Merge branch 'main' into universal_wheel

Author: twiecki

.github/workflows/pypi.yml

@@ -29,12 +29,13 @@ jobs:
       - name: Build SDist
         run: pipx run build --sdist
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: sdist
           path: dist/*.tar.gz
 
   build_wheels:
-    name: Build ${{ matrix.python-version }} wheels on ${{ matrix.platform }}
+    name: Build wheels for ${{ matrix.platform }}
     runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
@@ -50,8 +51,9 @@ jobs:
       - name: Build wheels
         uses: pypa/[email protected]
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: wheels-${{ matrix.platform }}
           path: ./wheelhouse/*.whl
 
   build_universal_wheel:
@@ -84,10 +86,17 @@ jobs:
     needs: [make_sdist,build_wheels]
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          pattern: wheels-*
           path: dist
+          merge-multiple: true
+
       - name: Check SDist
         run: |
           mkdir -p test-sdist
@@ -107,16 +116,22 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          name: sdist
           path: dist
 
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: universal_wheel
           path: dist
 
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
       - uses: pypa/[email protected]
         with:
           user: __token__

.github/workflows/test.yml

@@ -187,9 +187,9 @@ jobs:
           FLOAT32: ${{ matrix.float32 }}
 
       - name: Upload coverage file
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: coverage
+          name: coverage-${{ steps.matrix-id.outputs.id }}
           path: coverage/coverage-${{ steps.matrix-id.outputs.id }}.xml
 
   benchmarks:
@@ -273,10 +273,11 @@ jobs:
           python -m pip install -U coverage>=5.1 coveralls
 
       - name: Download coverage file
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: coverage
+          pattern: coverage-*
           path: coverage
+          merge-multiple: true
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
           )$
       - id: check-merge-conflict
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.1
+    rev: v0.5.6
     hooks:
       - id: ruff
         args: ["--fix", "--output-format=full"]

CONTRIBUTING.md

@@ -21,7 +21,7 @@ For issues a minimal working example (MWE) is strongly recommended when relevant
 (fixing a typo in the documentation does not require a MWE). For discussions,
 MWEs are generally required. All MWEs must be implemented using PyTensor. Please
 do not submit MWEs if they are not implemented in PyTensor. In certain cases,
-pseudocode may be acceptable, but an PyTensor implementation is always preferable.
+pseudocode may be acceptable, but a PyTensor implementation is always preferable.
 
 ## Quick links
 

MANIFEST.in

@@ -8,5 +8,4 @@ global-include *.h
 global-include *.hh
 global-include *.sh
 recursive-include doc *
-include versioneer.py
 include pytensor/_version.py

README.rst

@@ -133,7 +133,7 @@ A good place to start contributing is by looking through the issues
 
 
 .. |Project Name| replace:: PyTensor
-.. |Tests Status| image:: https://github.com/pymc-devs/pytensor/workflows/Tests/badge.svg
-  :target: https://github.com/pymc-devs/pytensor/actions?query=workflow%3ATests
+.. |Tests Status| image:: https://github.com/pymc-devs/pytensor/workflows/Tests/badge.svg?branch=main
+  :target: https://github.com/pymc-devs/pytensor/actions?query=workflow%3ATests+branch%3Amain
 .. |Coverage| image:: https://codecov.io/gh/pymc-devs/pytensor/branch/main/graph/badge.svg?token=WVwr8nZYmc
   :target: https://codecov.io/gh/pymc-devs/pytensor

doc/generate_dtype_tensor_table.py

@@ -31,7 +31,7 @@
         if len(shape[1]) < 6 or len(set(shape[1])) > 1:
             broadcastable_str = str(shape[1])
         else:
-            broadcastable_str = '(%s,) * %d' % (str(shape[1][0]), len(shape[1]))
+            broadcastable_str = f'({shape[1][0]},) * {len(shape[1])}'
         print('%s%-10s  %-10s  %-4s %-15s  %-20s' %(
                 letter[0], shape[0], letter[1], len(shape[1]), s, broadcastable_str
                 ))

doc/introduction.rst

@@ -157,9 +157,9 @@ to extend PyTensor, please feel free to ask.
    install
    tutorial/index
 
-.. _LISA:  https://mila.umontreal.ca/
+.. _LISA:  https://mila.quebec/en
 .. _Greek mathematician: http://en.wikipedia.org/wiki/Theano_(mathematician)
-.. _numpy: http://numpy.scipy.org/
+.. _numpy: https://numpy.org/
 .. _BLAS: http://en.wikipedia.org/wiki/Basic_Linear_Algebra_Subprograms
 
 .. _sympy: http://www.sympy.org/

doc/library/config.rst

@@ -103,14 +103,6 @@ import ``pytensor`` and print the config variable, as in:
 
     String value: either ``'cpu'``
 
-.. attribute:: force_device
-
-    Bool value: either ``True`` or ``False``
-
-    Default: ``False``
-
-    This flag's value cannot be modified during the program execution.
-
 .. attribute:: print_active_device
 
     Bool value: either ``True`` or ``False``
@@ -139,16 +131,6 @@ import ``pytensor`` and print the config variable, as in:
     equal to ``float64`` is created.
     This can be used to help find upcasts to ``float64`` in user code.
 
-.. attribute:: deterministic
-
-    String value: either ``'default'``, ``'more'``
-
-    Default: ``'default'``
-
-    If ``more``, sometimes PyTensor will select :class:`Op` implementations that
-    are more "deterministic", but slower.  See the ``dnn.conv.algo*``
-    flags for more cases.
-
 .. attribute:: allow_gc
 
     Bool value: either ``True`` or ``False``
@@ -373,7 +355,7 @@ import ``pytensor`` and print the config variable, as in:
 
     When ``True``, ignore the first call to an PyTensor function while profiling.
 
-.. attribute:: config.lib__amblibm
+.. attribute:: config.lib__amdlibm
 
     Bool value: either ``True`` or ``False``
 
@@ -412,16 +394,6 @@ import ``pytensor`` and print the config variable, as in:
     ignore it (i.e. ``'ignore'``).
     We suggest never using ``'ignore'`` except during testing.
 
-.. attribute:: assert_no_cpu_op
-
-    String value: ``'ignore'`` or ``'warn'`` or ``'raise'`` or ``'pdb'``
-
-    Default: ``'ignore'``
-
-    If there is a CPU :class:`Op` in the computational graph, depending on its value,
-    this flag can either raise a warning, an exception or drop into the frame
-    with ``pdb``.
-
 .. attribute:: on_shape_error
 
     String value: ``'warn'`` or ``'raise'``
@@ -797,18 +769,3 @@ import ``pytensor`` and print the config variable, as in:
     The verbosity level of the meta-rewriter: ``0`` for silent, ``1`` to only
     warn when PyTensor cannot meta-rewrite an :class:`Op`, ``2`` for full output (e.g.
     timings and the rewrites selected).
-
-
-.. attribute:: config.metaopt__optimizer_excluding
-
-    Default: ``""``
-
-    A list of rewrite tags that we don't want included in the meta-rewriter.
-    Multiple tags are separate by ``':'``.
-
-.. attribute:: config.metaopt__optimizer_including
-
-    Default: ``""``
-
-    A list of rewriter tags to be included during meta-rewriting.
-    Multiple tags are separate by ``':'``.

doc/links.rst

@@ -39,18 +39,18 @@ This is a sort of memo for developers and would-be developers.
 
 .. _git: http://git-scm.com/
 .. _pytest: http://docs.pytest.org/en/latest/
-.. _numpy: http://numpy.scipy.org/
+.. _numpy: https://numpy.org/
 .. _python: http://www.python.org
 .. _scipy: http://scipy.org/
 
 .. _autodiff: http://www.autodiff.org
-.. _boost.python: http://www.boost.org/doc/libs/1_38_0/libs/python/doc/index.html
+.. _boost.python: https://www.boost.org/doc/libs/1_85_0/libs/python/doc/html/index.html
 .. _cython: http://www.cython.org/
 .. _liboil: http://liboil.freedesktop.org/wiki/
 .. _llvm: http://llvm.org/
-.. _networkx: http://networkx.lanl.gov/
-.. _pypy: http://codespeak.net/pypy/dist/pypy/doc/
+.. _networkx: https://networkx.org/
+.. _pypy: https://doc.pypy.org/en/latest/
 .. _swig: http://www.swig.org/
-.. _unpython: http://code.google.com/p/unpython/
-.. _pycppad: http://www.seanet.com/~bradbell/pycppad/index.xml
-.. _shedskin: http://shed-skin.blogspot.com/
+.. _unpython: https://code.google.com/archive/p/unpython/
+.. _pycppad: https://github.com/Simple-Robotics/pycppad
+.. _shedskin: https://shedskin.github.io/shedskin/