New packages for openCARP (#25909)

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

var/spack/repos/builtin/packages/meshtool/package.py

@@ -0,0 +1,23 @@
+# Copyright 2013-2021 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 Meshtool(MakefilePackage):
+    """Meshtool - A mesh manipulation utility"""
+
+    homepage = "https://bitbucket.org/aneic/meshtool/"
+    git      = "https://bitbucket.org/aneic/meshtool.git"
+
+    maintainers = ['MarieHouillon']
+
+    version('master', branch='master')
+    # Version to use with opencarp@7.0
+    version('oc7.0', commit="6c5cfbd067120901f15a04bf63beec409bda6dc9")
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('meshtool', prefix.bin)

var/spack/repos/builtin/packages/opencarp/opencarp7.patch

@@ -0,0 +1,52 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1c77521..ac421ca 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -145,4 +145,4 @@ install(CODE "execute_process(COMMAND sh -c \"bash ${CMAKE_CURRENT_LIST_DIR}/cma
+ )
+ 
+ 
+-include(CPackConfig)
++#include(CPackConfig)
+diff --git a/cmake/postinst b/cmake/postinst
+index 7f1e249..0df6777 100644
+--- a/cmake/postinst
++++ b/cmake/postinst
+@@ -1,16 +1,16 @@
+ #!/bin/bash
+ 
+-INST_DIR="/usr/local/lib/opencarp"
++#INST_DIR="/usr/local/lib/opencarp"
+ 
+-if [ "$(uname -s)" == "Linux" ]; then
+-    echo $INST_DIR/lib > /etc/ld.so.conf.d/opencarp.conf
+-    ldconfig
+-fi
++#if [ "$(uname -s)" == "Linux" ]; then
++#    echo $INST_DIR/lib > /etc/ld.so.conf.d/opencarp.conf
++#    ldconfig
++#fi
+ 
+ # link binaries
+-ln -sf $INST_DIR/bin/* /usr/local/bin/
+-ln -sf $INST_DIR/lib/openmpi/bin/mpirun /usr/local/bin/mpirun
+-ln -sf $INST_DIR/lib/openmpi/bin/mpiexec /usr/local/bin/mpiexec
++#ln -sf $INST_DIR/bin/* /usr/local/bin/
++#ln -sf $INST_DIR/lib/openmpi/bin/mpirun /usr/local/bin/mpirun
++#ln -sf $INST_DIR/lib/openmpi/bin/mpiexec /usr/local/bin/mpiexec
+ 
+ # install carputils
+ if [ -d "$INST_DIR/share/carputils" ]; then
+diff --git a/simulator/build_info.py b/simulator/build_info.py
+index 7ef8aec..0b51aaa 100644
+--- a/simulator/build_info.py
++++ b/simulator/build_info.py
+@@ -168,7 +168,7 @@ TEMPLATE = """#ifndef __BUILD_INFO__
+ 
+ def generate():
+ 
+-    info = git()
++    info = git(os.path.dirname(os.path.abspath(__file__)))
+ 
+     # Get subrepo info
+     repo_versions = []

var/spack/repos/builtin/packages/opencarp/package.py

@@ -0,0 +1,68 @@
+# Copyright 2013-2021 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)
+
+import os
+from datetime import datetime
+
+from spack import *
+
+
+class Opencarp(CMakePackage):
+    """The openCARP simulation software,
+       an open cardiac electrophysiology simulator for in-silico experiments."""
+
+    homepage = "https://www.opencarp.org"
+    git = "https://git.opencarp.org/openCARP/openCARP.git"
+
+    maintainers = ['MarieHouillon']
+
+    version('7.0', commit='78da9195', submodules=False, no_cache=True, preferred=True)
+    version('master', branch='master', submodules=False, no_cache=True)
+
+    variant('carputils', default=False, description='Installs the carputils framework')
+    variant('meshtool', default=False, description='Installs the meshtool software')
+
+    # Patch removing problematic steps in CMake process
+    patch('opencarp7.patch', when='@7.0')
+
+    depends_on('git')
+    depends_on('petsc')
+    depends_on('binutils')
+    depends_on('gengetopt')
+    depends_on('pkgconfig')
+    depends_on('python@:3.8')
+    depends_on('zlib')
+    depends_on('perl')
+
+    depends_on('py-carputils')
+    depends_on('meshtool')
+    # Use specific versions of carputils and meshtool for releases
+    for ver in ['7.0']:
+        depends_on('py-carputils@oc' + ver, when='@' + ver + ' +carputils')
+        depends_on('meshtool@oc' + ver, when='@' + ver + ' +meshtool')
+
+    def cmake_args(self):
+        return [
+            self.define('DLOPEN', True),
+            self.define('SPACK_BUILD', True)
+        ]
+
+    @run_after('install')
+    def post_install(self):
+        # If carputils has been installed, a new settings file
+        # with right executable paths is generated
+        if '+carputils' in self.spec:
+            settings_prefix = os.path.expanduser(join_path('~', '.config', 'carputils'))
+            settings_file = join_path(settings_prefix, 'settings.yaml')
+            if os.path.exists(settings_file):
+                print('Backup the existing settings.yaml...')
+                os.rename(settings_file,
+                          join_path(
+                              settings_prefix,
+                              'settings.yaml.'
+                              + datetime.today().strftime('%Y-%m-%d-%H:%M:%S')))
+            cusettings = Executable('cusettings')
+            cusettings(settings_file, '--flavor', 'petsc',
+                       '--software-root', self.prefix.bin)

var/spack/repos/builtin/packages/py-carputils/package.py

@@ -0,0 +1,31 @@
+# Copyright 2013-2021 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)
+
+
+class PyCarputils(PythonPackage):
+    """The carputils framework for running simulations with the openCARP software."""
+
+    homepage = "https://www.opencarp.org"
+    git      = "https://git.opencarp.org/openCARP/carputils.git"
+
+    maintainers = ['MarieHouillon']
+
+    version('master', branch='master')
+    # Version to use with openCARP 7.0
+    version('oc7.0', commit='4c04db61744f2fb7665594d7c810699c5c55c77c')
+
+    depends_on('git')
+
+    depends_on('python@:3.8', type=('build', 'run'))
+    depends_on('py-pip', type='build')
+    depends_on('py-numpy@1.14.5:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-python-dateutil', type='run')
+    depends_on('py-scipy@:1.5.4', type='run')
+    depends_on('py-matplotlib@:3.3.3', type='run')
+    depends_on('py-pandas@:1.1.4', type='run')
+    depends_on('py-tables@3.6.1', type='run')
+    depends_on('py-six@:1.14.0', type='run')
+    depends_on('py-ruamel-yaml', type='run')