--- doc/conf.py.orig	2020-11-23 15:59:25.572772033 -0700
+++ doc/conf.py	2020-11-23 15:59:35.724796795 -0700
@@ -136,7 +136,7 @@ if os.environ.get('READTHEDOCS') != 'Tru
     html_theme = 'sphinx_rtd_theme'
 
 def setup(app):
-    app.add_stylesheet("fix_rtd.css")
+    app.add_css_file("fix_rtd.css")
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
--- doc/extending/extending_theano_gpu.txt.orig	2020-11-14 20:22:36.000000000 -0700
+++ doc/extending/extending_theano_gpu.txt	2020-11-23 16:48:56.092972525 -0700
@@ -264,14 +264,14 @@ CGpuKernelBase
 Python File
 ~~~~~~~~~~~
 
-.. literalinclude:: ../../theano/gpuarray/tests/test_cgpukernelbase.py
+.. literalinclude:: ../../tests/gpuarray/test_cgpukernelbase.py
     :language: python
     :pyobject: GpuEye
 
 ``tstgpueye.c``
 ~~~~~~~~~~~~~~~
 
-.. literalinclude:: ../../theano/gpuarray/tests/c_code/tstgpueye.c
+.. literalinclude:: ../../tests/gpuarray/c_code/tstgpueye.c
     :language: C
 
 Wrapping Exisiting Libraries
--- doc/library/scan.txt.orig	2020-11-14 20:22:36.000000000 -0700
+++ doc/library/scan.txt	2020-11-23 16:23:49.166254031 -0700
@@ -682,4 +682,4 @@ reference
 .. autofunction:: theano.foldl
 .. autofunction:: theano.foldr
 .. autofunction:: theano.scan
-.. autofunction:: theano.scan_checkpoints
+.. autofunction:: theano.scan.checkpoints.scan_checkpoints
--- doc/library/sparse/sandbox.txt.orig	2020-11-14 20:22:36.000000000 -0700
+++ doc/library/sparse/sandbox.txt	2020-11-23 16:25:00.134423267 -0700
@@ -19,5 +19,3 @@ API
     :members:
 .. automodule:: theano.sparse.sandbox.sp2
     :members:
-.. automodule:: theano.sparse.sandbox.truedot
-    :members:
--- doc/library/tests.txt.orig	2020-11-14 20:22:36.000000000 -0700
+++ doc/library/tests.txt	2020-11-23 16:33:08.245587256 -0700
@@ -4,5 +4,5 @@
 :mod:`tests` -- Tests
 =====================
 
-.. automodule:: tests.breakpoint
+.. automodule:: theano.breakpoint
     :members:
--- theano/gof/op.py.orig	2020-11-14 20:22:36.000000000 -0700
+++ theano/gof/op.py	2020-11-23 15:59:35.726796800 -0700
@@ -341,13 +341,13 @@ class CLinkerOp(CLinkerObject):
             string is the name of a C variable pointing to that input.
             The type of the variable depends on the declared type of
             the input.  There is a corresponding python variable that
-            can be accessed by prepending "py_" to the name in the
+            can be accessed by prepending ```"py_"``` to the name in the
             list.
         outputs : list of strings
             Each string is the name of a C variable where the Op should
             store its output.  The type depends on the declared type of
             the output.  There is a corresponding python variable that
-            can be accessed by prepending "py_" to the name in the
+            can be accessed by prepending ```"py_"``` to the name in the
             list.  In some cases the outputs will be preallocated and
             the value of the variable may be pre-filled.  The value for
             an unallocated output is type-dependent.
@@ -404,13 +404,13 @@ class CLinkerOp(CLinkerObject):
             string is the name of a C variable pointing to that input.
             The type of the variable depends on the declared type of
             the input. There is a corresponding python variable that
-            can be accessed by prepending "py_" to the name in the
+            can be accessed by prepending ```"py_"``` to the name in the
             list.
         outputs : list of strings
             Each string is the name of a C variable correspoinding to
             one of the outputs of the Op. The type depends on the
             declared type of the output. There is a corresponding
-            python variable that can be accessed by prepending "py_" to
+            python variable that can be accessed by prepending ```"py_"``` to
             the name in the list.
         sub : dict of strings
             extra symbols defined in `CLinker` sub symbols (such as 'fail').
--- theano/gof/opt.py.orig	2020-11-14 20:22:36.000000000 -0700
+++ theano/gof/opt.py	2020-11-23 15:59:35.728796804 -0700
@@ -102,9 +102,9 @@ class Optimizer:
 
         Add features to the fgraph that are required to apply the optimization.
         For example:
-          fgraph.attach_feature(History())
-          fgraph.attach_feature(MyFeature())
-          etc.
+        fgraph.attach_feature(History())
+        fgraph.attach_feature(MyFeature())
+        etc.
 
         """
 
--- theano/scan/__init__.py.orig	2020-11-14 20:22:36.000000000 -0700
+++ theano/scan/__init__.py	2020-11-23 16:21:47.909964873 -0700
@@ -25,9 +25,9 @@ of using ``scan`` over `for` loops in py
 * it allows the number of iterations to be part of the symbolic graph
 * it allows computing gradients through the for loop
 * there exist a bunch of optimizations that help re-write your loop
-such that less memory is used and that it runs faster
+  such that less memory is used and that it runs faster
 * it ensures that data is not copied from host to gpu and gpu to
-host at each step
+  host at each step
 
 The Scan Op should typically be used by calling any of the following
 functions: ``scan()``, ``map()``, ``reduce()``, ``foldl()``,
--- theano/sparse/basic.py.orig	2020-11-14 20:22:36.000000000 -0700
+++ theano/sparse/basic.py	2020-11-23 15:59:35.729796807 -0700
@@ -4342,9 +4342,9 @@ class ConstructSparseFromList(gof.Op):
         This create a sparse matrix with the same shape as `x`. Its
         values are the rows of `values` moved. Pseudo-code::
 
-            output = csc_matrix.zeros_like(x, dtype=values.dtype)
-            for in_idx, out_idx in enumerate(ilist):
-                output[out_idx] = values[in_idx]
+        output = csc_matrix.zeros_like(x, dtype=values.dtype)
+        for in_idx, out_idx in enumerate(ilist):
+            output[out_idx] = values[in_idx]
 
         """
         x_ = theano.tensor.as_tensor_variable(x)
--- theano/tensor/extra_ops.py.orig	2020-11-14 20:22:36.000000000 -0700
+++ theano/tensor/extra_ops.py	2020-11-23 17:01:03.085630196 -0700
@@ -1464,7 +1464,7 @@ def broadcast_shape(*arrays, **kwargs):
 
     Parameters
     ----------
-    *arrays: `TensorVariable`s
+    *arrays: `TensorVariable` instances
         The tensor variables, or their shapes (as tuples),
         for which the broadcast shape is computed.
     arrays_are_shapes: bool (Optional)
--- versioneer.py.orig	2020-11-14 20:22:36.000000000 -0700
+++ versioneer.py	2020-11-23 15:59:35.730796809 -0700
@@ -418,7 +418,7 @@ def run_command(commands, args, cwd=None
     return stdout, p.returncode
 
 
-LONG_VERSION_PY['git'] = '''
+LONG_VERSION_PY['git'] = r'''
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build