ENH: stats: test marray support for hypothesis tests

.github/workflows/array_api.yml

@@ -74,6 +74,10 @@ jobs:
       run: |
         python -m pip install dask[array]
 
+    - name: Install MArray
+      run: |
+        python -m pip install marray
+
     - name:  Prepare compiler cache
       id:    prep-ccache
       shell: bash

.github/workflows/linux.yml

@@ -26,7 +26,7 @@ jobs:
     uses: ./.github/workflows/commit_message.yml
 
   test_meson:
-    name: mypy (py3.10) & dev deps (py3.13), fast, dev.py
+    name: mypy (py3.11) & dev deps (py3.13), fast, dev.py
     needs: get_commit_message
     # If using act to run CI locally the github object does not exist and
     # the usual skipping should not be enforced
@@ -36,7 +36,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ['3.10', '3.13-dev'] # this run will use python dev versions when available
+        python-version: ['3.11', '3.13-dev'] # this run will use python dev versions when available
         maintenance-branch:
           - ${{ contains(github.ref, 'maintenance/') || contains(github.base_ref, 'maintenance/') }}
         exclude:
@@ -63,7 +63,7 @@ jobs:
         sudo apt-get install -y libopenblas-dev libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libsuitesparse-dev ccache libmpc-dev
 
     - name: Install Python packages
-      if: matrix.python-version == '3.10'
+      if: matrix.python-version == '3.11'
       run: |
         python -m pip install numpy cython pytest pytest-xdist pytest-timeout pybind11 mpmath gmpy2 pythran ninja meson click rich-click doit pydevtool pooch hypothesis
 
@@ -95,7 +95,7 @@ jobs:
         path: ${{ steps.prep-ccache.outputs.dir }}
         # Restores ccache from either a previous build on this branch or on main
         key:  ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-${{ steps.prep-ccache.outputs.timestamp }}
-        # This evaluates to `Linux Tests-3.10-ccache-linux-` which is not unique. As the CI matrix is expanded, this will
+        # This evaluates to `Linux Tests-3.11-ccache-linux-` which is not unique. As the CI matrix is expanded, this will
         # need to be updated to be unique so that the cache is not restored from a different job altogether.
         restore-keys: |
           ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-
@@ -128,7 +128,7 @@ jobs:
       run: ninja -C build -t missingdeps
 
     - name: Mypy
-      if: matrix.python-version == '3.10'
+      if: matrix.python-version == '3.11'
       run: |
         # Packages that are only needed for their annotations
         python -m pip install mypy==1.10.0 types-psutil typing_extensions
@@ -148,7 +148,7 @@ jobs:
     if: >
       needs.get_commit_message.outputs.message == 1
       && (github.repository == 'scipy/scipy' || github.repository == '')
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
     - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
       with:
@@ -202,12 +202,12 @@ jobs:
   #################################################################################
   python_debug:
     # also uses the vcs->sdist->wheel route.
-    name: Python-debug & ATLAS & sdist+wheel, fast, py3.10/npMin, pip+pytest
+    name: Python-debug & ATLAS & sdist+wheel, fast, py3.12/npMin, pip+pytest
     needs: get_commit_message
     if: >
       needs.get_commit_message.outputs.message == 1
       && (github.repository == 'scipy/scipy' || github.repository == '')
-    runs-on: ubuntu-22.04  # provides python3.10-dbg
+    runs-on: ubuntu-24.04  # provides python3.12-dbg
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
@@ -232,7 +232,7 @@ jobs:
   #################################################################################
   gcc9:
     # Purpose is to examine builds with oldest-supported gcc and test with pydata/sparse.
-    name: Oldest GCC & pydata/sparse, fast, py3.10/npMin, pip+pytest
+    name: Oldest GCC & pydata/sparse, fast, py3.11/npMin, pip+pytest
     needs: get_commit_message
     if: >
       needs.get_commit_message.outputs.message == 1
@@ -246,7 +246,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Setup system dependencies
         run: |
@@ -271,7 +271,7 @@ jobs:
       - name: Install test dependencies
         run: |
           # Downgrade numpy to oldest supported version
-          pip install gmpy2 threadpoolctl mpmath pooch pytest pytest-xdist==2.5.0 pytest-timeout hypothesis sparse "numpy==1.23.5"
+          pip install gmpy2 threadpoolctl mpmath pooch pytest pytest-xdist==2.5.0 pytest-timeout hypothesis sparse "numpy==1.25.2"
 
       - name: Run tests
         run: |
@@ -284,17 +284,17 @@ jobs:
   #################################################################################
   prerelease_deps_coverage_64bit_blas:
     # TODO: re-enable ILP64 build.
-    name: Prerelease deps & coverage report, full, py3.10/npMin & py3.11/npPre, dev.py
+    name: Prerelease deps & coverage report, full, py3.11/npMin & py3.11/npPre, dev.py
     needs: get_commit_message
     if: >
       needs.get_commit_message.outputs.message == 1
       && (github.repository == 'scipy/scipy' || github.repository == '')
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # Both use numpy 2.x-dev at build time; 3.10 job then downgrades to
+        # Both use numpy 2.x-dev at build time; 3.11 job then downgrades to
         # lowest supported NumPy version in order to test ABI compatibility.
-        python-version: ['3.10', '3.11']
+        python-version: ['3.11', '3.12']
 
     steps:
     - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
@@ -321,10 +321,7 @@ jobs:
     - name: Install Python packages
       run: |
         python -m pip install cython pythran ninja meson-python pybind11 click rich_click pydevtool
-        python -m pip install --pre --upgrade pytest pytest-cov pytest-xdist gmpy2 threadpoolctl pooch hypothesis matplotlib
-        # Move mpmath back into `install --pre` above once mpmath 1.4.0 with
-        # the fix is out (xref gh-22395)
-        python -m pip install mpmath
+        python -m pip install --pre --upgrade pytest pytest-cov pytest-xdist mpmath gmpy2 threadpoolctl pooch hypothesis matplotlib
         python -m pip install -r requirements/openblas.txt
         # Install numpy last, to ensure we get nightly (avoid possible <2.0 constraints).
         python -m pip install --pre --upgrade --timeout=60 -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
@@ -357,9 +354,9 @@ jobs:
       run: ccache -s
 
     - name: Downgrade NumPy from 2.0-dev to lowest supported
-      if: matrix.python-version == '3.10'
+      if: matrix.python-version == '3.11'
       run: |
-        python -m pip install "numpy==1.23.5"
+        python -m pip install "numpy==1.25.2"
 
     - name: Test SciPy
       run: |
@@ -368,7 +365,7 @@ jobs:
 
   #################################################################################
   linux_32bit:
-    name: 32-bit, fast, py3.10/npMin, dev.py
+    name: 32-bit, fast, py3.11/npMin, dev.py
     needs: get_commit_message
     if: >
       needs.get_commit_message.outputs.message == 1
@@ -388,7 +385,7 @@ jobs:
         docker pull quay.io/pypa/manylinux2014_i686
         docker run -v $(pwd):/scipy --platform=linux/i386 quay.io/pypa/manylinux2014_i686 /bin/bash -c "cd /scipy && \
         uname -a && \
-        python3.10 -m venv test && \
+        python3.11 -m venv test && \
         source test/bin/activate && \
         python -m pip install doit click rich_click pydevtool meson ninja && \
         python -m pip install -r requirements/openblas.txt && \
@@ -401,7 +398,7 @@ jobs:
         runtime_library_dirs = \$(python -c 'import scipy_openblas32; print(scipy_openblas32.get_lib_dir())')
         symbol_prefix = scipy_
         EOL
-        python -m pip install numpy==1.23.5 cython pybind11 pytest pytest-timeout pytest-xdist pytest-env 'Pillow<10.0.0' mpmath pythran pooch meson hypothesis && \
+        python -m pip install numpy==1.25.2 cython pybind11 pytest pytest-timeout pytest-xdist pytest-env 'Pillow<10.0.0' mpmath pythran pooch meson hypothesis && \
         python -c 'import numpy as np; np.show_config()' && \
         python dev.py build --with-scipy-openblas && \
         python dev.py --no-build test"
@@ -411,12 +408,12 @@ jobs:
     # Purpose is to build for a non-default Python interpreter in a Linux distro
     # For such a build config, `python`/`python3` executables may not have
     # build dependencies like Cython or NumPy installed.
-    name: non-default Python interpreter, fast, py3.10/npMin, pip+pytest
+    name: non-default Python interpreter, fast, py3.11/npMin, pip+pytest
     needs: get_commit_message
     if: >
       needs.get_commit_message.outputs.message == 1
       && (github.repository == 'scipy/scipy' || github.repository == '')
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
@@ -425,8 +422,10 @@ jobs:
       - name: Setup system dependencies
         run: |
           sudo apt-get -y update
-          # `python3-dev` yields Python 3.10 on Ubuntu 22.04
-          sudo apt install -y python3-dev python3.11-dev ninja-build pkg-config libatlas-base-dev liblapack-dev
+          sudo apt install software-properties-common
+          sudo add-apt-repository ppa:deadsnakes/ppa
+          sudo apt update -y
+          sudo apt install -y python3.11-dev ninja-build pkg-config libatlas-base-dev liblapack-dev
 
       - name: Setup Python build deps
         run: |
@@ -440,7 +439,7 @@ jobs:
       - name: Install test dependencies
         run: |
           python3.11 -m pip install pytest hypothesis
-          python3.10 -m pip install meson  # ensure compile test work with this
+          python3.12 -m pip install meson  # ensure compile test work with this
 
       - name: Run tests
         run: |

.github/workflows/macos.yml

@@ -68,7 +68,7 @@ jobs:
       with:
         path: ${{ steps.prep-ccache.outputs.dir }}
         key:  ${{ github.workflow }}-${{ matrix.python-version }}-ccache-macos-${{ steps.prep-ccache.outputs.timestamp }}
-        # This evaluates to `macOS Tests-3.10-ccache-macos-` which is not
+        # This evaluates to `macOS Tests-3.11-ccache-macos-` which is not
         # unique. As the CI matrix is expanded, this will need to be updated to
         # be unique so that the cache is not restored from a different job altogether.
         restore-keys: |

.github/workflows/musllinux.yml

@@ -24,7 +24,7 @@ jobs:
     uses: ./.github/workflows/commit_message.yml
 
   musllinux_x86_64:
-    name: musl Ubuntu-latest, fast, py3.10/npAny, dev.py
+    name: musl Ubuntu-latest, fast, py3.11/npAny, dev.py
     needs: get_commit_message
     runs-on: ubuntu-latest
     # If using act to run CI locally the github object does not exist and
@@ -57,7 +57,7 @@ jobs:
             git -c user.email="you@example.com" merge --no-commit my_ref_name
         fi
 
-        ln -s /usr/local/bin/python3.10 /usr/local/bin/python
+        ln -s /usr/local/bin/python3.11 /usr/local/bin/python
         git submodule update --init
 
 

.github/workflows/wheels.yml

@@ -88,7 +88,7 @@ jobs:
         - [macos-14, macosx, arm64, openblas, "12.3"]
         - [macos-14, macosx, arm64, accelerate, "14.0"]
         - [windows-2019, win, AMD64, "", ""]
-        python: [["cp310", "3.10"], ["cp311", "3.11"], ["cp312", "3.12"], ["cp313", "3.13"], ["cp313t", "3.13"]]
+        python: [["cp311", "3.11"], ["cp312", "3.12"], ["cp313", "3.13"], ["cp313t", "3.13"]]
         # python[0] is used to specify the python versions made by cibuildwheel
 
     env:
@@ -243,7 +243,7 @@ jobs:
           # Note that this step is *after* specific pythons have been used to
           # build and test the wheel
           auto-update-conda: true
-          python-version: "3.10"
+          python-version: "3.11"
           miniforge-version: latest
           conda-remove-defaults: "true"
 

.github/workflows/windows.yml

@@ -65,7 +65,7 @@ jobs:
 
   #############################################################################
   full_dev_py_min_numpy_fail_slow:
-    name: fail slow, full, py3.10/npMin, dev.py
+    name: fail slow, full, py3.11/npMin, dev.py
     needs: get_commit_message
     if: >
       needs.get_commit_message.outputs.message == 1
@@ -79,7 +79,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
-          python-version: '3.10'
+          python-version: '3.11'
           cache: 'pip'
           cache-dependency-path: 'environment.yml'
 
@@ -90,9 +90,8 @@ jobs:
 
       - name: pip-packages
         run: |
-          # 1.23.5 is currently the oldest numpy usable on cp3.10 according
-          # to pyproject.toml
-          python -m pip install numpy==1.23.5 cython pybind11 pythran meson-python meson ninja pytest pytest-xdist pytest-timeout pytest-fail-slow pooch rich_click click doit pydevtool hypothesis
+          # 1.25.2 is currently our oldest supported NumPy version
+          python -m pip install numpy==1.25.2 cython pybind11 pythran meson-python meson ninja pytest pytest-xdist pytest-timeout pytest-fail-slow pooch rich_click click doit pydevtool hypothesis
           python -m pip install -r requirements/openblas.txt
 
       - name: Build

benchmarks/benchmarks/sparse_csgraph_yen.py

@@ -0,0 +1,38 @@
+"""benchmarks for the scipy.sparse.csgraph module"""
+import numpy as np
+import scipy.sparse
+
+from .common import Benchmark, safe_import
+
+with safe_import():
+    from scipy.sparse.csgraph import yen
+
+
+class Yen(Benchmark):
+    params = [
+        [30, 300, 3000],
+        [10, 100, 300],
+    ]
+    param_names = ['n', 'K']
+
+    def setup(self, n, K):
+        # make a random connectivity matrix
+        data = scipy.sparse.rand(
+            n, n, density=0.4, format='lil', random_state=42, dtype=np.bool_
+        )
+        data.setdiag(np.zeros(n, dtype=np.bool_))
+        self.data = data
+        self.source = np.random.randint(n)
+        sink = np.random.randint(n)
+        while self.source == sink:
+            sink = np.random.randint(n)
+        self.sink = sink
+
+    def time_yen(self, n, K):
+        yen(
+            csgraph=self.data,
+            source=self.source,
+            sink=self.sink,
+            K=K,
+            directed=False,
+        )

dev.py

@@ -310,7 +310,7 @@ def __init__(self, args=None):
             self.installed = self.build.parent / (self.build.stem + "-install")
 
         # relative path for site-package with py version
-        # i.e. 'lib/python3.10/site-packages'
+        # i.e. 'lib/python3.11/site-packages'
         self.site = self.get_site_packages()
 
     def add_sys_path(self):
@@ -1449,7 +1449,7 @@ class ShowDirs(Python):
 
     PYTHONPATH sets the default search path for module files for the
     interpreter. Here, it includes the path to the local SciPy build
-    (typically `.../build-install/lib/python3.10/site-packages`).
+    (typically `.../build-install/lib/python3.11/site-packages`).
 
     Use the global option `-n` to skip the building step, e.g.:
     `python dev.py -n show_PYTHONPATH`
@@ -1544,8 +1544,7 @@ def cpu_count(only_physical_cores=False):
     or the LOKY_MAX_CPU_COUNT environment variable. If the number of physical
     cores is not found, return the number of logical cores.
 
-    Note that on Windows, the returned number of CPUs cannot exceed 61 (or 60 for
-    Python < 3.10), see:
+    Note that on Windows, the returned number of CPUs cannot exceed 61, see:
     https://bugs.python.org/issue26903.
 
     It is also always larger or equal to 1.