Merge remote-tracking branch 'upstream/main'

Author: fonnesbeck

.github/workflows/pypi.yml

@@ -30,12 +30,13 @@ 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:
@@ -49,21 +50,29 @@ jobs:
           fetch-depth: 0
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.18.1
+        uses: pypa/cibuildwheel@v2.19.2
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: wheels-${{ matrix.platform }}
           path: ./wheelhouse/*.whl
 
   check_dist:
     name: Check dist
     needs: [make_sdist,build_wheels]
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          name: sdist
           path: dist
+
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
       - name: Check SDist
         run: |
           mkdir -p test-sdist
@@ -83,12 +92,18 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-    - uses: actions/download-artifact@v3
-      with:
-        name: artifact
-        path: dist
+      - uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
 
-    - uses: pypa/[email protected]
-      with:
-        user: __token__
-        password: ${{ secrets.pypi_password }}
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}

.github/workflows/test.yml

@@ -76,7 +76,9 @@ jobs:
         float32: [0, 1]
         install-numba: [0]
         install-jax: [0]
+        install-torch: [0]
         part:
+          - "--doctest-modules --ignore=pytensor/misc/check_duplicate_key.py pytensor --ignore=pytensor/link"
           - "tests --ignore=tests/tensor --ignore=tests/scan --ignore=tests/sparse"
           - "tests/scan"
           - "tests/sparse"
@@ -95,6 +97,10 @@ 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"
+            float32: 1
+          - part: "--doctest-modules --ignore=pytensor/misc/check_duplicate_key.py pytensor --ignore=pytensor/link"
+            fast-compile: 1
         include:
           - install-numba: 1
             python-version: "3.10"
@@ -116,6 +122,11 @@ jobs:
             fast-compile: 0
             float32: 0
             part: "tests/link/jax"
+          - install-torch: 1
+            python-version: "3.10"
+            fast-compile: 0
+            float32: 0
+            part: "tests/link/pytorch"
     steps:
       - uses: actions/checkout@v4
         with:
@@ -142,9 +153,13 @@ jobs:
       - name: Install dependencies
         shell: micromamba-shell {0}
         run: |
-          micromamba install --yes -q "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service graphviz cython pytest coverage pytest-cov pytest-benchmark pytest-mock sympy
+
+          micromamba install --yes -q "python~=${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
+          pip install pytest-sphinx
+          
           pip install -e ./
           micromamba list && pip freeze
           python -c 'import pytensor; print(pytensor.config.__str__(print_doc=False))'
@@ -153,6 +168,7 @@ jobs:
           PYTHON_VERSION: ${{ matrix.python-version }}
           INSTALL_NUMBA: ${{ matrix.install-numba }}
           INSTALL_JAX: ${{ matrix.install-jax }}
+          INSTALL_TORCH: ${{ matrix.install-torch}}
 
       - name: Run tests
         shell: micromamba-shell {0}
@@ -171,9 +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:
@@ -199,7 +215,7 @@ jobs:
       - name: Install dependencies
         shell: micromamba-shell {0}
         run: |
-          micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service cython pytest "numba>=0.57" jax jaxlib pytest-benchmark
+          micromamba install --yes -q -c conda-forge "python~=${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
           pip install -e ./
           micromamba list && pip freeze
           python -c 'import pytensor; print(pytensor.config.__str__(print_doc=False))'
@@ -257,14 +273,16 @@ 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
         with:
           directory: ./coverage/
           fail_ci_if_error: true
           token: ${{ secrets.CODECOV_TOKEN }}
+

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
           )$
       - id: check-merge-conflict
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.8
+    rev: v0.5.5
     hooks:
       - id: ruff
         args: ["--fix", "--output-format=full"]

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/conf.py

@@ -12,11 +12,12 @@
 # serve to show the default value.
 
 # If your extensions are in another directory, add it here. If the directory
-# is relative to the documentation root, use os.path.abspath to make it
+# is relative to the documentation root, use Path.absolute to make it
 # absolute, like shown here.
-# sys.path.append(os.path.abspath('some/directory'))
+# sys.path.append(str(Path("some/directory").absolute()))
 
 import os
+import inspect
 import sys
 import pytensor
 
@@ -32,8 +33,16 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.linkcode",
     "sphinx.ext.mathjax",
+    "sphinx_design",
+    "sphinx.ext.intersphinx"
 ]
 
+intersphinx_mapping = {
+    "jax": ("https://jax.readthedocs.io/en/latest", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "torch": ("https://pytorch.org/docs/stable", None),
+}
+
 needs_sphinx = "3"
 
 todo_include_todos = True
@@ -228,11 +237,9 @@ def find_source():
         obj = sys.modules[info["module"]]
         for part in info["fullname"].split("."):
             obj = getattr(obj, part)
-        import inspect
-        import os
 
-        fn = inspect.getsourcefile(obj)
-        fn = os.path.relpath(fn, start=os.path.dirname(pytensor.__file__))
+        fn = Path(inspect.getsourcefile(obj))
+        fn = fn.relative_to(Path(__file__).parent)
         source, lineno = inspect.getsourcelines(obj)
         return fn, lineno, lineno + len(source) - 1
 

doc/environment.yml

@@ -13,6 +13,7 @@ dependencies:
   - mock
   - pillow
   - pymc-sphinx-theme
+  - sphinx-design
   - pip
   - pip:
     - -e ..