merge

doc/README.txt

@@ -65,7 +65,12 @@ Software Requirements
 
 - python 2.5
 
-- SciPy (specifically numpy, sparse, weave).  Numpy version >= 1.1 fixes memory leak. Numpy version >=1.2 fixes more memory leak.
+- SciPy (specifically numpy, sparse, weave). We recommend scipy >=0.7 if you
+are using sparse matrices, because scipy.sparse is buggy in 0.6.
+(scipy.csc_matrix dot has a bug with singleton dimensions. There may be more
+bugs.)
+Numpy version >= 1.1 fixes
+memory leak. Numpy version >=1.2 fixes more memory leak.
 
 - docutils, pygments (optional, to build documentation)
 

doc/api/epydoc.conf

@@ -7,7 +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: theano
+modules: theano scipy.sparse
 
 # The type of output that should be generated.  Should be one
 # of: html, text, latex, dvi, ps, pdf.

theano/compile/module.py

 
-from .. import gof
-from ..printing import pprint
+from theano import gof
+from theano.printing import pprint
 from collections import defaultdict
 from itertools import chain
 from functools import partial
@@ -791,31 +791,29 @@ def wrap(x):
             return wrapper(x)
     return x
 
+def dict_wrap(d):
+    for k,v in d.iteritems():
+        d[k]=wrap(v)
+    return d
+
+# Result -> Member
+register_wrapper(lambda x: isinstance(x, gof.Result) and not x.owner,
+                 lambda x: Member(x))
+
 # Result -> External
-register_wrapper(lambda x: isinstance(x, gof.Result),
+register_wrapper(lambda x: isinstance(x, gof.Result) and x.owner,
                  lambda x: External(x))
 
-# [Component1, Component2, ...] -> ComponentList(Component1, Component2, ...)
-register_wrapper(lambda x: isinstance(x, (list, tuple)) and all(isinstance(r, Component) for r in x),
-                 lambda x: ComponentList(*x))
-
-# [Result1, Result2, ...] -> ComponentList(Member(Result1), Member(Result2), ...)
+# [[Result1], {Result2}, Result3...] -> ComponentList(Member(Result1), Member(Result2), ...)
 register_wrapper(lambda x: isinstance(x, (list, tuple)) \
-                     and all(isinstance(r, gof.Result) and not r.owner for r in x),
-                 lambda x: ComponentList(*map(Member, x)))
-#{ "name1":Result1,...} -> ComponentDict(Member(Result1),...)
-def dict_member(d):
-    nd={}
-    for k,v in d.iteritems():
-        nd[k]=Member(v)
-    return nd
-register_wrapper(lambda x: isinstance(x, dict) \
-                     and all(isinstance(r,gof.Result) \
-                                 and not r.owner for r in x.itervalues()),
-                 lambda x: ComponentDict(dict_member(x)))
+                     and all(isinstance(r, (gof.Result,Component,list,
+                                            tuple, dict)) for r in x),
+                 lambda x: ComponentList(*map(wrap, x)))
+
+#{ "name1":{Component,Result,list,tuple,dict},...} -> ComponentDict({Component,Result,list,tuple,dict},...)
 register_wrapper(lambda x: isinstance(x, dict) \
-                     and all(isinstance(r,Component) for r in x.itervalues()),
-                 lambda x: ComponentDict(x))
+                     and all(isinstance(r,(Component,gof.Result,list,tuple,dict)) for r in x.itervalues()),
+                 lambda x: ComponentDict(dict_wrap(x)))
 
 class Curry:
     def __init__(self, obj, name, arg):
@@ -869,13 +867,9 @@ class Module(ComponentDict):
         if attr == '_components' and '_components' not in self.__dict__:
             self.__dict__['_components'] = {}
         try:
-            rval = self[attr]
+            rval = self.__dict__["local_attr"][attr]
         except KeyError:
             raise AttributeError('%s has no %s attribute.' % (self.__class__, attr))
-        if isinstance(rval, (External, Member)):
-            # Special treatment for External and Member, so that
-            # the user may use them to build graphs more easily.
-            return rval.r
         return rval
 
     def __setattr__(self, attr, value):
@@ -885,17 +879,35 @@ class Module(ComponentDict):
         elif attr == 'name':
             self.__set_name__(value)
             return
-            
-        value = self.__wrapper__(value)
-        try:
-            self[attr] = value
-        except:
-            if isinstance(value, Component):
-                raise
+
+        def remove_member(v):
+            if isinstance(v, (Member, External)):
+                return v.r
+            elif isinstance(v, (gof.Result,Method,Module)):
+                return v
+            elif isinstance(v,(int,bool)):
+                return v
+            elif isinstance(v, (list,tuple)):
+                return map(remove_member,v)
+            elif isinstance(v,dict):
+                for k,vv in v.iteritems():
+                    v[k]=remove_member(vv)
+                return v
             else:
-                self.__dict__[attr] = value
+#                raise NotImplementedError
+#                print "WARNING: unknow:",v
+                return v
+
+        value=remove_member(value)
+
+        if not hasattr(self,"local_attr"):
+            self.__dict__["local_attr"]={}
+
+        self.__dict__["local_attr"][attr]=value
 
     def build(self, mode, memo):
+        for k,v in self.local_attr.iteritems():
+            self.__setattr__(k,v)
         inst = super(Module, self).build(mode, memo)
         for method in dir(self):
             # Any method with a name like '_instance_XXX' is added to
@@ -911,6 +923,64 @@ class Module(ComponentDict):
         for name, value in chain(init.iteritems(), kwinit.iteritems()):
             inst[name] = value
 
+    def make_mi(self, *args, **kwargs):
+        meth=[]#we put the method after the member to be sure of the ordering.
+        for k,v in self.local_attr.iteritems():
+            if isinstance(v,Module):
+                v=v.make_mi(args,kwargs)
+            if isinstance(v,Method):
+                meth.append((k,v))
+            else:
+                v = self.__wrapper__(v)
+                try:
+                    self[k] = v
+                except:
+                    if isinstance(v, Component):
+                        raise
+                    else:
+                        self.__dict__[k] = v
+#                self.__setitem__(k,v)
+
+        for k,v in meth:
+            self.__setitem__(k,v)
+
+        return self
+
+    def make(self, *args, **kwargs):
+        """
+        Allocates the necessary containers using allocate() and uses
+        build() to make an instance which will be returned. The
+        initialize() method of the instance will be called with the
+        arguments and the keyword arguments. If 'mode' is in the
+        keyword arguments it will be passed to build().
+        """
+        self.make_mi(args,kwargs)
+
+        mode = kwargs.pop('mode', 'FAST_COMPILE')
+        rval = self.make_no_init(mode)
+        if hasattr(rval, 'initialize'):
+            rval.initialize(*args, **kwargs)
+        return rval
+
+    def __str__(self):
+        return self.__class__.__name__+"(%s)" % ', '.join(x for x in sorted(map(str, self.local_attr)) if x[0] != '_')
+
+    def __get_name__(self):
+        """
+        Getter for self.name
+        """
+        return self._name
+
+    def __set_name__(self, name):
+        """
+        Setter for self.name
+        """
+        self._name = name
+
+    name = property(lambda self: self.__get_name__(),
+                    lambda self, value: self.__set_name__(value),
+                    "Contains the name of this Component")
+
 FancyModule = Module
 FancyModuleInstance = ModuleInstance
 

theano/compile/tests/test_module.py

@@ -10,7 +10,7 @@ class T_test_module(unittest.TestCase):
     def test_whats_up_with_submembers(self):
         class Blah(FancyModule):
             def __init__(self, stepsize):
-                super(Blah, self).__init__(self)
+                super(Blah, self).__init__()
                 self.stepsize = Member(T.value(stepsize))
                 x = T.dscalar()
             

theano/sparse/basic.py

@@ -22,6 +22,8 @@ def register_specialize(lopt, *tags, **kwargs):
 """ Types of sparse matrices to use for testing """
 _mtypes = [sparse.csc_matrix, sparse.csr_matrix]
 #_mtypes = [sparse.csc_matrix, sparse.csr_matrix, sparse.dok_matrix, sparse.lil_matrix, sparse.coo_matrix]
+#* new class ``dia_matrix`` : the sparse DIAgonal format
+#* new class ``bsr_matrix`` : the Block CSR format
 _mtype_to_str = {sparse.csc_matrix: "csc", sparse.csr_matrix: "csr"}
 
 
@@ -673,16 +675,14 @@ class StructuredDot(gof.Op):
     """
     def make_node(self, a, b):
         assert a.type.dtype == b.type.dtype
-        if type(a) is not SparseResult:
-            raise TypeError('First argument must be of type SparseResult');
+        if type(a) is not SparseResult and type(a) is not SparseConstant:
+            raise TypeError('First argument must be of type SparseResult or SparseConstant');
 
         return gof.Apply(self, [a,b], [tensor.tensor(a.type.dtype, (False, False))])
 
     def perform(self, node, (a,b), (out,)):
         if a.shape[1] != b.shape[0]:
             raise ValueError('shape mismatch in StructuredDot.perform', (a.shape, b.shape))
-        if b.shape[0] == 1:
-            raise NotImplemented('ERROR: scipy.csc_matrix dot has bug with singleton dimensions')
 
         result = a.dot(b)
 
@@ -699,6 +699,12 @@ class StructuredDot(gof.Op):
 
         assert result.ndim == 2
 
+        if result.shape != (a.shape[0], b.shape[1]):
+            if b.shape[0] == 1:
+                raise Exception("a.shape=%s, b.shape=%s, result.shape=%s ??? This is probably because scipy.csc_matrix dot has a bug with singleton dimensions (i.e. b.shape[0]=1), for scipy 0.6. Use scipy 0.7" % (a.shape, b.shape, result.shape))
+            else:
+                raise Exception("a.shape=%s, b.shape=%s, result.shape=%s ??? I have no idea why")
+
         ## Commenting this out because result should be a numpy.ndarray since the assert above
         ## (JB 20090109)
         #out[0] = numpy.asarray(result)  #TODO: fix this really bad implementation

theano/tensor/raw_random.py

@@ -245,7 +245,7 @@ class RModule(compile.Module):
     def __init__(self, components = {}, **kwcomponents):
         super(RModule, self).__init__(components, **kwcomponents)
         self.random = RandomKit('rkit')
-        self._components['_rkit'] = compile.KitComponent(self.random)
+        self._rkit = compile.KitComponent(self.random)
 
     def __wrapper__(self, x):
         x = compile.module.wrap(x)

theano/tensor/tests/test_raw_random.py

@@ -32,7 +32,7 @@ class T_test_module(unittest.TestCase):
         """
         class B(RModule):
             def __init__(self):
-                super(B, self).__init__(self)
+                super(B, self).__init__()
                 
                 self.x = compile.Member(tensor.dvector())
                 self.r = self.random.uniform(tensor.shape(self.x))
@@ -40,7 +40,7 @@ class T_test_module(unittest.TestCase):
                 self.f = compile.Method([self.x], self.r)
         class E(RModule):
             def __init__(self):
-                super(E, self).__init__(self)
+                super(E, self).__init__()
                 self.b = B()
                 self.f = compile.Method([self.b.x], self.b.r)