neuron: add new versions and clean-up the recipe (#41931)
* update tarball urls, add new versions and update maintainers * remove unnecessary variant like cross-compile * use self.define and self.define_from_variant * improve regex / bug that matches with -DMPICH_SKIP_MPICXX=1 Co-authored-by: Matthias Wolf <matthias.wolf@epfl.ch> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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Pramod Kumbhar
GitHub
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commit
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@ -16,86 +16,137 @@ class Neuron(CMakePackage):
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"""
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homepage = "https://www.neuron.yale.edu/"
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url = "https://neuron.yale.edu/ftp/neuron/versions/v7.7/nrn-7.7.tar.gz"
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url = "https://github.com/neuronsimulator/nrn/releases/download/8.2.3/nrn-full-src-package-8.2.3.tar.gz"
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git = "https://github.com/neuronsimulator/nrn"
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maintainers("pramodk", "nrnhines", "iomaganaris", "alexsavulescu")
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maintainers("pramodk", "nrnhines", "iomaganaris", "ohm314", "matz-e")
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license("BSD-3-Clause")
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version("develop", branch="master", submodules="True")
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version(
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"8.2.3", tag="8.2.3", commit="f0ed3701059aa53ce93387f3d73d13c45de6d87f", submodules="True"
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)
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version(
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"8.1.0", tag="8.1.0", commit="047dd8240c2badadf5ea154b563b29369db1303f", submodules="True"
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)
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version(
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"8.0.0", tag="8.0.0", commit="429d11ef34b1d860b3ddbfffc9f7960acb399b0c", submodules="True"
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)
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version(
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"7.8.2", tag="7.8.2", commit="09b151ecb2b3984335c265932dc6ba3e4fcb318e", submodules="True"
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)
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version(
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"7.8.1", tag="7.8.1", commit="47cd8c85aa3fde5dbb7319facd6f475438235d7d", submodules="True"
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)
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variant("coreneuron", default=False, description="Enable CoreNEURON as submodule")
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variant("cross-compile", default=False, description="Build for cross-compile environment")
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variant("backtrace", default=False, description="Enable printing backtraces on failure")
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variant("interviews", default=False, description="Enable GUI with INTERVIEWS")
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variant("legacy-unit", default=False, description="Enable legacy units")
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variant("mpi", default=True, description="Enable MPI parallelism")
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variant("python", default=True, description="Enable python")
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variant("rx3d", default=False, description="Enable cython translated 3-d rxd")
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variant("tests", default=False, description="Enable unit tests")
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variant("caliper", default=False, description="Add LLNL/Caliper support")
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variant("shared", default=True, description="Build shared library (CoreNEURON)")
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variant("tests", default=False, description="Enable building tests")
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variant("rx3d", default=False, description="Enable cython translated 3-d rxd.", when="+python")
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depends_on("bison", type="build")
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depends_on("flex", type="build")
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depends_on("py-cython", when="+rx3d", type="build")
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# variants from coreneuron support
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variant("coreneuron", default=True, description="Enable CoreNEURON support")
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variant(
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"gpu", default=False, description="Enable GPU build (with NVHPC)", when="@9:+coreneuron"
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)
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variant(
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"openmp", default=False, description="Enable CoreNEURON OpenMP support", when="+coreneuron"
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)
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variant(
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"sympy",
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default=False,
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description="Use NMODL with SymPy to solve ODEs",
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when="@9:+coreneuron",
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)
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variant("caliper", default=False, description="Add Caliper support")
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generator("ninja")
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depends_on("bison@3:", type="build")
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depends_on("flex@2.6:", type="build")
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depends_on("ninja", type="build")
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depends_on("gettext")
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depends_on("libdwarf", when="+backtrace")
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depends_on("mpi", when="+mpi")
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depends_on("ncurses")
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depends_on("python@2.7:", when="+python")
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depends_on("readline")
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depends_on("python", when="+python")
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depends_on("py-pytest", when="+python+tests")
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depends_on("py-mpi4py", when="+mpi+python+tests")
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depends_on("readline")
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depends_on("caliper", when="+caliper")
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depends_on("py-numpy", type="run")
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depends_on("py-numpy", when="+python")
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depends_on("py-cython", when="+rx3d", type="build")
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depends_on("py-pytest-cov", when="+tests")
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conflicts("+rx3d", when="~python")
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# next two needed after neuronsimulator/nrn#2235.
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depends_on("py-pip", type="build")
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depends_on("py-setuptools", type="build")
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depends_on("py-packaging", type="run")
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depends_on("boost", when="+coreneuron+tests")
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depends_on("cuda", when="+coreneuron+gpu")
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depends_on("py-sympy@1.3:", when="+coreneuron")
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depends_on("caliper", when="+caliper")
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gpu_compiler_message = "neuron+gpu needs %nvhpc"
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requires("%nvhpc", when="+gpu", msg=gpu_compiler_message)
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patch("patch-v782-git-cmake-avx512.patch", when="@7.8.2")
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def cmake_args(self):
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spec = self.spec
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args = []
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for variant in ["backtrace", "coreneuron", "interviews", "mpi", "python", "rx3d", "tests"]:
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args.append(self.define_from_variant("NRN_ENABLE_" + variant.upper(), variant))
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def cmake_options(spec_options):
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value = "TRUE" if spec_options in spec else "FALSE"
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cmake_name = spec_options[1:].upper().replace("-", "_")
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return "-DNRN_ENABLE_" + cmake_name + ":BOOL=" + value
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args.append(self.define_from_variant("CORENRN_ENABLE_SHARED", "shared"))
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args = [
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cmake_options(variant)
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for variant in [
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"+coreneuron",
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"+interviews",
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"+mpi",
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"+python",
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"+rx3d",
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"+coreneuron",
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"+tests",
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]
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]
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args.append("-DNRN_ENABLE_BINARY_SPECIAL=ON")
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if spec.satisfies("@:8"):
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args.append(self.define("NRN_ENABLE_BINARY_SPECIAL", "ON"))
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if "~mpi" in spec and "+coreneuron" in spec:
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args.append("-DCORENRN_ENABLE_MPI=OFF")
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if "+python" in spec:
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args.append(self.define("PYTHON_EXECUTABLE", spec["python"].command.path))
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if spec.variants["build_type"].value == "Debug":
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args.append("-DCMAKE_C_FLAGS=-g -O0")
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args.append("-DCMAKE_CXX_FLAGS=-g -O0")
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args.append("-DCMAKE_BUILD_TYPE=Custom")
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if "+legacy-unit" in spec:
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args.append("-DNRN_DYNAMIC_UNITS_USE_LEGACY=ON")
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if "+legacy-unit" in spec and spec.satisfies("@:8"):
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args.append(self.define("NRN_DYNAMIC_UNITS_USE_LEGACY", "ON"))
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if "+caliper" in spec:
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args.append("-DCORENRN_CALIPER_PROFILING=ON")
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args.append(self.define("NRN_ENABLE_PROFILING", "ON"))
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args.append(self.define("NRN_PROFILER", "caliper"))
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if spec.satisfies("+coreneuron"):
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options = [
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self.define("CORENRN_ENABLE_SPLAYTREE_QUEUING", "ON"),
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self.define("CORENRN_ENABLE_TIMEOUT", "OFF"),
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self.define_from_variant("CORENRN_ENABLE_OPENMP", "openmp"),
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self.define_from_variant("CORENRN_ENABLE_LEGACY_UNITS", "legacy-unit"),
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self.define_from_variant("CORENRN_ENABLE_UNIT_TESTS", "tests"),
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]
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nmodl_options = "codegen --force"
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if spec.satisfies("+sympy"):
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nmodl_options += " sympy --analytic"
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options.append(self.define("CORENRN_NMODL_FLAGS", nmodl_options))
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if spec.satisfies("+gpu"):
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nvcc = spec["cuda"].prefix.bin.nvcc
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options.append(self.define("CMAKE_CUDA_COMPILER", nvcc))
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options.append(self.define("CORENRN_ENABLE_GPU", True))
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args.extend(options)
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# Enable math optimisations to enable SIMD/vectorisation in release modes
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if spec.satisfies("build_type=Release") or spec.satisfies("build_type=RelWithDebInfo"):
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args.append(self.define("NRN_ENABLE_MATH_OPT", "ON"))
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# add cpu arch specific optimisation flags to CMake so that they are passed
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# to embedded Makefile that neuron has for compiling MOD files
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compilation_flags = self.spec.architecture.target.optimization_flags(self.spec.compiler)
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args.append(self.define("CMAKE_CXX_FLAGS", compilation_flags))
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return args
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@ -117,30 +168,21 @@ def filter_compilers(self):
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cxx_compiler = self.compiler.cxx
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kwargs = {"backup": False, "string": True}
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nrnmech_makefile = join_path(self.prefix, "./bin/nrnmech_makefile")
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nrnmech_makefile = join_path(self.prefix, "bin/nrnmech_makefile")
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# assign_operator is changed to fix wheel support
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if self.spec.satisfies("@:7"):
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assign_operator = "?="
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else:
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assign_operator = "="
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assign_operator = "?=" if spec.satisfies("@:7") else "="
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filter_file(
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"CC {0} {1}".format(assign_operator, env["CC"]),
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"CC = {0}".format(cc_compiler),
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nrnmech_makefile,
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**kwargs,
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)
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filter_file(
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"CXX {0} {1}".format(assign_operator, env["CXX"]),
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"CXX = {0}".format(cxx_compiler),
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nrnmech_makefile,
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**kwargs,
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)
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# replace compilers from makefile
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compilers = [("CC", "cc_compiler"), ("CXX", "cxx_compiler")]
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for compiler_var, compiler_env in compilers:
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pattern = "(?:^|\\s){0}\\s*{1}.+".format(compiler_var, assign_operator)
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replacement = "{0} = {1}".format(compiler_var, locals()[compiler_env])
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filter_file(pattern, replacement, nrnmech_makefile)
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if spec.satisfies("+coreneuron"):
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corenrn_makefile = join_path(self.prefix, "share/coreneuron/nrnivmodl_core_makefile")
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filter_file(env["CXX"], cxx_compiler, corenrn_makefile, **kwargs)
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if spec.satisfies("@8:+coreneuron"):
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nrnmakefile = join_path(self.prefix, "share/coreneuron/nrnivmodl_core_makefile")
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filter_file("(?:^|\\s)CXX\\s*=.+", "CXX = {0}".format(cxx_compiler), nrnmakefile)
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def setup_run_environment(self, env):
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env.prepend_path("PATH", join_path(self.prefix, "bin"))
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