more old todo/comment and pep8 doc/tutorial

doc/tutorial/adding.txt

@@ -178,13 +178,11 @@ with NumPy arrays may be found here: :ref:`tensor creation<libdoc_tensor_creatio
 
   import theano
   a = theano.tensor.vector() # declare variable
-  out = a + a**10               # build symbolic expression
+  out = a + a ** 10               # build symbolic expression
   f = theano.function([a], out)   # compile function
-  print f([0,1,2])  # prints `array([0,2,1026])`
+  print f([0, 1, 2])  # prints `array([0, 2, 1026])`
   
-Modify and execute this code to compute this expression: a**2 + b**2 + 2*a*b.
+Modify and execute this code to compute this expression: a ** 2 + b ** 2 + 2 * a * b.
 
 
-.. TODO: repair this link
-
 :download:`Solution<adding_solution_1.py>`

doc/tutorial/aliasing.txt

@@ -231,7 +231,7 @@ that control how ``theano.function`` handles its argument[s] and return value[s]
     import theano, theano.tensor
 
     x = theano.tensor.matrix()
-    y = 2*x
+    y = 2 * x
     f = theano.function([theano.In(x, borrow=True)], theano.Out(y, borrow=True))
 
 Borrowing an input means that Theano will treat the argument you provide as if

doc/tutorial/conditions.txt

@@ -24,33 +24,33 @@ IfElse vs Switch
   from theano.ifelse import ifelse
   import theano, time, numpy
 
-  a,b = T.scalars('a','b')
-  x,y = T.matrices('x','y')
+  a,b = T.scalars('a', 'b')
+  x,y = T.matrices('x', 'y')
   
-  z_switch = T.switch(T.lt(a,b), T.mean(x), T.mean(y))
-  z_lazy = ifelse(T.lt(a,b), T.mean(x), T.mean(y))
+  z_switch = T.switch(T.lt(a, b), T.mean(x), T.mean(y))
+  z_lazy = ifelse(T.lt(a, b), T.mean(x), T.mean(y))
 
-  f_switch = theano.function([a,b,x,y], z_switch, 
+  f_switch = theano.function([a, b, x, y], z_switch,
                       mode=theano.Mode(linker='vm'))
-  f_lazyifelse = theano.function([a,b,x,y], z_lazy,
+  f_lazyifelse = theano.function([a, b, x, y], z_lazy,
                       mode=theano.Mode(linker='vm'))
 
   val1 = 0.
   val2 = 1.
-  big_mat1 = numpy.ones((10000,1000))
-  big_mat2 = numpy.ones((10000,1000))
+  big_mat1 = numpy.ones((10000, 1000))
+  big_mat2 = numpy.ones((10000, 1000))
 
   n_times = 10
 
   tic = time.clock()
   for i in xrange(n_times):
       f_switch(val1, val2, big_mat1, big_mat2)
-  print 'time spent evaluating both values %f sec'%(time.clock()-tic)
+  print 'time spent evaluating both values %f sec' % (time.clock() - tic)
 
   tic = time.clock()
   for i in xrange(n_times):
       f_lazyifelse(val1, val2, big_mat1, big_mat2)
-  print 'time spent evaluating one value %f sec'%(time.clock()-tic)
+  print 'time spent evaluating one value %f sec' % (time.clock() - tic)
 
 In this example, the ``IfElse`` op spends less time (about half as much) than ``Switch``
 since it computes only one variable out of the two.

doc/tutorial/debug_faq.txt

@@ -35,27 +35,27 @@ following example.
     theano.config.compute_test_value = 'off'
 
     # configure shared variables
-    W1val = numpy.random.rand(2,10,10).astype(theano.config.floatX)
+    W1val = numpy.random.rand(2, 10, 10).astype(theano.config.floatX)
     W1 = theano.shared(W1val, 'W1')
-    W2val = numpy.random.rand(15,20).astype(theano.config.floatX)
+    W2val = numpy.random.rand(15, 20).astype(theano.config.floatX)
     W2 = theano.shared(W2val, 'W2')
 
     # input which will be of shape (5,10)
     x  = T.matrix('x')
 
     # transform the shared variable in some way. Theano does not
-    # know off hand that the matrix func_of_W1 has shape (20,10)
-    func_of_W1 = W1.dimshuffle(2,0,1).flatten(2).T
+    # know off hand that the matrix func_of_W1 has shape (20, 10)
+    func_of_W1 = W1.dimshuffle(2, 0, 1).flatten(2).T
 
     # source of error: dot product of 5x10 with 20x10
-    h1 = T.dot(x,func_of_W1)  
+    h1 = T.dot(x, func_of_W1)
 
     # do more stuff
-    h2 = T.dot(h1,W2.T)  
+    h2 = T.dot(h1, W2.T)
 
     # compile and call the actual function
     f = theano.function([x], h2)
-    f(numpy.random.rand(5,10))
+    f(numpy.random.rand(5, 10))
    
 Running the above code generates the following error message:
 
@@ -98,10 +98,10 @@ can get Theano to reveal the exact source of the error.
 
     ...
 
-    # input which will be of shape (5,10)
+    # input which will be of shape (5, 10)
     x  = T.matrix('x')
     # provide Theano with a default test-value
-    x.tag.test_value = numpy.random.rand(5,10)
+    x.tag.test_value = numpy.random.rand(5, 10)
 
 In the above, we are tagging the symbolic matrix *x* with a special test
 value. This allows Theano to evaluate symbolic expressions on-the-fly (by
@@ -159,10 +159,10 @@ Theano provides a 'Print' op to do this.
     f_with_print = theano.function([x], x_printed * 5)
 
     #this runs the graph without any printing
-    assert numpy.all( f([1,2,3]) == [5, 10, 15])
+    assert numpy.all( f([1, 2, 3]) == [5, 10, 15])
 
     #this runs the graph with the message, and value printed
-    assert numpy.all( f_with_print([1,2,3]) == [5, 10, 15])
+    assert numpy.all( f_with_print([1, 2, 3]) == [5, 10, 15])
 
 
 Since Theano runs your program in a topological order, you won't have precise
@@ -242,7 +242,7 @@ along with its position in the graph, the arguments to the functions ``perform``
 ``c_code`` and the output it computed.  
 
 >>> x = T.dscalar('x')
->>> f = function([x], [5*x], mode=PrintEverythingMode())
+>>> f = function([x], [5 * x], mode=PrintEverythingMode())
 >>> f(3)
 >>> # print: 0 Elemwise{mul,no_inplace}(5, x) [array(5, dtype=int8), array(3.0)] [array(15.0)]
 >>> # print: [array(15.0)]
@@ -280,11 +280,11 @@ Consider this example script ("ex.py"):
         a = T.dmatrix('a')
         b = T.dmatrix('b')
 
-        f = theano.function([a,b], [a*b])
+        f = theano.function([a, b], [a * b])
 
         # matrices chosen so dimensions are unsuitable for multiplication
-        mat1 = numpy.arange(12).reshape((3,4))
-        mat2 = numpy.arange(25).reshape((5,5))
+        mat1 = numpy.arange(12).reshape((3, 4))
+        mat2 = numpy.arange(25).reshape((5, 5))
 
         f(mat1, mat2)
 

doc/tutorial/examples.txt

@@ -412,11 +412,11 @@ The preceding elements are featured in this more realistic example.  It will be
   print w.get_value(), b.get_value()
 
   # Construct Theano expression graph
-  p_1 = 1 / (1 + T.exp(-T.dot(x, w)-b))     # Probability that target = 1
+  p_1 = 1 / (1 + T.exp(-T.dot(x, w) - b))   # Probability that target = 1
   prediction = p_1 > 0.5                    # The prediction thresholded
-  xent = -y*T.log(p_1) - (1-y)*T.log(1-p_1) # Cross-entropy loss function
-  cost = xent.mean() + 0.01*(w**2).sum()    # The cost to minimize
-  gw,gb = T.grad(cost, [w,b])               # Compute the gradient of the cost
+  xent = -y * T.log(p_1) - (1-y) * T.log(1-p_1) # Cross-entropy loss function
+  cost = xent.mean() + 0.01 * (w ** 2).sum()# The cost to minimize
+  gw,gb = T.grad(cost, [w, b])              # Compute the gradient of the cost
                                             # (we shall return to this in a
                                             # following section of this tutorial)
 
@@ -424,7 +424,7 @@ The preceding elements are featured in this more realistic example.  It will be
   train = theano.function(
             inputs=[x,y],
             outputs=[prediction, xent],
-            updates={w:w-0.1*gw, b:b-0.1*gb})
+            updates={w: w - 0.1 * gw, b: b - 0.1 * gb})
   predict = theano.function(inputs=[x], outputs=prediction)
 
   # Train

doc/tutorial/extending_theano_solution_1.py

@@ -121,13 +121,13 @@ class TestOp(utt.InferShapeTester):
         y = tensor.dmatrix()
 
         # adapt the choice of the next instruction to the op under test
-       
+
         self._compile_and_check([x, y], [self.op_class()(x, y)],  # case 1
                                 [numpy.random.rand(5, 6),
                                  numpy.random.rand(5, 6)],
                                 self.op_class)
         """
-        
+
         self._compile_and_check([x, y], self.op_class()(x, y),  # case 2
                                 [numpy.random.rand(5, 6),
                                  numpy.random.rand(5, 6)],
@@ -141,5 +141,5 @@ if __name__ == "__main__":
     t.test_perform()
     # comment out next instruction in case 2 since autotesting of
     # gradient of multiple output functions is not implemented yet
-    t.test_gradient() # enable in case 1, disable in case 2
+    t.test_gradient()  # enable in case 1, disable in case 2
     t.test_infer_shape()

doc/tutorial/gpu_data_convert.txt

@@ -100,9 +100,9 @@ You can use a GPU function compiled with PyCUDA in a Theano op:
         def make_thunk(self, node, storage_map, _, _2):
             mod = SourceModule("""
         __global__ void my_fct(float * i0, float * o0, int size) {
-        int i = blockIdx.x*blockDim.x + threadIdx.x;
+        int i = blockIdx.x * blockDim.x + threadIdx.x;
         if(i<size){
-            o0[i] = i0[i]*2;
+            o0[i] = i0[i] * 2;
         }
       }""")
             pycuda_fct = mod.get_function("my_fct")
@@ -114,7 +114,7 @@ You can use a GPU function compiled with PyCUDA in a Theano op:
                     z[0] = cuda.CudaNdarray.zeros(inputs[0][0].shape)
                 grid = (int(numpy.ceil(inputs[0][0].size / 512.)),1)
                 pycuda_fct(inputs[0][0], z[0], numpy.intc(inputs[0][0].size),
-                           block=(512,1,1), grid=grid)
+                           block=(512, 1, 1), grid=grid)
             return thunk
     
 CUDAMat

doc/tutorial/gradients.txt

@@ -25,7 +25,7 @@ Here is the code to compute this gradient:
 
 >>> from theano import pp
 >>> x = T.dscalar('x')
->>> y = x**2
+>>> y = x ** 2
 >>> gy = T.grad(y, x)
 >>> pp(gy)  # print out the gradient prior to optimization
 '((fill((x ** 2), 1.0) * 2) * (x ** (2 - 1)))'
@@ -118,10 +118,10 @@ do is to loop over the entries in *y* and compute the gradient of
     shall return to :ref:`scan<tutloop>` later in this tutorial.
 
 >>> x = T.dvector('x')
->>> y = x**2
->>> J, updates = theano.scan(lambda i, y,x : T.grad(y[i], x), sequences = T.arange(y.shape[0]), non_sequences = [y,x])
->>> f = function([x], J, updates = updates)
->>> f([4,4])
+>>> y = x ** 2
+>>> J, updates = theano.scan(lambda i, y,x : T.grad(y[i], x), sequences=T.arange(y.shape[0]), non_sequences=[y,x])
+>>> f = function([x], J, updates=updates)
+>>> f([4, 4])
 array([[ 8.,  0.],
        [ 0.,  8.]])
     
@@ -156,12 +156,12 @@ scalar.
 
 
 >>> x = T.dvector('x')
->>> y = x**2
+>>> y = x ** 2
 >>> cost = y.sum()
 >>> gy = T.grad(cost, x)
->>> H, updates = theano.scan(lambda i, gy,x : T.grad(gy[i], x), sequences = T.arange(gy.shape[0]), non_sequences = [gy,x])
->>> f = function([x], H, updates = updates)
->>> f([4,4])
+>>> H, updates = theano.scan(lambda i, gy,x : T.grad(gy[i], x), sequences=T.arange(gy.shape[0]), non_sequences=[gy, x])
+>>> f = function([x], H, updates=updates)
+>>> f([4, 4])
 array([[ 2.,  0.],
        [ 0.,  2.]])
 
@@ -200,10 +200,10 @@ you need to do something similar to this:
 >>> W = T.dmatrix('W')
 >>> V = T.dmatrix('V')
 >>> x = T.dvector('x')
->>> y = T.dot(x,W)
+>>> y = T.dot(x, W)
 >>> JV = T.Rop(y, W, V)
->>> f = theano.function([W,V,x], JV)
->>> f([[1,1],[1,1]], [[2,2,],[2,2]], [0,1])
+>>> f = theano.function([W, V, x], JV)
+>>> f([[1, 1], [1, 1]], [[2, 2], [2, 2]], [0,1])
 array([ 2.,  2.])
 
 :ref:`List <R_op_list>` of Op that implement Rop.
@@ -219,10 +219,10 @@ f(x)}{\partial x}`. The *L-operator* is also supported for generic tensors
 >>> W = T.dmatrix('W')
 >>> v = T.dvector('v')
 >>> x = T.dvector('x')
->>> y = T.dot(x,W)
+>>> y = T.dot(x, W)
 >>> VJ = T.Lop(y, W, v)
 >>> f = theano.function([W,v,x], JV)
->>> f([[1,1],[1,1]], [2,2,], [0,1])
+>>> f([[1, 1], [1, 1]], [2, 2], [0, 1])
 array([[ 0.,  0.],
        [ 2.,  2.]])
 
@@ -250,11 +250,11 @@ Hence, we suggest profiling the methods before using either one of the two:
 
 >>> x = T.dvector('x')
 >>> v = T.dvector('v')
->>> y = T.sum(x**2)
+>>> y = T.sum(x ** 2)
 >>> gy = T.grad(y, x)
->>> vH = T.grad( T.sum(gy*v), x)
->>> f = theano.function([x,v], vH)
->>> f([4,4],[2,2])
+>>> vH = T.grad(T.sum(gy * v), x)
+>>> f = theano.function([x, v], vH)
+>>> f([4, 4], [2, 2])
 array([ 4.,  4.])
 
 
@@ -262,11 +262,11 @@ or, making use of the *R-operator*:
 
 >>> x = T.dvector('x')
 >>> v = T.dvector('v')
->>> y = T.sum(x**2)
+>>> y = T.sum(x ** 2)
 >>> gy = T.grad(y, x)
->>> Hv = T.Rop(gy,x,v)
->>> f = theano.function([x,v], Hv)
->>> f([4,4],[2,2])
+>>> Hv = T.Rop(gy, x, v)
+>>> f = theano.function([x, v], Hv)
+>>> f([4, 4], [2, 2])
 array([ 4.,  4.])
 
 

doc/tutorial/loop.txt

@@ -43,11 +43,11 @@ The full documentation can be found in the library: :ref:`Scan <lib_scan>`.
                               outputs_info=T.ones_like(A),
                               non_sequences=A, n_steps=k)
 
-  # Scan has provided us with A**1 through A**k.  Keep only the last
+  # Scan has provided us with A ** 1 through A ** k.  Keep only the last
   # value. Scan notices this and does not waste memory saving them.
   final_result = result[-1]
   
-  power = theano.function(inputs=[A,k], outputs=final_result,
+  power = theano.function(inputs=[A, k], outputs=final_result,
                         updates=updates)
   
   print power(range(10),2)
@@ -94,6 +94,4 @@ Run both examples.
 Modify and execute the polynomial example to have the reduction done by ``scan``.
 
 
-.. TODO: repair this link as well as the code in the target file
-
 :download:`Solution<loop_solution_1.py>`

doc/tutorial/loop_solution_1.py

@@ -23,7 +23,7 @@ result, updates = theano.scan(fn=inner_fct,
                             outputs_info=T.ones_like(A),
                             non_sequences=A, n_steps=k)
 
-# Scan has provided us with A**1 through A**k.  Keep only the last
+# Scan has provided us with A ** 1 through A ** k.  Keep only the last
 # value. Scan notices this and does not waste memory saving them.
 final_result = result[-1]
 
@@ -83,10 +83,10 @@ outputs_info = T.as_tensor_variable(numpy.asarray(0, 'float64'))
 
 components, updates = theano.scan(fn=lambda prior_value, coeff, power, free_var:
                                  prior_value + (coeff * (free_var ** power)),
-                                outputs_info=outputs_info,
-                                sequences=[coefficients, full_range],
-                                non_sequences=x)
-                                
+                                 outputs_info=outputs_info,
+                                 sequences=[coefficients, full_range],
+                                 non_sequences=x)
+
 polynomial = components[-1]
 calculate_polynomial = theano.function(inputs=[coefficients, x],
                                      outputs=polynomial, updates=updates)
@@ -94,4 +94,3 @@ calculate_polynomial = theano.function(inputs=[coefficients, x],
 test_coeff = numpy.asarray([1, 0, 2], dtype=numpy.float32)
 print calculate_polynomial(test_coeff, 3)
 # 19.0
-

doc/tutorial/modes.txt

@@ -108,12 +108,6 @@ Modify and execute this example to run on CPU (the default) with floatX=float32
 time the execution using the command line ``time python file.py``.  Save your code 
 as it will be useful later on. 
 
-.. TODO: To be resolved:
- 
-.. Solution said:
-
-.. You will need to use: ``theano.config.floatX`` and ``ndarray.astype("str")``
-
 .. Note::
 
    * Apply the Theano flag ``floatX=float32`` through (``theano.config.floatX``) in your code.
@@ -124,8 +118,6 @@ as it will be useful later on.
      * Insert manual cast around the mean operator (this involves division by length, which is an *int64*).
      * Notice that a new casting mechanism is being developed.
 
-.. TODO: repair this link
-
 :download:`Solution<modes_solution_1.py>`
 
 -------------------------------------------

doc/tutorial/modes_solution_1.py

@@ -63,4 +63,3 @@ print D[1]
 
 print "prediction on D"
 print predict(D[0])
-

doc/tutorial/numpy.txt

@@ -37,7 +37,7 @@ This is a 3x2 matrix, i.e. there are 3 rows and 2 columns.
 
 To access the entry in the 3rd row (row #2) and the 1st column (column #0):
 
->>> numpy.asarray([[1., 2], [3, 4], [5, 6]])[2,0]
+>>> numpy.asarray([[1., 2], [3, 4], [5, 6]])[2, 0]
 5.0
 
 

doc/tutorial/printing_drawing.txt

@@ -42,20 +42,20 @@ The following output depicts the pre- and post- compilation graphs.
 
 
     # Construct Theano expression graph
-    p_1 = 1 / (1 + T.exp(-T.dot(x, w)-b)) # Probabily of having a one
+    p_1 = 1 / (1 + T.exp(-T.dot(x, w) - b)) # Probabily of having a one
     prediction = p_1 > 0.5 # The prediction that is done: 0 or 1
-    xent = -y*T.log(p_1) - (1-y)*T.log(1-p_1) # Cross-entropy
-    cost = xent.mean() + 0.01*(w**2).sum() # The cost to optimize
-    gw,gb = T.grad(cost, [w,b])
+    xent = -y * T.log(p_1) - (1 - y) * T.log(1 - p_1) # Cross-entropy
+    cost = xent.mean() + 0.01 * (w ** 2).sum() # The cost to optimize
+    gw,gb = T.grad(cost, [w, b])
 
     # Compile expressions to functions
     train = theano.function(
-                inputs=[x,y],
+                inputs=[x, y],
                 outputs=[prediction, xent],
-                updates={w:w-0.01*gw, b:b-0.01*gb},
-                name = "train")
+                updates={w: w - 0.01 * gw, b: b - 0.01 * gb},
+                name="train")
     predict = theano.function(inputs=[x], outputs=prediction,
-                name = "predict")
+                name="predict")
 
     if any( [x.op.__class__.__name__=='Gemv' for x in
     train.maker.fgraph.toposort()]):

doc/tutorial/shape_info.txt

@@ -24,7 +24,7 @@ Currently, information regarding shape is used in two ways in Theano:
 
      import theano
      x = theano.tensor.matrix('x')
-     f = theano.function([x], (x**2).shape)
+     f = theano.function([x], (x ** 2).shape)
      theano.printing.debugprint(f)
      #MakeVector [@43860304] ''   2
      # |Shape_i{0} [@43424912] ''   1
@@ -48,9 +48,9 @@ can lead to errors. Consider this example:
    import theano
    x = theano.tensor.matrix('x')
    y = theano.tensor.matrix('y')
-   z = theano.tensor.join(0,x,y)
-   xv = numpy.random.rand(5,4)
-   yv = numpy.random.rand(3,3)
+   z = theano.tensor.join(0, x, y)
+   xv = numpy.random.rand(5, 4)
+   yv = numpy.random.rand(3, 3)
 
    f = theano.function([x,y], z.shape)
    theano.printing.debugprint(f)
@@ -119,7 +119,7 @@ upgrade.  Here is the current state of what can be done:
 
 .. code-block:: python
 
-    theano.tensor.nnet.conv2d(..., image_shape=(7,3,5,5), filter_shape=(2,3,4,4))
+    theano.tensor.nnet.conv2d(..., image_shape=(7, 3, 5, 5), filter_shape=(2, 3, 4, 4))
 
 - You can use the ``SpecifyShape`` op to add shape information anywhere in the
   graph. This allows to perform some optimizations. In the following example,
@@ -129,8 +129,8 @@ upgrade.  Here is the current state of what can be done:
 
    import theano
    x = theano.tensor.matrix()
-   x_specify_shape = theano.tensor.specify_shape(x, (2,2))
-   f = theano.function([x], (x_specify_shape**2).shape)
+   x_specify_shape = theano.tensor.specify_shape(x, (2, 2))
+   f = theano.function([x], (x_specify_shape ** 2).shape)
    theano.printing.debugprint(f)
    # [2 2] [@72791376]
 

doc/tutorial/symbolic_graphs.txt

@@ -67,7 +67,7 @@ Take for example the following code:
 .. code-block:: python
 
     x = T.dmatrix('x')
-    y = x*2.
+    y = x * 2.
 
 If you enter ``type(y.owner)`` you get ``<class 'theano.gof.graph.Apply'>``, 
 which is the apply node that connects the op and the inputs to get this
@@ -156,9 +156,9 @@ as we apply it. Consider the following example of optimization:
 
 >>> import theano
 >>> a = theano.tensor.vector("a")      # declare symbolic variable
->>> b = a + a**10                      # build symbolic expression
+>>> b = a + a ** 10                    # build symbolic expression
 >>> f = theano.function([a], b)        # compile function
->>> print f([0,1,2])                   # prints `array([0,2,1026])`
+>>> print f([0, 1, 2])                 # prints `array([0,2,1026])`
 
 
 ======================================================  =====================================================

doc/tutorial/using_gpu.txt

@@ -389,8 +389,6 @@ What can be done to further increase the speed of the GPU version? Put your idea
      * Insert manual cast around the mean operator (this involves division by length, which is an *int64*).
      * Notice that a new casting mechanism is being developed.
 
-.. TODO: repair this link
-
 :download:`Solution<using_gpu_solution_1.py>`
 
 -------------------------------------------

doc/tutorial/using_gpu_solution_1.py

@@ -321,4 +321,4 @@ Include the training steps inside the definition of the Theano function.
 Implement this solution and put it to test.
 
 
-"""
\ No newline at end of file
+"""