learning techniques.
+arrays. Theano was written at the LISA_ lab to support the development
+of efficient machine learning algorithms while minimizing human time. We
+use it especially in gradient-based learning techniques.
+
+Theano melds some aspects of a computer algebra system (CAS) with
+aspects of an optimizing compiler. It can even transform some or all
+of the expression into C code and compile it into native machine
+instructions. This combination of CAS with optimizing compilation
+is particularly useful for computational fields in which complicated
+mathematical expressions are evaluated numerous times over large data
+sets.
 
 Theano supports a range of numerical types in multiple dimensions and
 a number of well-tested operations. It also allows you to compute the

ez_setup.py

+#!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 = "0.6c9"
+DEFAULT_URL     = "http://pypi.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',
+    'setuptools-0.6c6-py2.3.egg': '35686b78116a668847237b69d549ec20',
+    'setuptools-0.6c6-py2.4.egg': '3c56af57be3225019260a644430065ab',
+    'setuptools-0.6c6-py2.5.egg': 'b2f8a7520709a5b34f80946de5f02f53',
+    'setuptools-0.6c7-py2.3.egg': '209fdf9adc3a615e5115b725658e13e2',
+    'setuptools-0.6c7-py2.4.egg': '5a8f954807d46a0fb67cf1f26c55a82e',
+    'setuptools-0.6c7-py2.5.egg': '45d2ad28f9750e7434111fde831e8372',
+    'setuptools-0.6c8-py2.3.egg': '50759d29b349db8cfd807ba8303f1902',
+    'setuptools-0.6c8-py2.4.egg': 'cba38d74f7d483c06e9daa6070cce6de',
+    'setuptools-0.6c8-py2.5.egg': '1721747ee329dc150590a58b3e1ac95b',
+    'setuptools-0.6c9-py2.3.egg': 'a83c4020414807b496e4cfbe08507c03',
+    'setuptools-0.6c9-py2.4.egg': '260a2be2e5388d66bdaee06abec6342a',
+    'setuptools-0.6c9-py2.5.egg': 'fe67c3e5a17b12c0e7c541b7ea43a8e6',
+    'setuptools-0.6c9-py2.6.egg': 'ca37b1ff16fa2ede6e19383e7b59245a',
+}
+
+import sys, os
+try: from hashlib import md5
+except ImportError: from md5 import md5
+
+def _validate_md5(egg_name, data):
+    if egg_name in md5_data:
+        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.
+    """
+    was_imported = 'pkg_resources' in sys.modules or 'setuptools' in sys.modules
+    def do_download():
+        egg = download_setuptools(version, download_base, to_dir, download_delay)
+        sys.path.insert(0, egg)
+        import setuptools; setuptools.bootstrap_install_from = egg
+    try:
+        import pkg_resources
+    except ImportError:
+        return do_download()       
+    try:
+        pkg_resources.require("setuptools>="+version); return
+    except pkg_resources.VersionConflict, e:
+        if was_imported:
+            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, using 'easy_install -U setuptools'."
+            "\n\n(Currently using %r)"
+            ) % (version, e.args[0])
+            sys.exit(2)
+        else:
+            del pkg_resources, sys.modules['pkg_resources']    # reload ok
+            return do_download()
+    except pkg_resources.DistributionNotFound:
+        return do_download()
+
+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':
+            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)
+
+    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
+
+    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.cfg

+[nosetests]
+match=^test
+nocapture=1

setup.py

-#!/bin/env python
+#!/usr/bin/env python
+#
+#  TODO:
+#   * Figure out how to compile and install documentation automatically
+#   * Add back in installation requirements
+#   * Add download_url
+
+from ez_setup import use_setuptools
+use_setuptools()
 
 from setuptools import setup, find_packages
 
 setup(name="Theano",
       version="0.1",
-      description="Theano",
-      long_description="""Machine learning toolkit""",
-      author="LISA",
+      description="Optimizing compiler for mathematical expressions",
+      long_description="""Theano is a Python library that allows you to define, optimize, and efficiently evaluate mathematical expressions involving multi-dimensional arrays. Theano was written at the LISA lab to support the development of efficient machine learning algorithms while minimizing human time. We use it especially in gradient-based learning techniques.""",
+      author="LISA laboratory, University of Montreal",
       author_email="theano-dev@googlegroups.com",
-      packages=find_packages(exclude='tests'),
-      url="http://lgcm.iro.umontreal.ca/theano",
+      packages=find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests"]),
+      url="http://pylearn.org/theano",
+      keywords="machine learning ai gradient compiler math science",
+
+      test_suite = "nose.collector",
+
+#      install_requires = ["numpy>=1.2", "scipy"],
+
+      extras_require = {
+        'doc':      ["sphinx>=0.5.1", "pygments"],
+        'test':     ["nose"],
+#        'sparse':   ["scipy>=0.7"]
+      },
       license = "BSD",
 )
 

theano/sandbox/softsign.py

@@ -21,4 +21,3 @@ class ScalarSoftsign(theano.scalar.UnaryScalarOp):
         raise NotImplementedError('only floating point x is implemented')
 scalar_softsign = ScalarSoftsign(theano.scalar.upgrade_to_float, name='scalar_softsign')
 softsign = theano.tensor.Elemwise(scalar_softsign, name='softsign')
-