add spack post-installation testing

This Merge Request:

• adds or fixes tests for most EBRAINS (top-level) Spack packages
• adapts gitlab CI and installation script to run tests at installation time

packages/neuron/package.py

+# this package was adapted from the spack v0.18.1 upstream to fix an issue with
+# setting the PYTHONPATH of dependents for installation time tests
+
+# Copyright 2013-2022 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 import *
+
+
+class Neuron(CMakePackage):
+    """NEURON is a simulation environment for single and networks of neurons.
+
+    NEURON is a simulation environment for modeling individual and networks of
+    neurons. NEURON models individual neurons via the use of sections that are
+    automatically subdivided into individual compartments, instead of
+    requiring the user to manually create compartments.
+    """
+
+    homepage = "https://www.neuron.yale.edu/"
+    url      = "https://neuron.yale.edu/ftp/neuron/versions/v7.7/nrn-7.7.tar.gz"
+    git      = "https://github.com/neuronsimulator/nrn"
+    maintainers = ['pramodk', 'nrnhines', 'iomaganaris', 'alexsavulescu']
+
+    version('develop', branch='master', submodules='True')
+    version("8.0.0", tag="8.0.0", submodules='True')
+    version("7.8.2", tag="7.8.2", submodules='True')
+    version("7.8.1", tag="7.8.1", submodules='True')
+
+    variant("coreneuron",    default=False, description="Enable CoreNEURON as submodule")
+    variant("cross-compile", default=False, description="Build for cross-compile environment")
+    variant("interviews",    default=False, description="Enable GUI with INTERVIEWS")
+    variant("legacy-unit",   default=False, description="Enable legacy units")
+    variant("mpi",           default=True,  description="Enable MPI parallelism")
+    variant("python",        default=True,  description="Enable python")
+    variant("rx3d",          default=False,  description="Enable cython translated 3-d rxd")
+    variant("tests",         default=False, description="Enable unit tests")
+    variant("caliper",       default=False, description="Add LLNL/Caliper support")
+
+    depends_on("bison",     type="build")
+    depends_on("flex",      type="build")
+    depends_on("py-cython", when="+rx3d", type="build")
+
+    depends_on("gettext")
+    depends_on("mpi",         when="+mpi")
+    depends_on("ncurses")
+    depends_on("python@2.7:", when="+python")
+    depends_on("py-pytest",   when="+python+tests")
+    depends_on("py-mpi4py",   when="+mpi+python+tests")
+    depends_on("readline")
+    depends_on("caliper",     when="+caliper")
+    depends_on("py-numpy",    type='run')
+
+    conflicts("+rx3d",        when="~python")
+
+    patch("patch-v782-git-cmake-avx512.patch", when="@7.8.2")
+
+    def cmake_args(self):
+        spec = self.spec
+
+        def cmake_options(spec_options):
+            value = "TRUE" if spec_options in spec else "FALSE"
+            cmake_name = spec_options[1:].upper().replace("-", "_")
+            return "-DNRN_ENABLE_" + cmake_name + ":BOOL=" + value
+
+        args = [cmake_options(variant) for variant in ["+coreneuron",
+                                                       "+interviews",
+                                                       "+mpi",
+                                                       "+python",
+                                                       "+rx3d",
+                                                       "+coreneuron",
+                                                       "+tests"]]
+        args.append("-DNRN_ENABLE_BINARY_SPECIAL=ON")
+
+        if "~mpi" in spec and '+coreneuron' in spec:
+            args.append("-DCORENRN_ENABLE_MPI=OFF")
+
+        if "+python" in spec:
+            args.append("-DPYTHON_EXECUTABLE:FILEPATH="
+                        + spec["python"].command.path)
+
+        if spec.variants['build_type'].value == 'Debug':
+            args.append("-DCMAKE_C_FLAGS=-g -O0")
+            args.append("-DCMAKE_CXX_FLAGS=-g -O0")
+            args.append("-DCMAKE_BUILD_TYPE=Custom")
+
+        if "+legacy-unit" in spec:
+            args.append('-DNRN_DYNAMIC_UNITS_USE_LEGACY=ON')
+
+        if "+caliper" in spec:
+            args.append('-DCORENRN_CALIPER_PROFILING=ON')
+
+        return args
+
+    @run_after("install")
+    def filter_compilers(self):
+        """run after install to avoid spack compiler wrappers
+        getting embded into nrnivmodl script"""
+
+        spec = self.spec
+
+        if "cray" in spec.architecture:
+            cc_compiler = "cc"
+            cxx_compiler = "CC"
+        elif spec.satisfies("+mpi"):
+            cc_compiler = spec["mpi"].mpicc
+            cxx_compiler = spec["mpi"].mpicxx
+        else:
+            cc_compiler = self.compiler.cc
+            cxx_compiler = self.compiler.cxx
+
+        kwargs = {"backup": False, "string": True}
+        nrnmech_makefile = join_path(self.prefix,
+                                     "./bin/nrnmech_makefile")
+
+        # assign_operator is changed to fix wheel support
+        if self.spec.satisfies("@:7"):
+            assign_operator = "?="
+        else:
+            assign_operator = "="
+
+        filter_file("CC {0} {1}".format(assign_operator, env["CC"]),
+                    "CC = {0}".format(cc_compiler),
+                    nrnmech_makefile,
+                    **kwargs)
+        filter_file("CXX {0} {1}".format(assign_operator, env["CXX"]),
+                    "CXX = {0}".format(cxx_compiler),
+                    nrnmech_makefile,
+                    **kwargs)
+
+        if spec.satisfies("+coreneuron"):
+            corenrn_makefile = join_path(self.prefix,
+                                         "share/coreneuron/nrnivmodl_core_makefile")
+            filter_file(env["CXX"], cxx_compiler, corenrn_makefile, **kwargs)
+
+    def setup_run_environment(self, env):
+        env.prepend_path("PATH", join_path(self.prefix, "bin"))
+        env.prepend_path("LD_LIBRARY_PATH", join_path(self.prefix, "lib"))
+        if self.spec.satisfies("+python"):
+            env.prepend_path("PYTHONPATH", self.spec.prefix.lib.python)
+    
+    # necessary for installation time tests of dependents
+    def setup_dependent_build_environment(self, env, dependent_spec):
+        self.setup_run_environment(env)