Update9.1.0 (#128)

* Update to SuiteSparse:GraphBLAS 9.1.0

* maybe fix? (path and extra constant)

* Update default include path to include "suitesparse"

* Try this

* Maybe don't need this anymore for arm on mac os

* Explicit macos x86 and arm runners

* Add dir dump

* Look in "/usr/local"

* Try installing to prefix

* Cmake from .

* Add lib64

* Try installing to . instead of /tmp

* Set MACOSX_DEPLOYMENT_TARGET

* Try installing to /usr/local/graphblas

* Try installing to {package}

* Fix

* Add prints

* Add print

* Try installing to .

* parent

* retry

* Disable JIT on Windows

* retry

* Fix if

* Revert to sys install

* Fix sudo

* Disable JIT on Windows

* tweaks

* MSVC complex values

* Revert prints

* Silence workflow warnings

* Delete no longer used script

* Undo run tests on push

* Make linter happy

* Linter

* Support both suitesparse.sh and conda install paths

* Fix cibw_test_skip typo

* Build with numpy 2; add Python 3.13; drop Python 3.8

* Bump

* Try setuptools<74

* experiment w/ setuptools as runtime dep

* undo

* Update cibuildwheel

We need pypa/cibuildwheel#1915 to `yum install`

* Use cibuildwheel 2.21, not 2.21.3

* Delete unnecessary code b/c we dropped Python 3.8

---------

Co-authored-by: Erik Welch <[email protected]>

Author: alugowski

.github/workflows/test.yml

@@ -18,7 +18,7 @@ jobs:
         source: ["conda-forge"]
         # os: ["ubuntu-latest"]
         # source: ["source"]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
     - name: Checkout
       uses: actions/checkout@v4

.github/workflows/wheels.yml

@@ -84,16 +84,14 @@ jobs:
             cibw_skip: "pp* *musl*"
 
           # macOS x86
-          - os: macos-latest
+          # Note: keep as old as possible as due to libomp this will be the oldest supported macOS version.
+          - os: macos-12
             cibw_archs: "x86_64"
 
-          # macOS Apple Silicon cross-compiled on x86 macOS runner.
-          # GitHub does not offer Apple Silicon yet (only for self-hosted).
-          # See https://github.com/github/roadmap/issues/528
-          - os: macos-latest
+          # macOS Apple Silicon
+          # Note: keep as old as possible as due to libomp this will be the oldest supported macOS version.
+          - os: macos-14
             cibw_archs: "arm64"
-            # Skip macOS ARM tests on Intel runner.
-            cibw_test_skip: "*-macosx_arm64"
 
     steps:
       - uses: actions/checkout@v4
@@ -139,17 +137,15 @@ jobs:
         if: contains(matrix.os, 'macos')
         # Install coreutils which includes `nproc` used by `make -j` in suitesparse.sh
         #
-        # GitHub actions comes with libomp already installed, but for its native arch only. Must build universal one
-        # manually so that both x86 and arm builds can be built.
+        # Explicitly install libomp to be clear about the dependency.
+        #
+        # libomp determines the minimum macOS version that we can build for
         run: |
           brew fetch --retry coreutils && brew install coreutils
-          brew fetch --retry libomp && brew install libomp
-          if [[ ${{ matrix.cibw_archs }} == "arm64" ]] ; then
-            echo "Building universal libomp manually"
-            sh add_arm_to_libomp_dylib.sh || exit 1
-          fi
+          brew fetch --retry libomp && brew reinstall libomp
+          echo MACOSX_DEPLOYMENT_TARGET=$(otool -l $(brew --prefix libomp)/lib/libomp.dylib | grep minos | awk '{print $2}') >> $GITHUB_ENV
 
-      - uses: pypa/cibuildwheel@v2.16
+      - uses: pypa/cibuildwheel@v2.21
         with:
           output-dir: wheelhouse
         env:

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ default_language_version:
     python: python3
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -20,43 +20,43 @@ repos:
       - id: mixed-line-ending
       # - id: trailing-whitespace
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.14
+    rev: v0.20.2
     hooks:
       - id: validate-pyproject
         name: Validate pyproject.toml
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.2.1
+    rev: v2.3.1
     hooks:
       - id: autoflake
         args: [--in-place]
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.13.0
+    rev: v3.18.0
     hooks:
       - id: pyupgrade
-        args: [--py38-plus]
+        args: [--py39-plus]
   # - repo: https://github.com/MarcoGorelli/auto-walrus
   #   rev: v0.2.2
   #   hooks:
   #     - id: auto-walrus
   #       args: [--line-length, "100"]
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.10.0
     hooks:
       - id: black
       # - id: black-jupyter
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         additional_dependencies: &flake8_dependencies
         # These versions need updated manually
-        - flake8==6.1.0
-        - flake8-comprehensions==3.14.0
-        - flake8-bugbear==23.9.16
+        - flake8==7.1.1
+        - flake8-comprehensions==3.15.0
+        - flake8-bugbear==24.8.19
         # - flake8-simplify==0.20.0
   - repo: https://github.com/asottile/yesqa
     rev: v1.5.0
@@ -71,6 +71,6 @@ repos:
   #     - id: pyroma
   #       args: [-n, "10", .]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: no-commit-to-branch  # no commit directly to main

GB_VERSION.txt

@@ -1 +1 @@
-8.2.1
+9.1.0

add_arm_to_libomp_dylib.sh

@@ -14,17 +14,30 @@
 # Expected subdirectories: include/ (contains GraphBLAS.h), lib/, and bin/ (on Windows only)
 # Otherwise fallback to default system folders.
 graphblas_root = os.environ.get("GraphBLAS_ROOT", None)
+
 if not graphblas_root:
     # Windows wheels.yml configures suitesparse.sh to install GraphBLAS to "C:\\GraphBLAS".
-    graphblas_root = "C:\\GraphBLAS" if is_win else sys.prefix
-
-include_dirs = [os.path.join(graphblas_root, "include")]
-library_dirs = [os.path.join(graphblas_root, "lib")]
+    if is_win:
+        graphblas_root = "C:\\GraphBLAS"
+    elif Path("/usr/local/include/suitesparse").exists():
+        # SuiteSparse:GraphBLAS 9.1+ built by suitesparse.sh
+        graphblas_root = "/usr/local"
+    else:
+        # Conda install
+        graphblas_root = sys.prefix
+
+include_dirs = [
+    os.path.join(graphblas_root, "include"),
+    os.path.join(graphblas_root, "include", "suitesparse"),
+]
+library_dirs = [os.path.join(graphblas_root, "lib"), os.path.join(graphblas_root, "lib64")]
 if is_win:
     include_dirs.append(os.path.join(sys.prefix, "Library", "include"))
+    include_dirs.append(os.path.join(sys.prefix, "Library", "include", "suitesparse"))
     library_dirs.append(os.path.join(sys.prefix, "Library", "lib"))
 
     include_dirs.append(os.path.join(graphblas_root, "include"))
+    include_dirs.append(os.path.join(graphblas_root, "include", "suitesparse"))
     library_dirs.append(os.path.join(graphblas_root, "lib"))
     library_dirs.append(os.path.join(graphblas_root, "bin"))
 
@@ -68,6 +81,9 @@ def get_extension(apply_msvc_patch: bool = None, extra_compile_args=()):
         msvc_code = msvc_code.replace("double _Complex", "_Dcomplex")
         code_path.write_text(msvc_code)
 
+        # Hack: tell GraphBLAS.h that we need MSVC-style complex values
+        extra_compile_args = list(extra_compile_args) + ["-DGxB_HAVE_COMPLEX_MSVC"]
+
     return Extension(
         "suitesparse_graphblas._graphblas",
         [os.path.join("suitesparse_graphblas", "_graphblas.c")],

build_graphblas_cffi.py

@@ -1,23 +1,21 @@
 [build-system]
 build-backend = "setuptools.build_meta"
 requires = [
-    "setuptools >=64",
+    # setuptools<74 until PyPy vendors cffi 1.15.1
+    "setuptools >=64, <74",
     "setuptools-git-versioning",
     "wheel",
     "cffi>=1.11",
     "cython",
-    "oldest-supported-numpy; platform_python_implementation != 'PyPy'",
-    # Inspired by SciPy: unpin numpy version for PyPy builds,
-    # as oldest-supported-numpy does not take PyPy into account.
-    "numpy; platform_python_implementation=='PyPy'",
+    "numpy>=2.0",
 ]
 
 [project]
 name = "suitesparse-graphblas"
 dynamic = ["version"]
 description = "SuiteSparse:GraphBLAS Python bindings."
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = {file = "LICENSE"}
 authors = [
     {name = "Erik Welch", email = "[email protected]"},
@@ -53,11 +51,11 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3 :: Only",
     "Intended Audience :: Developers",
     "Intended Audience :: Other Audience",
@@ -68,9 +66,8 @@ classifiers = [
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 dependencies = [
-    # These are super-old; can/should we update them?
-    "cffi>=1.11",
-    "numpy>=1.19",
+    "cffi>=1.15",
+    "numpy>=1.23",
 ]
 [project.urls]
 homepage = "https://github.com/GraphBLAS/python-suitesparse-graphblas"
@@ -96,7 +93,7 @@ dirty_template = "{tag}+{ccount}.g{sha}.dirty"
 
 [tool.black]
 line-length = 100
-target-version = ["py38", "py39", "py310", "py311"]
+target-version = ["py39", "py310", "py311", "py312", "py313"]
 
 [tool.isort]
 sections = ["FUTURE", "STDLIB", "THIRDPARTY", "FIRSTPARTY", "LOCALFOLDER"]

pyproject.toml

@@ -113,11 +113,29 @@ if [ -n "${SUITESPARSE_FASTEST_BUILD}" ]; then
     cmake_params+=(-DCMAKE_CUDA_DEV=1)
 fi
 
-# Use `-DJITINIT=2` so that the JIT functionality is available, but disabled by default.
-# Level 2, "run", means that pre-JIT kernels may be used, which does not require a compiler at runtime.
-cmake .. -DJITINIT=2 -DCMAKE_BUILD_TYPE=Release -G 'Unix Makefiles' "${cmake_params[@]}"
+if [ -n "${CMAKE_GNUtoMS}" ]; then
+    # Windows options
+    echo "Skipping JIT on Windows for now because it fails to build."
+    cmake_params+=(-DGRAPHBLAS_USE_JIT=OFF)
+else
+    # Use `-DJITINIT=2` so that the JIT functionality is available, but disabled by default.
+    # Level 2, "run", means that pre-JIT kernels may be used, which does not require a compiler at runtime.
+    cmake_params+=(-DJITINIT=2)
+
+    # Disable JIT here too to not segfault in tests
+    cmake_params+=(-DGRAPHBLAS_USE_JIT=OFF)
+fi
+
+# some platforms require sudo for installation, some don't have sudo at all
+if [ "$(uname)" == "Darwin" ]; then
+    SUDO=sudo
+else
+    SUDO=""
+fi
+
+cmake .. -DCMAKE_BUILD_TYPE=Release -G 'Unix Makefiles' "${cmake_params[@]}"
 make -j$NPROC
-make install
+$SUDO make install
 
 if [ -n "${CMAKE_GNUtoMS}" ]; then
     if [ -z "${GRAPHBLAS_PREFIX}" ]; then

suitesparse.sh

@@ -21,6 +21,7 @@
 Run `python create_headers.py --help` to see more help.
 
 """
+
 import argparse
 import os
 import re
@@ -325,6 +326,7 @@ def groupby(index, seq):
     "RMM_WRAP_H",
     "GXB_COMPLEX_H",
     "GxB_STATIC_INLINE_VOID",
+    "GxB_HAVE_COMPLEX_C99",
     # deprecated
     "GxB_HYPER",
 }
@@ -633,6 +635,7 @@ def handle_function_node(node):
                 "init": "core",
                 "wait": "core",
                 "deserialize": "core",
+                "Serialized": "core",  # Added in version 9
             }[group]
         return {
             "name": node.name,
@@ -782,7 +785,7 @@ def main():
     parser.add_argument(
         "--graphblas",
         help="Path to GraphBLAS.h of SuiteSparse.  Default will look in Python prefix path.",
-        default=os.path.join(sys.prefix, "include", "GraphBLAS.h"),
+        default=os.path.join(sys.prefix, "include", "suitesparse", "GraphBLAS.h"),
     )
     parser.add_argument(
         "--show-skipped",