Merge branch 'main' into torch_dot

Author: HangenYuu

.github/workflows/pypi.yml

@@ -49,7 +49,7 @@ jobs:
           fetch-depth: 0
 
       - name: Build wheels
-        uses: pypa/[email protected].1
+        uses: pypa/[email protected].2
 
       - uses: actions/upload-artifact@v3
         with:

.github/workflows/test.yml

@@ -78,6 +78,7 @@ jobs:
         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"
@@ -96,6 +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"
@@ -149,11 +154,12 @@ jobs:
         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))'

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
           )$
       - id: check-merge-conflict
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.10
+    rev: v0.5.1
     hooks:
       - id: ruff
         args: ["--fix", "--output-format=full"]

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 ..