eef9939c21
Use full length commit sha instead of short prefixes, to improve reproducibility (future clashes) and guard against compromised repos and man in the middle attacks. Abbreviated commit shas are expanded to full length, to guard against future clashes on short hash. It also guards against compromised repos and man in the middle attacks, where attackers can easily fabricate a malicious commit with a shasum prefix collision. Versions with just tags now also get a commit sha, which can later be used to check for retagged commits.
151 lines
5.5 KiB
Python
151 lines
5.5 KiB
Python
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Neuron(CMakePackage):
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"""NEURON is a simulation environment for single and networks of neurons.
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NEURON is a simulation environment for modeling individual and networks of
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neurons. NEURON models individual neurons via the use of sections that are
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automatically subdivided into individual compartments, instead of
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requiring the user to manually create compartments.
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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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git = "https://github.com/neuronsimulator/nrn"
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maintainers("pramodk", "nrnhines", "iomaganaris", "alexsavulescu")
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version("develop", branch="master", submodules="True")
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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("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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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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depends_on("gettext")
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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("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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conflicts("+rx3d", when="~python")
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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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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 = [
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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 "~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("-DPYTHON_EXECUTABLE:FILEPATH=" + 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 "+caliper" in spec:
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args.append("-DCORENRN_CALIPER_PROFILING=ON")
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return args
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@run_after("install")
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def filter_compilers(self):
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"""run after install to avoid spack compiler wrappers
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getting embded into nrnivmodl script"""
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spec = self.spec
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if "cray" in spec.architecture:
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cc_compiler = "cc"
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cxx_compiler = "CC"
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elif spec.satisfies("+mpi"):
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cc_compiler = spec["mpi"].mpicc
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cxx_compiler = spec["mpi"].mpicxx
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else:
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cc_compiler = self.compiler.cc
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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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# 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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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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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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def setup_run_environment(self, env):
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env.prepend_path("PATH", join_path(self.prefix, "bin"))
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env.prepend_path("LD_LIBRARY_PATH", join_path(self.prefix, "lib"))
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if self.spec.satisfies("+python"):
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env.prepend_path("PYTHONPATH", self.spec.prefix.lib.python)
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