[dolfin] 02/04: Merge tag 'upstream/2016.2.0'
Johannes Ring
johannr-guest at moszumanska.debian.org
Fri Dec 2 11:08:33 UTC 2016
This is an automated email from the git hooks/post-receive script.
johannr-guest pushed a commit to branch master
in repository dolfin.
commit 8af2e3ae40a5d2a801efbfa1ec369bf852238396
Merge: 5b8a232 0f81084
Author: Johannes Ring <johannr at simula.no>
Date: Fri Dec 2 10:22:41 2016 +0100
Merge tag 'upstream/2016.2.0'
Upstream version 2016.2.0
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dolfin/io/X3DOM.h | 73 +-
dolfin/io/XDMFFile.cpp | 2688 +-
dolfin/io/XDMFFile.h | 262 +-
dolfin/io/XDMFxml.cpp | 539 -
dolfin/io/XDMFxml.h | 146 -
dolfin/io/XMLFile.cpp | 16 +-
dolfin/io/XMLTable.cpp | 61 +
dolfin/io/XMLTable.h | 4 +
dolfin/la/CMakeLists.txt | 98 +
dolfin/la/PETScKrylovSolver.cpp | 6 +-
dolfin/la/PETScLUSolver.cpp | 2 +-
dolfin/la/PETScLinearOperator.cpp | 4 +
dolfin/la/PETScObject.cpp | 57 +
dolfin/la/PETScObject.h | 16 +-
dolfin/la/PETScOptions.cpp | 15 +-
dolfin/la/PETScOptions.h | 19 +-
dolfin/log/CMakeLists.txt | 21 +
dolfin/math/CMakeLists.txt | 12 +
dolfin/mesh/CMakeLists.txt | 91 +
dolfin/mesh/Cell.h | 27 +-
dolfin/mesh/CellType.cpp | 24 +-
dolfin/mesh/CellType.h | 13 +-
dolfin/mesh/DistributedMeshTools.cpp | 33 +-
dolfin/mesh/DistributedMeshTools.h | 6 +-
dolfin/mesh/HexahedronCell.cpp | 3 +-
dolfin/mesh/HexahedronCell.h | 2 +-
dolfin/mesh/IntervalCell.cpp | 2 +-
dolfin/mesh/IntervalCell.h | 2 +-
dolfin/mesh/Mesh.cpp | 7 +
dolfin/mesh/Mesh.h | 3 +
dolfin/mesh/MeshEntity.h | 19 +-
dolfin/mesh/MeshFunction.h | 2 +-
dolfin/mesh/MeshGeometry.h | 8 -
dolfin/mesh/MeshOrdering.cpp | 4 +-
dolfin/mesh/MeshPartitioning.h | 3 +-
dolfin/mesh/MeshTopology.cpp | 2 +-
dolfin/mesh/MeshTopology.h | 6 +-
dolfin/mesh/PointCell.cpp | 2 +-
dolfin/mesh/PointCell.h | 2 +-
dolfin/mesh/QuadrilateralCell.cpp | 3 +-
dolfin/mesh/QuadrilateralCell.h | 2 +-
dolfin/mesh/TetrahedronCell.cpp | 2 +-
dolfin/mesh/TetrahedronCell.h | 2 +-
dolfin/mesh/TopologyComputation.cpp | 5 +-
dolfin/mesh/TriangleCell.cpp | 2 +-
dolfin/mesh/TriangleCell.h | 2 +-
dolfin/multistage/CMakeLists.txt | 12 +
dolfin/multistage/MultiStageScheme.cpp | 102 +-
dolfin/nls/CMakeLists.txt | 16 +
dolfin/nls/PETScSNESSolver.cpp | 47 +-
dolfin/nls/TAOLinearBoundSolver.cpp | 3 +
dolfin/parameter/CMakeLists.txt | 12 +
dolfin/plot/CMakeLists.txt | 25 +
dolfin/plot/VTKPlotter.h | 8 -
dolfin/refinement/CMakeLists.txt | 18 +
dolfin/refinement/LocalMeshCoarsening.cpp | 4 +-
dolfin/refinement/ParallelRefinement.cpp | 2 +-
dolfin/swig/CMakeLists.txt | 19 +-
dolfin/swig/adaptivity/docstrings.i | 2 +-
dolfin/swig/ale/docstrings.i | 2 +-
dolfin/swig/common/docstrings.i | 8 +-
dolfin/swig/common/pre.i | 23 +-
dolfin/swig/fem/docstrings.i | 31 +-
dolfin/swig/function/docstrings.i | 67 +-
dolfin/swig/function/post.i | 28 +-
dolfin/swig/function/pre.i | 77 +-
dolfin/swig/generation/docstrings.i | 2 +-
dolfin/swig/geometry/docstrings.i | 2 +-
dolfin/swig/graph/docstrings.i | 2 +-
dolfin/swig/io/docstrings.i | 124 +-
dolfin/swig/io/post.i | 3 +-
dolfin/swig/la/docstrings.i | 2 +-
dolfin/swig/la/post.i | 10 +-
dolfin/swig/log/docstrings.i | 2 +-
dolfin/swig/math/docstrings.i | 2 +-
dolfin/swig/mesh/docstrings.i | 29 +-
dolfin/swig/mesh/post.i | 21 +-
dolfin/swig/modules/common/CMakeLists.txt | 11 +-
dolfin/swig/modules/common/dependencies.txt | 2 +-
dolfin/swig/modules/common/module.i | 7 +-
dolfin/swig/modules/fem/CMakeLists.txt | 11 +-
dolfin/swig/modules/fem/dependencies.txt | 2 +-
dolfin/swig/modules/fem/module.i | 2 +-
dolfin/swig/modules/function/CMakeLists.txt | 11 +-
dolfin/swig/modules/function/dependencies.txt | 2 +-
dolfin/swig/modules/function/module.i | 2 +-
dolfin/swig/modules/io/CMakeLists.txt | 11 +-
dolfin/swig/modules/io/dependencies.txt | 2 +-
dolfin/swig/modules/io/module.i | 2 +-
dolfin/swig/modules/la/CMakeLists.txt | 11 +-
dolfin/swig/modules/la/dependencies.txt | 2 +-
dolfin/swig/modules/la/module.i | 2 +-
dolfin/swig/modules/mesh/CMakeLists.txt | 11 +-
dolfin/swig/modules/mesh/dependencies.txt | 2 +-
dolfin/swig/modules/mesh/module.i | 2 +-
dolfin/swig/multistage/docstrings.i | 2 +-
dolfin/swig/nls/docstrings.i | 2 +-
dolfin/swig/parameter/docstrings.i | 2 +-
dolfin/swig/parameter/post.i | 13 +-
dolfin/swig/plot/docstrings.i | 2 +-
dolfin/swig/refinement/docstrings.i | 2 +-
dolfin/swig/shared_ptr_classes.i | 1 +
dolfin/swig/typemaps/std_vector.i | 2 +
site-packages/dolfin/common/plotting.py | 44 +-
.../dolfin/compilemodules/compilemodule.py | 133 +-
site-packages/dolfin/compilemodules/expressions.py | 65 +-
site-packages/dolfin/compilemodules/jit.py | 26 +-
site-packages/dolfin/compilemodules/subdomains.py | 20 +-
.../dolfin/compilemodules/swigimportinfo.py | 1815 +-
site-packages/dolfin/deprecation.py | 13 -
site-packages/dolfin/fem/assembling.py | 39 +-
site-packages/dolfin/fem/bcs.py | 4 +-
site-packages/dolfin/fem/form.py | 24 +-
site-packages/dolfin/fem/formmanipulations.py | 37 +-
site-packages/dolfin/fem/norms.py | 3 +-
site-packages/dolfin/fem/projection.py | 29 +-
site-packages/dolfin/functions/__init__.py | 5 +-
site-packages/dolfin/functions/expression.py | 24 +-
site-packages/dolfin/functions/function.py | 14 +-
site-packages/dolfin/functions/functionspace.py | 134 +-
.../dolfin/functions/multimeshfunction.py | 126 +
site-packages/dolfin/importhandler/__init__.py | 2 +-
site-packages/dolfin_utils/cppparser/utils.py | 10 +-
site-packages/dolfin_utils/pjobs/pjobs.py | 23 +-
site-packages/dolfin_utils/test/skips.py | 17 +
test/codingstyle/test_coding_style.py.in | 2 +-
test/data/README | 5 +-
test/data/aneurysm.xml | 85368 +++++++++++++++++++
test/data/aneurysm.xml.gz | Bin 703208 -> 0 bytes
test/data/boxes.xml | 2473 +
test/data/boxes.xml.gz | Bin 16611 -> 0 bytes
test/data/doughnut.xml | 1072 +
test/data/doughnut.xml.gz | Bin 15843 -> 0 bytes
test/data/intersecting_surfaces.xml | 5515 ++
test/data/intersecting_surfaces.xml.gz | Bin 39191 -> 0 bytes
test/data/manifest.xml | 62 +
test/data/snake.xml | 9487 +++
test/data/snake.xml.gz | Bin 95055 -> 0 bytes
test/documentation/README | 1 -
test/documentation/test.py | 40 -
test/documentation/verify_demo_code_snippets.py | 196 -
test/regression/test.py | 36 +-
test/unit/CMakeLists.txt | 2 +-
test/unit/cpp/CMakeLists.txt | 12 +-
test/unit/cpp/function/Projection.h | 910 +-
test/unit/cpp/function/compile.log | 260 -
test/unit/cpp/la/forms/ReactionDiffusion.h | 296 +-
test/unit/cpp/la/forms/ReactionDiffusionAction.h | 275 +-
test/unit/cpp/la/forms/compile.log | 319 -
test/unit/python/book/test_chapter_10.py | 16 +-
test/unit/python/fem/test_assembler.py | 2 +-
test/unit/python/fem/test_dirichlet_bc.py | 2 +-
test/unit/python/fem/test_local_solver.py | 8 +-
test/unit/python/fem/test_manifolds.py | 2 +-
test/unit/python/fem/test_solving.py | 26 +
.../python/fem/test_symbolic_geometry_assembly.py | 15 +-
test/unit/python/fem/tetrahedron.xml | 15 +
test/unit/python/fem/tetrahedron.xml.gz | Bin 254 -> 0 bytes
test/unit/python/function/test_expression.py | 6 +-
test/unit/python/function/test_function_space.py | 41 +
test/unit/python/io/test_HDF5.py | 10 +
test/unit/python/io/test_XDMF.py | 366 +-
test/unit/python/io/test_XML_table.py | 48 +
test/unit/python/jit/test_jit.py | 4 +-
test/unit/python/la/test_petsc.py | 1 +
test/unit/python/mesh/test_cell.py | 17 +-
test/unit/python/mesh/test_mesh.py | 18 +-
test/unit/python/mesh/test_mesh_quality.py | 4 +-
test/unit/python/mesh/test_sub_domain.py | 28 +-
test/unit/python/mesh/test_sub_mesh.py | 2 +-
test/unit/python/multimesh/test_multimesh.py | 62 +
test/unit/python/nls/test_PETScSNES_solver.py | 4 +-
.../python/nls/test_TAO_linear_bound_solver.py | 2 +-
.../test_solve_result_against_reference.py | 6 +-
utils/pylit/LICENSE | 341 +
utils/pylit/README.rst | 51 +
utils/pylit/pylit.py | 1873 +
utils/x3dom/README.rst | 27 +
utils/x3dom/x3dom_support.css | 162 +
utils/x3dom/x3dom_support.js | 364 +
571 files changed, 173539 insertions(+), 160900 deletions(-)
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