Maintenance, scipy update, and automated scipy update script

.github/dependabot.yml

@@ -0,0 +1,16 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    target-branch: "main"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "06:00"
+  - package-ecosystem: "github-actions"
+    target-branch: "main"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "06:00"

.github/workflows/dependabot_helper.yml

@@ -0,0 +1,39 @@
+name: Dependabot helper
+on: pull_request
+
+permissions:
+  pull-requests: write
+  issues: write
+  contents: write
+
+jobs:
+  dependabot:
+    runs-on: ubuntu-latest
+    if: github.event.pull_request.user.login == 'dependabot[bot]' && github.repository == 'numba/numba-scipy'
+    steps:
+      - name: Dependabot metadata
+        id: metadata
+        uses: dependabot/fetch-metadata@v2
+        with:
+          github-token: "${{ secrets.GITHUB_TOKEN }}"
+
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ref: ${{ github.head_ref }}
+
+      - name: Scipy check
+        if: contains(steps.metadata.outputs.dependency-names, 'scipy')
+        shell: bash -l {0}
+        run: |
+          prev_version=${{ steps.metadata.outputs.previous-version }}
+          new_version=${{ steps.metadata.outputs.new-version }}
+          sed -i s/$prev_version/$new_version/g .github/workflows/test_and_deploy.yml buildscripts/conda_recipes/numba-scipy/meta.yaml
+          git config user.email "49699333+dependabot[bot]@users.noreply.github.com"
+          git config user.name "dependabot[bot]"
+          git add .github/workflows/test_and_deploy.yml buildscripts/conda_recipes/numba-scipy/meta.yaml
+          if [[ -n $(git status --porcelain) ]] ; then
+            git commit -m "Updated scipy in build scripts"
+            git push
+          fi

.github/workflows/deploy_release.yml

@@ -1,35 +1,38 @@
 name: Deploy Release
 
 on:
-  push:
-    tags:
-      - '*'
+  release:
+    types: [published]
+
+permissions:
+  contents: read
 
 jobs:
   deploy_pypi:
     runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Setup Miniconda
-        uses: conda-incubator/[email protected]
+      - uses: actions/setup-python@v5
         with:
-          auto-update-conda: true
-          auto-activate-base: false
-          activate-environment: test_env
+          python-version: |
+            3.9
+            3.10
+            3.11
+            3.12
+          cache: "pip"
       - name: Install dependencies
         shell: bash -l {0}
         run: |
-          conda install -c numba python=3.8 numba>=0.45 'scipy>=0.16,<1.4' wheel
-      - name: Build PyPI artifacts
-        shell: bash -l {0}
-        run: |
-          python setup.py sdist bdist_wheel
+          python -m pip install --upgrade pip
+          pip install hatch
+      - name: Build package
+        run: hatch build
       - name: Publish to PyPI
-        uses: pypa/[email protected]
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_SECRET }}
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test_and_deploy.yml

@@ -18,8 +18,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        scipy-version: [">=1.4,<1.11.0"]
-        numpy-version: ["<1.22.0", ">=1.22.0"]
+        scipy-version: [">=1.4,<=1.14.1"]
+        numpy-version: [">=1.22.0"]
     steps:
       - name: Install glibc-tools
         shell: bash -l {0}
@@ -40,12 +40,13 @@ jobs:
       - name: Install dependencies
         shell: bash -l {0}
         run: |
-          conda install -c numba conda-build python=${{ env.MAIN_PYVER }} numba>=0.45 'scipy${{ matrix.scipy-version }}' 'numpy${{ matrix.numpy-version }}' flake8 pytest pip
+          conda install -c numba conda-build python=${{ env.MAIN_PYVER }} numba>=0.45 'scipy${{ matrix.scipy-version }}' 'numpy${{ matrix.numpy-version }}' ruff pytest pip
           pip install --no-deps -e .
-      - name: Lint with flake8
+      - name: Lint
         shell: bash -l {0}
         run: |
-          flake8 numba_scipy
+          ruff check .
+          ruff format .
       - name: Pytest
         shell: bash -l {0}
         run: |
@@ -70,26 +71,10 @@ jobs:
     needs: build
     strategy:
       matrix:
-        scipy-version: [">=1.4,<1.11.0"]
-        pyver: [3.8, 3.9, "3.10", 3.11]
+        scipy-version: [">=1.4,<=1.14.1"]
+        pyver: [3.9, "3.10", 3.11, 3.12]
         runs-on: [macos-latest, ubuntu-latest, windows-latest]
-        numpy-version: ["<1.22.0", ">=1.22.0"]
-        exclude:
-          - pyver: 3.11
-            numpy-version: "<1.22.0"
-        include:
-          - pyver: 3.8
-            scipy-version: ">=0.16,<1.4"
-            numpy-version: "<1.22.0"
-            runs-on: macos-latest
-          - pyver: 3.8
-            scipy-version: ">=0.16,<1.4"
-            numpy-version: "<1.22.0"
-            runs-on: ubuntu-latest
-          - pyver: 3.8
-            scipy-version: ">=0.16,<1.4"
-            numpy-version: "<1.22.0"
-            runs-on: windows-latest
+        numpy-version: [">=1.22.0"]
 
     runs-on: ${{ matrix.runs-on }}
     steps:

.gitignore

@@ -23,3 +23,5 @@ htmlcov/
 .vscode/
 .ipynb_checkpoints/
 __pycache__/
+
+numba_scipy/_version.py

buildscripts/conda_recipes/numba-scipy/meta.yaml

@@ -18,16 +18,16 @@ requirements:
   host:
     - python
     - numba
-    - scipy<1.11.0
+    - scipy<=1.14.1
     - setuptools
   run:
     - python
     - numba
-    - scipy<1.11.0
+    - scipy<=1.14.1
 
 test:
   requires:
-    - scipy<1.11.0
+    - scipy<=1.14.1
     - pytest
     - setuptools
     - faulthandler             # [py27 and (not (armv6l or armv7l))]

buildscripts/incremental/setup_conda_environment.sh

@@ -23,10 +23,6 @@ PIP_INSTALL="pip install -q"
 source deactivate
 # Display root environment (for debugging)
 conda list
-# Clean up any left-over from a previous build
-# (note workaround for https://github.com/conda/conda/issues/2679:
-#  `conda env remove` issue)
-conda remove --all -q -y -n $CONDA_ENV
 
 # Create a base env
 conda create -n $CONDA_ENV -q -y python=$PYTHON numpy=$NUMPY scipy=$SCIPY pip
@@ -36,20 +32,7 @@ set +v
 source activate $CONDA_ENV
 set -v
 
-# 32bit linux needs the numba channel to get a conda package as the distro
-# channels stopped shipping for 32bit linux packages, this branching is
-# superfluous but sets up for adding later conditional package installation.
-if [[ $(uname) == Linux ]]; then
-    if [[ "$CONDA_SUBDIR" == "linux-32" || "$BITS32" == "yes" ]] ; then
-        $CONDA_INSTALL -c numba numba
-        # Work around https://github.com/pytest-dev/pytest/issues/3280
-        $CONDA_INSTALL pytest attrs==19.1.0
-    else
-        $CONDA_INSTALL numba pytest
-    fi
-elif  [[ $(uname) == Darwin ]]; then
-    $CONDA_INSTALL numba pytest
-fi
+$CONDA_INSTALL numba pytest
 
 # environment dump for debug
 echo "-------------------------------------------------------------------------"

docs/environment.yml

@@ -4,7 +4,7 @@ channels:
   - numba
 
 dependencies:
-  - python=3.7
+  - python=3.12
   - pip
   - setuptools
   - numba

docs/source/conf.py

@@ -17,8 +17,8 @@
     import numba_scipy
 except ImportError:
     # Numba is run from its source checkout
-    sys.path.insert(0, os.path.abspath('../..'))
-    import numba
+    sys.path.insert(0, os.path.abspath("../.."))
+    import numba  # noqa: F401
     import numba_scipy
 
 
@@ -35,33 +35,33 @@
 
 # -- Project information -----------------------------------------------------
 
-project = u'numba-scipy'
-copyright = u'2019, Anaconda, Inc.'
-author = u'Anaconda, Inc.'
+project = "numba-scipy"
+copyright = "2019, Anaconda, Inc."
+author = "Anaconda, Inc."
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-version = '.'.join(numba_scipy.__version__.split('.')[:2])
+version = ".".join(numba_scipy.__version__.split(".")[:2])
 # The full version, including alpha/beta/rc tags.
 release = numba_scipy.__version__
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.autodoc',
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autodoc",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['../_templates']
+templates_path = ["../_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -75,13 +75,13 @@
 # a list of builtin themes.
 #
 # pip install sphinx_bootstrap_theme
-html_theme = 'bootstrap'
+html_theme = "bootstrap"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
-  'bootswatch_theme': "paper",
+    "bootswatch_theme": "paper",
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -90,19 +90,19 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['../_static']
+html_static_path = ["../_static"]
 
 
 # -- Intersphinx -------------------------------------------------------------
 # Configuration for intersphinx: refer to the Python standard library
 # and the Numpy documentation.
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3', None),
-    'numpy': ('http://docs.scipy.org/doc/numpy', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
-    'numba': ('http://numba.pydata.org/numba-doc/latest', None),
-    'llvmlite': ('http://llvmlite.pydata.org/en/latest/', None),
-    }
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("http://docs.scipy.org/doc/numpy", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
+    "numba": ("https://numba.readthedocs.io/en/stable/index.html", None),
+    "llvmlite": ("http://llvmlite.pydata.org/en/latest/", None),
+}
 
 
 # numpydoc options
@@ -112,4 +112,4 @@
 
 
 def setup(app):
-    app.add_stylesheet("numba-scipy-docs.css")
+    app.add_css_file("numba-scipy-docs.css")

numba_scipy/__init__.py

@@ -1,11 +1,11 @@
-
 from . import _version
-__version__ = _version.get_versions()['version']
+
+__version__ = _version.version
 
 
 def _init_extension():
-    '''Register SciPy functions with Numba.
+    """Register SciPy functions with Numba.
 
     This entry_point is called by Numba when it initializes.
-    '''
+    """
     from . import special, sparse