FEniCS: update of packages to support 2019.1.0 (#21207)

3 files changed, 173 insertions, 119 deletions

diff --git a/var/spack/repos/builtin/packages/fenics/header_fix.patch b/var/spack/repos/builtin/packages/fenics/header_fix.patch
new file mode 100644
index 0000000000..f5622d7e9d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fenics/header_fix.patch
@@ -0,0 +1,36 @@
+From 3d3916e01f22c20eb4aa80d1ed784402a17422f6 Mon Sep 17 00:00:00 2001
+Date: Thu, 10 Sep 2020 23:16:31 +0200
+Subject: [PATCH] fixed compilation errors by adding the algorithm header
+
+---
+ dolfin/geometry/IntersectionConstruction.cpp | 1 +
+ dolfin/mesh/MeshFunction.h                   | 1 +
+ 2 files changed, 2 insertions(+)
+
+diff --git a/dolfin/geometry/IntersectionConstruction.cpp b/dolfin/geometry/IntersectionConstruction.cpp
+index 765dbb674..fe72ee5f6 100644
+--- a/dolfin/geometry/IntersectionConstruction.cpp
++++ b/dolfin/geometry/IntersectionConstruction.cpp
+@@ -18,6 +18,7 @@
+ // First added:  2014-02-03
+ // Last changed: 2017-12-12
+ 
++#include <algorithm> 	// fix compiling problem with min_element
+ #include <iomanip>
+ #include <dolfin/mesh/MeshEntity.h>
+ #include "predicates.h"
+diff --git a/dolfin/mesh/MeshFunction.h b/dolfin/mesh/MeshFunction.h
+index 08cbc824f..6d4a22f6e 100644
+--- a/dolfin/mesh/MeshFunction.h
++++ b/dolfin/mesh/MeshFunction.h
+@@ -26,6 +26,7 @@
+ 
+ #include <map>
+ #include <vector>
++#include <algorithm>	// EM: fix for compile error, line 652
+ 
+ #include <memory>
+ #include <unordered_set>
+-- 
+2.25.1
+
diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py
index 95fa85ef07..01a2f16019 100644
--- a/var/spack/repos/builtin/packages/fenics/package.py
+++ b/var/spack/repos/builtin/packages/fenics/package.py
@@ -10,26 +10,43 @@ class Fenics(CMakePackage):
     """FEniCS is organized as a collection of interoperable components
     that together form the FEniCS Project. These components include
     the problem-solving environment DOLFIN, the form compiler FFC, the
-    finite element tabulator FIAT, the just-in-time compiler Instant,
-    the code generation interface UFC, the form language UFL and a
-    range of additional components."""
+    finite element tabulator FIAT, the just-in-time compiler Instant / Dijitso,
+    the code generation interface UFC, the form language UFL and a range of
+    additional components."""
 
     homepage = "http://fenicsproject.org/"
-    url      = "https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-1.6.0.tar.gz"
-    base_url = "https://bitbucket.org/fenics-project/{pkg}/downloads/{pkg}-{version}.tar.gz"
-
-    python_components = ['ufl', 'ffc', 'fiat', 'instant']
-
+    git      = "https://bitbucket.org/fenics-project/dolfin.git"
+    url      = "https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-2019.1.0.post0.tar.gz"
+
+    version('2019.1.0.post0', sha256='61abdcdb13684ba2a3ba4afb7ea6c7907aa0896a46439d3af7e8848483d4392f')
+    version('2018.1.0.post1', sha256='425cc49b90e0f5c2ebdd765ba9934b1ada97e2ac2710d982d6d267a5e2c5982d')
+    # Pre 2018.1.0 versions are deprecated due to expected compatibility issues
+    version('2017.2.0.post0',
+            sha256='d3c40cd8c1c882f517999c25ea4220adcd01dbb1d829406fce99b1fc40184c82',
+            deprecated=True)
+    version('2016.2.0',
+            sha256='c6760996660a476f77889e11e4a0bc117cc774be0eec777b02a7f01d9ce7f43d',
+            deprecated=True)
+    version('1.6.0',
+            sha256='67f66c39983a8c5a1ba3c0787fa9b9082778bc7227b25c7cad80dc1299e0a201',
+            deprecated=True)
+
+    dolfin_versions = ['2019.1.0', '2018.1.0', '2017.2.0', '2016.2.0', '1.6.0']
+
+    variant('python',       default=True,  description='Compile with Python interface')
     variant('hdf5',         default=True,  description='Compile with HDF5')
     variant('parmetis',     default=True,  description='Compile with ParMETIS')
     variant('scotch',       default=True,  description='Compile with Scotch')
     variant('petsc',        default=True,  description='Compile with PETSc')
     variant('slepc',        default=True,  description='Compile with SLEPc')
-    variant('trilinos',     default=True,  description='Compile with Trilinos')
+    variant('petsc4py',     default=True,  description='Use PETSC4py')
+    variant('slepc4py',     default=True,  description='Use SLEPc4py')
+    variant('trilinos',     default=False, description='Compile with Trilinos')
     variant('suite-sparse', default=True,
             description='Compile with SuiteSparse solvers')
     variant('vtk',          default=False, description='Compile with VTK')
     variant('qt',           default=False, description='Compile with QT')
+    variant('zlib',         default=False, description='Compile with ZLIB')
     variant('mpi',          default=True,
             description='Enables the distributed memory support')
     variant('openmp',       default=True,
@@ -43,135 +60,105 @@ class Fenics(CMakePackage):
             values=('Debug', 'Release', 'RelWithDebInfo',
                     'MinSizeRel', 'Developer'))
 
-    # not part of spack list for now
-    # variant('petsc4py',     default=True,  description='Uses PETSc4py')
-    # variant('slepc4py',     default=True,  description='Uses SLEPc4py')
-    # variant('pastix',       default=True,  description='Compile with Pastix')
-
-    patch('petsc-3.7.patch', when='@1.6.1^petsc@3.7:')
-    patch('petsc-version-detection.patch', when='@:1.6.1')
-    patch('hdf5~cxx-detection.patch')
-
-    extends('python')
-
+    # Conflics for PETSC4PY / SLEPC4PY
+    conflicts('+petsc4py', when='~python')
+    conflicts('+petsc4py', when='~petsc')
+    conflicts('+slepc4py', when='~python')
+    conflicts('+slepc4py', when='~slepc')
+
+    # Patches
+    # patch('petsc-3.7.patch', when='petsc@3.7:')
+    patch('petsc-version-detection.patch', when='@1.6.0')
+    patch('hdf5~cxx-detection.patch', when='@:1.6.0')
+
+    patch('header_fix.patch', when='@2019.1.0.post0')
+    patch('petsc_3_11.patch', when='@2018.1.0.post1')
+
+    # enable extension support for fenics package
+    extends('python', when='+python')
+
+    # fenics python package dependencies
+    for ver in dolfin_versions:
+        wver = '@' + ver
+        depends_on('py-fenics-fiat{0}'.format(wver), type=('build', 'run'), when=wver + '+python')
+        if(Version(ver) < Version('2018.1.0')):
+            depends_on('py-fenics-instant{0}'.format(wver), type=('build', 'run'), when=wver + '+python')
+        else:
+            depends_on('py-fenics-dijitso{0}'.format(wver), type=('build', 'run'), when=wver + '+python')
+        depends_on('py-fenics-ufl{0}'.format(wver), type=('build', 'run'), when=wver + '+python')
+        if ver in ['2019.1.0', '2017.2.0']:
+            wver = '@' + ver + '.post0'
+        depends_on('py-fenics-ffc{0}'.format(wver), type=('build', 'run'), when=wver + '+python')
+
+    # package dependencies
+    depends_on('python@3.5:', type=('build', 'run'), when='+python')
     depends_on('eigen@3.2.0:')
-    depends_on('boost+filesystem+program_options+system+iostreams+timer+regex+chrono')
+    depends_on('pkgconfig', type='build')
+    depends_on('zlib', when='+zlib')
+
+    for ver in dolfin_versions:
+        if Version(ver) == Version('2019.1.0'):
+            depends_on('boost+filesystem+program_options+system+iostreams+timer+regex+chrono')
+        else:
+            depends_on('boost+filesystem+program_options+system+iostreams+timer+regex+chrono@1.68.0')
 
     depends_on('mpi', when='+mpi')
-    # FIXME: next line fixes concretization with petsc
     depends_on('hdf5+hl+fortran', when='+hdf5+petsc')
     depends_on('hdf5+hl', when='+hdf5~petsc')
-    depends_on('parmetis@4.0.2:', when='+parmetis')
     depends_on('metis+real64', when='+parmetis')
+    depends_on('parmetis', when='+parmetis')
     depends_on('scotch~metis', when='+scotch~mpi')
     depends_on('scotch+mpi~metis', when='+scotch+mpi')
-    depends_on('petsc@3.4:', when='+petsc')
-    depends_on('slepc@3.4:', when='+slepc')
+    depends_on('petsc', when='+petsc')
+    depends_on('slepc', when='+slepc')
+    depends_on('py-petsc4py@3.6:', when='+petsc+python')
     depends_on('trilinos', when='+trilinos')
     depends_on('vtk', when='+vtk')
     depends_on('suite-sparse', when='+suite-sparse')
     depends_on('qt', when='+qt')
 
-    depends_on('py-ply', type=('build', 'run'))
-    depends_on('py-six', type=('build', 'run'))
-    depends_on('py-numpy', type=('build', 'run'))
-    depends_on('py-sympy', type=('build', 'run'))
-    depends_on('swig@3.0.3:', type=('build', 'run'))
-    depends_on('cmake@2.8.12:', type='build')
+    depends_on('py-pybind11@2.2.4', type=('build', 'run'))
+    depends_on('cmake@3.17.3:', type='build')
 
-    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools', type='build', when='+python')
+    depends_on('py-pkgconfig', type=('build', 'run'), when='+python')
     depends_on('py-sphinx@1.0.1:', when='+doc', type='build')
 
-    releases = [
-        {
-            'version': '2016.1.0',
-            'sha256': '6228b4d641829a4cd32141bfcd217a1596a27d5969aa00ee64ebba2b1c0fb148',
-            'resources': {
-                'ffc': '52430ce4c7d57ce1b81eb5fb304992247c944bc6a6054c8b6f42bac81702578d',
-                'fiat': '851723126a71bc1ae2dc4ad6e9330bd9b54d52db390dcbbc1f3c759fb49c6aeb',
-                'instant': '7bf03c8a7b61fd1e432b8f3a0405410ae68892ebb1a62a9f8118e8846bbeb0c6',
-                'ufl': '8dccfe10d1251ba48a4d43a4c6c89abe076390223b500f4baf06f696294b8dd0',
-            }
-        },
-        {
-            'version': '1.6.0',
-            'sha256': '67eaac5fece6e71da0559b4ca8423156f9e99a952f0620adae449ebebb6695d1',
-            'resources': {
-                'ffc': '382e7713fe759694e5f07506b144eeead681e169e5a34c164ef3da30eddcc1c6',
-                'fiat': '858ea3e936ad3b3558b474ffccae8a7b9dddbaafeac77e307115b23753cb1cac',
-                'instant': '2347e0229531969095911fdb1de30bd77bdd7f81521ba84d81b1b4a564fc906c',
-                'ufl': 'c75c4781e5104504f158cb42cd87aceffa9052e8e9db6e9764e6a5b6115d7f73',
-            }
-        },
-    ]
-
-    for release in releases:
-        version(release['version'], release['sha256'], url=base_url.format(
-            pkg='dolfin', version=release['version']))
-        for rname, sha256 in release['resources'].items():
-            resource(name=rname,
-                     url=base_url.format(pkg=rname, **release),
-                     sha256=sha256,
-                     destination='depends',
-                     when='@{version}'.format(**release),
-                     placement=rname)
-
-    def cmake_is_on(self, option):
-        return 'ON' if option in self.spec else 'OFF'
-
     def cmake_args(self):
         return [
-            '-DDOLFIN_ENABLE_DOCS:BOOL={0}'.format(
-                self.cmake_is_on('+doc')),
-            '-DBUILD_SHARED_LIBS:BOOL={0}'.format(
-                self.cmake_is_on('+shared')),
-            '-DDOLFIN_SKIP_BUILD_TESTS:BOOL=ON',
-            '-DDOLFIN_ENABLE_OPENMP:BOOL={0}'.format(
-                self.cmake_is_on('+openmp')),
-            '-DDOLFIN_ENABLE_CHOLMOD:BOOL={0}'.format(
-                self.cmake_is_on('suite-sparse')),
-            '-DDOLFIN_ENABLE_HDF5:BOOL={0}'.format(
-                self.cmake_is_on('hdf5')),
-            '-DDOLFIN_ENABLE_MPI:BOOL={0}'.format(
-                self.cmake_is_on('mpi')),
-            '-DDOLFIN_ENABLE_PARMETIS:BOOL={0}'.format(
-                self.cmake_is_on('parmetis')),
-            '-DDOLFIN_ENABLE_PASTIX:BOOL={0}'.format(
-                self.cmake_is_on('pastix')),
-            '-DDOLFIN_ENABLE_PETSC:BOOL={0}'.format(
-                self.cmake_is_on('petsc')),
-            '-DDOLFIN_ENABLE_PETSC4PY:BOOL={0}'.format(
-                self.cmake_is_on('py-petsc4py')),
-            '-DDOLFIN_ENABLE_PYTHON:BOOL={0}'.format(
-                self.cmake_is_on('python')),
-            '-DDOLFIN_ENABLE_QT:BOOL={0}'.format(
-                self.cmake_is_on('qt')),
-            '-DDOLFIN_ENABLE_SCOTCH:BOOL={0}'.format(
-                self.cmake_is_on('scotch')),
-            '-DDOLFIN_ENABLE_SLEPC:BOOL={0}'.format(
-                self.cmake_is_on('slepc')),
-            '-DDOLFIN_ENABLE_SLEPC4PY:BOOL={0}'.format(
-                self.cmake_is_on('py-slepc4py')),
-            '-DDOLFIN_ENABLE_SPHINX:BOOL={0}'.format(
-                self.cmake_is_on('py-sphinx')),
-            '-DDOLFIN_ENABLE_TRILINOS:BOOL={0}'.format(
-                self.cmake_is_on('trilinos')),
-            '-DDOLFIN_ENABLE_UMFPACK:BOOL={0}'.format(
-                self.cmake_is_on('suite-sparse')),
-            '-DDOLFIN_ENABLE_VTK:BOOL={0}'.format(
-                self.cmake_is_on('vtk')),
-            '-DDOLFIN_ENABLE_ZLIB:BOOL={0}'.format(
-                self.cmake_is_on('zlib')),
+            self.define_from_variant('BUILD_SHARED_LIBS', 'shared'),
+            self.define('DOLFIN_SKIP_BUILD_TESTS', True),
+            self.define_from_variant('DOLFIN_ENABLE_OPENMP', 'openmp'),
+            self.define_from_variant('DOLFIN_ENABLE_CHOLMOD', 'suite-sparse'),
+            self.define_from_variant('DOLFIN_ENABLE_HDF5', 'hdf5'),
+            self.define_from_variant('DOLFIN_ENABLE_MPI', 'mpi'),
+            self.define_from_variant('DOLFIN_ENABLE_PARMETIS', 'parmetis'),
+            self.define_from_variant('DOLFIN_ENABLE_PETSC', 'petsc'),
+            self.define_from_variant('DOLFIN_ENABLE_PETSC4PY', 'petsc4py'),
+            self.define_from_variant('DOLFIN_ENABLE_PYTHON', 'python'),
+            self.define_from_variant('DOLFIN_ENABLE_QT', 'qt'),
+            self.define_from_variant('DOLFIN_ENABLE_SCOTCH', 'scotch'),
+            self.define_from_variant('DOLFIN_ENABLE_SLEPC', 'slepc'),
+            self.define_from_variant('DOLFIN_ENABLE_SLEPC4PY', 'slepc4py'),
+            self.define_from_variant('DOLFIN_ENABLE_DOCS', 'doc'),
+            self.define_from_variant('DOLFIN_ENABLE_SPHINX', 'doc'),
+            self.define_from_variant('DOLFIN_ENABLE_TRILINOS', 'trilinos'),
+            self.define_from_variant('DOLFIN_ENABLE_UMFPACK', 'suite-sparse'),
+            self.define_from_variant('DOLFIN_ENABLE_VTK', 'vtk'),
+            self.define_from_variant('DOLFIN_ENABLE_ZLIB', 'zlib'),
         ]
 
-    @run_after('build')
-    def build_python_components(self):
-        for package in self.python_components:
-            with working_dir(join_path('depends', package)):
-                setup_py('build')
+    # set environment for bulding python interface
+    def setup_build_environment(self, env):
+        env.set('DOLFIN_DIR', self.prefix)
+
+    def setup_run_environment(self, env):
+        env.set('DOLFIN_DIR', self.prefix)
 
+    # build python interface of dolfin
     @run_after('install')
-    def install_python_components(self):
-        for package in self.python_components:
-            with working_dir(join_path('depends', package)):
-                setup_py('install', '--prefix={0}'.format(self.prefix))
+    def install_python_interface(self):
+        if '+python' in self.spec:
+            with working_dir('python'):
+                setup_py('install', '--single-version-externally-managed',
+                         '--root=/', '--prefix={0}'.format(self.prefix))
diff --git a/var/spack/repos/builtin/packages/fenics/petsc_3_11.patch b/var/spack/repos/builtin/packages/fenics/petsc_3_11.patch
new file mode 100644
index 0000000000..98c0d94618
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fenics/petsc_3_11.patch
@@ -0,0 +1,31 @@
+diff --git a/dolfin/la/PETScOptions.h b/dolfin/la/PETScOptions.h
+index 37e5054b3..5ae24e6f5 100644
+--- a/dolfin/la/PETScOptions.h
++++ b/dolfin/la/PETScOptions.h
+@@ -22,7 +22,7 @@
+ 
+ #include <string>
+ #include <boost/lexical_cast.hpp>
+-#include <petscoptions.h>
++#include <petscsys.h>
+ #include <dolfin/common/SubSystemsManager.h>
+ #include <dolfin/log/log.h>
+ #include "PETScObject.h"
+diff --git a/dolfin/nls/PETScSNESSolver.cpp b/dolfin/nls/PETScSNESSolver.cpp
+index b3e1d62c5..43923ca7b 100644
+--- a/dolfin/nls/PETScSNESSolver.cpp
++++ b/dolfin/nls/PETScSNESSolver.cpp
+@@ -48,7 +48,10 @@ PETScSNESSolver::_methods
+ = { {"default",      {"default SNES method", ""}},
+     {"newtonls",     {"Line search method", SNESNEWTONLS}},
+     {"newtontr",     {"Trust region method", SNESNEWTONTR}},
++#if PETSC_VERSION_LT(3,9,0)
++    // SNESTEST functionality removed in petsc 3.9
+     {"test",         {"Tool to verify Jacobian approximation", SNESTEST}},
++#endif
+     {"ngmres",       {"Nonlinear generalised minimum residual method",
+                       SNESNGMRES}},
+     {"nrichardson",  {"Richardson nonlinear method (Picard iteration)",
+diff --git a/petsc_3_11.patch b/petsc_3_11.patch
+new file mode 100644
+index 000000000..e69de29bb