final clean-up before v0.12

.github/workflows/benchmarks.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Set up cmake
         uses: jwlawson/actions-setup-cmake@v2.2
         with:
-          cmake-version: 3.25.x
+          cmake-version: 4.x
       - name: Clone w/ submodules
         uses: actions/checkout@v6
         with:

.github/workflows/build-pip-wheels.yml

@@ -67,7 +67,7 @@ jobs:
       - name: Update pip and setup venv
         run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo PATH=$PATH >> $GITHUB_ENV
       - name: Get packages
-        run: python3 -m pip install build
+        run: python3 -m pip install build mpi4py
       - name: Get Arbor
         uses: actions/checkout@v6
         with:

.github/workflows/codeql.yml

@@ -52,7 +52,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v4
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -61,7 +61,10 @@ jobs:
 
         # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
         # queries: security-extended,security-and-quality
-
+    - name: Set up cmake
+      uses: jwlawson/actions-setup-cmake@v2.2
+      with:
+        cmake-version: 4.x
     - name: Build arbor
       run: |
            mkdir build
@@ -81,6 +84,6 @@ jobs:
     #     ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v4
       with:
         category: "/language:${{matrix.language}}"

.github/workflows/sanitize.yml

@@ -38,7 +38,7 @@ jobs:
       - name: Set up cmake
         uses: jwlawson/actions-setup-cmake@v2.2
         with:
-          cmake-version: 3.25.x
+          cmake-version: 4.x
       - name: Clone w/ submodules
         uses: actions/checkout@v6
         with:

.github/workflows/test-matrix.yml

@@ -22,7 +22,7 @@ jobs:
             cc:    "gcc-12",
             cxx:   "g++-12",
             py:    "3.10",
-            cmake: "3.25.x",
+            cmake: "4.0.x",
             mpi:   "ON",
             simd:  "OFF"
           }
@@ -32,7 +32,7 @@ jobs:
             cc:    "clang-13",
             cxx:   "clang++-13",
             py:    "3.10",
-            cmake: "3.25.x",
+            cmake: "4.0.x",
             mpi:   "ON",
             simd:  "OFF"
           }
@@ -42,7 +42,7 @@ jobs:
             cc:    "clang",
             cxx:   "clang++",
             py:    "3.10",
-            cmake: "3.25.x",
+            cmake: "4.0.x",
             mpi:   "ON",
             simd:  "OFF"
           }

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.25)
+cmake_minimum_required(VERSION 4.0.0)
 include(CMakeDependentOption)
 include(CheckIPOSupported)
 

VERSION

@@ -1 +1 @@
-0.12.0-dev
+0.12.0-rc

doc/dependencies.csv

@@ -1,5 +1,5 @@
 Build option/target,Tool name,Minimum version,Notes,Update criteria
---,CMake,3.25,,"* Is available as a module on HPC systems
+--,CMake,4.0.0,,"* Is available as a module on HPC systems
 * When arbitrary changes in more recently released versions make supported"
 --,C++ compiler,,C++17 support. See below,
 --,GCC,12.0.0,,"* it is supported by the minimum version of CUDA.
@@ -14,11 +14,11 @@ html,     .. literalinclude:: ../requirements.txt,,See ``doc/requirements.txt``,
 unit,googletest,1.12.1,CPM,
 bench,Google-benchmark,1.8.3,CPM,
 --,json,3.12.0,CPM,
---,pugi,1.13,CPM,
+--,pugi,1.15,CPM,
 --,random123,1.14.0,CPM,
---,fmt,10.0.0,CPM,
+--,fmt,12.0.0,CPM,
 --,tinyopt,,CPM,
 --,units,0.13.1,CPM,
 --,unordered_dense,4.5.0,CPM,
-ARB_WITH_PYTHON,pybind11,3.0.0,CPM,
-ARB_WITH_PYTHON,Python,3.10,Python compatiblity is the range between the latest officially released point version and the minimum here specified.,"* it is not more advanced than the version specified by NEP 29."
+ARB_WITH_PYTHON,pybind11,3.0.2,CPM,
+ARB_WITH_PYTHON,Python,3.11,Python compatiblity is the range between the latest officially released point version and the minimum here specified.,"* it is not more advanced than the version specified by NEP 29."

pyproject.toml

@@ -59,6 +59,7 @@ exclude = [
     ".venv",
     ".vscode",
     "build",
+    "spack",
     "dist",
     "ext",
     "install-*",
@@ -69,7 +70,7 @@ exclude = [
 
 line-length = 88
 indent-width = 4
-target-version = "py312"
+target-version = "py314"
 
 [tool.ruff.lint]
 ignore = [ # for black
@@ -124,7 +125,7 @@ build-frontend = "build"
 build = ["*linux*","*macosx*"]
 manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
-skip = ["cp36*", "cp37*", "cp38*", "cp39*", "*musllinux*", "pp*"]
+skip = ["cp38*", "cp39*", "cp310*", "*musllinux*", "pp*"]
 test-command = "python -m unittest discover -v -s {project}/python"
 dependency-versions = "latest"
 

spack/package.py

@@ -0,0 +1,174 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class Arbor(CMakePackage, CudaPackage):
+    """Arbor is a high-performance library for computational neuroscience
+    simulations."""
+
+    homepage = "https://arbor-sim.org"
+    git = "https://github.com/arbor-sim/arbor.git"
+    url = "https://github.com/arbor-sim/arbor/releases/download/v0.8.1/arbor-v0.9.0-full.tar.gz"
+    maintainers = ("thorstenhater", "haampie")
+    submodules = True
+
+    version("master", branch="master", submodules=True)
+    version("develop", branch="master", submodules=True)
+    version(
+        "0.10.0",
+        sha256="6b6cc900b85fbf833fae94817b9406a0d690dc28",
+        url="https://github.com/arbor-sim/arbor/releases/download/v0.10.1/arbor-v0.10.0-full.tar.gz",
+        submodules=True,
+    )
+
+    version(
+        "0.9.0",
+        sha256="5f9740955c821aca81e23298c17ad64f33f635756ad9b4a0c1444710f564306a",
+        url="https://github.com/arbor-sim/arbor/releases/download/v0.9.0/arbor-v0.9.0-full.tar.gz",
+        submodules=True,
+    )
+    version(
+        "0.8.1",
+        sha256="caebf96676ace6a9c50436541c420ca4bb53f0639dcab825de6fa370aacf6baa",
+        url="https://github.com/arbor-sim/arbor/releases/download/v0.8.1/arbor-v0.8.1-full.tar.gz",
+    )
+    version(
+        "0.8.0",
+        sha256="18df5600308841616996a9de93b55a105be0f59692daa5febd3a65aae5bc2c5d",
+        url="https://github.com/arbor-sim/arbor/releases/download/v0.8/arbor-v0.8-full.tar.gz",
+    )
+    version(
+        "0.7.0",
+        sha256="c3a6b7193946aee882bb85f9c38beac74209842ee94e80840968997ba3b84543",
+        url="https://github.com/arbor-sim/arbor/releases/download/v0.7/arbor-v0.7-full.tar.gz",
+    )
+    version(
+        "0.6.0",
+        sha256="4cd333b18effc8833428ddc0b99e7dc976804771bc85da90034c272c7019e1e8",
+        url="https://github.com/arbor-sim/arbor/releases/download/v0.6/arbor-v0.6-full.tar.gz",
+    )
+    version(
+        "0.5.2",
+        sha256="290e2ad8ca8050db1791cabb6b431e7c0409c305af31b559e397e26b300a115d",
+        url="https://github.com/arbor-sim/arbor/releases/download/v0.5.2/arbor-v0.5.2-full.tar.gz",
+    )
+
+    variant(
+        "assertions",
+        default=False,
+        description="Enable arb_assert() assertions in code.",
+    )
+    variant("doc", default=False, description="Build documentation.")
+    variant("mpi", default=False, description="Enable MPI support")
+    variant("python", default=True, description="Enable Python frontend support")
+    variant(
+        "pystubs", default=True, when="@0.11:", description="Python stub generation"
+    )
+    variant(
+        "vectorize",
+        default=False,
+        description="Enable vectorization of computational kernels",
+    )
+    variant("hwloc", default=False, description="support for thread pinning via HWLOC")
+    variant(
+        "gpu_rng",
+        default=False,
+        description="Use GPU generated random numbers -- not bitwise equal to CPU version",
+        when="+cuda",
+    )
+
+    # https://docs.arbor-sim.org/en/latest/install/build_install.html#compilers
+    conflicts("%gcc@:8")
+    conflicts("%clang@:9")
+    # Cray compiler v9.2 and later is Clang-based.
+    conflicts("%cce@:9.1")
+    conflicts("%intel")
+
+    depends_on("cmake@3.19:", type="build")
+    depends_on("c", type="build")  # generated
+    depends_on("cxx", type="build")  # generated
+
+    # misc dependencies
+    depends_on("fmt@7.1:", when="@0.5.3:")  # required by the modcc compiler
+    depends_on("fmt@9.1:", when="@0.7.1:")
+    depends_on("fmt@10.2:", when="@0.9.1:")
+    depends_on("fmt@10.2:", when="@0.10.0:")
+    depends_on("fmt@12.0:", when="@0.12.0:")
+    depends_on("googletest@1.12.1:", when="@0.7.1:")
+    depends_on("pugixml@1.11:", when="@0.7.1:")
+    depends_on("pugixml@1.13:", when="@0.9.1:")
+    depends_on("pugixml@1.14:", when="@0.10.0:")
+    depends_on("pugixml@1.15:", when="@0.12.0:")
+    depends_on("nlohmann-json@3.11.3:")
+    depends_on("nlohmann-json@3.12:", when="@0.12.0:")
+    depends_on("random123@1.14.0:")
+    with when("+cuda"):
+        depends_on("cuda@10:")
+        depends_on("cuda@11:", when="@0.7.1:")
+        depends_on("cuda@12:", when="@0.9.1:")
+        depends_on("cuda@12:", when="@0.10.0:")
+
+    # mpi
+    depends_on("mpi", when="+mpi")
+    depends_on("py-mpi4py", when="+mpi+python", type=("build", "run"))
+
+    # hwloc
+    depends_on("hwloc@2:", when="+hwloc", type=("build", "run"))
+
+    # python (bindings)
+    with when("+python"):
+        extends("python")
+        depends_on("python@3.7:", type=("build", "run"))
+        depends_on("python@3.9:", when="@0.9.1:", type=("build", "run"))
+        depends_on("python@3.10:", when="@0.10.0:", type=("build", "run"))
+        depends_on("python@3.10:", when="@0.11.0:", type=("build", "run"))
+        depends_on("python@3.11:", when="@0.12.0:", type=("build", "run")) #
+        depends_on("py-numpy", type=("build", "run"))
+        depends_on("py-numpy@2.0.0:", when="@0.12.0:", type=("build", "run"))
+        depends_on("py-pybind11@2.6:", type="build")
+        depends_on("py-pybind11@2.8.1:", when="@0.5.3:", type="build")
+        depends_on("py-pybind11@2.10.1:", when="@0.7.1:", type="build")
+        depends_on("py-pybind11@2.11.1:", when="@0.9.1:", type="build")
+        depends_on("py-pybind11@2.10.1:", when="@0.7.1:", type="build")
+        depends_on("py-pybind11@3.0.2:", when="@0.12.0:", type="build")
+        depends_on("py-pybind11-stubgen@2.5:", when="+pystubs", type="build")
+
+    # sphinx based documentation
+    with when("+doc"):
+        depends_on("python@3.11:", type="build")
+        depends_on("py-sphinx", type="build")
+        depends_on("py-svgwrite", type="build")
+
+    @property
+    def build_targets(self):
+        return ["all", "html"] if "+doc" in self.spec else ["all"]
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            self.define_from_variant("ARB_WITH_ASSERTIONS", "assertions"),
+            self.define_from_variant("ARB_WITH_MPI", "mpi"),
+            self.define_from_variant("ARB_WITH_PYTHON", "python"),
+            self.define_from_variant("ARB_VECTORIZE", "vectorize"),
+            self.define("ARB_ARCH", "none"),
+            self.define("ARB_CXX_FLAGS_TARGET", optimization_flags(self.compiler, spec.target)),
+        ]
+
+        if self.spec.satisfies("+cuda"):
+            args.extend(
+                [
+                    self.define("ARB_GPU", "cuda"),
+                    self.define_from_variant("ARB_USE_GPU_RNG", "gpu_rng"),
+                ]
+            )
+
+        return args
+
+    @run_after("install", when="+python")
+    @on_package_attributes(run_tests=True)
+    def install_test(self):
+        python("-c", "import arbor")