Remove deprecated modules

.github/workflows/test.yml

@@ -77,7 +77,7 @@ jobs:
           - "tests/tensor tests/sparse --ignore=tests/tensor/test_basic.py --ignore=tests/tensor/test_math.py --ignore=tests/tensor/test_math_scipy.py --ignore=tests/tensor/test_inplace.py --ignore=tests/tensor/test_elemwise.py --ignore=tests/tensor/rewriting/test_basic.py --ignore=tests/tensor/rewriting/test_math.py --ignore=tests/tensor/nnet --ignore=tests/tensor/signal"
           - "tests/tensor/test_basic.py tests/tensor/test_math.py tests/tensor/test_math_scipy.py tests/tensor/test_inplace.py"
           - "tests/tensor/test_elemwise.py tests/tensor/rewriting/test_basic.py tests/tensor/rewriting/test_math.py"
-          - "tests/tensor/nnet/test_conv.py"
+          - "tests/tensor/conv/test_abstract_conv.py"
         include:
           - python-version: "3.7"
             fast-compile: 1

doc/conf.py

@@ -113,7 +113,8 @@
 
 # html4_writer added to Fix colon & whitespace misalignment
 # https://github.com/readthedocs/sphinx_rtd_theme/issues/766#issuecomment-513852197
-html4_writer = True
+# https://github.com/readthedocs/sphinx_rtd_theme/issues/766#issuecomment-629666319
+# html4_writer = False
 
 html_logo = "images/pytensor_logo.svg"
 html_theme = "pymc_sphinx_theme"

doc/environment.yml

@@ -9,7 +9,7 @@ dependencies:
   - numpy
   - scipy
   - six
-  - sphinx>=3
+  - sphinx>=5.1.0
   - mock
   - pillow
   - pip

doc/extending/type.rst

@@ -324,8 +324,8 @@ For certain mechanisms, you can register functions and other such
 things to plus your type into pytensor's mechanisms.  These are optional
 but will allow people to use you type with familiar interfaces.
 
-`transfer`
-~~~~~~~~~~
+**`transfer`**
+
 
 To plug in additional options for the transfer target, define a
 function which takes an PyTensor variable and a target argument and

doc/extending/using_params.rst

@@ -76,7 +76,6 @@ attribute :attr:`params_type` to an instance of your params Type.
    If you want to have multiple parameters, PyTensor provides the convenient class
    :class:`pytensor.link.c.params_type.ParamsType` that allows to bundle many parameters into
    one object that will be available in both Python (as a Python object) and C code (as a struct).
-   See :ref:`ParamsType tutorial and API documentation <libdoc_graph_params_type>` for more infos.
 
 For example if we decide to use an int as the params the following
 would be appropriate:

doc/library/compile/io.rst

@@ -6,9 +6,9 @@
 
 .. _function_inputs:
 
-===========================================
+============================================
 :mod:`io` - defines pytensor.function [TODO]
-===========================================
+============================================
 
 .. module:: pytensor.compile.io
    :platform: Unix, Windows

doc/library/compile/opfromgraph.rst

@@ -2,9 +2,9 @@
 
 .. _opfromgraph:
 
-============
+=============
 `OpFromGraph`
-============
+=============
 
 This page describes :class:`pytensor.compile.builders.OpFromGraph
 <pytensor.compile.builders.OpFromGraph>`, an `Op` constructor that allows one to

doc/library/graph/index.rst

@@ -18,5 +18,4 @@
     features
     op
     type
-    params_type
     utils

doc/library/index.rst

@@ -19,7 +19,6 @@ Modules
    config
    d3viz/index
    graph/index
-   gpuarray/index
    gradient
    misc/pkl_utils
    printing

doc/library/sandbox/index.rst

@@ -14,5 +14,3 @@
     :maxdepth: 1
 
     linalg
-    neighbours
-    rng_mrg

doc/library/tensor/basic.rst

@@ -557,6 +557,7 @@ them perfectly, but a `dscalar` otherwise.
     .. method:: astype(dtype)
     .. method:: take(indices, axis=None, mode='raise')
     .. method:: copy()
+       :noindex:
 
         Return a new symbolic variable that is a copy of the variable. Does not copy the tag.
 
@@ -667,11 +668,7 @@ dimensions, see :meth:`_tensor_py_operators.dimshuffle`.
     >>> pytensor.tensor.shape_padaxis(tensor, axis=-1)
     InplaceDimShuffle{0,1,2,x}.0
 
-.. autofunction:: unbroadcast(x, *axes)
-
-.. autofunction:: addbroadcast(x, *axes)
-
-.. autofunction:: patternbroadcast(x, broadcastable)
+.. autofunction:: specify_shape(x, shape)
 
 .. function:: flatten(x, ndim=1)
 

doc/library/tensor/conv.rst

@@ -0,0 +1,11 @@
+=========================================
+:mod:`tensor.conv` -- Tensor Convolutions
+=========================================
+
+.. module:: tensor.conv
+   :platform: Unix, Windows
+   :synopsis: Tensor Convolutions
+.. moduleauthor:: LISA, PyMC Developers, PyTensor Developers
+
+.. automodule:: pytensor.tensor.conv
+    :members:

doc/library/tensor/index.rst

@@ -26,5 +26,6 @@ They are grouped into the following sections:
     slinalg
     nlinalg
     fft
+    conv
     math_opt
     basic_opt

doc/library/tensor/io.rst

@@ -12,11 +12,6 @@ File operation
 
 - Load from disk with the function :func:`load <pytensor.tensor.io.load>` and its associated op :class:`LoadFromDisk <pytensor.tensor.io.LoadFromDisk>`
 
-MPI operation
-=============
-- Non-blocking transfer: :func:`isend <pytensor.tensor.io.isend>` and :func:`irecv <pytensor.tensor.io.irecv>`.
-- Blocking transfer: :func:`send <pytensor.tensor.io.send>` and :func:`recv <pytensor.tensor.io.recv>`
-
 Details
 =======
 

doc/library/tensor/slinalg.rst

@@ -20,8 +20,4 @@ API
 
 .. automodule:: pytensor.tensor.slinalg
     :members:
-    :exclude-members: solve, solve_lower_triangular, solve_upper_triangular
 
-.. autofunction:: solve(a, b)
-.. autofunction:: solve_lower_triangular(a, b)
-.. autofunction:: solve_upper_triangular(a, b)

doc/sandbox/sparse.rst

@@ -120,7 +120,7 @@ Misc
 The sparse equivalent of `dmatrix` is `csc_matrix` and `csr_matrix`.
 
 :class:`~pytensor.sparse.basic.Dot` vs. :class:`~pytensor.sparse.basic.StructuredDot`
----------------------------------------------------------------------------------
+-------------------------------------------------------------------------------------
 
 Often when you use a sparse matrix it is because there is a meaning to the
 structure of non-zeros. The gradient on terms outside that structure

doc/troubleshooting.rst

@@ -16,7 +16,7 @@ Here are Linux troubleshooting instructions. There is a specific `MacOS`_ sectio
 .. _network_error_proxy:
 
 Why do I get a network error when I install PyTensor
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 If you are behind a proxy, you must do some extra configuration steps
 before starting the installation. You must set the environment
@@ -69,7 +69,7 @@ large enough.
 .. _float64_output:
 
 pytensor.function returns a float64 when the inputs are float32 and int{32, 64}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 It should be noted that using float32 and int{32, 64} together
 inside a function would provide float64 as output.
@@ -80,7 +80,7 @@ To help you find where float64 are created, see the
 .. _test_pytensor:
 
 How to test that PyTensor works properly
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 An easy way to check something that could be wrong is by making sure ``PYTENSOR_FLAGS``
 have the desired values as well as the ``~/.pytensorrc``

doc/tutorial/profiling.rst

@@ -27,9 +27,10 @@ of the following two options:
 2. Pass the argument :attr:`profile=True` to the function :func:`pytensor.function
    <function.function>` and then call :attr:`f.profile.summary()` for a single
    function.
-    - Use this option when you want to profile not all the
-      functions but only one or more specific function(s).
-    - You can also combine the profile results of many functions:
+
+   - Use this option when you want to profile not all the
+     functions but only one or more specific function(s).
+   - You can also combine the profile results of many functions:
 
       .. doctest::
           :hide:

environment.yml

@@ -16,6 +16,7 @@ dependencies:
   - logical-unification
   - miniKanren
   - cons
+  - pydeprecate
   # Intel BLAS
   - mkl
   - mkl-service
@@ -30,7 +31,7 @@ dependencies:
   - pytest-cov
   - pytest-xdist
   # For building docs
-  - sphinx>=1.3
+  - sphinx>=5.1.0
   - sphinx_rtd_theme
   - pygments
   - pydot
@@ -47,5 +48,5 @@ dependencies:
   - packaging
   - typing_extensions
   # optional
-  - sympy
   - cython
+

pytensor/__init__.py

@@ -171,27 +171,3 @@ def get_scalar_constant_value(v):
 # imports were executed, we can warn about remaining flags provided by the user
 # through PYTENSOR_FLAGS.
 config.warn_unused_flags()
-
-DEPRECATED_NAMES = [
-    (
-        "change_flags",
-        "`pytensor.change_flags` is deprecated: use `pytensor.config.change_flags` instead.",
-        config.change_flags,
-    ),
-]
-
-
-def __getattr__(name):
-    """Intercept module-level attribute access of deprecated symbols.
-
-    Adapted from https://stackoverflow.com/a/55139609/3006474.
-
-    """
-    from warnings import warn
-
-    for old_name, msg, old_object in DEPRECATED_NAMES:
-        if name == old_name:
-            warn(msg, DeprecationWarning, stacklevel=2)
-            return old_object
-
-    raise AttributeError(f"module {__name__} has no attribute {name}")

pytensor/compile/function/types.py

@@ -1158,7 +1158,7 @@ def _constructor_Function(maker, input_storage, inputs_data, trust_input=False):
     if not config.unpickle_function:
         return None
 
-    f = maker.create(input_storage, trustme=True)
+    f = maker.create(input_storage)
     assert len(f.input_storage) == len(inputs_data)
     for container, x in zip(f.input_storage, inputs_data):
         assert (
@@ -1574,7 +1574,7 @@ def __init__(
             for i in self.inputs
         ]
 
-    def create(self, input_storage=None, trustme=False, storage_map=None):
+    def create(self, input_storage=None, storage_map=None):
         """
         Create a function.
 
@@ -1584,9 +1584,6 @@ def create(self, input_storage=None, trustme=False, storage_map=None):
             A list matching the inputs list and providing default values if the
             default for an input is None, then that input is a required input.
             For an input with an update, the default acts as initialization.
-        trustme
-            Disables some exceptions, used internally.
-
         """
 
         if input_storage is None:

pytensor/compile/profiling.py

@@ -1485,7 +1485,6 @@ def print_tips(self, file):
         from pytensor import scalar as aes
         from pytensor.tensor.elemwise import Elemwise
         from pytensor.tensor.math import Dot
-        from pytensor.tensor.random.op import RandomVariable
 
         scalar_op_amdlibm_no_speed_up = [
             aes.LT,
@@ -1628,18 +1627,7 @@ def exp_float32_op(op):
                 printed_tip = True
 
         # tip 5
-        for (fgraph, a) in self.apply_time:
-            node = a
-            if isinstance(node.op, RandomVariable):
-                printed_tip = True
-                print(
-                    "  - Replace the default random number generator by "
-                    "'from pytensor.sandbox.rng_mrg import MRG_RandomStream "
-                    "as RandomStream', as this is is faster. It is still "
-                    "experimental, but seems to work correctly.",
-                    file=file,
-                )
-                break
+        # The tip was about MRG_RandomStream which is removed
 
         # tip 6
         for (fgraph, a) in self.apply_time: