mofem: add new releases and minor changes (#9138)

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

@@ -19,6 +19,7 @@ class Moab(AutotoolsPackage):
     homepage = "https://bitbucket.org/fathomteam/moab"
     url = "http://ftp.mcs.anl.gov/pub/fathom/moab-5.0.0.tar.gz"
 
+    version('5.0.2', '00a6f96f2e6591ab087548839fa3825e')
     version('5.0.0', '1840ca02366f4d3237d44af63e239e3b')
     version('4.9.2', '540931a604c180bbd3c1bb3ee8c51dd0')
     version('4.9.1', '19cc2189fa266181ad9109b18d0b2ab8')

var/spack/repos/builtin/packages/mofem-cephas/package.py

@@ -8,31 +8,41 @@
 
 
 class MofemCephas(CMakePackage):
-    """mofem-cephas core library"""
+    """MoFEM is finite element core library"""
 
     homepage = "http://mofem.eng.gla.ac.uk"
-    git      = "https://bitbucket.org/likask/mofem-cephas.git"
+    git = "https://bitbucket.org/likask/mofem-cephas.git"
 
     maintainers = ['likask']
 
-    version('develop', branch='develop', submodules=True)
+    version('develop', branch='develop')
-    version('0.8.7', tag='v0.8.7', submodules=True)
+    version('0.8.17', tag='v0.8.17')
+    version('0.8.16', tag='v0.8.16')
+    version('0.8.15', tag='v0.8.15')
+    version('0.8.14', tag='v0.8.14')
+    version('0.8.13', tag='v0.8.13')
+    version('0.8.12', tag='v0.8.12')
+    version('0.8.11', tag='v0.8.11')
+    version('0.8.10', tag='v0.8.10')
+    version('0.8.9', tag='v0.8.9')
+    version('0.8.8', tag='v0.8.8')
+    version('0.8.7', tag='v0.8.7')
 
     # This option can be only used for development of core lib
     variant('copy_user_modules', default=True,
         description='Copy user modules directory instead linking to source')
-    variant('adol-c', default=True, description='Compile with Adol-C')
+    variant('adol-c', default=True, description='Compile with ADOL-C')
     variant('tetgen', default=True, description='Compile with Tetgen')
     variant('med', default=True, description='Compile with Med')
     variant('slepc', default=False, description='Compile with Slepc')
 
     depends_on("mpi")
-    depends_on("boost")
+    depends_on("boost@:1.68")
     depends_on("parmetis")
     # Fixed version of hdf5, to remove some problems with dependent
     # packages, f.e. MED format
     depends_on("hdf5@:1.8.19+hl+mpi")
-    depends_on("petsc@:3.9.2+mumps+mpi")
+    depends_on("petsc@:3.9.3+mumps+mpi")
     depends_on('slepc', when='+slepc')
     depends_on("moab")
     # Upper bound set to ADOL-C until issues with memory leaks
@@ -58,7 +68,7 @@ def cmake_args(self):
             '-DBOOST_DIR=%s' % spec['boost'].prefix])
 
         # build tests
-        options.append('-DMOFEM_BUILD_TETS={0}'.format(
+        options.append('-DMOFEM_BUILD_TESTS={0}'.format(
             'ON' if self.run_tests else 'OFF'))
 
         # variant packages

var/spack/repos/builtin/packages/mofem-fracture-module/package.py

@@ -16,12 +16,22 @@ class MofemFractureModule(CMakePackage):
     maintainers = ['likask']
 
     version('develop', branch='develop')
+    version('0.9.50', tag='v0.9.50')
+    version('0.9.49', tag='v0.9.49')
+    version('0.9.48', tag='v0.9.48')
+    version('0.9.47', tag='v0.9.47')
+    version('0.9.46', tag='v0.9.46')
+    version('0.9.45', tag='v0.9.45')
+    version('0.9.44', tag='v0.9.44')
     version('0.9.42', tag='v0.9.42')
 
     variant('copy_user_modules', default=True,
         description='Copy user modules directory instead linking')
 
     extends('mofem-cephas')
+    depends_on('mofem-users-modules@0.8.17', when='@0.9.50')
+    depends_on('mofem-users-modules@0.8.16', when='@0.9.49')
+    depends_on('mofem-users-modules@0.8.15', when='@0.9.48')
     depends_on("mofem-users-modules", type=('build', 'link', 'run'))
 
     # The CMakeLists.txt installed with mofem-cephas package set cmake
@@ -40,7 +50,7 @@ def root_cmakelists_dir(self):
         :return: directory containing CMakeLists.txt
         """
         spec = self.spec
-        return spec['mofem-cephas'].prefix.users_modules
+        return spec['mofem-users-modules'].prefix.users_modules
 
     def cmake_args(self):
         spec = self.spec
@@ -70,15 +80,15 @@ def cmake_args(self):
                 '-DFM_VERSION_BUILD=%s' % self.spec.version[2]])
 
         # build tests
-        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+        options.append('-DMOFEM_UM_BUILD_TESTS={0}'.format(
             'ON' if self.run_tests else 'OFF'))
 
         return options
 
     # This function is not needed to run code installed by extension, nor in
-    # the install process. However for users like to have access to source code
+    # the install process. However, for users like to have access to source
-    # to play and make with it. Having source code at hand one can compile in
+    # code to play, change and make it. Having source code at hand one can
-    # own build directory it in mofem-cephas view when the extension is
+    # compile in own build directory it in package view when the extension is
     # activated.
     @run_after('install')
     def copy_source_code(self):

var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py

@@ -11,11 +11,12 @@ class MofemMinimalSurfaceEquation(CMakePackage):
     """mofem minimal surface equation"""
 
     homepage = "http://mofem.eng.gla.ac.uk"
-    git      = "https://bitbucket.org/likask/mofem_um_minimal_surface_equation.git"
+    git = "https://bitbucket.org/likask/mofem_um_minimal_surface_equation.git"
 
     maintainers = ['likask']
 
     version('develop', branch='develop')
+    version('0.3.10', tag='v0.3.10')
     version('0.3.9', tag='v0.3.9')
 
     variant('copy_user_modules', default=True,
@@ -40,7 +41,7 @@ def root_cmakelists_dir(self):
         :return: directory containing CMakeLists.txt
         """
         spec = self.spec
-        return spec['mofem-cephas'].prefix.users_modules
+        return spec['mofem-users-modules'].prefix.users_modules
 
     def cmake_args(self):
         spec = self.spec
@@ -58,15 +59,15 @@ def cmake_args(self):
             ('YES' if '+copy_user_modules' in spec else 'NO')])
 
         # build tests
-        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+        options.append('-DMOFEM_UM_BUILD_TESTS={0}'.format(
             'ON' if self.run_tests else 'OFF'))
 
         return options
 
     # This function is not needed to run code installed by extension, nor in
-    # the install process. However for users like to have access to source code
+    # the install process. However, for users like to have access to source
-    # to play and make with it. Having source code at hand one can compile in
+    # code to play, change and make it. Having source code at hand one can
-    # own build directory it in mofem-cephas view when the extension is
+    # compile in own build directory it in package view when the extension is
     # activated.
     @run_after('install')
     def copy_source_code(self):

var/spack/repos/builtin/packages/mofem-users-modules/package.py

@@ -9,25 +9,23 @@
 
 class MofemUsersModules(CMakePackage):
     """MofemUsersModules creates installation environment for user-provided
-    modules and extends of mofem-cephas package. The CMakeList.txt file for
+    modules and extends of mofem-cephas package. For more information how to
-    user modules is located in mofem-cephas/user_modules prefix.
+    work with Spack and MoFEM see
-    MofemUsersModules itself does not contain any code (is a dummy with a
-    single dummy version). It provide sources location of users modules, i.e.
-    mofem-fracture-module. Those are kept as a stand-alone package (instead
-    of resources) as they have different versions and developers. One can
-    install the extension, f.e. spack installs extension spack install
-    mofem-fracture-module. Next, create a symlink to run the code, f.e. spack
-    view symlink um_view mofem-cephas, and activate the extension, i.e. spack
-    activate um_view mofem-minimal-surface-equation. Basic mofem
-    functionality is available when with spack install mofem-users-modules,
-    it provides simple examples for calculating elasticity problems,
-    magnetostatics, saturated and unsaturated flow and a couple more. For
-    more information how to work with Spack and MoFEM see
     http://mofem.eng.gla.ac.uk/mofem/html/install_spack.html"""
 
     homepage = "http://mofem.eng.gla.ac.uk"
-    url = "https://bitbucket.org/likask/mofem-joseph/downloads/users_modules_dummy"
+    git = "https://likask@bitbucket.org/mofem/users-modules-cephas.git"
-    version('1.0', '5a8b22c9cdcad7bbad92b1590d55edb1', expand=False)
+
+    version('develop', branch='develop')
+    version('0.8.17', commit='60b2341f1635f595d571096dd8c70a7cf7538aeb')
+    version('0.8.16', commit='f6af51ad7db5b5dbc9d9acc6e753277a857c9f24')
+    version('0.8.15', commit='4843b2d92ec21ad100a8d637698f56b3a2e14af3')
+    version('0.8.14', commit='cfaa32133c574a31beaeb36202d033280521ddff')
+    version('0.8.12', commit='7b2ce5595a95d1b919f50103513c44bb2bc9e6d2')
+    version('0.8.11', commit='329b06d758137f1ec830f157d383b5ea415963de')
+    version('0.8.10', commit='ca03a8222b20f9c8ff93a2d6f4c3babbcfde2058')
+    version('0.8.8', commit='eb40f3c218badcd528ab08ee952835fb2ff07fd3')
+    version('0.8.7', commit='a83b236f26f258f4d6bafc379ddcb9503088df56')
 
     maintainers = ['likask']
 
@@ -35,18 +33,16 @@ class MofemUsersModules(CMakePackage):
         description='Copy user modules directory instead linking')
 
     extends('mofem-cephas')
-
+    depends_on('mofem-cephas@0.8.17', when='@0.8.17')
-    @property
+    depends_on('mofem-cephas@0.8.16', when='@0.8.16')
-    def root_cmakelists_dir(self):
+    depends_on('mofem-cephas@0.8.15', when='@0.8.15')
-        """The relative path to the directory containing CMakeLists.txt
+    depends_on('mofem-cephas@0.8.14', when='@0.8.14')
-
+    depends_on('mofem-cephas@0.8.12:0.8.13', when='@0.8.12')
-        This path is relative to the root of the extracted tarball,
+    depends_on('mofem-cephas@0.8.11', when='@0.8.11')
-        not to the ``build_directory``. Defaults to the current directory.
+    depends_on('mofem-cephas@0.8.10', when='@0.8.10')
-
+    depends_on('mofem-cephas@0.8.8:0.8.9', when='@0.8.8')
-        :return: directory containing CMakeLists.txt
+    depends_on('mofem-cephas@0.8.7', when='@0.8.7')
-        """
+    depends_on('mofem-cephas@develop', when='@develop')
-        spec = self.spec
-        return spec['mofem-cephas'].prefix.users_modules
 
     def cmake_args(self):
         spec = self.spec
@@ -55,12 +51,25 @@ def cmake_args(self):
 
         # obligatory options
         options.extend([
+            '-DMOFEM_DIR=%s' % spec['mofem-cephas'].prefix.users_module,
             '-DWITH_SPACK=YES',
             '-DSTAND_ALLONE_USERS_MODULES=%s' %
             ('YES' if '+copy_user_modules' in spec else 'NO')])
 
         # build tests
-        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+        options.append('-DMOFEM_UM_BUILD_TESTS={0}'.format(
             'ON' if self.run_tests else 'OFF'))
 
         return options
+
+    # This function is not needed to run code installed by extension, nor in
+    # the install process. However, the source code of users modules is
+    # necessary to compile other sub-modules. Also, for users like to have
+    # access to source code to play, change and make it. Having source code at
+    # hand one can compile in own build directory it in package view when the
+    # extension is activated.
+    @run_after('install')
+    def copy_source_code(self):
+        source = self.stage.source_path
+        prefix = self.prefix
+        install_tree(source, prefix.users_modules)