Merge branch 'main' into scalarloop

Author: Ch0ronomato

.github/workflows/mypy.yml

@@ -15,7 +15,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: mamba-org/setup-micromamba@v1
         with:
-          micromamba-version: "latest" # any version from https://github.com/mamba-org/micromamba-releases
+          micromamba-version: "1.5.10-0" # until https://github.com/mamba-org/setup-micromamba/issues/225 is resolved
           environment-file: environment.yml
           init-shell: bash
           cache-environment: true

.github/workflows/pypi.yml

@@ -35,6 +35,18 @@ jobs:
           name: sdist
           path: dist/*.tar.gz
 
+  run_checks:
+    name: Build & inspect our package.
+    # Note: the resulting builds are not actually published.
+    # This is purely for additional testing and diagnostic purposes.
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: hynek/build-and-inspect-python-package@v2
+
   build_wheels:
     name: Build wheels for ${{ matrix.platform }}
     runs-on: ${{ matrix.platform }}
@@ -50,7 +62,7 @@ jobs:
           fetch-depth: 0
 
       - name: Build wheels
-        uses: pypa/[email protected].0
+        uses: pypa/[email protected].2
 
       - uses: actions/upload-artifact@v4
         with:
@@ -133,7 +145,7 @@ jobs:
           name: universal_wheel
           path: dist
 
-      - uses: pypa/gh-action-pypi-publish@v1.9.0
+      - uses: pypa/gh-action-pypi-publish@v1.10.3
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/rtd-link-preview.yml

@@ -0,0 +1,16 @@
+name: Read the Docs Pull Request Preview
+on:
+  pull_request_target:
+    types:
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: "pytensor"

.github/workflows/test.yml

@@ -78,7 +78,7 @@ jobs:
         install-jax: [0]
         install-torch: [0]
         part:
-          - "--doctest-modules --ignore=pytensor/misc/check_duplicate_key.py pytensor --ignore=pytensor/link"
+          - "--doctest-modules pytensor --ignore=pytensor/misc/check_duplicate_key.py --ignore=pytensor/link"
           - "tests --ignore=tests/tensor --ignore=tests/scan --ignore=tests/sparse"
           - "tests/scan"
           - "tests/sparse"
@@ -97,9 +97,9 @@ jobs:
             part: "tests/tensor/test_math.py"
           - fast-compile: 1
             float32: 1
-          - part: "--doctest-modules --ignore=pytensor/misc/check_duplicate_key.py pytensor --ignore=pytensor/link"
+          - part: "--doctest-modules pytensor --ignore=pytensor/misc/check_duplicate_key.py --ignore=pytensor/link"
             float32: 1
-          - part: "--doctest-modules --ignore=pytensor/misc/check_duplicate_key.py pytensor --ignore=pytensor/link"
+          - part: "--doctest-modules pytensor --ignore=pytensor/misc/check_duplicate_key.py --ignore=pytensor/link"
             fast-compile: 1
         include:
           - install-numba: 1
@@ -135,7 +135,7 @@ jobs:
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-name: pytensor-test
-          micromamba-version: "latest"
+          micromamba-version: "1.5.10-0" # until https://github.com/mamba-org/setup-micromamba/issues/225 is resolved
           init-shell: bash
           post-cleanup: "all"
           create-args: python=${{ matrix.python-version }}
@@ -157,7 +157,7 @@ jobs:
           micromamba install --yes -q "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service graphviz cython pytest coverage pytest-cov pytest-benchmark pytest-mock
           if [[ $INSTALL_NUMBA == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" "numba>=0.57"; fi
           if [[ $INSTALL_JAX == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" jax jaxlib numpyro && pip install tensorflow-probability; fi
-          if [[ $INSTALL_TORCH == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" pytorch pytorch-cuda=12.1 -c pytorch -c nvidia; fi
+          if [[ $INSTALL_TORCH == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" pytorch pytorch-cuda=12.1 "mkl<=2024.0" -c pytorch -c nvidia; fi
           pip install pytest-sphinx
           
           pip install -e ./
@@ -209,13 +209,13 @@ jobs:
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-name: pytensor-test
-          micromamba-version: "latest"
+          micromamba-version: "1.5.10-0" # until https://github.com/mamba-org/setup-micromamba/issues/225 is resolved
           init-shell: bash
           post-cleanup: "all"
       - name: Install dependencies
         shell: micromamba-shell {0}
         run: |
-          micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service cython pytest "numba>=0.57" jax jaxlib pytest-benchmark  pytorch pytorch-cuda=12.1 -c pytorch -c nvidia
+          micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service cython pytest "numba>=0.57" jax jaxlib pytest-benchmark
           pip install -e ./
           micromamba list && pip freeze
           python -c 'import pytensor; print(pytensor.config.__str__(print_doc=False))'

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ exclude: |
     )$
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: debug-statements
         exclude: |
@@ -27,7 +27,7 @@ repos:
     - id: sphinx-lint 
       args: ["."]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.5
+    rev: v0.6.9
     hooks:
       - id: ruff
         args: ["--fix", "--output-format=full"]

doc/library/graph/graph.rst

@@ -4,12 +4,5 @@
 :mod:`graph` -- Interface for the PyTensor graph
 ================================================
 
----------
-Reference
----------
-
 .. automodule:: pytensor.graph.basic
-   :platform: Unix, Windows
-   :synopsis: Interface for types of symbolic variables
    :members:
-.. moduleauthor:: LISA

doc/library/graph/index.rst

@@ -1,20 +1,20 @@
 
 .. _libdoc_graph:
 
-================================================
-:mod:`graph` -- Theano Internals [doc TODO]
-================================================
+========================================
+:mod:`graph` -- PyTensor Graph Internals
+========================================
 
 .. module:: graph
-   :platform: Unix, Windows
-   :synopsis: Theano Internals
+
 .. moduleauthor:: LISA
 
 .. toctree::
     :maxdepth: 1
 
     graph
     fgraph
+    replace
     features
     op
     type

doc/library/graph/op.rst

@@ -1,12 +1,8 @@
-
 .. _libdoc_graph_op:
 
-==============================================================
-:mod:`graph` -- Objects and functions for computational graphs
-==============================================================
+===========================================
+:mod:`op` -- Objects that define operations
+===========================================
 
 .. automodule:: pytensor.graph.op
-   :platform: Unix, Windows
-   :synopsis: Interface for types of symbolic variables
    :members:
-.. moduleauthor:: LISA

doc/library/graph/replace.rst

@@ -0,0 +1,8 @@
+.. _libdoc_graph_replace:
+
+==================================================
+:mod:`replace` -- High level graph transformations
+==================================================
+
+.. automodule:: pytensor.graph.replace
+   :members:

doc/library/tensor/functional.rst

@@ -0,0 +1,2 @@
+.. automodule:: pytensor.tensor.functional
+    :members: vectorize