pytensor 2.18.6__tar.gz → 2.20.0__tar.gz

{pytensor-2.18.6/pytensor.egg-info → pytensor-2.20.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pytensor
-Version: 2.18.6
+Version: 2.20.0
 Summary: Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs.
 Author-email: pymc-devs <pymc.devs@gmail.com>
 License: .. _license:
@@ -66,10 +66,10 @@ Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
 Classifier: Operating System :: MacOS
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: <3.12,>=3.9
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
 Requires-Dist: setuptools>=48.0.0
@@ -105,8 +105,7 @@ Provides-Extra: jax
 Requires-Dist: jax; extra == "jax"
 Requires-Dist: jaxlib; extra == "jax"
 Provides-Extra: numba
-Requires-Dist: numba>=0.55; extra == "numba"
-Requires-Dist: numba-scipy>=0.3.0; extra == "numba"
+Requires-Dist: numba>=0.57; extra == "numba"
 
 .. image:: https://cdn.rawgit.com/pymc-devs/pytensor/main/doc/images/PyTensor_RGB.svg
     :height: 100px
@@ -115,8 +114,9 @@ Requires-Dist: numba-scipy>=0.3.0; extra == "numba"
 
 |Tests Status| |Coverage|
 
-|Project Name| is a fork of `Aesara <https://github.com/aesara-devs/aesara>`__ -- a Python library that allows one to define, optimize, and
+|Project Name| is a Python library that allows one to define, optimize, and
 efficiently evaluate mathematical expressions involving multi-dimensional arrays.
+It provides the computational backend for `PyMC <https://github.com/pymc-devs/pymc>`__.
 
 Features
 ========
@@ -125,7 +125,8 @@ Features
 - Extensible graph framework suitable for rapid development of custom operators and symbolic optimizations
 - Implements an extensible graph transpilation framework that currently provides
   compilation via C, `JAX <https://github.com/google/jax>`__, and `Numba <https://github.com/numba/numba>`__
-- Based on one of the most widely-used Python tensor libraries: `Theano <https://github.com/Theano/Theano>`__
+- Contrary to PyTorch and TensorFlow, PyTensor maintains a static graph which can be modified in-place to
+  allow for advanced optimizations
 
 Getting started
 ===============
@@ -223,6 +224,11 @@ The current development branch of |Project Name| can be installed from GitHub, a
     pip install git+https://github.com/pymc-devs/pytensor
 
 
+Background
+==========
+
+PyTensor is a fork of `Aesara <https://github.com/aesara-devs/aesara>`__, which is a fork of `Theano <https://github.com/Theano/Theano>`__.
+
 Contributing
 ============
 

{pytensor-2.18.6 → pytensor-2.20.0}/README.rst

@@ -5,8 +5,9 @@
 
 |Tests Status| |Coverage|
 
-|Project Name| is a fork of `Aesara <https://github.com/aesara-devs/aesara>`__ -- a Python library that allows one to define, optimize, and
+|Project Name| is a Python library that allows one to define, optimize, and
 efficiently evaluate mathematical expressions involving multi-dimensional arrays.
+It provides the computational backend for `PyMC <https://github.com/pymc-devs/pymc>`__.
 
 Features
 ========
@@ -15,7 +16,8 @@ Features
 - Extensible graph framework suitable for rapid development of custom operators and symbolic optimizations
 - Implements an extensible graph transpilation framework that currently provides
   compilation via C, `JAX <https://github.com/google/jax>`__, and `Numba <https://github.com/numba/numba>`__
-- Based on one of the most widely-used Python tensor libraries: `Theano <https://github.com/Theano/Theano>`__
+- Contrary to PyTorch and TensorFlow, PyTensor maintains a static graph which can be modified in-place to
+  allow for advanced optimizations
 
 Getting started
 ===============
@@ -113,6 +115,11 @@ The current development branch of |Project Name| can be installed from GitHub, a
     pip install git+https://github.com/pymc-devs/pytensor
 
 
+Background
+==========
+
+PyTensor is a fork of `Aesara <https://github.com/aesara-devs/aesara>`__, which is a fork of `Theano <https://github.com/Theano/Theano>`__.
+
 Contributing
 ============
 

{pytensor-2.18.6 → pytensor-2.20.0}/bin/__init__.py

@@ -1,5 +1,6 @@
 import warnings
 
+
 warnings.warn(
     message= "Importing 'bin.pytensor_cache' is deprecated. Import from "
     "'pytensor.bin.pytensor_cache' instead.",

{pytensor-2.18.6 → pytensor-2.20.0}/doc/environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python=3.9
+  - python=3.10
   - gcc_linux-64
   - gxx_linux-64
   - numpy

{pytensor-2.18.6 → pytensor-2.20.0}/pyproject.toml

@@ -1,24 +1,20 @@
 [build-system]
 requires = [
-  "setuptools>=48.0.0",
-  "cython",
-  "numpy>=1.17.0",
-  "versioneer[toml]==0.28",
+    "setuptools>=48.0.0",
+    "cython",
+    "numpy>=1.17.0",
+    "versioneer[toml]>=0.28",
 ]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "pytensor"
-dynamic = [
-  'version'
-]
-requires-python = ">=3.9,<3.12"
-authors = [
-    {name = "pymc-devs", email = "pymc.devs@gmail.com"}
-]
+dynamic = ['version']
+requires-python = ">=3.10,<3.13"
+authors = [{ name = "pymc-devs", email = "pymc.devs@gmail.com" }]
 description = "Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs."
 readme = "README.rst"
-license = {file = "LICENSE.txt"}
+license = { file = "LICENSE.txt" }
 classifiers = [
     "Development Status :: 6 - Mature",
     "Intended Audience :: Education",
@@ -34,9 +30,9 @@ classifiers = [
     "Operating System :: Unix",
     "Operating System :: MacOS",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 
 keywords = [
@@ -71,15 +67,8 @@ documentation = "https://pytensor.readthedocs.io/en/latest/"
 pytensor-cache = "pytensor.bin.pytensor_cache:main"
 
 [project.optional-dependencies]
-complete = [
-    "pytensor[jax]",
-    "pytensor[numba]",
-]
-development = [
-    "pytensor[complete]",
-    "pytensor[tests]",
-    "pytensor[rtd]"
-]
+complete = ["pytensor[jax]", "pytensor[numba]"]
+development = ["pytensor[complete]", "pytensor[tests]", "pytensor[rtd]"]
 tests = [
     "pytest",
     "pre-commit",
@@ -88,34 +77,16 @@ tests = [
     "pytest-benchmark",
     "pytest-mock",
 ]
-rtd = [
-    "sphinx>=5.1.0,<6",
-    "pygments",
-    "pydot",
-    "pydot2",
-    "pydot-ng",
-]
-jax = [
-    "jax",
-    "jaxlib",
-]
-numba = [
-    "numba>=0.55",
-    "numba-scipy>=0.3.0"
-]
+rtd = ["sphinx>=5.1.0,<6", "pygments", "pydot", "pydot2", "pydot-ng"]
+jax = ["jax", "jaxlib"]
+numba = ["numba>=0.57"]
 
 [tool.setuptools.packages.find]
 include = ["pytensor*", "bin"]
 
 [tool.setuptools.package-data]
-pytensor = [
-    "py.typed"
-]
-"pytensor.d3viz" = [
-    "html/*",
-    "css/*",
-    "js/*",
-]
+pytensor = ["py.typed"]
+"pytensor.d3viz" = ["html/*", "css/*", "js/*"]
 
 [tool.coverage.run]
 omit = [
@@ -129,21 +100,13 @@ omit = [
     "pytensor/graph/unify.py",
     "pytensor/link/jax/jax_linker.py",
     "pytensor/link/jax/jax_dispatch.py",
-    "pytensor/graph/toolbox.py",
-    "pytensor/scalar/basic_scipy.py",
 ]
 branch = true
 relative_files = true
 
 [tool.coverage.report]
-omit = [
-    "pytensor/_version.py",
-    "tests/",
-]
-exclude_lines = [
-    "pragma: no cover",
-    "if TYPE_CHECKING:",
-]
+omit = ["pytensor/_version.py", "tests/"]
+exclude_lines = ["pragma: no cover", "if TYPE_CHECKING:"]
 show_missing = true
 
 [tool.versioneer]
@@ -157,50 +120,40 @@ tag_prefix = "rel-"
 addopts = "--durations=50"
 testpaths = "tests/"
 
-[tool.pylint]
-max-line-length = 88
+[tool.ruff]
+line-length = 88
+exclude = ["doc/", "pytensor/_version.py", "bin/pytensor_cache.py"]
 
-[tool.pylint.messages_control]
-disable = ["C0330", "C0326"]
+[tool.ruff.lint]
+select = ["C", "E", "F", "I", "UP", "W", "RUF"]
+ignore = ["C408", "C901", "E501", "E741", "RUF012"]
 
-[tool.isort]
-profile = "black"
-lines_after_imports = 2
-lines_between_sections = 1
-honor_noqa = true
-skip_gitignore = true
-skip = "pytensor/version.py"
-skip_glob = "**/*.pyx"
 
-[tool.ruff]
-select=["C","E","F","W"]
-ignore=["E501","E741","C408","C901"]
-exclude = [
-    "doc/",
-    "pytensor/_version.py",
-    "bin/pytensor_cache.py",
-]
+[tool.ruff.lint.isort]
+lines-after-imports = 2
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # TODO: Get rid of these:
-    "**/__init__.py"=["F401","E402","F403"]
-    "pytensor/tensor/linalg.py"=["F401","F403"]
-    "pytensor/scalar/basic_scipy.py"=["E402","F403","F401"]
-    "pytensor/graph/toolbox.py"=["E402","F403","F401"]
-    "pytensor/link/jax/jax_dispatch.py"=["E402","F403","F401"]
-    "pytensor/link/jax/jax_linker.py"=["E402","F403","F401"]
-    "pytensor/sparse/sandbox/sp2.py"=["F401"]
-    "tests/tensor/test_math_scipy.py"=["E402"]
-    "tests/sparse/test_basic.py"=["E402"]
-    "tests/sparse/test_opt.py"=["E402"]
-    "tests/sparse/test_sp2.py"=["E402"]
-    "tests/sparse/test_utils.py"=["E402","F401"]
-    "tests/sparse/sandbox/test_sp.py"=["E402","F401"]
-    "tests/scalar/test_basic_sympy.py"=["E402"]
-    "pytensor/graph/rewriting/unify.py"=["F811"]
+"**/__init__.py" = ["F401", "E402", "F403"]
+"pytensor/tensor/linalg.py" = ["F403"]
+# For the tests we skip because `pytest.importorskip` is used:
+"tests/link/jax/test_scalar.py" = ["E402"]
+"tests/link/jax/test_tensor_basic.py" = ["E402"]
+"tests/link/numba/test_basic.py" = ["E402"]
+"tests/link/numba/test_cython_support.py" = ["E402"]
+"tests/link/numba/test_performance.py" = ["E402"]
+"tests/link/numba/test_sparse.py" = ["E402"]
+"tests/link/numba/test_tensor_basic.py" = ["E402"]
+"tests/tensor/test_math_scipy.py" = ["E402"]
+"tests/sparse/test_basic.py" = ["E402"]
+"tests/sparse/test_sp2.py" = ["E402"]
+"tests/sparse/test_utils.py" = ["E402"]
+"tests/sparse/sandbox/test_sp.py" = ["E402", "F401"]
+"versioneer.py" = ["I"]
 
 
 [tool.mypy]
+python_version = "3.10"
 ignore_missing_imports = true
 no_implicit_optional = true
 check_untyped_defs = false

{pytensor-2.18.6 → pytensor-2.20.0}/pytensor/__init__.py

@@ -18,7 +18,6 @@ To learn more, check out:
 
 """
 
-
 __docformat__ = "restructuredtext en"
 
 # Set a default logger. It is important to do this before importing some other
@@ -77,7 +76,7 @@ from pytensor.graph.replace import clone_replace, graph_replace
 # isort: on
 
 
-def as_symbolic(x: Any, name: Optional[str] = None, **kwargs) -> Variable:
+def as_symbolic(x: Any, name: str | None = None, **kwargs) -> Variable:
     """Convert `x` into an equivalent PyTensor `Variable`.
 
     Parameters

{pytensor-2.18.6 → pytensor-2.20.0}/pytensor/_version.py

@@ -1,5 +1,5 @@
 
-# This file was generated by 'versioneer.py' (0.28) from
+# This file was generated by 'versioneer.py' (0.29) from
 # revision-control system data, or from the parent directory name of an
 # unpacked source archive. Distribution tarballs contain a pre-generated copy
 # of this file.
@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-01-12T14:29:52+0100",
+ "date": "2024-03-28T18:19:27+0100",
  "dirty": false,
  "error": null,
- "full-revisionid": "0666fd564d2d67384051c5bb6e0c09e713e0329c",
- "version": "2.18.6"
+ "full-revisionid": "ef22377d7e6ea6c74c36a8dc634ef7f1f1f8f9c6",
+ "version": "2.20.0"
 }
 '''  # END VERSION_JSON
 

{pytensor-2.18.6 → pytensor-2.20.0}/pytensor/breakpoint.py

@@ -92,7 +92,7 @@ class PdbBreakpoint(Op):
             new_op.inp_types.append(monitored_vars[i].type)
 
         # Build the Apply node
-        inputs = [condition] + list(monitored_vars)
+        inputs = [condition, *monitored_vars]
         outputs = [inp.type() for inp in monitored_vars]
         return Apply(op=new_op, inputs=inputs, outputs=outputs)
 
@@ -142,7 +142,7 @@ class PdbBreakpoint(Op):
                 output_storage[i][0] = inputs[i + 1]
 
     def grad(self, inputs, output_gradients):
-        return [DisconnectedType()()] + output_gradients
+        return [DisconnectedType()(), *output_gradients]
 
     def infer_shape(self, fgraph, inputs, input_shapes):
         # Return the shape of every input but the condition (first input)

{pytensor-2.18.6 → pytensor-2.20.0}/pytensor/compile/builders.py

@@ -1,9 +1,10 @@
 """Define new Ops from existing Ops"""
+
 from collections import OrderedDict
 from collections.abc import Sequence
 from copy import copy
 from functools import partial
-from typing import Optional, cast
+from typing import cast
 
 import pytensor.tensor as pt
 from pytensor import function
@@ -91,38 +92,29 @@ def construct_nominal_fgraph(
     dict[Variable, Variable],
 ]:
     """Construct an inner-`FunctionGraph` with ordered nominal inputs."""
-    dummy_inputs = []
-    for n, inp in enumerate(inputs):
-        if (
-            not isinstance(inp, Variable)
-            or isinstance(inp, Constant)
-            or isinstance(inp, SharedVariable)
-        ):
-            raise TypeError(
-                f"Inputs and outputs must be non-Constant/shared Variable instances; got {inp}"
-            )
+    implicit_shared_inputs = []
 
-        dummy_inputs.append(inp.type())
-
-    dummy_shared_inputs = []
-    shared_inputs = []
+    dummy_inputs = [inp.type() for inp in inputs]
+    dummy_implicit_shared_inputs = []
     for var in graph_inputs(outputs, inputs):
+        if var in inputs:
+            continue
         if isinstance(var, SharedVariable):
-            # To correctly support shared variables the inner-graph should
-            # not see them; otherwise, there will be problems with
-            # gradients.
-            # That's why we collect the shared variables and replace them
-            # with dummies.
-            shared_inputs.append(var)
-            dummy_shared_inputs.append(var.type())
-        elif var not in inputs and not isinstance(var, Constant):
-            raise MissingInputError(f"OpFromGraph is missing an input: {var}")
-
-    replacements = dict(zip(inputs + shared_inputs, dummy_inputs + dummy_shared_inputs))
+            # We allow shared inputs to be added automatically to the graph
+            implicit_shared_inputs.append(var)
+            dummy_implicit_shared_inputs.append(var.type())
+        elif not isinstance(var, Constant):
+            raise MissingInputError(f"NominalGraph is missing an input: {var}")
+
+    replacements = dict(
+        zip(
+            inputs + implicit_shared_inputs, dummy_inputs + dummy_implicit_shared_inputs
+        )
+    )
 
     new = rebuild_collect_shared(
         cast(Sequence[Variable], outputs),
-        inputs=inputs + shared_inputs,
+        inputs=inputs + implicit_shared_inputs,
         replace=replacements,
         copy_inputs_over=False,
     )
@@ -132,7 +124,7 @@ def construct_nominal_fgraph(
         (clone_d, update_d, update_expr, new_shared_inputs),
     ) = new
 
-    assert len(local_inputs) == len(inputs) + len(shared_inputs)
+    assert len(local_inputs) == len(inputs) + len(implicit_shared_inputs)
     assert len(local_outputs) == len(outputs)
     assert not update_d
     assert not update_expr
@@ -154,7 +146,7 @@ def construct_nominal_fgraph(
         fgraph.clients.pop(inp, None)
         fgraph.add_input(nom_inp)
 
-    return fgraph, shared_inputs, update_d, update_expr
+    return fgraph, implicit_shared_inputs, update_d, update_expr
 
 
 class OpFromGraph(Op, HasInnerGraph):
@@ -176,8 +168,6 @@ class OpFromGraph(Op, HasInnerGraph):
         - grad() make it support DisconnectedType and the new interface
         - add support for NullType and DisconnectedType when R_op supports them
         - check how it works with updates.
-        - add test with constant as input or inside the inner graph.
-        - Add support for the GPU? Probably just need an opt to remove transfer
         - Add support to pickle this Op.
         - Add support/test with random generator
         - Add optimization to removing unused inputs/outputs
@@ -285,7 +275,7 @@ class OpFromGraph(Op, HasInnerGraph):
         #
         # For now, this converts NullType or DisconnectedType into zeros_like.
         # other types are unmodified: overrider_var -> None
-        if isinstance(grad.type, (NullType, DisconnectedType)):
+        if isinstance(grad.type, NullType | DisconnectedType):
             if hasattr(inp, "zeros_like"):
                 return inp.zeros_like(), grad
             else:
@@ -309,12 +299,14 @@ class OpFromGraph(Op, HasInnerGraph):
         self,
         inputs: list[Variable],
         outputs: list[Variable],
+        *,
         inline: bool = False,
         lop_overrides: str = "default",
         grad_overrides: str = "default",
         rop_overrides: str = "default",
-        connection_pattern: Optional[list[list[bool]]] = None,
-        name: Optional[str] = None,
+        connection_pattern: list[list[bool]] | None = None,
+        strict: bool = False,
+        name: str | None = None,
         **kwargs,
     ):
         """
@@ -398,6 +390,10 @@ class OpFromGraph(Op, HasInnerGraph):
             must be equal to number of outputs.  connection_pattern If not
             ``None``, this will be used as the connection_pattern for this
             :class:`Op`.
+        strict: bool, default False
+            If true, it raises when any variables needed to compute the inner graph
+            are not provided as explici inputs. This can only happen for graphs with
+            shared variables.
         name
             A name for debugging purposes.
         kwargs
@@ -423,6 +419,12 @@ class OpFromGraph(Op, HasInnerGraph):
             inputs, outputs
         )
 
+        if strict and self.shared_inputs:
+            raise ValueError(
+                "All variables needed to compute inner-graph must be provided as inputs under strict=True. "
+                f"The inner-graph implicitly depends on the following shared variables {self.shared_inputs}"
+            )
+
         self.kwargs = kwargs
         self.input_types = [inp.type for inp in inputs]
         self.output_types = [out.type for out in outputs]
@@ -465,7 +467,7 @@ class OpFromGraph(Op, HasInnerGraph):
     def __str__(self):
         name = self.__class__.__name__ if self.name is None else self.name
         is_inline = self.is_inline
-        return "%(name)s{inline=%(is_inline)s}" % locals()
+        return "{name}{{inline={is_inline}}}".format(**locals())
 
     @config.change_flags(compute_test_value="off")
     def _recompute_lop_op(self):
@@ -533,7 +535,7 @@ class OpFromGraph(Op, HasInnerGraph):
             all_grads_l = list(all_grads_l)
             all_grads_ov_l = list(all_grads_ov_l)
         elif isinstance(lop_op, Variable):
-            if isinstance(lop_op.type, (DisconnectedType, NullType)):
+            if isinstance(lop_op.type, DisconnectedType | NullType):
                 all_grads_l = [inp.zeros_like() for inp in local_inputs]
                 all_grads_ov_l = [lop_op.type() for _ in range(inp_len)]
             else:
@@ -560,7 +562,7 @@ class OpFromGraph(Op, HasInnerGraph):
                     all_grads_l.append(gnext)
                     all_grads_ov_l.append(gnext_ov)
                 elif isinstance(fn_gov, Variable):
-                    if isinstance(fn_gov.type, (DisconnectedType, NullType)):
+                    if isinstance(fn_gov.type, DisconnectedType | NullType):
                         all_grads_l.append(inp.zeros_like())
                         all_grads_ov_l.append(fn_gov.type())
                     else:

{pytensor-2.18.6 → pytensor-2.20.0}/pytensor/compile/compiledir.py

@@ -2,6 +2,7 @@
 This module contains housekeeping functions for cleaning/purging the "compiledir".
 It is used by the "pytensor-cache" CLI tool, located in the /bin folder of the repository.
 """
+
 import logging
 import os
 import pickle
@@ -54,7 +55,7 @@ def cleanup():
                                     have_npy_abi_version = True
                                 elif obj.startswith("c_compiler_str="):
                                     have_c_compiler = True
-                            elif isinstance(obj, (Op, CType)) and hasattr(
+                            elif isinstance(obj, Op | CType) and hasattr(
                                 obj, "c_code_cache_version"
                             ):
                                 v = obj.c_code_cache_version()

{pytensor-2.18.6 → pytensor-2.20.0}/pytensor/compile/compilelock.py

@@ -2,10 +2,10 @@
 Locking mechanism to ensure no two compilations occur simultaneously
 in the same compilation directory (which can cause crashes).
 """
+
 import os
 import threading
 from contextlib import contextmanager
-from typing import Optional, Union
 
 import filelock
 
@@ -46,7 +46,9 @@ def force_unlock(lock_dir: os.PathLike):
 
 @contextmanager
 def lock_ctx(
-    lock_dir: Union[str, os.PathLike] = None, *, timeout: Optional[float] = None
+    lock_dir: str | os.PathLike | None = None,
+    *,
+    timeout: float | None = None,
 ):
     """Context manager that wraps around FileLock and SoftFileLock from filelock package.