merge

__transit/conf.py

+# -*- coding: utf-8 -*-
+#
+# theano documentation build configuration file, created by
+# sphinx-quickstart on Tue Oct  7 02:53:58 2008.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# The contents of this file are pickled, so don't put values in the namespace
+# that aren't pickleable (module imports are okay, they're removed automatically).
+#
+# All configuration values have a default value; values that are commented out
+# serve to show the default value.
+
+import sys, os
+
+# If your extensions are in another directory, add it here. If the directory
+# is relative to the documentation root, use os.path.abspath to make it
+# absolute, like shown here.
+#sys.path.append(os.path.abspath('some/directory'))
+
+# General configuration
+# ---------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['.templates']
+
+# The suffix of source filenames.
+source_suffix = '.txt'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General substitutions.
+project = 'theano'
+copyright = '2008, Olivier Breuleux, James Bergstra'
+
+# The default replacements for |version| and |release|, also used in various
+# other places throughout the built documents.
+#
+# The short X.Y version.
+version = '0.1'
+# The full version, including alpha/beta/rc tags.
+release = '0.1'
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+today_fmt = '%B %d, %Y'
+
+# List of documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directories, that shouldn't be searched
+# for source files.
+#exclude_dirs = []
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# Options for HTML output
+# -----------------------
+
+# The style sheet to use for HTML and HTML Help pages. A file of that name
+# must exist either in Sphinx' static/ path, or in one of the custom paths
+# given in html_static_path.
+html_style = 'default.css'
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (within the static path) to place at the top of
+# the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['.static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_use_modindex = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, the reST sources are included in the HTML build as _sources/<name>.
+#html_copy_source = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'theanodoc'
+
+
+# Options for LaTeX output
+# ------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, document class [howto/manual]).
+latex_documents = [
+  ('index', 'theano.tex', 'theano Documentation',
+   'Olivier Breuleux, James Bergstra', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True

gen_oplist.py → __transit/scripts/gen_oplist.py

 """script to generate doc/oplist.txt, which compiles to :doc:`oplist`. """
 __docformat__ = "restructuredtext en"
 import sys
-import gof
+from theano import gof
 
 def print_title(title_string, under_char, over_char=''):
     l = len(title_string)
@@ -94,15 +94,25 @@ class EntryConstructor(Entry):
         Entry.__init__(self, symbol, name, module)
 
 
-def search_entries(module_list):
-    ops = []
-    constructors = []
+def search_entries(module_list, ops = None, constructors = None, seen = None):
+    if ops is None: ops = []
+    if constructors is None: constructors = []
+    if seen is None: seen = set()
+    modules = []
 
     for module in module_list:
         symbol_name_list = [s for s in dir(module) if not s[0] == '_']
-
+        
 	for symbol_name in symbol_name_list:
 	    symbol = getattr(module, symbol_name)
+            try:
+                if symbol in seen:
+                    continue
+                seen.add(symbol)
+            except TypeError:
+                pass
+            if type(symbol) == type(module): # module
+                modules.append(symbol)
             try:
                 ops.append(EntryOp(symbol, symbol_name, module))
             except TypeError:
@@ -111,6 +121,9 @@ def search_entries(module_list):
                 except TypeError:
                     pass
 
+    for symbol in modules:
+        search_entries([symbol], ops, constructors, seen)
+
     return ops, constructors
 
 def print_entries(ops, constructors):
@@ -141,7 +154,7 @@ def print_entries(ops, constructors):
 
 if __name__ == "__main__":
     """Generate the op list"""
-    import scalar, sparse, tensor
+    import theano
 
     print_title("Op List", "~", "~")
     print """
@@ -156,11 +169,8 @@ In the future, this list may distinguish `constructors` that are Op instances fr
     print ".. contents:: "
     print ""
 
-    ops, constructors = search_entries([scalar, sparse, tensor])
+    ops, constructors = search_entries([theano])
 
     print_entries(ops, constructors)
 
     print ""
-
-    for line in open("doc/header.txt"):
-        print line[:-1]

autotest.py

-import unittest, os, sys, traceback
-
-def test_root_dir(debugmode=False):
-    suite = None
-    filenames = os.listdir('.')
-    for filename in filenames:
-        if filename[-3:] == '.py' and filename[0:5] == '_test':
-            #print >>sys.stderr, 'Loading', modname
-            modname = filename[0:-3]
-
-            try:
-                module = __import__(modname)
-            except Exception, e:
-                print >>sys.stderr, "===================================================="
-                print >>sys.stderr, "Failed to load %s.py" % modname
-                print >>sys.stderr, "===================================================="
-                traceback.print_exc()
-                print >>sys.stderr, "===================================================="
-                continue
-                
-            tests = unittest.TestLoader().loadTestsFromModule(module)
-            if tests.countTestCases() > 0:
-                print >>sys.stderr, 'Testing', modname
-                if suite is None:
-                    suite = tests
-                else:
-                    suite.addTests(tests)
-    if debugmode:
-        suite.debug()
-    else:
-        unittest.TextTestRunner(verbosity=1).run(suite)
-
-if __name__ == '__main__':
-
-    def printUsage():
-        print >>sys.stderr, "Bad argument: ",sys.argv
-        print >>sys.stderr, "only --debug is supported"
-        sys.exit(1)
-    debugparam=""
-
-    if len(sys.argv)==2:
-        if sys.argv[1]=="--debug":
-            debugparam="--debug"
-            sys.argv.remove(debugparam)
-        else:
-            printUsage()
-    elif len(sys.argv)>2:
-        printUsage()
-
-    if len(sys.argv) >= 2:
-        cmd = sys.argv[1]
-    else:
-        cmd = 'python'
-
-    for dir in 'gof compile scalar tensor sparse'.split():
-        os.system('cd %s; %s autotest.py %s' % (dir, cmd, debugparam))
-    test_root_dir(debugparam!="")
-
-

compile/autotest.py

-import unittest, os, sys, traceback
-
-if __name__ == '__main__':
-    def printUsage():
-        print >>sys.stderr, "Bad argument: ",sys.argv
-        print >>sys.stderr, "only --debug is supported"
-        sys.exit(1)
-    debugparam=""
-
-    if len(sys.argv)==2:
-        if sys.argv[1]=="--debug":
-            debugparam="--debug"
-            sys.argv.remove(debugparam)
-        else:
-            printUsage()
-    elif len(sys.argv)>2:
-        printUsage()
-
-
-
-    suite = None
-    filenames = os.listdir('.')
-    for filename in filenames:
-        if filename[-3:] == '.py':
-            modname = filename[:-3]
-            if modname in ['__init__', 'autotest']: continue
-            #print >>sys.stderr, 'Loading', modname
-
-            try:
-                module = __import__(modname)
-            except Exception, e:
-                if 'relative import' not in e.message:
-                    print >>sys.stderr, "===================================================="
-                    print >>sys.stderr, "Failed to load module %s" % modname
-                    print >>sys.stderr, "===================================================="
-                    traceback.print_exc()
-                    print >>sys.stderr, "===================================================="
-                continue
-                
-            tests = unittest.TestLoader().loadTestsFromModule(module)
-            if tests.countTestCases() > 0:
-                print >>sys.stderr, 'Testing', modname
-                if suite is None:
-                    suite = tests
-                else:
-                    suite.addTests(tests)
-    if debugparam:
-        suite.debug()
-    else:
-        unittest.TextTestRunner(verbosity=1).run(suite)
-

README.txt → doc/README.txt

@@ -194,18 +194,9 @@ Getting Help
 If these installation instructions don't work, search the theano-users archive for similar cases.  If you don't find a solution, write to theano-users and explain the situation.
 
 
-.. header:: |THEANO| - README_ - Download_ - Documentation_ - Wiki_ - `Task List`_
-
 .. _README: README.html
 .. _Download: README.html#downloading-theano
 .. _Documentation: doc/index.html
 .. _Wiki: http://pylearn.org/theano
 .. _task list: http://lgcm.iro.umontreal.ca/theano/query?status=accepted&status=assigned&status=new&status=reopened&group=milestone&max=200&col=id&col=summary&col=status&col=owner&col=type&col=priority&col=component&col=time&report=9&order=priority
 
-.. |THEANO| image:: http://lgcm.iro.umontreal.ca/theano/chrome/site/theano_logo.png
-   :target: http://pylearn.org/auto_theano
-   :alt: THEANO
-   :align: top
-   :class: borderless
-   :width: 60
-   :height: 18

local.epydoc → doc/api/epydoc.conf

@@ -7,12 +7,7 @@
 # The list of objects to document.  Objects can be named using
 # dotted names, module filenames, or package directory names.
 # Alases for this option include "objects" and "values".
-modules: __init__.py,
-    [a-z]*.py,
-    [A-Z]*.py,
-    gof/__init__.py,
-    gof/[a-z]*.py,
-    gof/[A-Z]*.py
+modules: theano
 
 # The type of output that should be generated.  Should be one
 # of: html, text, latex, dvi, ps, pdf.
@@ -125,9 +120,9 @@ separate-classes: no
 
 # Use this URL prefix to configure the string returned for external API.
 #external-api-root: epydoc:http://epydoc.sourceforge.net/api
-external-api: wiki doc
-external-api-root: wiki:http://lgcm.iro.umontreal.ca/theano/wiki/ doc:http://lgcm.iro.umontreal.ca/auto_theano/doc/
-external-api-file: wiki:wiki.idx doc:doc/doc.idx
+# external-api: wiki doc
+# external-api-root: wiki:http://lgcm.iro.umontreal.ca/theano/wiki/ doc:http://lgcm.iro.umontreal.ca/auto_theano/doc/
+# external-api-file: wiki:wiki.idx doc:doc/doc.idx
 
 ### Graph options
 

doc/conf.py

+# -*- coding: utf-8 -*-
+#
+# theano documentation build configuration file, created by
+# sphinx-quickstart on Tue Oct  7 16:34:06 2008.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# The contents of this file are pickled, so don't put values in the namespace
+# that aren't pickleable (module imports are okay, they're removed automatically).
+#
+# All configuration values have a default value; values that are commented out
+# serve to show the default value.
+
+import sys, os
+
+# If your extensions are in another directory, add it here. If the directory
+# is relative to the documentation root, use os.path.abspath to make it
+# absolute, like shown here.
+#sys.path.append(os.path.abspath('some/directory'))
+
+# General configuration
+# ---------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'ext']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['.templates']
+
+# The suffix of source filenames.
+source_suffix = '.txt'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General substitutions.
+project = 'theano'
+copyright = '2008, Olivier Breuleux, James Bergstra'
+
+# The default replacements for |version| and |release|, also used in various
+# other places throughout the built documents.
+#
+# The short X.Y version.
+version = '0.1'
+# The full version, including alpha/beta/rc tags.
+release = '0.1'
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+today_fmt = '%B %d, %Y'
+
+# List of documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directories, that shouldn't be searched
+# for source files.
+#exclude_dirs = []
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# Options for HTML output
+# -----------------------
+
+# The style sheet to use for HTML and HTML Help pages. A file of that name
+# must exist either in Sphinx' static/ path, or in one of the custom paths
+# given in html_static_path.
+html_style = 'default.css'
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (within the static path) to place at the top of
+# the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['.static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_use_modindex = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, the reST sources are included in the HTML build as _sources/<name>.
+#html_copy_source = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'theanodoc'
+
+
+# Options for LaTeX output
+# ------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, document class [howto/manual]).
+latex_documents = [
+  ('index', 'theano.tex', 'theano Documentation',
+   'Olivier Breuleux, James Bergstra', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True

doc/DevStartGuide.txt → doc/doc/dev_start_guide.txt

@@ -60,16 +60,6 @@ When you install a package, only the package name can be imported directly. If y
 .. _basicnumpy: http://lgcm.iro.umontreal.ca/theano/wiki/BasicNumpy
 
 
-.. header:: |THEANO| - README_ - Download_ - Documentation_ - Wiki_ - `Task List`_
-
-.. |THEANO| image:: http://lgcm.iro.umontreal.ca/theano/chrome/site/theano_logo.png
-   :target: http://pylearn.org/auto_theano
-   :alt: THEANO
-   :align: top
-   :class: borderless
-   :width: 60
-   :height: 18
-
 .. _README: ../README.html
 .. _Download: ../README.html#downloading-theano
 .. _Documentation: index.html

doc/graph.txt → doc/doc/graph.txt

@@ -87,16 +87,6 @@ If we had wanted a more brute-force approach to graph construction, we could hav
 Note how the call to `Apply` modifies the `owner` and `index` fields of the `Result` s passed as outputs to point to itself and the rank they occupy in the output list. This whole machinery builds a DAG (Directed Acyclic Graph) representing the computation, a graph that theano can compile and optimize.
 
 
-.. header:: |THEANO| - README_ - Download_ - Documentation_ - Wiki_ - `Task List`_
-
-.. |THEANO| image:: http://lgcm.iro.umontreal.ca/theano/chrome/site/theano_logo.png
-   :target: http://pylearn.org/auto_theano
-   :alt: THEANO
-   :align: top
-   :class: borderless
-   :width: 60
-   :height: 18
-
 .. _README: ../README.html
 .. _Download: ../README.html#downloading-theano
 .. _Documentation: index.html

doc/doc/index.txt

+=====================================
+Theano Project Documentation Overview
+=====================================
+
+.. toctree::
+   :glob:
+
+   *
+
+Documentation is divided broadly into two kinds: user documentation and
+developer documentation.  
+
+- `Using Theano` covers how to *use* what is already in the Theano library to
+  build graphs and evaluate them.
+
+- `Extending Theano` introduces how Theano works and explains how to add new
+  data and expression types, as well as optimizations to accompany them.
+
+- `Hacking Theano` introduces you to what's under the hood: the compilation
+  process, the Env, C code generation.
+
+
+Using Theano
+============
+
+- First of all, read the `n00b guide`_.  It is a cut-and-paste, tutorial-style intro to what Theano can do.
+
+- Familiarize yourself with the `glossary of terminology`_.
+
+- Join `theano-users`_.
+
+- Learn to use the typelist_, and the oplist_.  These are the building blocks
+  of theano expression graphs.
+
+- Browse through some of the `Howto`_ recipes on the wiki.
+
+.. _Howto: 
+.. _theano-users: http://groups.google.com/group/theano-users?pli=1
+.. _theano-dev: http://groups.google.com/group/theano-dev?pli=1
+.. _n00b guide: n00b.html
+.. _glossary of terminology: ../api/term-index.html
+.. _typelist: typelist.html
+.. _oplist: oplist.html
+
+Extending Theano
+================
+
+- Read about `How Theano Works <UserAdvanced.html>`__.  This introduces the
+  major interface data structures: Op, Type, Result, Apply.
+
+- How to make a new Op.
+
+- How to make a new Optimization.
+
+- How to make a new data Type.
+
+Hacking Theano
+==============
+
+- `Get Started as a Developer <DevStartGuide.html>`__ by setting up mercurial, getting a few accounts,
+  setting up your environment, and getting some background in mercurial, python,
+  and numpy.
+
+- Join `theano-dev`_ to participate in development discussion.
+
+- Pick a task from the `task list`_, or suggest one on `theano-users`_.
+  Features/ideas are generally discussed on `theano-users`_.   Technical
+  discussions of how to actually implement something should be on
+  `theano-dev`_.
+
+- Browse `Theano's API <../api/>`__.
+
+- Keep an eye on the `Mercurial Changelog <http://pylearn.org/hg/theano>`__.
+
+- Send us your work as a patch to `theano-dev`_ or commit directly to the trunk.
+
+.. _theano-dev: http://groups.google.com/group/theano-dev?pli=1
+.. _task list: http://lgcm.iro.umontreal.ca/theano/query?status=accepted&status=assigned&status=new&status=reopened&group=milestone&max=200&col=id&col=summary&col=status&col=owner&col=type&col=priority&col=component&col=time&report=9&order=priority
+.. _reStructuredText: http://docutils.sourceforge.net/rst.html
+
+
+
+

doc/n00b.txt → doc/doc/n00b.txt

@@ -237,16 +237,6 @@ code. The question is how to automatically extract the source files and inline
 them into this documentation.*
 
 
-.. header:: |THEANO| - README_ - Download_ - Documentation_ - Wiki_ - `Task List`_
-
-.. |THEANO| image:: http://lgcm.iro.umontreal.ca/theano/chrome/site/theano_logo.png
-   :target: http://pylearn.org/auto_theano
-   :alt: THEANO
-   :align: top
-   :class: borderless
-   :width: 60
-   :height: 18
-
 .. _README: ../README.html
 .. _Download: ../README.html#downloading-theano
 .. _Documentation: index.html

doc/ext.py

+
+import os
+from docutils import nodes
+import epydoc.docwriter.xlink as xlink
+
+def role_fn(name, rawtext, text, lineno, inliner,
+            options={}, content=[]):
+    node = nodes.reference(rawtext, text, refuri = "http://pylearn.org/theano/wiki/%s" % text)
+    return [node], []
+
+
+def setup(app):
+    help(xlink)
+    #role = xlink.create_api_role('api', True)
+    #print role
+
+    xlink.register_api('api', xlink.DocUrlGenerator())
+    xlink.set_api_file('api', os.path.join(app.outdir, 'api', 'api-objects.txt'))
+    xlink.set_api_root('api', os.path.join(app.outdir, 'api', ''))
+    xlink.create_api_role('api', True)
+    
+    app.add_role("wiki", role_fn)

doc/index.txt

-=====================================
-Theano Project Documentation Overview
-=====================================
 
-Documentation is divided broadly into two kinds: user documentation and
-developer documentation.  
+======
+Theano
+======
 
-- `Using Theano` covers how to *use* what is already in the Theano library to
-  build graphs and evaluate them.
+.. toctree::
+   :maxdepth: 2
 
-- `Extending Theano` introduces how Theano works and explains how to add new
-  data and expression types, as well as optimizations to accompany them.
+   README
+   doc/index
 
-- `Hacking Theano` introduces you to what's under the hood: the compilation
-  process, the Env, C code generation.
+-------------------------------------------------------------------
+A python library for manipulating and evaluating matrix expressions
+-------------------------------------------------------------------
 
+Theano is a library in Python, built to evaluate complicated
+expressions (especially matrix-valued ones) as quickly as possible.
+It was written at LISA_ to explore techniques for machine learning.
+Our project uses the name to honour the ancient Greek mathematician. 
 
-Using Theano
-============
+--------------------------------------------------------------------------------
 
-- First of all, read the `n00b guide`_.  It is a cut-and-paste, tutorial-style intro to what Theano can do.
+.. _not in the normal sense: :wiki:`WhatIsTheano`
 
-- Familiarize yourself with the `glossary of terminology`_.
+Overview
+========
 
-- Join `theano-users`_.
+**To get up & running quickly** see README_.
 
-- Learn to use the typelist_, and the oplist_.  These are the building blocks
-  of theano expression graphs.
+All **documentation** can be reached from the `Theano Project Documentation Overview`_.
 
-- Browse through some of the `Howto`_ recipes on the wiki.
+As developers of an open source project, we rely on **feedback** for
+determining what features to implement, and what documentation needs to be
+improved.  The best forum for feedback is the theano-users_ mailing list.
 
-.. _Howto: 
-.. _theano-users: http://groups.google.com/group/theano-users?pli=1
-.. _theano-dev: http://groups.google.com/group/theano-dev?pli=1
-.. _n00b guide: n00b.html
-.. _glossary of terminology: ../api/term-index.html
-.. _typelist: typelist.html
-.. _oplist: oplist.html
-
-Extending Theano
-================
+All **discussion** about theano also takes place on the theano-users_ mailing list.
 
-- Read about `How Theano Works <UserAdvanced.html>`__.  This introduces the
-  major interface data structures: Op, Type, Result, Apply.
+If you find a **bug**, please file a `bug report`_ or send email to
+the theano-users_ mailing list.  **Patch** submissions should be
+sent to theano-dev_.
 
-- How to make a new Op.
+We welcome all kinds of **contributions**.  Our `task list`_ is
+full of interesting ideas awaiting a champion.  If you have any
+questions regarding how to extend Theano, please feel free to ask on
+the Theano-dev_ mailing list.
 
-- How to make a new Optimization.
+Theano is in active development and should be considered **experimental**.
+APIs are subject to change at any time.
 
-- How to make a new data Type.
 
-Hacking Theano
-==============
+Download
+========
 
-- `Get Started as a Developer <DevStartGuide.html>`__ by setting up mercurial, getting a few accounts,
-  setting up your environment, and getting some background in mercurial, python,
-  and numpy.
+We recommend that you use the `latest snapshot`_,
+Better yet, use `mercurial`_ to keep your installation fresh.
+The snapshots usually contain *more features* and *fewer bugs* than the
+"official" releases |---| they're not only for developers!
 
-- Join `theano-dev`_ to participate in development discussion.
 
-- Pick a task from the `task list`_, or suggest one on `theano-users`_.
-  Features/ideas are generally discussed on `theano-users`_.   Technical
-  discussions of how to actually implement something should be on
-  `theano-dev`_.
+Indices and tables
+==================
 
-- Browse `Theano's API <../api/>`__.
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
 
-- Keep an eye on the `Mercurial Changelog <http://pylearn.org/hg/theano>`__.
-
-- Send us your work as a patch to `theano-dev`_ or commit directly to the trunk.
 
+.. |---| unicode:: U+02014 .. em dash
+   :trim:
+.. _latest snapshot: http://pylearn.org/hg/theano/archive/tip.tar.gz
+.. _bug report: http://lgcm.iro.umontreal.ca/theano/newticket
+.. _theano-users: http://groups.google.com/group/theano-users?pli=1
 .. _theano-dev: http://groups.google.com/group/theano-dev?pli=1
+.. _reStructuredText: rst.html
 .. _task list: http://lgcm.iro.umontreal.ca/theano/query?status=accepted&status=assigned&status=new&status=reopened&group=milestone&max=200&col=id&col=summary&col=status&col=owner&col=type&col=priority&col=component&col=time&report=9&order=priority
-.. _reStructuredText: http://docutils.sourceforge.net/rst.html
-
-
-.. header:: |THEANO| - README_ - Download_ - Documentation_ - Wiki_ - `Task List`_
-
-.. |THEANO| image:: http://lgcm.iro.umontreal.ca/theano/chrome/site/theano_logo.png
-   :target: http://pylearn.org/auto_theano
-   :alt: THEANO
-   :align: top
-   :class: borderless
-   :width: 60
-   :height: 18
-
-.. _README: ../README.html
-.. _Download: ../README.html#downloading-theano
-.. _Documentation: index.html
-.. _Wiki: http://pylearn.org/theano
+.. _README: README.html
+.. _Quick-Start: README.html#quick-start
+
+.. _Theano Project Documentation Overview: doc/index.html
+.. _Mercurial: http://www.selenic.com/mercurial/wiki/
+.. _docutils: http://docutils.sourceforge.net
+.. _epydoc: http://epydoc.sourceforge.net/
+.. _scipy: http://scipy.org/
+.. _Python: http://www.python.org/
 .. _TRAC: http://trac.edgewall.org/
-.. _task list: http://lgcm.iro.umontreal.ca/theano/query?status=accepted&status=assigned&status=new&status=reopened&group=milestone&max=200&col=id&col=summary&col=status&col=owner&col=type&col=priority&col=component&col=time&report=9&order=priority
-
-
+.. _LISA:  http://www.iro.umontreal.ca/rubrique.php3?id_rubrique=27
 

gof/_test_type.py

-
-import unittest
-from type import *
-
-
-# todo: test generic
-
-
-
-
-if __name__ == '__main__':
-    unittest.main()

gof/autotest.py

-import unittest, os, sys, traceback
-
-if __name__ == '__main__':
-    def printUsage():
-        print >>sys.stderr, "Bad argument: ",sys.argv
-        print >>sys.stderr, "only --debug is supported"
-        sys.exit(1)
-    debugparam=""
-
-    if len(sys.argv)==2:
-        if sys.argv[1]=="--debug":
-            debugparam="--debug"
-            sys.argv.remove(debugparam)
-        else:
-            printUsage()
-    elif len(sys.argv)>2:
-        printUsage()
-
-
-
-    suite = None
-    filenames = os.listdir('.')
-    for filename in filenames:
-        if filename[-3:] == '.py':
-            modname = filename[:-3]
-            if modname in ['__init__', 'autotest']: continue
-            #print >>sys.stderr, 'Loading', modname
-
-            try:
-                module = __import__(modname)
-            except Exception, e:
-                print >>sys.stderr, "===================================================="
-                print >>sys.stderr, "Failed to load module %s" % modname
-                print >>sys.stderr, "===================================================="
-                traceback.print_exc()
-                print >>sys.stderr, "===================================================="
-                continue
-                
-            tests = unittest.TestLoader().loadTestsFromModule(module)
-            if tests.countTestCases() > 0:
-                print >>sys.stderr, 'Testing', modname
-                if suite is None:
-                    suite = tests
-                else:
-                    suite.addTests(tests)
-    if debugparam:
-        suite.debug()
-    else:
-        unittest.TextTestRunner(verbosity=1).run(suite)
-

index.txt

-======
-Theano
-======
--------------------------------------------------------------------
-A python library for manipulating and evaluating matrix expressions
--------------------------------------------------------------------
-
-Theano is a library in Python, built to evaluate complicated
-expressions (especially matrix-valued ones) as quickly as possible.
-It was written at LISA_ to explore techniques for machine learning.
-Our project uses the name to honour the ancient Greek mathematician. 
-
---------------------------------------------------------------------------------
-
-.. _not in the normal sense: :wiki:`WhatIsTheano`
-
-Overview
-========
-
-**To get up & running quickly** see README_.
-
-All **documentation** can be reached from the `Theano Project Documentation Overview`_.
-
-As developers of an open source project, we rely on **feedback** for
-determining what features to implement, and what documentation needs to be
-improved.  The best forum for feedback is the theano-users_ mailing list.
-
-All **discussion** about theano also takes place on the theano-users_ mailing list.
-
-If you find a **bug**, please file a `bug report`_ or send email to
-the theano-users_ mailing list.  **Patch** submissions should be
-sent to theano-dev_.
-
-We welcome all kinds of **contributions**.  Our `task list`_ is
-full of interesting ideas awaiting a champion.  If you have any
-questions regarding how to extend Theano, please feel free to ask on
-the Theano-dev_ mailing list.
-
-Theano is in active development and should be considered **experimental**.
-APIs are subject to change at any time.
-
-
-Download
-========
-
-We recommend that you use the `latest snapshot`_,
-Better yet, use `mercurial`_ to keep your installation fresh.
-The snapshots usually contain *more features* and *fewer bugs* than the
-"official" releases |---| they're not only for developers!
-
-.. class:: credits
-
-    Project by Mercurial_ and TRAC_.
-    Powered by Python_ and SciPy_.
-    Coded at the LISA_ lab.
-
-.. class:: hidden
-
-    Google should index the mailing lists: 
-    `theano-users <http://groups.google.com/group/theano-users?pli=1>`__,
-    and
-    `theano-dev <http://groups.google.com/group/theano-dev?pli=1>`__.
-
-.. |---| unicode:: U+02014 .. em dash
-   :trim:
-.. _latest snapshot: http://pylearn.org/hg/theano/archive/tip.tar.gz
-.. _bug report: http://lgcm.iro.umontreal.ca/theano/newticket
-.. _theano-users: http://groups.google.com/group/theano-users?pli=1
-.. _theano-dev: http://groups.google.com/group/theano-dev?pli=1
-.. _reStructuredText: rst.html
-.. _task list: http://lgcm.iro.umontreal.ca/theano/query?status=accepted&status=assigned&status=new&status=reopened&group=milestone&max=200&col=id&col=summary&col=status&col=owner&col=type&col=priority&col=component&col=time&report=9&order=priority
-.. _README: README.html
-.. _Quick-Start: README.html#quick-start
-
-.. _Theano Project Documentation Overview: doc/index.html
-.. _Mercurial: http://www.selenic.com/mercurial/wiki/
-.. _docutils: http://docutils.sourceforge.net
-.. _epydoc: http://epydoc.sourceforge.net/
-.. _scipy: http://scipy.org/
-.. _Python: http://www.python.org/
-.. _TRAC: http://trac.edgewall.org/
-.. _LISA:  http://www.iro.umontreal.ca/rubrique.php3?id_rubrique=27
-
-.. |TRAC| image:: http://www.edgewall.org/gfx/trac_logo.png
-   :target: http://www.edgewall.org/
-   :alt: Trac Logo
-   :align: middle
-   :class: borderless
-   :width: 193
-   :height: 32
-.. |Python| image:: python.png
-   :alt: Python Logo
-   :align: middle
-   :class: borderless
-   :width: 193
-   :height: 32
-.. |LISA| image:: http://www.iro.umontreal.ca/images/neurone_chip2.jpg
-   :target: http://www.iro.umontreal.ca/rubrique.php3?id_rubrique=27
-   :width: 193
-   :height: 32
-   :alt: LISA Logo
-   :align: middle
-   :class: borderless
-
-.. header:: |THEANO| - README_ - Download_ - Documentation_ - Wiki_ - `Task List`_
-
-.. _Download: README.html#downloading-theano
-.. _Documentation: doc/index.html
-.. _Wiki: http://pylearn.org/theano
-
-.. |THEANO| image:: http://lgcm.iro.umontreal.ca/theano/chrome/site/theano_logo.png
-   :target: http://pylearn.org/auto_theano
-   :alt: THEANO
-   :align: top
-   :class: borderless
-   :width: 60
-   :height: 18
-
-..
-   Local Variables:
-   mode: indented-text
-   indent-tabs-mode: nil
-   sentence-end-double-space: t
-   fill-column: 70
-   End:
-

scalar/_test_opt.py

-
-## PENDING REWRITE OF opt.py

scalar/autotest.py

-import unittest, os, sys, traceback
-
-if __name__ == '__main__':
-    def printUsage():
-        print >>sys.stderr, "Bad argument: ",sys.argv
-        print >>sys.stderr, "only --debug is supported"
-        sys.exit(1)
-    debugparam=""
-
-    if len(sys.argv)==2:
-        if sys.argv[1]=="--debug":
-            debugparam="--debug"
-            sys.argv.remove(debugparam)
-        else:
-            printUsage()
-    elif len(sys.argv)>2:
-        printUsage()
-
-
-
-    suite = None
-    filenames = os.listdir('.')
-    for filename in filenames:
-        if filename[-3:] == '.py':
-            modname = filename[:-3]
-            if modname in ['__init__', 'autotest']: continue
-            #print >>sys.stderr, 'Loading', modname
-
-            try:
-                module = __import__(modname)
-            except Exception, e:
-                if 'relative import' not in e.message:
-                    print >>sys.stderr, "===================================================="
-                    print >>sys.stderr, "Failed to load module %s" % modname
-                    print >>sys.stderr, "===================================================="
-                    traceback.print_exc()
-                    print >>sys.stderr, "===================================================="
-                continue
-                
-            tests = unittest.TestLoader().loadTestsFromModule(module)
-            if tests.countTestCases() > 0:
-                print >>sys.stderr, 'Testing', modname
-                if suite is None:
-                    suite = tests
-                else:
-                    suite.addTests(tests)
-    if debugparam:
-        suite.debug()
-    else:
-        unittest.TextTestRunner(verbosity=1).run(suite)
-

scalar/opt.py

-
-# TODO: everything?
-

scripts/docgen.py

+
+import sys
+import os
+import inspect
+
+from epydoc import docintrospecter 
+from epydoc.apidoc import RoutineDoc
+
+def Op_to_RoutineDoc(op, routine_doc, module_name=None):
+    routine_doc.specialize_to(RoutineDoc)
+
+    #NB: this code is lifted from
+    # /u/bergstrj/pub/prefix/x86_64-unknown-linux-gnu-Fedora_release_7__Moonshine_/lib/python2.5/site-packages/epydoc
+    # /u/bergstrj/pub/prefix/x86_64-unknown-linux-gnu-Fedora_release_7__Moonshine_/lib/python2.5/site-packages/epydoc/docintrospecter.py
+
+
+    # op should be an op instance
+    assert hasattr(op, 'perform')
+
+    # Record the function's docstring.
+    routine_doc.docstring = getattr(op, '__doc__', '')
+
+    # Record the function's signature.
+    func = op.__epydoc_asRoutine
+    if isinstance(func, type(Op_to_RoutineDoc)):
+        (args, vararg, kwarg, defaults) = inspect.getargspec(func)
+
+        # Add the arguments.
+        routine_doc.posargs = args
+        routine_doc.vararg = vararg
+        routine_doc.kwarg = kwarg
+
+        # Set default values for positional arguments.
+        routine_doc.posarg_defaults = [None]*len(args)
+
+        # Set the routine's line number.
+        if hasattr(func, 'func_code'):
+            routine_doc.lineno = func.func_code.co_firstlineno
+    else:
+        # [XX] I should probably use UNKNOWN here??
+        # dvarrazzo: if '...' is to be changed, also check that
+        # `docstringparser.process_arg_field()` works correctly.
+        # See SF bug #1556024.
+        routine_doc.posargs = ['...']
+        routine_doc.posarg_defaults = [None]
+        routine_doc.kwarg = None
+        routine_doc.vararg = None
+
+    return routine_doc
+
+docintrospecter.register_introspecter(
+    lambda value: getattr(value, '__epydoc_asRoutine', False), 
+    Op_to_RoutineDoc, 
+    priority=-1)
+
+
+
+if __name__ == '__main__':
+
+    throot = "/".join(sys.path[0].split("/")[:-1])
+
+    os.chdir(throot)
+
+    def mkdir(path):
+        try:
+            os.mkdir(path)
+        except OSError:
+            pass
+
+    mkdir("html")
+    mkdir("html/doc")
+    mkdir("html/api")
+
+    if len(sys.argv) == 1 or sys.argv[1] != 'rst':
+        from epydoc.cli import cli
+        sys.path[0:0] = os.path.realpath('.')
+        sys.argv[:] = ['', '--config', 'doc/api/epydoc.conf', '-o', 'html/api']
+        cli()
+#        os.system("epydoc --config doc/api/epydoc.conf -o html/api")
+
+    if len(sys.argv) == 1 or sys.argv[1] != 'epydoc':
+        import sphinx
+        sys.path[0:0] = [os.path.realpath('doc')]
+        sphinx.main(['', 'doc', 'html'])
+
+

scripts/test.py

+
+import unittest, os, sys, traceback, commands
+theano_path = os.path.realpath("%s/.." % sys.path[0])
+sys.path[0:0] = [theano_path]
+
+def test_module(module_path, debugmode = False):
+    files = commands.getoutput("find %s -name _test_*.py" % module_path)
+    suite = None
+    tocut = len("/".join(module_path.split("/")[:-1])) + 1
+    for file in files.split("\n"):
+        file = file[tocut:]
+        try:
+            module = __import__(file[:-3])
+        except Exception, e:
+            print >>sys.stderr, "===================================================="
+            print >>sys.stderr, "Failed to load %s" % file
+            print >>sys.stderr, "===================================================="
+            traceback.print_exc()
+            print >>sys.stderr, "===================================================="
+            continue
+
+        tests = unittest.TestLoader().loadTestsFromModule(module)
+        if tests.countTestCases() > 0:
+            print >>sys.stderr, 'Testing', file
+            if suite is None:
+                suite = tests
+            else:
+                suite.addTests(tests)
+    if suite is None:
+        return
+    if debugmode:
+        suite.debug()
+    else:
+        unittest.TextTestRunner(verbosity=1).run(suite)
+
+def py_test(module_path):
+    py.test.cmdline.main([module_path])
+
+def nopy_test(module_path):
+    print >>sys.stderr, "py.test is not installed!"
+    print >>sys.stderr, "  easy_install py"
+    print >>sys.stderr, "or if you are installing locally"
+    print >>sys.stderr, "  easy_install --prefix=/some/local/dir py"
+    return None
+
+    files = commands.getoutput("find %s -name test_*.py" % module_path)
+    suite = None
+    tocut = len("/".join(module_path.split("/")[:-1])) + 1
+    for file in files.split("\n"):
+        file = file[tocut:]
+        try:
+            module = __import__(file[:-3])
+        except Exception, e:
+            print >>sys.stderr, "===================================================="
+            print >>sys.stderr, "Failed to load %s" % file
+            print >>sys.stderr, "===================================================="
+            traceback.print_exc()
+            print >>sys.stderr, "===================================================="
+            continue
+    for method in dir(module):
+        if method.startswith("test_"):
+            method = getattr(module, method)
+            try:
+                r = method()
+            except Exception, e:
+                print >>sys.stderr, "===================================================="
+                print >>sys.stderr, "Exception in %s.%s" % (file, method.__name__)
+                print >>sys.stderr, "===================================================="
+                traceback.print_exc()
+                print >>sys.stderr, "===================================================="
+            if hasattr(r, 'next'):
+                for fargs in r:
+                    try:
+                        fargs[0](*fargs[1:])
+                    except Exception, e:
+                        print >>sys.stderr, "===================================================="
+                        print >>sys.stderr, "Exception in %s.%s, %s%s" % (file, method.__name__, fargs[0], fargs[1:])
+                        print >>sys.stderr, "===================================================="
+                        traceback.print_exc()
+                        print >>sys.stderr, "===================================================="
+
+
+if __name__ == '__main__':
+
+    def printUsage():
+        print >>sys.stderr, "Bad argument: ",sys.argv
+        print >>sys.stderr, "only --debug is supported"
+        sys.exit(1)
+    debugparam=""
+
+    if len(sys.argv)==2:
+        if sys.argv[1]=="--debug":
+            debugparam="--debug"
+            sys.argv.remove(debugparam)
+        else:
+            printUsage()
+    elif len(sys.argv)>2:
+        printUsage()
+
+    mname = os.path.join(theano_path, "theano")
+    test_module(mname)
+    try:
+        import py.test
+        py_test(mname)
+    except ImportError:
+        nopy_test(mname)
+
+

sparse/autotest.py

-import unittest, os, sys, traceback
-
-if __name__ == '__main__':
-    def printUsage():
-        print >>sys.stderr, "Bad argument: ",sys.argv
-        print >>sys.stderr, "only --debug is supported"
-        sys.exit(1)
-    debugparam=""
-
-    if len(sys.argv)==2:
-        if sys.argv[1]=="--debug":
-            debugparam="--debug"
-            sys.argv.remove(debugparam)
-        else:
-            printUsage()
-    elif len(sys.argv)>2:
-        printUsage()
-
-
-
-    suite = None
-    filenames = os.listdir('.')
-    for filename in filenames:
-        if filename[-3:] == '.py':
-            modname = filename[:-3]
-            if modname in ['__init__', 'autotest']: continue
-            #print >>sys.stderr, 'Loading', modname
-
-            try:
-                module = __import__(modname)
-            except Exception, e:
-                if 'relative import' not in e.message:
-                    print >>sys.stderr, "===================================================="
-                    print >>sys.stderr, "Failed to load module %s" % modname
-                    print >>sys.stderr, "===================================================="
-                    traceback.print_exc()
-                    print >>sys.stderr, "===================================================="
-                continue
-                
-            tests = unittest.TestLoader().loadTestsFromModule(module)
-            if tests.countTestCases() > 0:
-                print >>sys.stderr, 'Testing', modname
-                if suite is None:
-                    suite = tests
-                else:
-                    suite.addTests(tests)
-    if debugparam:
-        suite.debug()
-    else:
-        unittest.TextTestRunner(verbosity=1).run(suite)
-

tensor/autotest.py

-import unittest, os, sys, traceback
-
-if __name__ == '__main__':
-    def printUsage():
-        print >>sys.stderr, "Bad argument: ",sys.argv
-        print >>sys.stderr, "only --debug is supported"
-        sys.exit(1)
-    debugparam=""
-
-    if len(sys.argv)==2:
-        if sys.argv[1]=="--debug":
-            debugparam="--debug"
-            sys.argv.remove(debugparam)
-        else:
-            printUsage()
-    elif len(sys.argv)>2:
-        printUsage()
-
-
-
-    suite = None
-    filenames = os.listdir('.')
-    for filename in filenames:
-        if filename[-3:] == '.py':
-            modname = filename[:-3]
-            if modname in ['__init__', 'autotest']: continue
-            #print >>sys.stderr, 'Loading', modname
-
-            try:
-                module = __import__(modname)
-            except Exception, e:
-                if 'relative import' not in e.message:
-                    print >>sys.stderr, "===================================================="
-                    print >>sys.stderr, "Failed to load module %s" % modname
-                    print >>sys.stderr, "===================================================="
-                    traceback.print_exc()
-                    print >>sys.stderr, "===================================================="
-                continue
-                
-            tests = unittest.TestLoader().loadTestsFromModule(module)
-            if tests.countTestCases() > 0:
-                print >>sys.stderr, 'Testing', modname
-                if suite is None:
-                    suite = tests
-                else:
-                    suite.addTests(tests)
-    if debugparam:
-        suite.debug()
-    else:
-        unittest.TextTestRunner(verbosity=1).run(suite)
-

gof/cc.py → theano/gof/cc.py

@@ -19,53 +19,7 @@ import graph
 import link
 import utils
 
-def set_compiledir(path=None):
-    """Set the directory into which theano will compile code objects
-
-    @param path: an absolute path or relative path. An argument of None will
-    trigger one of two default paths: firstly an environment variable called
-    'THEANO_COMPILEDIR' will be sought; failing that, an architecture-specific
-    directory will be chosen within $HOME/.theano.
-
-    @type path: string or None
-
-    @return: None
-
-    @note:  This function will create the path (recursively) as a folder if it
-    is not present, not readable, or not writable.  New folders will be created
-    with mode 0700.
-
-    """
-    # N.B. The path is stored as an attribute of this function
-
-    if path is None:
-        # we need to set the default, which can come from one of two places
-        if os.getenv('THEANO_COMPILEDIR'):
-            path = os.getenv('THEANO_COMPILEDIR')
-        else:
-            platform_id = platform.platform() + '-' + platform.processor()
-            platform_id = re.sub("[\(\)\s]+", "_", platform_id)
-            path = os.path.join(os.getenv('HOME'), '.theano', 'compiledir_'+platform_id)
-
-    if not os.access(path, os.R_OK | os.W_OK):
-        os.makedirs(path, 7<<6) #read-write-execute for this user only
-
-    # PROBLEM: sometimes the first approach based on os.system('touch')
-    # returned -1 for an unknown reason; the alternate approach here worked
-    # in all cases... it was weird.
-    open(os.path.join(path, '__init__.py'), 'w').close()
-
-    set_compiledir.compiledir = path
-
-def get_compiledir():
-    """Return the directory where theano code objects should be compiled
-
-    @rtype: string
-    """
-    if not hasattr(set_compiledir, 'compiledir'):
-        set_compiledir()
-    return set_compiledir.compiledir
-
+from compiledir import *
 
 class CodeBlock:
     """WRITEME

theano/gof/compiledir.py

+
+import os
+import platform
+import re
+
+def set_compiledir(path=None):
+    """Set the directory into which theano will compile code objects
+
+    @param path: an absolute path or relative path. An argument of None will
+    trigger one of two default paths: firstly an environment variable called
+    'THEANO_COMPILEDIR' will be sought; failing that, an architecture-specific
+    directory will be chosen within $HOME/.theano.
+
+    @type path: string or None
+
+    @return: None
+
+    @note:  This function will create the path (recursively) as a folder if it
+    is not present, not readable, or not writable.  New folders will be created
+    with mode 0700.
+
+    """
+    # N.B. The path is stored as an attribute of this function
+
+    if path is None:
+        # we need to set the default, which can come from one of two places
+        if os.getenv('THEANO_COMPILEDIR'):
+            path = os.getenv('THEANO_COMPILEDIR')
+        else:
+            platform_id = platform.platform() + '-' + platform.processor()
+            platform_id = re.sub("[\(\)\s]+", "_", platform_id)
+            path = os.path.join(os.getenv('HOME'), '.theano', 'compiledir_'+platform_id)
+
+    if not os.access(path, os.R_OK | os.W_OK):
+        os.makedirs(path, 7<<6) #read-write-execute for this user only
+
+    # PROBLEM: sometimes the first approach based on os.system('touch')
+    # returned -1 for an unknown reason; the alternate approach here worked
+    # in all cases... it was weird.
+    open(os.path.join(path, '__init__.py'), 'w').close()
+
+    set_compiledir.compiledir = path
+
+def get_compiledir():
+    """Return the directory where theano code objects should be compiled
+
+    @rtype: string
+    """
+    if not hasattr(set_compiledir, 'compiledir'):
+        set_compiledir()
+    return set_compiledir.compiledir

gof/cutils.py → theano/gof/cutils.py

 
+from compiledir import *
+import sys
+
+
+
 try:
+    sys.path.append(get_compiledir())
     from cutils_ext import *
 
 except ImportError:
@@ -27,6 +33,5 @@ except ImportError:
     fun =weave.ext_tools.ext_function('run_cthunk', single_runner, ['cthunk'])
     fun.customize.add_extra_compile_arg('--permissive')
     mod.add_function(fun)
-    mod.compile()
-
+    mod.compile(location = get_compiledir())
     from cutils_ext import *

gof/_test_cc.py → theano/gof/tests/test_cc.py

 
 import unittest
 
-from link import PerformLinker, Profiler
-from cc import *
-from type import Type
-from graph import Result, Apply, Constant
-from op import Op
-import env
-import toolbox
+from theano.gof.link import PerformLinker, Profiler
+from theano.gof.cc import *
+from theano.gof.type import Type
+from theano.gof.graph import Result, Apply, Constant
+from theano.gof.op import Op
+from theano.gof import env
+from theano.gof import toolbox
 
 def as_result(x):
     assert isinstance(x, Result)
@@ -135,77 +135,76 @@ def Env(inputs, outputs):
     return e
 
 
-class _test_CLinker(unittest.TestCase):
-
-    def test_straightforward(self):
-        x, y, z = inputs()
-        e = add(mul(add(x, y), div(x, y)), sub(sub(x, y), z))
-        lnk = CLinker().accept(Env([x, y, z], [e]))
-        fn = lnk.make_function()
-        self.failUnless(fn(2.0, 2.0, 2.0) == 2.0)
-
-#     def test_orphan(self):
-#         x, y, z = inputs()
-#         z = Constant(tdouble, 4.12345678)
-#         e = add(mul(add(x, y), div(x, y)), sub(sub(x, y), z))
-#         lnk = CLinker(Env([x, y], [e]))
-#         fn = lnk.make_function()
-#         self.failUnless(abs(fn(2.0, 2.0) + 0.12345678) < 1e-9)
-#         print lnk.code_gen()
-#         self.failUnless("4.12345678" not in lnk.code_gen()) # we do not expect the number to be inlined
-
-    def test_literal_inlining(self):
-        x, y, z = inputs()
-        z = Constant(tdouble, 4.12345678)
-        e = add(mul(add(x, y), div(x, y)), sub(sub(x, y), z))
-        lnk = CLinker().accept(Env([x, y], [e]))
-        fn = lnk.make_function()
-        self.failUnless(abs(fn(2.0, 2.0) + 0.12345678) < 1e-9)
-        self.failUnless("4.12345678" in lnk.code_gen()) # we expect the number to be inlined
-
-    def test_single_node(self):
-        x, y, z = inputs()
-        node = add.make_node(x, y)
-        lnk = CLinker().accept(Env(node.inputs, node.outputs))
-        fn = lnk.make_function()
-        self.failUnless(fn(2.0, 7.0) == 9)
-    
-    def test_dups(self):
-        # Testing that duplicate inputs are allowed.
-        x, y, z = inputs()
-        e = add(x, x)
-        lnk = CLinker().accept(Env([x, x], [e]))
-        fn = lnk.make_function()
-        self.failUnless(fn(2.0, 2.0) == 4)
-        # note: for now the behavior of fn(2.0, 7.0) is undefined
-
-    def test_dups_inner(self):
-        # Testing that duplicates are allowed inside the graph
-        x, y, z = inputs()
-        e = add(mul(y, y), add(x, z))
-        lnk = CLinker().accept(Env([x, y, z], [e]))
-        fn = lnk.make_function()
-        self.failUnless(fn(1.0, 2.0, 3.0) == 8.0)
+################
+# Test CLinker #
+################
+
+def test_clinker_straightforward():
+    x, y, z = inputs()
+    e = add(mul(add(x, y), div(x, y)), sub(sub(x, y), z))
+    lnk = CLinker().accept(Env([x, y, z], [e]))
+    fn = lnk.make_function()
+    assert fn(2.0, 2.0, 2.0) == 2.0
+
+def test_clinker_literal_inlining():
+    x, y, z = inputs()
+    z = Constant(tdouble, 4.12345678)
+    e = add(mul(add(x, y), div(x, y)), sub(sub(x, y), z))
+    lnk = CLinker().accept(Env([x, y], [e]))
+    fn = lnk.make_function()
+    assert abs(fn(2.0, 2.0) + 0.12345678) < 1e-9
+    code = lnk.code_gen()
+    print "=== Code generated ==="
+    print code
+    assert "4.12345678" in code # we expect the number to be inlined
+
+def test_clinker_single_node():
+    x, y, z = inputs()
+    node = add.make_node(x, y)
+    lnk = CLinker().accept(Env(node.inputs, node.outputs))
+    fn = lnk.make_function()
+    assert fn(2.0, 7.0) == 9
+
+def test_clinker_dups():
+    # Testing that duplicate inputs are allowed.
+    x, y, z = inputs()
+    e = add(x, x)
+    lnk = CLinker().accept(Env([x, x], [e]))
+    fn = lnk.make_function()
+    assert fn(2.0, 2.0) == 4
+    # note: for now the behavior of fn(2.0, 7.0) is undefined
+
+def test_clinker_dups_inner():
+    # Testing that duplicates are allowed inside the graph
+    x, y, z = inputs()
+    e = add(mul(y, y), add(x, z))
+    lnk = CLinker().accept(Env([x, y, z], [e]))
+    fn = lnk.make_function()
+    assert fn(1.0, 2.0, 3.0) == 8.0
     
 
 
-class _test_OpWiseCLinker(unittest.TestCase):
+######################
+# Test OpWiseCLinker #
+######################
+
+def test_opwiseclinker_straightforward():
+    x, y, z = inputs()
+    e = add(mul(add(x, y), div(x, y)), sub(sub(x, y), z))
+    lnk = OpWiseCLinker().accept(Env([x, y, z], [e]))
+    fn = lnk.make_function()
+    assert fn(2.0, 2.0, 2.0) == 2.0
+
+def test_opwiseclinker_constant():
+    x, y, z = inputs()
+    x = Constant(tdouble, 7.2, name = 'x')
+    e = add(mul(x, y), mul(y, z))
+    lnk = OpWiseCLinker().accept(Env([y, z], [e]))
+    fn = lnk.make_function()
+    res = fn(1.5, 3.0)
+    assert res == 15.3
 
-    def test_straightforward(self):
-        x, y, z = inputs()
-        e = add(mul(add(x, y), div(x, y)), sub(sub(x, y), z))
-        lnk = OpWiseCLinker().accept(Env([x, y, z], [e]))
-        fn = lnk.make_function()
-        self.failUnless(fn(2.0, 2.0, 2.0) == 2.0)
 
-    def test_constant(self):
-        x, y, z = inputs()
-        x = Constant(tdouble, 7.2, name = 'x')
-        e = add(mul(x, y), mul(y, z))
-        lnk = OpWiseCLinker().accept(Env([y, z], [e]))
-        fn = lnk.make_function()
-        res = fn(1.5, 3.0)
-        self.failUnless(res == 15.3, res)
 
 
 class MyExc(Exception):
@@ -215,49 +214,34 @@ def _my_checker(x, y):
         raise MyExc("Output mismatch.", {'performlinker': x[0], 'clinker': y[0]})
 
 
-class _test_DualLinker(unittest.TestCase):
-
-    def test_straightforward(self):
-        x, y, z = inputs()
-        e = add(mul(x, y), mul(y, z)) # add and mul are correct in C and in Python
-        lnk = DualLinker(checker = _my_checker).accept(Env([x, y, z], [e]))
-        fn = lnk.make_function()
-        res = fn(7.2, 1.5, 3.0)
-        self.failUnless(res == 15.3, res)
-
-    def test_mismatch(self):
-        x, y, z = inputs()
-        e = sub(mul(x, y), mul(y, z)) # sub is correct in C but erroneous in Python
-        g = Env([x, y, z], [e])
-        lnk = DualLinker(checker = _my_checker).accept(g)
-        fn = lnk.make_function()
-
-        self.failUnless(CLinker().accept(g).make_function()(1.0, 2.0, 3.0) == -4.0) # good
-        self.failUnless(OpWiseCLinker().accept(g).make_function()(1.0, 2.0, 3.0) == -4.0) # good
-        self.failUnless(PerformLinker().accept(g).make_function()(1.0, 2.0, 3.0) == -10.0) # (purposely) wrong
-        
-        try:
-            # this runs OpWiseCLinker and PerformLinker in parallel and feeds
-            # results of matching operations to _my_checker to verify that they
-            # are the same.
-            res = fn(1.0, 2.0, 3.0)
-            self.fail()
-        except MyExc, e:
-            pass
-        else:
-            self.fail()
-
-#     def test_orphan(self):
-#         x, y, z = inputs()
-#         x = Constant(tdouble, 7.2, name = 'x')
-#         e = add(mul(x, y), mul(y, z)) # add and mul are correct in C and in Python
-#         lnk = DualLinker(Env([y, z], [e]), checker = _my_checker)
-#         fn = lnk.make_function()
-#         res = fn(1.5, 3.0)
-#         self.failUnless(res == 15.3, res)
-
-
-
-        
-if __name__ == '__main__':
-    unittest.main()
+###################
+# Test DualLinker #
+###################
+
+def test_duallinker_straightforward():
+    x, y, z = inputs()
+    e = add(mul(x, y), mul(y, z)) # add and mul are correct in C and in Python
+    lnk = DualLinker(checker = _my_checker).accept(Env([x, y, z], [e]))
+    fn = lnk.make_function()
+    res = fn(7.2, 1.5, 3.0)
+    assert res == 15.3
+
+def test_duallinker_mismatch():
+    x, y, z = inputs()
+    e = sub(mul(x, y), mul(y, z)) # sub is correct in C but erroneous in Python
+    g = Env([x, y, z], [e])
+    lnk = DualLinker(checker = _my_checker).accept(g)
+    fn = lnk.make_function()
+
+    assert CLinker().accept(g).make_function()(1.0, 2.0, 3.0) == -4.0 # good
+    assert OpWiseCLinker().accept(g).make_function()(1.0, 2.0, 3.0) == -4.0 # good
+    assert PerformLinker().accept(g).make_function()(1.0, 2.0, 3.0) == -10.0 # (purposely) wrong
+
+    try:
+        # this runs OpWiseCLinker and PerformLinker in parallel and feeds
+        # results of matching operations to _my_checker to verify that they
+        # are the same.
+        res = fn(1.0, 2.0, 3.0)
+        raise Exception("An exception should have been raised here!")
+    except MyExc, e:
+        pass

theano/gof/tests/test_destroyhandler.py

+
+import unittest
+
+from theano.gof.type import Type
+from theano.gof import graph
+from theano.gof.graph import Result, Apply
+from theano.gof.op import Op
+from theano.gof.opt import *
+
+from theano.gof import destroyhandler
+from theano.gof.env import Env, InconsistencyError
+from theano.gof.toolbox import ReplaceValidate
+
+from copy import copy
+
+PatternOptimizer = lambda p1, p2, ign=True: OpKeyOptimizer(PatternSub(p1, p2), ignore_newtrees=ign)
+OpSubOptimizer = lambda op1, op2, fail=keep_going, ign=True: TopoOptimizer(OpSub(op1, op2), ignore_newtrees=ign, failure_callback = fail)
+
+
+def as_result(x):
+    assert isinstance(x, Result)
+    return x
+
+
+class MyType(Type):
+
+    def filter(self, data):
+        return data
+
+    def __eq__(self, other):
+        return isinstance(other, MyType)
+
+
+def MyResult(name):
+    return Result(MyType(), None, None, name = name)
+
+def MyValue(data):
+    return graph.Value(MyType(), data = data)
+
+
+class MyOp(Op):
+
+    def __init__(self, nin, name, vmap = {}, dmap = {}, nout = 1, tolerate_same = []):
+        self.nin = nin
+        self.nout = nout
+        self.name = name
+        self.destroy_map = dmap
+        self.view_map = vmap
+        self.tolerate_same = tolerate_same
+    
+    def make_node(self, *inputs):
+        assert len(inputs) == self.nin
+        inputs = map(as_result, inputs)
+        for input in inputs:
+            if not isinstance(input.type, MyType):
+                raise Exception("Error 1")
+        outputs = [MyResult(self.name + "_R") for i in xrange(self.nout)]
+        return Apply(self, inputs, outputs)
+
+    def __str__(self):
+        return self.name
+
+
+sigmoid = MyOp(1, 'Sigmoid')
+transpose_view = MyOp(1, 'TransposeView', vmap = {0: [0]})
+add = MyOp(2, 'Add')
+add_in_place = MyOp(2, 'AddInPlace', dmap = {0: [0]})
+add_in_place_2 = MyOp(2, 'AddInPlace', dmap = {0: [0]}, tolerate_same = [(0, 1)])
+dot = MyOp(2, 'Dot')
+
+
+def inputs():
+    x = MyResult('x')
+    y = MyResult('y')
+    z = MyResult('z')
+    return x, y, z
+
+_Env = Env
+def Env(inputs, outputs, validate = True):
+    e = _Env(inputs, outputs)
+    e.extend(destroyhandler.DestroyHandler())
+    e.extend(ReplaceValidate())
+    if validate:
+        e.validate()
+    return e
+
+
+class FailureWatch:
+    # when passed to OpSubOptimizer or PatternOptimizer, counts the number of failures
+    def __init__(self):
+        self.failures = 0
+    def __call__(self, exc, nav, pairs):
+        assert isinstance(exc, InconsistencyError)
+        self.failures += 1
+
+
+def consistent(g):
+    print "Testing consistent:", g
+    try:
+        assert g.consistent()
+    except AssertionError:
+        print "Test failed! The graph was marked as NOT consistent."
+        raise
+    print "Test OK"
+
+def inconsistent(g):
+    print "Testing NOT consistent:", g
+    try:
+        assert not g.consistent()
+    except AssertionError:
+        print "Test failed! The graph was marked as consistent."
+        raise
+    print "Test OK"
+    
+
+
+
+#################
+# Test protocol #
+#################
+
+def test_misc():
+    x, y, z = inputs()
+    e = transpose_view(transpose_view(transpose_view(transpose_view(x))))
+    g = Env([x,y,z], [e])
+    consistent(g)
+    chk = g.checkpoint()
+    PatternOptimizer((transpose_view, (transpose_view, 'x')), 'x').optimize(g)
+    assert str(g) == "[x]"
+    new_e = add(x,y)
+    g.replace_validate(x, new_e)
+    assert str(g) == "[Add(x, y)]"
+    g.replace(new_e, dot(add_in_place(x,y), transpose_view(x)))
+    assert str(g) == "[Dot(AddInPlace(x, y), TransposeView(x))]"
+    inconsistent(g)
+    g.revert(chk)
+    consistent(g)
+    assert str(g) == "[TransposeView(TransposeView(TransposeView(TransposeView(x))))]"
+
+
+
+
+######################
+# Test protocol skip #
+######################
+
+def test_aliased_inputs_replacement():
+    x, y, z = inputs()
+    tv = transpose_view(x)
+    tvv = transpose_view(tv)
+    sx = sigmoid(x)
+    e = add_in_place(x, tv)
+    g = Env([x, y], [e], False)
+    inconsistent(g)
+    g.replace(tv, sx)
+    consistent(g)
+    g.replace(sx, tv)
+    inconsistent(g)
+    g.replace(tv, tvv)
+    inconsistent(g)
+    g.replace(tv, sx)
+    consistent(g)
+
+def test_indestructible():
+    x, y, z = inputs()
+    x.tag.indestructible = True
+    x = copy(x)
+    assert x.tag.indestructible  # checking if indestructible survives the copy!
+    e = add_in_place(x, y)
+    g = Env([x,y,z], [e], False)
+    inconsistent(g)
+    g.replace_validate(e, add(x, y))
+    consistent(g)
+
+def test_usage_loop_through_views_2():
+    x, y, z = inputs()
+    e0 = transpose_view(transpose_view(sigmoid(x)))
+    e = dot(add_in_place(x,y), transpose_view(e0))
+    g = Env([x,y,z], [e])
+    consistent(g) # because sigmoid can do the copy
+    g.replace(e0, x)
+    inconsistent(g) # we cut off the path to the sigmoid
+
+def test_destroyers_loop():
+    # AddInPlace(x, y) and AddInPlace(y, x) should not coexist
+    x, y, z = inputs()
+    e1 = add(x, y)
+    e2 = add(y, x)
+    g = Env([x,y,z], [e1, e2])
+    chk = g.checkpoint()
+    consistent(g)
+    g.replace_validate(e1, add_in_place(x, y))
+    consistent(g)
+    try:
+        g.replace_validate(e2, add_in_place(y, x))
+        raise Exception("Shouldn't have reached this point.")
+    except InconsistencyError:
+        pass
+    consistent(g)
+    g.revert(chk)
+    g.replace_validate(e2, add_in_place(y, x))
+    consistent(g)
+    try:
+        g.replace_validate(e1, add_in_place(x, y))
+        raise Exception("Shouldn't have reached this point.")
+    except InconsistencyError:
+        pass
+    consistent(g)
+
+
+########
+# Misc #
+########
+
+def test_aliased_inputs():
+    x, y, z = inputs()
+    e = add_in_place(x, x)
+    g = Env([x], [e], False)
+    inconsistent(g)
+
+def test_aliased_inputs2():
+    x, y, z = inputs()
+    e = add_in_place(x, transpose_view(x))
+    g = Env([x], [e], False)
+    inconsistent(g)
+
+def test_aliased_inputs_tolerate():
+    x, y, z = inputs()
+    e = add_in_place_2(x, x)
+    g = Env([x], [e], False)
+    consistent(g)
+
+def test_aliased_inputs_tolerate2():
+    x, y, z = inputs()
+    e = add_in_place_2(x, transpose_view(x))
+    g = Env([x], [e], False)
+    inconsistent(g)
+
+def test_indestructible_through_views():
+    x, y, z = inputs()
+    x.tag.indestructible = True
+    tv = transpose_view(x)
+    e = add_in_place(tv, y)
+    g = Env([x,y,z], [e], False)
+    inconsistent(g)
+    g.replace_validate(tv, sigmoid(x))
+    consistent(g)
+
+def test_indirect():
+    x, y, z = inputs()
+    e0 = add_in_place(x, y)
+    e = dot(sigmoid(e0), transpose_view(x))
+    g = Env([x,y,z], [e], False)
+    inconsistent(g)
+    new_e0 = add(x, y)
+    g.replace(e0, new_e0)
+    consistent(g)
+    g.replace(new_e0, add_in_place(x, y))
+    inconsistent(g)
+
+def test_indirect_2():
+    x, y, z = inputs()
+    e0 = transpose_view(x)
+    e = dot(sigmoid(add_in_place(x, y)), e0)
+    g = Env([x,y,z], [e], False)
+    inconsistent(g)
+    new_e0 = add(e0, y)
+    g.replace(e0, new_e0)
+    consistent(g)
+
+def test_long_destroyers_loop():
+    x, y, z = inputs()
+    e = dot(dot(add_in_place(x,y), add_in_place(y,z)), add(z,x))
+    g = Env([x,y,z], [e])
+    consistent(g)
+    OpSubOptimizer(add, add_in_place).optimize(g)
+    consistent(g)
+    assert str(g) != "[Dot(Dot(AddInPlace(x, y), AddInPlace(y, z)), AddInPlace(z, x))]" # we don't want to see that!
+    e2 = dot(dot(add_in_place(x,y), add_in_place(y,z)), add_in_place(z,x))
+    try:
+        g2 = Env(*graph.clone([x,y,z], [e2]))
+        raise Exception("Shouldn't have reached this point.")
+    except InconsistencyError:
+        pass
+
+def test_misc_2():
+    x, y, z = inputs()
+    tv = transpose_view(x)
+    e = add_in_place(x, tv)
+    g = Env([x,y], [e], False)
+    inconsistent(g)
+    g.replace(tv, x)
+    inconsistent(g)
+
+def test_multi_destroyers():
+    x, y, z = inputs()
+    e = add(add_in_place(x, y), add_in_place(x, y))
+    try:
+        g = Env([x,y,z], [e])
+        raise Exception("Shouldn't have reached this point.")
+    except InconsistencyError, e:
+        pass
+
+def test_multi_destroyers_through_views():
+    x, y, z = inputs()
+    e = dot(add(transpose_view(z), y), add(z, x))
+    g = Env([x,y,z], [e])
+    consistent(g)
+    fail = FailureWatch()
+    OpSubOptimizer(add, add_in_place, fail).optimize(g)
+    consistent(g)
+    assert fail.failures == 1 # should have succeeded once and failed once
+
+
+def test_repair_destroy_path():
+    x, y, z = inputs()
+    e1 = transpose_view(transpose_view(x))
+    e2 = transpose_view(transpose_view(e1))
+    e3 = add_in_place(e2, y)
+    e4 = add_in_place(e1, z)
+    g = Env([x,y,z], [e3, e4], False)
+    inconsistent(g)
+    g.replace(e2, transpose_view(x))
+    inconsistent(g)
+
+def test_usage_loop():
+    x, y, z = inputs()
+    g = Env([x,y,z], [dot(add_in_place(x, z), x)], False)
+    inconsistent(g)
+    OpSubOptimizer(add_in_place, add).optimize(g) # replace add_in_place with add
+    consistent(g)
+
+def test_usage_loop_through_views():
+    x, y, z = inputs()
+    aip = add_in_place(x, y)
+    e = dot(aip, transpose_view(x))
+    g = Env([x,y,z], [e], False)
+    inconsistent(g)
+    g.replace_validate(aip, add(x, z))
+    consistent(g)
+
+def test_usage_loop_insert_views():
+    x, y, z = inputs()
+    e = dot(add_in_place(x, add(y, z)), sigmoid(sigmoid(sigmoid(sigmoid(sigmoid(x))))))
+    g = Env([x,y,z], [e])
+    consistent(g)
+    fail = FailureWatch()
+    OpSubOptimizer(sigmoid, transpose_view, fail).optimize(g)
+    consistent(g)
+    assert fail.failures == 1 # it must keep one sigmoid in the long sigmoid chain
+
+def test_value_repl():
+    x, y, z = inputs()
+    sy = sigmoid(y)
+    e = add_in_place(x, sy)
+    g = Env([x,y], [e], False)
+    consistent(g)
+    g.replace(sy, MyValue("abc"))
+    consistent(g)
+
+def test_value_repl_2():
+    x, y, z = inputs()
+    sy = sigmoid(y)
+    e = add_in_place(x, sy)
+    g = Env([x,y], [e], False)
+    consistent(g)
+    g.replace(sy, transpose_view(MyValue("abc")))
+    consistent(g)
+
+
+

gof/_test_graph.py → theano/gof/tests/test_graph.py

 
 from collections import deque
-import unittest
-from graph import *
+from theano.gof.graph import *
 
-from op import Op
-from type import Type
-from graph import Result
-
-
-if 1:
-    testcase = unittest.TestCase
-else:
-    testcase = object
-    realtestcase = unittest.TestCase
+from theano.gof.op import Op
+from theano.gof.type import Type
+from theano.gof.graph import Result
 
 
 def as_result(x):
@@ -55,75 +47,31 @@ class MyOp(Op):
 MyOp = MyOp()
 
 
+##########
+# inputs #
+##########
 
-# class MyResult(Result):
-
-#     def __init__(self, thingy):
-#         self.thingy = thingy
-#         Result.__init__(self, role = None )
-#         self.data = [self.thingy]
-
-#     def __eq__(self, other):
-#         return self.same_properties(other)
-
-#     def same_properties(self, other):
-#         return isinstance(other, MyResult) and other.thingy == self.thingy
-
-#     def __str__(self):
-#         return str(self.thingy)
-
-#     def __repr__(self):
-#         return str(self.thingy)
-
+class TestInputs:
 
-# class MyOp(Op):
-
-#     def __init__(self, *inputs):
-#         for input in inputs:
-#             if not isinstance(input, MyResult):
-#                 raise Exception("Error 1")
-#         self.inputs = inputs
-#         self.outputs = [MyResult(sum([input.thingy for input in inputs]))]
-
-
-class _test_inputs(testcase):
-
-    def test_straightforward(self):
+    def test_inputs(self):
         r1, r2 = MyResult(1), MyResult(2)
         node = MyOp.make_node(r1, r2)
         assert inputs(node.outputs) == [r1, r2]
 
-    def test_deep(self):
+    def test_inputs_deep(self):
         r1, r2, r5 = MyResult(1), MyResult(2), MyResult(5)
         node = MyOp.make_node(r1, r2)
         node2 = MyOp.make_node(node.outputs[0], r5)
         i = inputs(node2.outputs)
-        self.failUnless(i == [r1, r2, r5], i)
-
-#     def test_unreached_inputs(self):
-#         r1, r2, r5 = MyResult(1), MyResult(2), MyResult(5)
-#         op = MyOp(r1, r2)
-#         op2 = MyOp(op.outputs[0], r5)
-#         try:
-#             # function doesn't raise if we put False instead of True
-#             ro = results_and_orphans([r1, r2, op2.outputs[0]], op.outputs, True)
-#         except Exception, e:
-#             if e[0] is results_and_orphans.E_unreached:
-#                 return
-#         self.fail()
-
-
-# class _test_orphans(testcase):
-
-#     def test_straightforward(self):
-#         r1, r2, r5 = MyResult(1), MyResult(2), MyResult(5)
-#         node = MyOp.make_node(r1, r2)
-#         node2 = MyOp.make_node(node.outputs[0], r5)
-#         orph = orphans([r1, r2], node2.outputs)
-#         self.failUnless(orph == [r5], orph)
-    
+        assert i == [r1, r2, r5], i
+
+
+#############
+# as_string #
+#############
+
 
-class _test_as_string(testcase):
+class X:
 
     leaf_formatter = lambda self, leaf: str(leaf.type)
     node_formatter = lambda self, node, argstrings: "%s(%s)" % (node.op,
@@ -133,19 +81,22 @@ class _test_as_string(testcase):
         return as_string(inputs, outputs,
                          leaf_formatter = self.leaf_formatter,
                          node_formatter = self.node_formatter)
+    
+
+class TestStr(X):
 
-    def test_straightforward(self):
+    def test_as_string(self):
         r1, r2 = MyResult(1), MyResult(2)
         node = MyOp.make_node(r1, r2)
         s = self.str([r1, r2], node.outputs)
-        self.failUnless(s == ["MyOp(R1, R2)"], s)
+        assert s == ["MyOp(R1, R2)"]
 
-    def test_deep(self):
+    def test_as_string_deep(self):
         r1, r2, r5 = MyResult(1), MyResult(2), MyResult(5)
         node = MyOp.make_node(r1, r2)
         node2 = MyOp.make_node(node.outputs[0], r5)
         s = self.str([r1, r2, r5], node2.outputs)
-        self.failUnless(s == ["MyOp(MyOp(R1, R2), R5)"], s)
+        assert s == ["MyOp(MyOp(R1, R2), R5)"]
 
     def test_multiple_references(self):
         r1, r2, r5 = MyResult(1), MyResult(2), MyResult(5)
@@ -161,16 +112,11 @@ class _test_as_string(testcase):
         assert self.str(node2.inputs, node2.outputs) == ["MyOp(R3, R3)"]
 
 
-class _test_clone(testcase):
-
-    leaf_formatter = lambda self, leaf: str(leaf.type)
-    node_formatter = lambda self, node, argstrings: "%s(%s)" % (node.op,
-                                                                ", ".join(argstrings))
+#########
+# clone #
+#########
 
-    def str(self, inputs, outputs):
-        return as_string(inputs, outputs,
-                         leaf_formatter = self.leaf_formatter,
-                         node_formatter = self.node_formatter)
+class TestClone(X):
 
     def test_accurate(self):
         r1, r2 = MyResult(1), MyResult(2)
@@ -198,6 +144,11 @@ class _test_clone(testcase):
         assert self.str(inputs(new_node.outputs), new_node.outputs) == ["MyOp(R7, R8)"]
         assert self.str(inputs(node.outputs), node.outputs) == ["MyOp(MyOp(R1, R2), R5)"]
 
+
+############
+# toposort #
+############
+
 def prenode(obj):
     if isinstance(obj, Result): 
         if obj.owner:
@@ -205,79 +156,64 @@ def prenode(obj):
     if isinstance(obj, Apply):
         return obj.inputs
 
-class _test_toposort(testcase):
-    def test0(self):
+class TestToposort:
+
+    def test_0(self):
         """Test a simple graph"""
         r1, r2, r5 = MyResult(1), MyResult(2), MyResult(5)
         o = MyOp.make_node(r1, r2)
         o2 = MyOp.make_node(o.outputs[0], r5)
 
         all = general_toposort(o2.outputs, prenode)
-        self.failUnless(all == [r5, r2, r1, o, o.outputs[0], o2, o2.outputs[0]], all)
+        assert all == [r5, r2, r1, o, o.outputs[0], o2, o2.outputs[0]]
 
         all = io_toposort([r5], o2.outputs)
-        self.failUnless(all == [o, o2], all)
+        assert all == [o, o2]
 
-    def test1(self):
+    def test_1(self):
         """Test a graph with double dependencies"""
         r1, r2, r5 = MyResult(1), MyResult(2), MyResult(5)
         o = MyOp.make_node(r1, r1)
         o2 = MyOp.make_node(o.outputs[0], r5)
         all = general_toposort(o2.outputs, prenode)
-        self.failUnless(all == [r5, r1, o, o.outputs[0], o2, o2.outputs[0]], all)
+        assert all == [r5, r1, o, o.outputs[0], o2, o2.outputs[0]]
 
-    def test2(self):
+    def test_2(self):
         """Test a graph where the inputs have owners"""
         r1, r2, r5 = MyResult(1), MyResult(2), MyResult(5)
         o = MyOp.make_node(r1, r1)
         r2b = o.outputs[0]
         o2 = MyOp.make_node(r2b, r2b)
         all = io_toposort([r2b], o2.outputs)
-        self.failUnless(all == [o2], all)
+        assert all == [o2]
 
         o2 = MyOp.make_node(r2b, r5)
         all = io_toposort([r2b], o2.outputs)
-        self.failUnless(all == [o2], all)
+        assert all == [o2]
 
-    def test3(self):
+    def test_3(self):
         """Test a graph which is not connected"""
         r1, r2, r3, r4 = MyResult(1), MyResult(2), MyResult(3), MyResult(4)
         o0 = MyOp.make_node(r1, r2)
         o1 = MyOp.make_node(r3, r4)
         all = io_toposort([r1, r2, r3, r4], o0.outputs + o1.outputs)
-        self.failUnless(all == [o1,o0], all)
+        assert all == [o1,o0]
 
-    def test4(self):
+    def test_4(self):
         """Test inputs and outputs mixed together in a chain graph"""
         r1, r2, r3, r4 = MyResult(1), MyResult(2), MyResult(3), MyResult(4)
         o0 = MyOp.make_node(r1, r2)
         o1 = MyOp.make_node(o0.outputs[0], r1)
         all = io_toposort([r1, o0.outputs[0]], [o0.outputs[0], o1.outputs[0]])
-        self.failUnless(all == [o1], all)
+        assert all == [o1]
 
-    def test5(self):
+    def test_5(self):
         """Test when outputs have clients"""
         r1, r2, r3, r4 = MyResult(1), MyResult(2), MyResult(3), MyResult(4)
         o0 = MyOp.make_node(r1, r2)
         o1 = MyOp.make_node(o0.outputs[0], r4)
         all = io_toposort([], o0.outputs)
-        self.failUnless(all == [o0], all)
-
-
-
-if __name__ == '__main__':
-    if 1:
-        #run all tests
-        unittest.main()
-    elif 1:
-        #load some TestCase classes
-        suite = unittest.TestLoader()
-        suite = suite.loadTestsFromTestCase(_test_toposort)
+        assert all == [o0]
 
-        #run just some of them
-        unittest.TextTestRunner(verbosity=2).run(suite)
 
-    else:
-        #run just a single test
-        _test_toposort('test0').debug()
 

gof/_test_link.py → theano/gof/tests/test_link.py

 
+from theano.gof import graph
+from theano.gof.graph import Result, Apply, Constant
+from theano.gof.type import Type
+from theano.gof.op import Op
+from theano.gof import env
+from theano.gof import toolbox
 
-import unittest
-
-import graph
-from graph import Result, Apply, Constant
-from type import Type
-from op import Op
-import env
-import toolbox
-
-from link import *
+from theano.gof.link import *
 
 #from _test_result import Double
 
@@ -78,7 +75,7 @@ def Env(inputs, outputs):
     return e
 
 
-class _test_PerformLinker(unittest.TestCase):
+class TestPerformLinker:
 
     def test_thunk(self):
         x, y, z = inputs()
@@ -105,14 +102,14 @@ class _test_PerformLinker(unittest.TestCase):
     def test_input_output_same(self):
         x, y, z = inputs()
         fn = perform_linker(Env([x], [x])).make_function()
-        self.failUnless(1.0 is fn(1.0))
+        assert 1.0 is fn(1.0)
 
     def test_input_dependency0(self):
         x, y, z = inputs()
         a,d = add(x,y), div(x,y)
         e = mul(a,d)
         fn = perform_linker(Env(*graph.clone([x, y, a], [e]))).make_function()
-        self.failUnless(fn(1.0,2.0,9.0) == 4.5)
+        assert fn(1.0,2.0,9.0) == 4.5
 
     def test_skiphole(self):
         x,y,z = inputs()
@@ -120,14 +117,16 @@ class _test_PerformLinker(unittest.TestCase):
         r = raise_err(a)
         e = add(r,a)
         fn = perform_linker(Env(*graph.clone([x, y,r], [e]))).make_function()
-        self.failUnless(fn(1.0,2.0,4.5) == 7.5)
+        assert fn(1.0,2.0,4.5) == 7.5
+
 
 def wrap_linker(env, linkers, wrapper):
     lnk = WrapLinker(linkers, wrapper).accept(env)
     return lnk
-class _test_WrapLinker(unittest.TestCase):
 
-    def test0(self):
+class TestWrapLinker:
+
+    def test_0(self):
         nodes = []
         def wrap(i, node, th):
             nodes.append(node.op)
@@ -138,10 +137,10 @@ class _test_WrapLinker(unittest.TestCase):
         i[0].data = 1
         i[1].data = 2
         fn()
-        self.failUnless(nodes == [div, add, mul], nodes)
-        self.failUnless(o[0].data is None)
+        assert nodes == [div, add, mul]
+        assert o[0].data is None
 
-    def test1(self):
+    def test_1(self):
         nodes = []
         def wrap(i, node, th):
             nodes.append(node.op)
@@ -153,44 +152,8 @@ class _test_WrapLinker(unittest.TestCase):
         i[0].data = 1
         i[1].data = 2
         fn()
-        self.failUnless(nodes == [div, add, mul], nodes)
-        self.failUnless(o[0].data == 1.5, o[0].data)
-        
-
-
-#     def test_disconnected_input_output(self):
-#         x,y,z = inputs()
-#         a = add(x,y)
-#         a.data = 3.0 # simulate orphan calculation
-#         fn = perform_linker(env([z], [a])).make_function(inplace=True)
-#         self.failUnless(fn(1.0) == 3.0)
-#         self.failUnless(fn(2.0) == 3.0)
-
-#     def test_thunk_inplace(self):
-#         x, y, z = inputs()
-#         e = mul(add(x, y), div(x, y))
-#         fn, i, o = perform_linker(Env([x, y, z], [e])).make_thunk(True)
-#         fn()
-#         assert e.data == 1.5
-
-#     def test_thunk_not_inplace(self):
-#         x, y, z = inputs()
-#         e = mul(add(x, y), div(x, y))
-#         fn, i, o = perform_linker(env([x, y, z], [e])).make_thunk(False)
-#         fn()
-#         assert o[0].data == 1.5
-#         assert e.data != 1.5
-
-#     def test_function(self):
-#         x, y, z = inputs()
-#         e = mul(add(x, y), div(x, y))
-#         fn = perform_linker(env([x, y, z], [e])).make_function()
-#         assert fn(1.0, 2.0, 3.0) == 1.5
-#         assert e.data != 1.5 # not inplace
-
-
-if __name__ == '__main__':
-    unittest.main()
+        assert nodes == [div, add, mul]
+        assert o[0].data == 1.5
         
 
 

gof/_test_op.py → theano/gof/tests/test_op.py

 
-import unittest
 from copy import copy
-from op import *
-from type import Type, Generic
-from graph import Apply, Result
+from theano.gof.op import *
+from theano.gof.type import Type, Generic
+from theano.gof.graph import Apply, Result
 
 def as_result(x):
     assert isinstance(x, Result)
@@ -38,7 +37,7 @@ class MyOp(Op):
 MyOp = MyOp()
 
 
-class _test_Op(unittest.TestCase):
+class TestOp:
 
     # Sanity tests
     def test_sanity_0(self):

gof/_test_opt.py → theano/gof/tests/test_opt.py

 
-import unittest
-
-from type import Type
-from graph import Result, Apply, Constant
-from op import Op
-from opt import *
-from env import Env
-from toolbox import *
+from theano.gof.type import Type
+from theano.gof.graph import Result, Apply, Constant
+from theano.gof.op import Op
+from theano.gof.opt import *
+from theano.gof.env import Env
+from theano.gof.toolbox import *
 
 
 def as_result(x):
@@ -73,7 +71,7 @@ def inputs():
 PatternOptimizer = lambda p1, p2, ign=False: OpKeyOptimizer(PatternSub(p1, p2), ignore_newtrees=ign)
 TopoPatternOptimizer = lambda p1, p2, ign=True: TopoOptimizer(PatternSub(p1, p2), ignore_newtrees=ign)
 
-class _test_PatternOptimizer(unittest.TestCase):
+class TestPatternOptimizer:
     
     def test_replace_output(self):
         # replacing the whole graph
@@ -250,7 +248,7 @@ class _test_PatternOptimizer(unittest.TestCase):
 OpSubOptimizer = lambda op1, op2: TopoOptimizer(OpSub(op1, op2))
 OpSubOptimizer = lambda op1, op2: OpKeyOptimizer(OpSub(op1, op2))
 
-class _test_OpSubOptimizer(unittest.TestCase):
+class TestOpSubOptimizer:
     
     def test_straightforward(self):
         x, y, z = inputs()
@@ -267,7 +265,7 @@ class _test_OpSubOptimizer(unittest.TestCase):
         assert str(g) == "[Op1(Op2(x), Op4(y), Op4(z))]"
 
 
-class _test_MergeOptimizer(unittest.TestCase):
+class TestMergeOptimizer:
 
     def test_straightforward(self):
         x, y, z = inputs()
@@ -330,42 +328,6 @@ class _test_MergeOptimizer(unittest.TestCase):
         g = Env([x, y, z], [e1])
         MergeOptimizer().optimize(g)
         strg = str(g)
-        self.failUnless(strg == '[Op1(y, y)]' or strg == '[Op1(z, z)]', strg)
-
-#     def test_identical_constant_args_with_destroymap(self):
-#         x, y, z = inputs()
-#         y.data = 2.0
-#         y.constant = False
-#         z.data = 2.0
-#         z.constant = True
-#         e1 = op_d(y, z)
-#         g = env([x, y, z], [e1])
-#         MergeOptimizer().optimize(g)
-#         strg = str(g)
-#         self.failUnless(strg == '[OpD(y, z)]', strg)
-
-#     def test_merge_with_destroyer_1(self):
-#         x, y, z = inputs()
-#         e1 = op_d(op1(x,y), y)
-#         e2 = op_d(op1(x,y), z)
-#         g = env([x, y, z], [e1,e2])
-#         MergeOptimizer().optimize(g)
-#         strg = str(g)
-#         self.failUnless(strg == '[OpD(Op1(x, y), y), OpD(Op1(x, y), z)]', strg)
-
-#     def test_merge_with_destroyer_2(self):
-#         x, y, z = inputs()
-#         e1 = op_d(op1(x,y), z)
-#         e2 = op_d(op1(x,y), z)
-#         g = env([x, y, z], [e1,e2])
-#         MergeOptimizer().optimize(g)
-#         strg = str(g)
-#         self.failUnless(strg == '[*1 -> OpD(Op1(x, y), z), *1]', strg)
-
-
-
-
-if __name__ == '__main__':
-    unittest.main()
+        assert strg == '[Op1(y, y)]' or strg == '[Op1(z, z)]'
 
 

gof/_test_toolbox.py → theano/gof/tests/test_toolbox.py

 
-import unittest
+from theano.gof.graph import Result, Apply
+from theano.gof.type import Type
+from theano.gof.op import Op
 
-from graph import Result, Apply
-from type import Type
-from op import Op
-
-from env import Env, InconsistencyError
-from toolbox import *
+from theano.gof.env import Env, InconsistencyError
+from theano.gof.toolbox import *
 
 
 def as_result(x):
@@ -63,22 +61,8 @@ def inputs():
     return x, y, z
 
 
-# class _test_EquivTool(unittest.TestCase):
-
-#     def test_straightforward(self):
-#         x, y, z = inputs()
-#         sx = sigmoid(x)
-#         e = add(sx, sigmoid(y))
-#         g = Env([x, y, z], [e])
-#         g.extend(EquivTool(g))
-#         assert hasattr(g, 'equiv')
-#         assert g.equiv(sx) is sx
-#         g.replace(sx, dot(x, z))
-#         assert g.equiv(sx) is not sx
-#         assert g.equiv(sx).owner.op is dot
-
 
-class _test_NodeFinder(unittest.TestCase):
+class TestNodeFinder:
 
     def test_straightforward(self):
         x, y, z = inputs()
@@ -89,7 +73,7 @@ class _test_NodeFinder(unittest.TestCase):
         assert hasattr(g, 'get_nodes')
         for type, num in ((add, 3), (sigmoid, 3), (dot, 2)):
             if not len([x for x in g.get_nodes(type)]) == num:
-                self.fail((type, num))
+                raise Exception("Expected: %i times %s" % (num, type))
         new_e0 = add(y, z)
         assert e0.owner in g.get_nodes(dot)
         assert new_e0.owner not in g.get_nodes(add)
@@ -98,21 +82,7 @@ class _test_NodeFinder(unittest.TestCase):
         assert new_e0.owner in g.get_nodes(add)
         for type, num in ((add, 4), (sigmoid, 3), (dot, 1)):
             if not len([x for x in g.get_nodes(type)]) == num:
-                self.fail((type, num))
-
-#     def test_robustness(self):
-#         # this test used to make sense to have, but it doesn't work like that anymore
-#         x, y, z = inputs()
-#         e = add(add(sigmoid(x), sigmoid(sigmoid(z))), dot(add(x, y), dot(y, z)))
-#         g = Env([x, y, z], [e])
-#         g.extend(NodeFinder())
-#         gen = g.get_nodes(sigmoid) # I want to get Sigmoid instances
-#         g.replace(e, add(x, y)) # but here I prune them all
-#         assert len([x for x in gen]) == 0 # the generator should not yield them
-
-
+                raise Exception("Expected: %i times %s" % (num, type))
 
-if __name__ == '__main__':
-    unittest.main()
 
     

theano/gof/tests/test_types.py

+
+from theano.gof.type import *
+
+# todo: test generic

scalar/__init__.py → theano/scalar/__init__.py

@@ -2,5 +2,4 @@
 from basic import *
 from basic import _abs
 
-import opt
 

tensor/basic.py → theano/tensor/basic.py

@@ -648,7 +648,7 @@ def cast(t, dtype):
 #to be removed as we get the epydoc routine-documenting thing going -JB 20080924
 def _conversion(real_value):
     __oplist_tag(real_value, 'casting')
-    real_value.__module__='tensor'
+    real_value.__module__='tensor.basic'
     return real_value
 
 convert_to_int8  = _conversion(elemwise.Elemwise(scal.Identity(scal.specific_out(scal.int8))))

tensor/raw_random.py → theano/tensor/raw_random.py

@@ -64,6 +64,20 @@ class RandomFunction(gof.Op):
         return hash(self.fn) ^ hash(self.outtype) ^ hash(self.args) ^ hash(self.inplace)
 
 
+__oplist_constructor_list = []
+"""List of functions to be listed as op constructors in the oplist (`gen_oplist`, doc/oplist.txt)."""
+def constructor(f):
+    """Add `f` to :doc:`oplist`.
+    
+    Make `f` appear as a constructor in the oplist (`gen_oplist`, doc/oplist.txt).
+    """
+    __oplist_constructor_list.append(f)
+    return f
+def __oplist_tag(thing, tag):
+    tags = getattr(thing, '__oplist_tags', [])
+    tags.append(tag)
+    thing.__oplist_tags = tags
+
 def random_function(fn, dtype, *rfargs, **rfkwargs):
     """
     Returns a wrapper around RandomFunction which automatically infers the number 
@@ -76,6 +90,7 @@ def random_function(fn, dtype, *rfargs, **rfkwargs):
     - make_lvector(x, y, z, ...)
     - constants
     """
+    @constructor
     def f(ndim, *args, **kwargs):
         if isinstance(ndim, int):
             r, shape, args = args[0], args[1], args[2:]
@@ -94,10 +109,48 @@ def random_function(fn, dtype, *rfargs, **rfkwargs):
 RS = numpy.random.RandomState
 
 # we need to provide defaults for all the functions in order to infer the argument types...
+
 uniform = random_function(RS.uniform, 'float64', 0.0, 1.0)
+uniform.__doc__ = """
+Usage: uniform(random_state, size, low=0.0, high=1.0)
+Sample from a uniform distribution between low and high.
+
+If the size argument is ambiguous on the number of
+dimensions, the first argument may be a plain integer
+to supplement the missing information.
+"""
+
 binomial = random_function(RS.binomial, 'int64', 1, 0.5)
+binomial.__doc__ = """
+Usage: binomial(random_state, size, n=1, prob=0.5)
+Sample n times with probability of success prob for each trial,
+return the number of successes.
+
+If the size argument is ambiguous on the number of
+dimensions, the first argument may be a plain integer
+to supplement the missing information.
+"""
+
 normal = random_function(RS.normal, 'float64', 0.0, 1.0)
+normal.__doc__ = """
+Usage: normal(random_state, size, avg=0.0, std=1.0)
+Sample from a normal distribution centered on avg with
+the specified standard deviation (std)
+
+If the size argument is ambiguous on the number of
+dimensions, the first argument may be a plain integer
+to supplement the missing information.
+"""
+
 random_integers = random_function(RS.random_integers, 'int64', 0, 1)
+random_integers.__doc__ = """
+Usage: random_integers(random_state, size, low=0, high=1)
+Sample a random integer between low and high, both inclusive.
+
+If the size argument is ambiguous on the number of
+dimensions, the first argument may be a plain integer
+to supplement the missing information.
+"""
 
 
 @gof.local_optimizer