Make scan to be a cython extension

.github/workflows/nightly.yml

@@ -9,10 +9,10 @@ jobs:
     if: github.repository == 'pymc-devs/pytensor'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         with:
           python-version: "3.9"
       - name: Install dependencies

.github/workflows/pypi.yml

@@ -17,28 +17,47 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  # The job to build pypi wheels users can installed precompiled for them.
+  # At the moment only linux wheels are build, Windows and MacOS will compile on installation
+  # Before prebuilds all users had to compile code anyway.
   build:
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         with:
-          python-version: "3.8"
+          python-version: ${{ matrix.python-version }}
       - name: Build the sdist and the wheel
         run: |
-          pip install wheel
-          python setup.py sdist bdist_wheel
+          pip install build
+          python -m build
       - name: Check the sdist installs and imports
         run: |
           mkdir -p test-sdist
           cd test-sdist
           python -m venv venv-sdist
           venv-sdist/bin/python -m pip install ../dist/pytensor-*.tar.gz
+          # check import
           venv-sdist/bin/python -c "import pytensor;print(pytensor.__version__)"
-      - uses: actions/upload-artifact@v2
+          # check import cython module
+          venv-sdist/bin/python -c 'from pytensor.scan import scan_perform; print(scan_perform.get_version())'
+      - name: Check the bdist installs and imports
+        run: |
+          mkdir -p test-bdist
+          cd test-bdist
+          python -m venv venv-bdist
+          venv-bdist/bin/python -m pip install ../dist/pytensor-*.whl
+          # check import
+          venv-bdist/bin/python -c "import pytensor;print(pytensor.__version__)"
+          # check import cython module
+          venv-bdist/bin/python -c 'from pytensor.scan import scan_perform; print(scan_perform.get_version())'
+      - uses: actions/upload-artifact@v3
         with:
           name: artifact
           path: dist/*
@@ -49,7 +68,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist

.github/workflows/test.yml

@@ -23,7 +23,7 @@ jobs:
     outputs:
       changes: ${{ steps.changes.outputs.src }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - uses: dorny/paths-filter@v2
@@ -52,7 +52,7 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ needs.changes.outputs.changes == 'true' }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - uses: actions/setup-python@v2
       with:
         python-version: '3.9'
@@ -90,7 +90,7 @@ jobs:
             install-numba: 1
             part: "tests --ignore=tests/tensor/nnet --ignore=tests/tensor/signal"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
@@ -110,7 +110,7 @@ jobs:
           echo $MATRIX_CONTEXT
           export MATRIX_ID=`echo $MATRIX_CONTEXT | md5sum | cut -c 1-32`
           echo $MATRIX_ID
-          echo "::set-output name=id::$MATRIX_ID"
+          echo "id=$MATRIX_ID" >> $GITHUB_OUTPUT
 
       - name: Install dependencies
         shell: bash -l {0}
@@ -143,7 +143,7 @@ jobs:
           FLOAT32: ${{ matrix.float32 }}
 
       - name: Upload coverage file
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: coverage
           path: coverage/coverage-${{ steps.matrix-id.outputs.id }}.xml
@@ -164,7 +164,7 @@ jobs:
     needs: [changes, all-checks]
     if: ${{ needs.changes.outputs.changes == 'true' && needs.all-checks.result == 'success' }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
         uses: actions/setup-python@v1

.gitignore

@@ -4,6 +4,7 @@ __pycache__
 .coverage
 *.linkinfo
 *.o
+*.c
 *.orig
 *.pyc
 *.pyo

pyproject.toml

@@ -0,0 +1,208 @@
+[build-system]
+requires = [
+  "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 = ">=3.7"
+authors = [
+    {name = "pymc-devs", email = "[email protected]"}
+]
+description = "Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs."
+readme = "DESCRIPTION.rst"
+license = {file = "LICENCE.txt"}
+classifiers = [
+    "Development Status :: 6 - Mature",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python",
+    "Topic :: Software Development :: Code Generators",
+    "Topic :: Software Development :: Compilers",
+    "Topic :: Scientific/Engineering :: Mathematics",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+]
+
+keywords = [
+    "pytensor",
+    "math",
+    "numerical",
+    "symbolic",
+    "blas",
+    "numpy",
+    "autodiff",
+    "differentiation",
+]
+dependencies = [
+    "setuptools>=48.0.0",
+    "scipy>=0.14",
+    "numpy>=1.17.0",
+    "filelock",
+    "etuples",
+    "logical-unification",
+    "miniKanren",
+    "cons",
+    "typing_extensions",
+]
+
+[project.urls]
+homepage = "https://github.com/pymc-devs/pytensor"
+repository = "https://github.com/pymc-devs/pytensor"
+documentation = "https://pytensor.readthedocs.io/en/latest/"
+
+
+[project.scripts]
+pytensor-cache = "bin.pytensor_cache:main"
+
+[project.optional-dependencies]
+complete = [
+    "pytensor[jax]",
+    "pytensor[numba]",
+]
+development = [
+    "pytensor[complete]",
+    "pytensor[tests]",
+    "pytensor[rtd]"
+]
+tests = [
+    "pytest",
+    "pre-commit",
+    "pytest-cov>=2.6.1",
+    "coverage>=5.1",
+]
+rtd = [
+    "sphinx>=1.3.0",
+    "sphinx_rtd_theme",
+    "pygments",
+    "pydot",
+    "pydot2",
+    "pydot-ng",
+]
+jax = [
+    "jax",
+    "jaxlib",
+]
+numba = [
+    "numba>=0.55",
+    "numba-scipy>=0.3.0"
+]
+
+[tool.setuptools.packages.find]
+exclude = [
+    "tests",
+    "tests.*"
+]
+
+[tool.setuptools.package-data]
+"*" = [
+    "*.txt",
+    "*.rst",
+    "*.cu",
+    "*.cuh",
+    "*.c",
+    "*.sh",
+    "*.pkl",
+    "*.h",
+    "*.cpp",
+    "ChangeLog",
+    "c_code/*",
+]
+pytensor = [
+    "py.typed"
+]
+"pytensor.misc" = [
+    "*.sh"
+]
+"pytensor.d3viz" = [
+    "html/*",
+    "css/*",
+    "js/*",
+]
+
+[tool.coverage.run]
+omit = [
+    "pytensor/_version.py",
+    "tests/*",
+    "pytensor/assert_op.py",
+    "pytensor/graph/opt.py",
+    "pytensor/graph/opt_utils.py",
+    "pytensor/graph/optdb.py",
+    "pytensor/graph/kanren.py",
+    "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:",
+]
+show_missing = true
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440"
+versionfile_source = "pytensor/_version.py"
+versionfile_build = "pytensor/_version.py"
+tag_prefix = "rel-"
+
+[tool.pytest]
+addopts = "--durations=50"
+testpaths = "tests/"
+
+[tool.pylint]
+max-line-length = 88
+
+[tool.pylint.messages_control]
+disable = ["C0330", "C0326"]
+
+[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.mypy]
+ignore_missing_imports = true
+no_implicit_optional = true
+check_untyped_defs = false
+strict_equality = true
+warn_redundant_casts = true
+warn_unused_configs = true
+warn_unused_ignores = true
+warn_return_any = true
+warn_no_return = false
+warn_unreachable = true
+show_error_codes = true
+allow_redefinition = false
+files = ["pytensor", "tests"]
+plugins = ["numpy.typing.mypy_plugin"]

pytensor/__init__.py

@@ -29,6 +29,8 @@
 from functools import singledispatch
 from typing import Any, NoReturn, Optional
 
+from pytensor.version import version as __version__
+
 
 pytensor_logger = logging.getLogger("pytensor")
 logging_default_handler = logging.StreamHandler()
@@ -49,10 +51,6 @@ def disable_log_handler(logger=pytensor_logger, handler=logging_default_handler)
         logger.removeHandler(handler)
 
 
-# Version information.
-from pytensor.version import version as __version__
-
-
 # Raise a meaningful warning/error if the pytensor directory is in the Python
 # path.
 rpath = os.path.realpath(__path__[0])