Mark ProfileMode as deprecated at many places

doc/library/compile/mode.txt

@@ -21,7 +21,7 @@ Theano defines the following modes by name:
 - ``'FAST_COMPILE'``: Apply just a few graph optimizations and only use Python implementations.
 - ``'FAST_RUN'``: Apply all optimizations, and use C implementations where possible.
 - ``'DebugMode'``: A mode for debuging. See :ref:`DebugMode <debugmode>` for details.
-- ``'ProfileMode'``: A mode for profiling. See :ref:`ProfileMode <profilemode>` for details.
+- ``'ProfileMode'``: Deprecated, use the Theano flag :attr:`config.profile`.
 - ``'DEBUG_MODE'``: Deprecated. Use the string DebugMode.
 - ``'PROFILE_MODE'``: Deprecated. Use the string ProfileMode.
 

doc/library/compile/profilemode.txt

@@ -14,6 +14,10 @@
 Guide
 =====
 
+.. note::
+
+    ProfileMode is deprecated. Use :attr:`config.profile` instead.
+
 To profile a Theano graph, a special mode called ProfileMode, must be passed as
 an argument when compiling your graph. Using ProfileMode is a three-step
 process.

doc/library/config.txt

@@ -258,7 +258,8 @@ import theano and print the config variable, as in:
 
 .. attribute:: mode
 
-    String value: 'Mode', 'ProfileMode', 'DebugMode', 'FAST_RUN', 'FAST_COMPILE'
+    String value: 'Mode', 'ProfileMode'(deprecated), 'DebugMode', 'FAST_RUN',
+    'FAST_COMPILE'
 
     Default 'Mode'
 

doc/tutorial/modes.txt

@@ -137,7 +137,7 @@ Theano defines the following modes by name:
 - ``'DebugMode``: Verify the correctness of all optimizations, and compare C and Python 
     implementations. This mode can take much longer than the other modes, but can identify
     several kinds of problems.
-- ``'ProfileMode'``: Same optimization as FAST_RUN, but print some profiling information
+- ``'ProfileMode'``(deprecated): Same optimization as FAST_RUN, but print some profiling information.
 
 The default mode is typically ``FAST_RUN``, but it can be controlled via
 the configuration variable :attr:`config.mode`,
@@ -150,7 +150,7 @@ short name        Full constructor
 ``FAST_COMPILE``  ``compile.mode.Mode(linker='py', optimizer='fast_compile')``    Python implementations only, quick and cheap graph transformations
 ``FAST_RUN``      ``compile.mode.Mode(linker='cvm', optimizer='fast_run')``       C implementations where available, all available graph transformations.
 ``DebugMode``     ``compile.debugmode.DebugMode()``                               Both implementations where available, all available graph transformations.
-``ProfileMode``   ``compile.profilemode.ProfileMode()``                           C implementations where available, all available graph transformations, print profile information.
+``ProfileMode``   ``compile.profilemode.ProfileMode()``                           Deprecated. C implementations where available, all available graph transformations, print profile information.
 ================= =============================================================== ===============================================================================
 
 .. Note::
@@ -180,7 +180,7 @@ c|py_nogc      no         yes                "++"       As c|py, but without gc
 c              no         yes                "+"        Use only C code (if none available for an op, raise an error)
 py             yes        yes                "+++"      Use only Python code
 c&py [#cpy2]_  no         yes                "+++++"    Use C and Python code
-ProfileMode    no         no                 "++++"     Compute some extra profiling info
+ProfileMode    no         no                 "++++"     (Deprecated) Compute some extra profiling info
 DebugMode      no         yes                VERY HIGH  Make many checks on what Theano computes
 =============  =========  =================  =========  ===
 
@@ -253,6 +253,11 @@ For more detail, see :ref:`DebugMode<debugmode>` in the library.
 ProfileMode
 ===========
 
+.. note::
+
+    ProfileMode is deprecated. Use :attr:`config.profile` instead.
+
+
 Besides checking for errors, another important task is to profile your
 code. For this Theano uses a special mode called ProfileMode which has
 to be passed as an argument to :func:`theano.function <function.function>`. 

theano/compile/function_module.py

@@ -1266,7 +1266,7 @@ def orig_function(inputs, outputs, mode=None, accept_inplace=False,
 
      - FAST_COMPILE (minimal optimization)
 
-     - ProfileMode: allow to print a profile mode with mode.print_summary
+     - ProfileMode(deprecated): allow to print a profile mode with mode.print_summary
 
      - DebugMode: verify many internal conditions that are normally assumed
        (slow)

theano/configdefaults.py

@@ -134,7 +134,7 @@ if rc == 0:
     # Keep the default linker the same as the one for the mode FAST_RUN
     AddConfigVar('linker',
                  ("Default linker used if the theano flags mode is Mode "
-                  "or ProfileMode"),
+                  "or ProfileMode(deprecated)"),
                  EnumStr('cvm', 'c|py', 'py', 'c', 'c|py_nogc', 'c&py',
                      'vm', 'vm_nogc', 'cvm_nogc'),
                  in_c_key=False)
@@ -142,7 +142,7 @@ else:
     # g++ is not present, linker should default to python only
     AddConfigVar('linker',
                  ("Default linker used if the theano flags mode is Mode "
-                  "or ProfileMode"),
+                  "or ProfileMode(deprecated)"),
                  EnumStr('py', 'vm', 'vm_nogc'),
                  in_c_key=False)
     _logger.warning('g++ not detected ! Theano will be unable to execute '
@@ -174,7 +174,7 @@ AddConfigVar('allow_gc',
 #Keep the default optimizer the same as the one for the mode FAST_RUN
 AddConfigVar('optimizer',
         ("Default optimizer. If not None, will use this linker with the Mode "
-         "object (not ProfileMode or DebugMode)"),
+         "object (not ProfileMode(deprecated) or DebugMode)"),
         EnumStr('fast_run', 'merge', 'fast_compile', 'None'),
         in_c_key=False)