Merge remote-tracking branch 'upstream/main' into lmoment

Author: mdhaber

.github/workflows/linux_intel_oneAPI.yml

@@ -55,7 +55,7 @@ jobs:
           channel-priority: true
           activate-environment: scipy-dev
           use-only-tar-bz2: false
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge3
           miniforge-version: latest
           use-mamba: true
 

.github/workflows/macos.yml

@@ -82,7 +82,7 @@ jobs:
         channel-priority: true
         activate-environment: scipy-dev
         use-only-tar-bz2: false
-        miniforge-variant: Mambaforge
+        miniforge-variant: Miniforge3
         miniforge-version: latest
         use-mamba: true
 

.github/workflows/wheels.yml

@@ -238,7 +238,7 @@ jobs:
           # build and test the wheel
           auto-update-conda: true
           python-version: "3.10"
-          miniconda-version: "latest"
+          miniforge-version: latest
 
       - name: Upload wheels
         if: success()

benchmarks/benchmarks/sparse.py

@@ -206,14 +206,17 @@ def time_block_diag(self, num_matrices):
 
 class BlockDiagSparseConstruction(Benchmark):
     param_names = ['num_matrices']
-    params = [100, 500, 1000, 1500, 2000]
+    params = [1000, 5000, 10000, 15000, 20000]
 
     def setup(self, num_matrices):
         self.matrices = []
         for i in range(num_matrices):
             rows = np.random.randint(1, 20)
             columns = np.random.randint(1, 20)
-            mat = np.random.randint(0, 10, (rows, columns))
+            density = 2e-3
+            nnz_per_row = int(density*columns)
+
+            mat = random_sparse(rows, columns, nnz_per_row)
             self.matrices.append(mat)
 
     def time_block_diag(self, num_matrices):

ci/cirrus_wheels.yml

@@ -24,19 +24,17 @@ cirrus_wheels_linux_aarch64_task:
     # single task takes longer than 60 mins (the default time limit for a
     # cirrus-ci task).
     - env:
-        CIBW_BUILD: cp310-manylinux*
+        CIBW_BUILD: cp313-manylinux* cp310-manylinux*
     - env:
         CIBW_BUILD: cp311-manylinux* cp312-manylinux*
   env:
     CIBW_PRERELEASE_PYTHONS: True
-    # TODO remove the CIBW_BEFORE_BUILD_LINUX line once there are numpy2.0 wheels available on PyPI.
-    # Also remove/comment out PIP_NO_BUILD_ISOLATION, PIP_EXTRA_INDEX_URL flags.
-    CIBW_BEFORE_BUILD_LINUX: "pip install numpy>=2.0.0.dev0 meson-python cython pythran pybind11 ninja;bash {project}/tools/wheels/cibw_before_build_linux.sh {project}"
-    CIBW_ENVIRONMENT: >
-      PIP_PRE=1
-      PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
-      PIP_NO_BUILD_ISOLATION=false
-      PKG_CONFIG_PATH=/project
+    # The following settings are useful when targetting an unreleased Python version.
+    #CIBW_BEFORE_BUILD_LINUX: "pip install numpy>=2.0.0.dev0 meson-python cython pythran pybind11 ninja;bash {project}/tools/wheels/cibw_before_build_linux.sh {project}"
+    #CIBW_ENVIRONMENT: >
+    #  PIP_PRE=1
+    #  PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+    #  PIP_NO_BUILD_ISOLATION=false
 
   build_script: |
     apt install -y python3-venv python-is-python3
@@ -88,14 +86,14 @@ cirrus_wheels_upload_task:
         apt-get update
         apt-get install -y curl wget
 
-        # install miniconda in the home directory. For some reason HOME isn't set by Cirrus
+        # install miniforge in the home directory. For some reason HOME isn't set by Cirrus
         export HOME=$PWD
         
-        # install miniconda for uploading to anaconda
-        wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
-        bash miniconda.sh -b -p $HOME/miniconda3
-        $HOME/miniconda3/bin/conda init bash
-        source $HOME/miniconda3/bin/activate
+        # install miniforge for uploading to anaconda
+        wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+        bash Miniforge3.sh -b -p "${HOME}/miniforge"
+        $HOME/miniforge/bin/conda init bash
+        source $HOME/miniforge/bin/activate
         conda install -y anaconda-client
         
         # The name of the zip file is derived from the `wheels_artifact` line.

doc/Makefile

@@ -53,8 +53,7 @@ clean:
 UPLOAD_DIR=/srv/docs_scipy_org/doc/scipy-$(RELEASE)
 
 SCIPYVER:=$(shell $(PYTHON) -c "import scipy; print(scipy.version.git_revision[:10])" 2>/dev/null)
-GITVER ?= $(shell cd ../tools; $(PYTHON) -c "from version_utils import git_version; \
-				print(git_version('..')[0][:10])")
+GITVER ?= $(shell (cd ..; set -o pipefail && git rev-parse HEAD 2>/dev/null | cut -c1-7) || echo Unknown)
 
 version-check:
 ifeq "$(GITVER)" "Unknown"

doc/source/_static/version_switcher.json

@@ -5,9 +5,14 @@
         "url": "https://scipy.github.io/devdocs/"
     },
     {
-        "name": "1.14.0 (stable)",
-        "version":"1.14.0",
+        "name": "1.14.1 (stable)",
+        "version":"1.14.1",
         "preferred": true,
+        "url": "https://docs.scipy.org/doc/scipy-1.14.1/"
+    },
+    {
+        "name": "1.14.0",
+        "version":"1.14.0",
         "url": "https://docs.scipy.org/doc/scipy-1.14.0/"
     },
     {

doc/source/building/index.rst

@@ -230,7 +230,7 @@ Otherwise, conda is recommended.
 .. note::
 
     If you don't have a conda installation yet, we recommend using
-    Mambaforge_; any conda flavor will work though.
+    Miniforge_; any conda flavor will work though.
 
 Building from source to use SciPy
 `````````````````````````````````
@@ -442,5 +442,5 @@ Background information
    distutils_equivalents
 
 
-.. _Mambaforge: https://github.com/conda-forge/miniforge#mambaforge
+.. _Miniforge: https://github.com/conda-forge/miniforge#miniforge
 .. _meson-python: https://mesonbuild.com/meson-python/

doc/source/dev/contributor/debugging_linalg_issues.rst

@@ -46,10 +46,10 @@ and LAPACK. E.g.::
     found:  True
     version:  0.3.23
     detection method:  pkgconfig
-    include directory:  /home/user/mambaforge/envs/scipy-dev/include
-    lib directory:  /home/user/mambaforge/envs/scipy-dev/lib
+    include directory:  /home/user/miniforge/envs/scipy-dev/include
+    lib directory:  /home/user/miniforge/envs/scipy-dev/lib
     openblas configuration:  USE_64BITINT=0 DYNAMIC_ARCH=1 DYNAMIC_OLDER= NO_CBLAS= NO_LAPACK=0 NO_LAPACKE= NO_AFFINITY=1 USE_OPENMP=0 PRESCOTT MAX_THREADS=128
-    pc file directory:  /home/user/mambaforge/envs/scipy-dev/lib/pkgconfig
+    pc file directory:  /home/user/miniforge/envs/scipy-dev/lib/pkgconfig
 
 This method will be correct for SciPy wheels and for local dev builds. It *may*
 be correct for other installs, however keep in mind that distros like
@@ -68,7 +68,7 @@ on plain Netlib BLAS, see
         "user_api": "blas",
         "internal_api": "openblas",
         "prefix": "libopenblas",
-        "filepath": "/home/user/mambaforge/envs/dev/lib/libopenblasp-r0.3.21.so",
+        "filepath": "/home/user/miniforge/envs/dev/lib/libopenblasp-r0.3.21.so",
         "version": "0.3.21",
         "threading_layer": "pthreads",
         "architecture": "SkylakeX",
@@ -89,7 +89,7 @@ Other ways of introspecting that can be helpful in local dev environments includ
 
        $ ldd build/scipy/linalg/_fblas.cpython-*.so
        ...
-       libopenblas.so.0 => /home/user/mambaforge/envs/scipy-dev/lib/libopenblas.so.0 (0x0000780d6d000000)
+       libopenblas.so.0 => /home/user/miniforge/envs/scipy-dev/lib/libopenblas.so.0 (0x0000780d6d000000)
 
   .. tab-item:: macOS
     :sync: macos
@@ -112,15 +112,15 @@ Other ways of introspecting that can be helpful in local dev environments includ
 
     ::
 
-        $ nm -gD ~/mambaforge/envs/scipy-dev/lib/libblas.so | rg openblas_set_num_threads
+        $ nm -gD ~/miniforge/envs/scipy-dev/lib/libblas.so | rg openblas_set_num_threads
         0000000000362990 T openblas_set_num_threads
 
   .. tab-item:: macOS
     :sync: macos
 
     ::
 
-        % nm ~/mambaforge/envs/scipy-dev/lib/libblas.3.dylib | rg openblas_set_num_threads
+        % nm ~/miniforge/envs/scipy-dev/lib/libblas.3.dylib | rg openblas_set_num_threads
         000000000015b6b0 T _openblas_set_num_threads
 
 
@@ -527,7 +527,7 @@ Here is an example ``gdb`` session::
     (Pdb) c     # continue execution until the C breakpoint
 
     Thread 1 "python" hit Breakpoint 1, 0x00007ffff4c48820 in dpotrf_ ()
-       from /home/br/mambaforge/envs/scipy-dev/lib/python3.10/site-packages/numpy/core/../../../../libcblas.so.3
+       from /home/br/miniforge/envs/scipy-dev/lib/python3.10/site-packages/numpy/core/../../../../libcblas.so.3
     (gdb) s     # step through the C function
     Single stepping until exit from function dpotrf_,
     which has no line number information.

doc/source/dev/core-dev/releasing.rst.inc

@@ -117,11 +117,9 @@ and PRs under the Milestone for the release
 (https://github.com/scipy/scipy/milestones), PRs labeled "backport-candidate",
 and that the release notes are up-to-date and included in the html docs.
 
-Then edit ``meson.build`` and ``tools/version_utils.py`` to get the correct version number (set
-``version:`` in the former, and ``ISRELEASED = True`` in the latter). It is
-also necessary to adjust the ``version`` in ``pyproject.toml``. Commit these
-changes with a message like ``REL: set version to <version-number>``.  Don't push
-this commit to the SciPy repo yet.
+Then update the ``version`` in ``pyproject.toml`` and commit the change with a
+message like ``REL: set version to <version-number>``.  Don't push this commit
+to the SciPy repo yet.
 
 Finally tag the release locally with ``git tag -s <v1.x.y>`` (the ``-s`` ensures
 the tag is signed). If ``gpg2`` is preferred, then