From a39ea97cd6f766e519ae9cdacc56b17867ed0190 Mon Sep 17 00:00:00 2001 From: Drew Parsons Date: Fri, 26 Oct 2018 11:45:58 +0800 Subject: [PATCH 1/1] Import mshr_2018.1.0+dfsg1-7.debian.tar.xz [dgit import tarball mshr 2018.1.0+dfsg1-7 mshr_2018.1.0+dfsg1-7.debian.tar.xz] --- changelog | 159 +++++++++++++++++++++++ compat | 1 + control | 74 +++++++++++ copyright | 25 ++++ docs | 1 + libmshr-dev.install | 5 + libmshr-dev.manpages | 1 + libmshr2018.1.install | 1 + mshrable.1 | 61 +++++++++ mshrable.sgml | 202 ++++++++++++++++++++++++++++++ patches/build_python.patch | 94 ++++++++++++++ patches/cmake_config_in_lib.patch | 15 +++ patches/demos_update.patch | 10 ++ patches/depython_main_build.patch | 23 ++++ patches/fix_mesh3_internal.patch | 27 ++++ patches/series | 6 + patches/test_controls.diff | 67 ++++++++++ python3-mshr.examples | 1 + python3-mshr.install | 1 + rules | 92 ++++++++++++++ source/format | 1 + tests/control | 3 + tests/test-mshr-python | 7 ++ watch | 3 + 24 files changed, 880 insertions(+) create mode 100644 changelog create mode 100644 compat create mode 100644 control create mode 100644 copyright create mode 100644 docs create mode 100644 libmshr-dev.install create mode 100644 libmshr-dev.manpages create mode 100644 libmshr2018.1.install create mode 100644 mshrable.1 create mode 100644 mshrable.sgml create mode 100644 patches/build_python.patch create mode 100644 patches/cmake_config_in_lib.patch create mode 100644 patches/demos_update.patch create mode 100644 patches/depython_main_build.patch create mode 100644 patches/fix_mesh3_internal.patch create mode 100644 patches/series create mode 100644 patches/test_controls.diff create mode 100644 python3-mshr.examples create mode 100644 python3-mshr.install create mode 100755 rules create mode 100644 source/format create mode 100644 tests/control create mode 100644 tests/test-mshr-python create mode 100644 watch diff --git a/changelog b/changelog new file mode 100644 index 0000000..2c111e5 --- /dev/null +++ b/changelog @@ -0,0 +1,159 @@ +mshr (2018.1.0+dfsg1-7) unstable; urgency=medium + + * Debian patch fix_mesh3_internal.patch updates namespace for + Mesh_3::internal::C3t3_initializer (CGAL 4.13). Closes: #911814. + + -- Drew Parsons Fri, 26 Oct 2018 11:45:58 +0800 + +mshr (2018.1.0+dfsg1-6) unstable; urgency=medium + + * apply strict versioned depends on pybind11, + python3-mshr Depends: pybind11 (>= 2.2.4), pybind11 (<= 2.2.5) + + -- Drew Parsons Tue, 25 Sep 2018 04:04:24 +0800 + +mshr (2018.1.0+dfsg1-5) unstable; urgency=medium + + * strip -g from dpkg-buildflags to reduce memory requirements of the + build (needed to build on Debian 32 bit and on ubuntu) + * Standards-Version: 4.2.1 + + -- Drew Parsons Tue, 04 Sep 2018 21:25:48 +0800 + +mshr (2018.1.0+dfsg1-4) unstable; urgency=medium + + * fix debian/tests: demos are now provided by python3-mshr + + -- Drew Parsons Sat, 11 Aug 2018 22:42:56 +0800 + +mshr (2018.1.0+dfsg1-3) unstable; urgency=medium + + * run autopkgtest on demos from mshr-demos package + - install demos in /usr/share/doc/mshr-demos/examples + * mark libmshr2018.1 as Multi-Arch: same + * drop mshr-demos (FTBFS on i386 interferes with package migration) + and install demos with python3-mshr. + + -- Drew Parsons Sat, 11 Aug 2018 02:47:12 +0800 + +mshr (2018.1.0+dfsg1-2) unstable; urgency=medium + + * Upload to unstable. Closes: #905369. + * Standards-Version: 4.2.0 + * Build-Depends: python3-setuptools + * Add debian/tests (autopkgtest) + - debian patch test_controls.diff provides test.py scripts + + -- Drew Parsons Sat, 04 Aug 2018 13:31:48 +0800 + +mshr (2018.1.0+dfsg1-1exp1) experimental; urgency=medium + + * New upstream release. + - debian patches applied upstream: + cgal_4.12.patch + tetgen_define_TETLIBRARY.patch + use_system_cgal_tetgen.patch + - removes python2 support (python-mshr is dropped) + - uses pybind11 instead of swig + * debian patch cmake_config_in_lib.patch places cmake config files + in lib not share, since MSHR_LIBRARIES_DIRS is arch-specific. + * apply dpkg-buildflags CXXFLAGS to cmake build (for hardening and + debug symbols) + * remove CGAL and tetgen licences from debian/copyright (these + 3rdParty sources have been removed from the source tarball) + * Standards-Version: 4.1.5 + * Build-Depends: python3-all-dev (i.e. add python3.7 support) + + -- Drew Parsons Tue, 10 Jul 2018 13:07:08 +0800 + +mshr (2017.2.0+dfsg1-1) unstable; urgency=medium + + * Upload mshr without embedded CGAL and tetgen code. Closes: #824716. + * debian/copyright Files-Excluded: 3rdparty/CGAL 3rdparty/tetgen1.5.0 + CGAL and tetgen are provided by their own packages, so exclude + them from mshr to save space. + * Debian patch cgal_4.12.patch builds against CGAL 4.12. + * Build against system CGAL and tetgen. + Thanks Johannes Ring (upstream branch + johannr/optional-use-system-packages, applied as Debian patch + use_system_cgal_tetgen.patch) + - Build-Depends: libcgal-dev (>= 4.12), libtet1.5-dev. + - debian patch tetgen_define_TETLIBRARY.patch ensures tetgen + library API is used (defines TETLIBRARY) + * Build-Depends: cmake (>= 3.5) + * Standards-Version: 4.1.4 + * Debian patch demos_update.patch keeps extrude demo running + + -- Drew Parsons Wed, 23 May 2018 03:10:08 +0800 + +mshr (2017.2.0-1) UNRELEASED; urgency=medium + + * Team upload. + * New upstream version. + * Standards-Version: 4.1.3 + * debhelper compatibility level 11 + + -- Drew Parsons Thu, 25 Jan 2018 16:59:08 +0800 + +mshr (2017.1.0-2) UNRELEASED; urgency=medium + + * Team upload. + * Standards-Version: 4.1.2 + * Provide python3 support in python3-mshr + + -- Drew Parsons Tue, 12 Dec 2017 14:56:09 +0800 + +mshr (2017.1.0-1) UNRELEASED; urgency=medium + + * Team upload. + + [ Johannes Ring ] + * New upstream release. + - Move debian/libmshr2016.2.install > debian/libmshr2017.1.install. + - Update package name for new SONAME 2017.1 (libmshr2016.2 -> + libmshr2017.1). + - Bump minimum required version of libdolfin-dev, python-ffc, + python-dolfin and dolfin-bin from 2016.2.0 to 2017.1.0. + + [ Drew Parsons ] + * Standards-Version: 4.1.0 + * debhelper compatibility level 10 + + -- Johannes Ring Thu, 11 May 2017 13:04:50 +0200 + +mshr (2016.2.0-1) UNRELEASED; urgency=medium + + * New upstream release. + - Move debian/libmshr2016.1.install > debian/libmshr2016.2.install. + - Update package name for new SONAME 2016.2 (libmshr2016.1 -> + libmshr2016.2). + - Bump minimum required version of libdolfin-dev, python-ffc, + python-dolfin and dolfin-bin from 2016.1.0 to 2016.2.0. + + -- Johannes Ring Fri, 02 Dec 2016 15:22:32 +0100 + +mshr (2016.1.0-2) UNRELEASED; urgency=medium + + * New upstream release. + * debian/control: + - Update package name for new SONAME 2016.1 (libmshr1.6 -> + libmshr2016.1). + - Bump minimum required version of libdolfin-dev, python-ffc, + python-dolfin and dolfin-bin from 1.6.0 to 2016.1.0. + - Add libproj-dev to Build-Depends and to Depends for binary package + libmshr-dev. + * Move debian/libmshr1.6.install -> debian/libmshr2016.1.install. + * Remove patch (fixed upstream). + * debian/rules: Add -fpermissive to CXX flags. + + -- Johannes Ring Fri, 02 Dec 2016 15:20:19 +0100 + +mshr (1.6.0-1) unstable; urgency=low + + [ Johannes Ring ] + * Initial release (Closes: #824716) + + [ Drew Parsons ] + * Team upload. + + -- Drew Parsons Fri, 20 May 2016 08:23:26 +0800 diff --git a/compat b/compat new file mode 100644 index 0000000..b4de394 --- /dev/null +++ b/compat @@ -0,0 +1 @@ +11 diff --git a/control b/control new file mode 100644 index 0000000..2867c2b --- /dev/null +++ b/control @@ -0,0 +1,74 @@ +Source: mshr +Section: math +Priority: optional +Maintainer: Debian Science Team +Uploaders: Johannes Ring , Drew Parsons +Build-Depends: debhelper (>= 11), + python3-all-dev, + dh-python, + python3-setuptools, + cmake (>= 3.5), + python3-pybind11 (>= 2.2.2), + libmpfr-dev, + libgmp-dev, + libcgal-dev (>= 4.13), + libtet1.5-dev, + libdolfin-dev (>= 2018.1), + python3-ffc (>= 2018.1), + python3-numpy, + python3-petsc4py, + python3-slepc4py, + libproj-dev +Standards-Version: 4.2.1 +X-Python3-Version: >= 3.5 +Homepage: http://fenicsproject.org +Vcs-Git: https://salsa.debian.org/science-team/fenics/mshr.git +Vcs-Browser: https://salsa.debian.org/science-team/fenics/mshr + +Package: libmshr2018.1 +Section: libs +Architecture: any +Multi-Arch: same +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: Shared libraries for mshr + mshr generates simplicial DOLFIN meshes in 2D and 3D from geometries + described by Constructive Solid Geometry (CSG) or from surface files, + utilizing CGAL and Tetgen as mesh generation backends. + . + This package contains the shared libraries. + +Package: libmshr-dev +Section: libdevel +Architecture: any +Depends: libmshr2018.1 (= ${binary:Version}), + libdolfin-dev (>= ${fenics:Upstream-Version}), + python3-ffc (>= ${fenics:Upstream-Version}), + cmake (>= 2.8.0), + libproj-dev, + ${shlibs:Depends}, + ${misc:Depends} +Description: Shared links and header files for mshr + mshr generates simplicial DOLFIN meshes in 2D and 3D from geometries + described by Constructive Solid Geometry (CSG) or from surface files, + utilizing CGAL and Tetgen as mesh generation backends. + . + This package contains the development files. + +Package: python3-mshr +Section: python +Architecture: any +Depends: libmshr-dev (= ${binary:Version}), + libmshr2018.1 (= ${binary:Version}), + python3-dolfin (>= ${fenics:Upstream-Version}), + dolfin-bin (>= ${fenics:Upstream-Version}), + python3-pybind11 (>= ${pybind11:Upstream-Version}), python3-pybind11 (<< ${pybind11:Next-Upstream-Version}), + ${python3:Depends}, + ${shlibs:Depends}, + ${misc:Depends} +Description: Python 3 interface for mshr + mshr generates simplicial DOLFIN meshes in 2D and 3D from geometries + described by Constructive Solid Geometry (CSG) or from surface files, + utilizing CGAL and Tetgen as mesh generation backends. + . + This package contains the Python 3 interface for mshr, and examples + and demo programs. diff --git a/copyright b/copyright new file mode 100644 index 0000000..bce0365 --- /dev/null +++ b/copyright @@ -0,0 +1,25 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: mshr +Source: http://fenicsproject.org +Comment: Lead Author: Benjamin Kehlet + Contributors: + Anders Logg + Johannes Ring + Garth N. Wells +Files-Excluded: 3rdparty/CGAL 3rdparty/tetgen1.5.0 + +Files: * +Copyright: © 2015 Benjamin Kehlet +License: GPL-3+ + +License: GPL-3+ + /usr/share/common-licenses/GPL-3 + +License: LGPL-3+ + /usr/share/common-licenses/LGPL-3 + +Files: debian/* +Copyright: © 2015 Johannes Ring , + 2016 Drew Parsons +License: GPL-2+ + /usr/share/common-licenses/GPL-2 diff --git a/docs b/docs new file mode 100644 index 0000000..a1320b1 --- /dev/null +++ b/docs @@ -0,0 +1 @@ +README.rst diff --git a/libmshr-dev.install b/libmshr-dev.install new file mode 100644 index 0000000..dcb8deb --- /dev/null +++ b/libmshr-dev.install @@ -0,0 +1,5 @@ +usr/lib/**/*.so +usr/include/mshr +usr/include/mshr.h +usr/lib/*/cmake/mshr/* +usr/bin/mshrable diff --git a/libmshr-dev.manpages b/libmshr-dev.manpages new file mode 100644 index 0000000..60ad814 --- /dev/null +++ b/libmshr-dev.manpages @@ -0,0 +1 @@ +debian/mshrable.1 diff --git a/libmshr2018.1.install b/libmshr2018.1.install new file mode 100644 index 0000000..8755c99 --- /dev/null +++ b/libmshr2018.1.install @@ -0,0 +1 @@ +usr/lib/**/lib*.so.* diff --git a/mshrable.1 b/mshrable.1 new file mode 100644 index 0000000..336f2f8 --- /dev/null +++ b/mshrable.1 @@ -0,0 +1,61 @@ +.TH "MSHRABLE" "1" +.SH "NAME" +mshrable \(em Generate mesh from surface file +.SH "SYNOPSIS" +.PP +\fBmshrable\fR [\-f \fIFILE\fR] +.SH "DESCRIPTION" +.PP +\fBmshrable\fR generates a mesh from a +surface file. It uses mshr, which is the mesh generation +component of FEniCS. It generates simplicial DOLFIN meshes in 2D +and 3D from geometries described by Constructive Solid Geometry +(CSG) or from surface files, utilizing CGAL and Tetgen as mesh +generation backends. + +.SH "OPTIONS" +.PP + +.IP "\-o [\-\-outfile] \fIarg\fR" 10 +Filename of generated Dolfin mesh. + +.IP "\-r [\-\-resolution] \fIarg (=15)\fR" 10 +Resolution of result mesh. + +.IP "\-s [\-\-stats]" 10 +Write some statistics of the mesh to stdout. + +.IP "\-\-polyout \fIarg\fR" 10 +Write the polyhedron to .poly which Tetgen can read +(and do not create a mesh). + +.IP "\-\-polystats" 10 +Write statistics of polyhedron (and do not create a +mesh). + +.IP "\-b [\-\-backend] \fIarg (=cgal)\fR" 10 +Use 3D mesh generation backend [tetgen|cgal]. + +.IP "\-\-degenerate_tolerance \fIarg (=9.9999999999999998e-13)\fR" 10 +Tolerance for considering a facet as degenerate. Set +to 0 to not remove degenerate facets. + +.IP "\-\-check-mesh" 10 +Check consistency of output mesh (most for debugging/testing. + +.IP "\-v [\-\-verbose]" 10 +Output more information about what is going on. + +.IP "\-h [\-\-help]" 10 +write help message. + +.SH "SEE ALSO" +.PP +dolfin-convert (1), dolfin-order (1) +.SH "AUTHOR" +.PP +\fBmshrable\fR was written by Benjamin +Kehlet benjamik@simula.no. This man page was written by +Drew Parsons dparsons@debian.org. + +.\" created by instant / docbook-to-man diff --git a/mshrable.sgml b/mshrable.sgml new file mode 100644 index 0000000..a7c8f4a --- /dev/null +++ b/mshrable.sgml @@ -0,0 +1,202 @@ +Drew"> + Parsons"> + + 19 May, 2016"> + 1"> + dparsons@debian.org"> + + MSHRABLE"> + + + Debian GNU/Linux"> + GNU"> +]> + + + + + +
+ &dhemail; +
+ + &dhfirstname; + &dhsurname; + + + 2001 + &dhusername; + + &dhdate; + + + &dhucpackage; + + &dhsection; + + + &dhpackage; + + Generate mesh from surface file + + + + &dhpackage; + -f FILE + + + + + DESCRIPTION + + &dhpackage; generates a mesh from a + surface file. It uses mshr, which is the mesh generation + component of FEniCS. It generates simplicial DOLFIN meshes in 2D + and 3D from geometries described by Constructive Solid Geometry + (CSG) or from surface files, utilizing CGAL and Tetgen as mesh + generation backends. + + + + + OPTIONS + + + + -o [--outfile] arg + + + Filename of generated Dolfin mesh. + + + + + + -r [--resolution] arg (=15) + + + Resolution of result mesh. + + + + + + -s [--stats] + + + Write some statistics of the mesh to stdout. + + + + + + --polyout arg + + + Write the polyhedron to .poly which Tetgen can read + (and do not create a mesh). + + + + + + --polystats + + + Write statistics of polyhedron (and do not create a + mesh). + + + + + + -b [--backend] arg (=cgal) + + + Use 3D mesh generation backend [tetgen|cgal]. + + + + + + --degenerate_tolerance arg (=9.9999999999999998e-13) + + + Tolerance for considering a facet as degenerate. Set + to 0 to not remove degenerate facets. + + + + + + --check-mesh + + + Check consistency of output mesh (most for debugging/testing. + + + + + + -v [--verbose] + + + Output more information about what is going on. + + + + + + -h [--help] + + + write help message. + + + + + + + + + SEE ALSO + + dolfin-convert (1), dolfin-order (1) + + + AUTHOR + &dhpackage; was written by Benjamin + Kehlet benjamik@simula.no. This man page was written by + &dhusername; &dhemail;. + + + + + + + + + + diff --git a/patches/build_python.patch b/patches/build_python.patch new file mode 100644 index 0000000..93207f6 --- /dev/null +++ b/patches/build_python.patch @@ -0,0 +1,94 @@ +Index: mshr/python/CMakeLists.txt +=================================================================== +--- mshr.orig/python/CMakeLists.txt ++++ mshr/python/CMakeLists.txt +@@ -7,6 +7,8 @@ cmake_minimum_required(VERSION 3.5.0) + + PROJECT(mshr_pybind11_config) + ++# Add cmake directory to mshr module path ++list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake") + + # pybind11_FOUND - true if pybind11 and all required components found on the system + # pybind11_VERSION - pybind11 version in format Major.Minor.Release +@@ -23,7 +25,7 @@ find_package(pybind11 CONFIG HINTS ${PYB + + find_package(DOLFIN) + +-find_package(mshr) ++find_package(mshr MODULE) + + configure_file("config.json.in" "config.json") + +Index: mshr/python/cmake/Findmshr.cmake +=================================================================== +--- /dev/null ++++ mshr/python/cmake/Findmshr.cmake +@@ -0,0 +1,51 @@ ++#.rst: ++# Findmshr ++# -------- ++# ++# Find mshr library ++# ++# Find the mshr includes and library. This module defines ++# ++# :: ++# ++# mshr_INCLUDE_DIRS, where to find mshr.h. ++# mshr_LIBRARIES, libraries to link against to use mshr ++# mshr_FOUND, If false (0), do not try to use mshr. ++# ++# ++# ++# ++# ++#============================================================================= ++find_path(mshr_INCLUDE_DIR mshr.h ++ DOC "The mshr include directory") ++ ++set(mshr_NAMES ${mshr_NAMES} libmshr mshr) ++find_library(mshr_LIBRARY NAMES ${mshr_NAMES} ++ DOC "The mshr library") ++ ++# handle the QUIETLY and REQUIRED arguments and set mshr_FOUND to TRUE if ++# all listed variables are TRUE ++include(FindPackageHandleStandardArgs) ++FIND_PACKAGE_HANDLE_STANDARD_ARGS(mshr ++ REQUIRED_VARS mshr_LIBRARY ++ mshr_INCLUDE_DIR ++ VERSION_VAR mshr_VERSION_STRING) ++ ++if(mshr_FOUND) ++ # FIND_PACKAGE_HANDLE_STANDARD_ARGS sets mshr_FOUND to TRUE not 1 ++ # which interferes with the json in config.json (must be true not TRUE) ++ # So set to 1 (following find_package(DOLFIN) ) ++ set( mshr_FOUND 1 ) ++ # use by setuptools.Extension, mshr_LIBRARIES must be in a form that appends to -l ++ # i.e. mshr not libmshr.so ++ set( mshr_LIBRARIES "mshr" ) ++ get_filename_component( mshr_LIBRARIES_DIRS ${mshr_LIBRARY} DIRECTORY ) ++ set( mshr_INCLUDE_DIRS ${mshr_INCLUDE_DIR} ) ++else() ++ set( mshr_FOUND 0) ++ set( mshr_LIBRARIES_DIRS "." ) ++ set( mshr_INCLUDE_DIRS "." ) ++endif() ++ ++mark_as_advanced(mshr_INCLUDE_DIR mshr_LIBRARY) +Index: mshr/python/setup.py +=================================================================== +--- mshr.orig/python/setup.py ++++ mshr/python/setup.py +@@ -9,7 +9,10 @@ from setuptools import setup, Extension + if not os.path.isfile(os.path.join("build", "config.json")) : + if not os.path.exists("build") : + os.mkdir("build") +- subprocess.check_call(["cmake", os.getcwd()], cwd=os.path.abspath("build")) ++ cmake_command=["cmake", os.getcwd()] ++ if os.environ.get('CMAKE_PREFIX_PATH'): ++ cmake_command.extend(['-DCMAKE_PREFIX_PATH={}'.format(os.environ['CMAKE_PREFIX_PATH'])]) ++ subprocess.check_call(cmake_command, cwd=os.path.abspath("build")) + + with open(os.path.join("build", "config.json"), 'r') as infile : + config = json.load(infile) diff --git a/patches/cmake_config_in_lib.patch b/patches/cmake_config_in_lib.patch new file mode 100644 index 0000000..0a52fe4 --- /dev/null +++ b/patches/cmake_config_in_lib.patch @@ -0,0 +1,15 @@ +Index: mshr/CMakeLists.txt +=================================================================== +--- mshr.orig/CMakeLists.txt ++++ mshr/CMakeLists.txt +@@ -218,8 +218,8 @@ configure_file(mshr-config.cmake.in + "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/mshr-config.cmake" @ONLY) + + # Install the FooBarConfig.cmake and FooBarConfigVersion.cmake +-install(FILES "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/mshrConfig.cmake" DESTINATION "${SHARE_DIR}/cmake" COMPONENT dev) +-install(FILES "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/mshr-config.cmake" DESTINATION "${SHARE_DIR}/cmake" COMPONENT dev) ++install(FILES "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/mshrConfig.cmake" DESTINATION "${INSTALL_LIB_DIR}/cmake/mshr" COMPONENT dev) ++install(FILES "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/mshr-config.cmake" DESTINATION "${INSTALL_LIB_DIR}/cmake/mshr" COMPONENT dev) + #install(FILES "Use-mshr.cmake" DESTINATION "${INSTALL_CMAKE_DIR}" COMPONENT dev) + + diff --git a/patches/demos_update.patch b/patches/demos_update.patch new file mode 100644 index 0000000..480d148 --- /dev/null +++ b/patches/demos_update.patch @@ -0,0 +1,10 @@ +Index: mshr/demo/python/extrude.py +=================================================================== +--- mshr.orig/demo/python/extrude.py ++++ mshr/demo/python/extrude.py +@@ -27,4 +27,4 @@ g3d = mshr.Extrude2D(g2d, + .2) # The z "thickness" + + m = mshr.generate_mesh(g3d, 15) +-plot(m, interactive=True) ++plot(m) diff --git a/patches/depython_main_build.patch b/patches/depython_main_build.patch new file mode 100644 index 0000000..22f81c3 --- /dev/null +++ b/patches/depython_main_build.patch @@ -0,0 +1,23 @@ +Index: mshr/CMakeLists.txt +=================================================================== +--- mshr.orig/CMakeLists.txt ++++ mshr/CMakeLists.txt +@@ -91,7 +91,6 @@ include_directories(BEFORE ${EXTERNAL_IN + add_definitions("${EXTERNAL_DEFINITIONS}") + + find_package(DOLFIN REQUIRED) +-include_directories(${DOLFIN_PYTHON_INCLUDE_DIRS}) + include(${DOLFIN_USE_FILE}) + + # Set installation directories +@@ -196,8 +195,8 @@ file(RELATIVE_PATH REL_INCLUDE_DIR "${IN + ### add cmake configuration file ### + + # common for both config files +-set(CONF_EXTERNAL_INCLUDE_DIRS "${DOLFIN_PYTHON_INCLUDE_DIRS};${DOLFIN_INCLUDE_DIRS};${DOLFIN_3RD_PARTY_INCLUDE_DIRS}") +-set(CONF_EXTERNAL_LIBRARIES "${DOLFIN_PYTHON_LIBRARIES};${DOLFIN_LIBRARIES};${DOLFIN_3RD_PARTY_LIBRARIES}") ++set(CONF_EXTERNAL_INCLUDE_DIRS "${DOLFIN_INCLUDE_DIRS};${DOLFIN_3RD_PARTY_INCLUDE_DIRS}") ++set(CONF_EXTERNAL_LIBRARIES "${DOLFIN_LIBRARIES};${DOLFIN_3RD_PARTY_LIBRARIES}") + set(CONF_CXX_DEFINITIONS "${DOLFIN_CXX_DEFINITIONS}") + string(REPLACE "\"" "\\\"" CONF_CXX_DEFINITIONS "${CONF_CXX_DEFINITIONS}") + set(CONF_CXX_FLAGS "${DOLFIN_CXX_FLAGS}") diff --git a/patches/fix_mesh3_internal.patch b/patches/fix_mesh3_internal.patch new file mode 100644 index 0000000..4309896 --- /dev/null +++ b/patches/fix_mesh3_internal.patch @@ -0,0 +1,27 @@ +Index: mshr/src/make_multicomponent_mesh_3.h +=================================================================== +--- mshr.orig/src/make_multicomponent_mesh_3.h ++++ mshr/src/make_multicomponent_mesh_3.h +@@ -37,11 +37,11 @@ void make_multicomponent_mesh_3_impl(C3T + //std::cout << "Number of vertices initially: " << c3t3.triangulation().number_of_vertices() << std::endl; + + // Initialize c3t3 with points from the special features +- CGAL::internal::Mesh_3::C3t3_initializer< ++ CGAL::Mesh_3::internal::C3t3_initializer< + C3T3, + MeshDomain, + MeshCriteria, +- CGAL::internal::Mesh_3::has_Has_features::value > () (c3t3, ++ CGAL::Mesh_3::internal::has_Has_features::value > () (c3t3, + domain, + criteria, + with_features); +@@ -49,7 +49,7 @@ void make_multicomponent_mesh_3_impl(C3T + // std::cout << "Number of vertices after features: " << c3t3.triangulation().number_of_vertices() << std::endl; + + // Inserts points from all connected components to the mesh +- CGAL::internal::Mesh_3::init_c3t3(c3t3, domain, criteria, 0); ++ CGAL::Mesh_3::internal::init_c3t3(c3t3, domain, criteria, 0); + // std::cout << "Number of vertices before meshing: " << c3t3.triangulation().number_of_vertices() << std::endl; + + // Build mesher and launch refinement process diff --git a/patches/series b/patches/series new file mode 100644 index 0000000..2436c48 --- /dev/null +++ b/patches/series @@ -0,0 +1,6 @@ +demos_update.patch +cmake_config_in_lib.patch +build_python.patch +depython_main_build.patch +test_controls.diff +fix_mesh3_internal.patch diff --git a/patches/test_controls.diff b/patches/test_controls.diff new file mode 100644 index 0000000..54d7dae --- /dev/null +++ b/patches/test_controls.diff @@ -0,0 +1,67 @@ +Index: mshr/demo/python/test.py +=================================================================== +--- /dev/null ++++ mshr/demo/python/test.py +@@ -0,0 +1,27 @@ ++import os ++import pathlib ++import subprocess ++import sys ++import pytest ++ ++ ++# Get directory of this file ++dir_path = pathlib.Path(__file__).resolve().parent ++ ++# Build list of demo programs ++demos = [] ++for subdir in ['.']: ++ p = pathlib.Path(dir_path, subdir) ++ demo_files = list(p.glob('*.py')) ++ for f in demo_files: ++ demos.append((f.parent, f.name)) ++ ++ ++@pytest.mark.parametrize("path,name", demos) ++def test_demos(path, name): ++ ++ # Run in serial ++ ret = subprocess.run([sys.executable, name], ++ cwd=str(path), ++ env={**os.environ, 'MPLBACKEND': 'agg'}, ++ check=True) +Index: mshr/test/test.py +=================================================================== +--- /dev/null ++++ mshr/test/test.py +@@ -0,0 +1,30 @@ ++import os ++import pathlib ++import subprocess ++import sys ++import pytest ++ ++ ++# Get directory of this file ++dir_path = pathlib.Path(__file__).resolve().parent ++ ++# Build list of demo programs ++tests = [] ++for subdir in ['.']: ++ p = pathlib.Path(dir_path, subdir) ++ test_files = list(p.glob('**/*.py')) ++ for f in test_files: ++ tests.append((f.parent, f.name)) ++ ++ ++# remove tests that are known to break ++tests = [d for d in tests if d[1] != 'test-fuzzypointmap.py'] ++ ++ ++@pytest.mark.parametrize("path,name", tests) ++def test_demos(path, name): ++ ++ ret = subprocess.run([sys.executable, name], ++ cwd=str(path), ++ env={**os.environ, 'MPLBACKEND': 'agg'}, ++ check=True) diff --git a/python3-mshr.examples b/python3-mshr.examples new file mode 100644 index 0000000..4b02f7b --- /dev/null +++ b/python3-mshr.examples @@ -0,0 +1 @@ +demo/python/* diff --git a/python3-mshr.install b/python3-mshr.install new file mode 100644 index 0000000..7aadc9c --- /dev/null +++ b/python3-mshr.install @@ -0,0 +1 @@ +usr/lib/python3*/*-packages/* diff --git a/rules b/rules new file mode 100755 index 0000000..cfbb048 --- /dev/null +++ b/rules @@ -0,0 +1,92 @@ +#!/usr/bin/make -f + +# FIXME: Is this needed? +#CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) +#CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) +#CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) $(CPPFLAGS) +#LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) + +DEB_BUILD_MULTIARCH ?= $(shell dpkg-architecture -qDEB_BUILD_MULTIARCH) + +MSHR_HOME = $(CURDIR)/$(DEB_SRCDIR) +USCAN_DESTDIR := $(CURDIR) +PY3VERS := $(shell py3versions --requested debian/control | tac -s' ') +PYVERS = $(PY3VERS) + +DEB_VERSION := $(shell dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ') +DEB_NOEPOCH_VERSION := $(shell echo $(DEB_VERSION) | cut -d: -f2-) +DEB_UPSTREAM_VERSION := $(shell echo $(DEB_NOEPOCH_VERSION) | sed 's/-[^-]*$$//') +DEB_STRIPPED_UPSTREAM_VERSION = $(shell echo $(DEB_UPSTREAM_VERSION) | sed -e 's/\+dfsg.*$$//p') + +FENICS_RELEASE_VERSION=$(DEB_STRIPPED_UPSTREAM_VERSION) +FENICS_MAJOR_VERSION=$(shell echo $(FENICS_RELEASE_VERSION) | sed "s/^\([^.]*\)\..*$$/\1/") +FENICS_MINOR_VERSION=$(shell echo $(FENICS_RELEASE_VERSION) | sed "s/^\([^.]*\)\.\([^.]*\)\..*$$/\2/") +FENICS_VERSION=$(FENICS_MAJOR_VERSION).$(FENICS_MINOR_VERSION) +FENICS_NEXT_VERSION=$(FENICS_MAJOR_VERSION).$(shell echo $$(( $(FENICS_MINOR_VERSION) + 1 )) ) + +# dolfin has a strict dependency on the pybind11 version it was built against, +# if pybind11.h will be used in C++ code fragments in python scripts. +# Extract pybind11 version from pybind11-dev +PYBIND11_DEB_VERSION=$(shell dpkg -s pybind11-dev | awk '/Version:/ {print $$2}') +# extract the current pybind11 version X.Y.Z (drop epoch and debian package version) +PYBIND11_UPSTREAM_VERSION=$(shell echo $(PYBIND11_DEB_VERSION) | sed "s/^.[^:]*://; s/-[^-]*$$//") +PYBIND11_X_Y_VERSION=$(shell echo $(PYBIND11_UPSTREAM_VERSION) | sed "s/^\(.*\)\.\([^.]*\)$$/\1/") +PYBIND11_Z_VERSION=$(shell echo $(PYBIND11_UPSTREAM_VERSION) | sed "s/^\(.*\)\.\([^.]*\)$$/\2/") +PYBIND11_NEXT_UPSTREAM_VERSION=$(PYBIND11_X_Y_VERSION).$(shell echo $$(( $(PYBIND11_Z_VERSION) + 1 )) ) + +# strip -g from dpkg-buildflags to reduce memory requirements of the build (needed to build on Debian 32 bit and on ubuntu) +CMAKE_OPTS := \ + -D CMAKE_BUILD_TYPE:STRING=Release \ + -D BUILD_SHARED_LIBS:BOOL=ON \ + -D USE_SYSTEM_CGAL:BOOL=ON \ + -D USE_SYSTEM_TETGEN:BOOL=ON \ + -D ENABLE_MSHRABLE:BOOL=ON \ + -D CMAKE_SKIP_RPATH:BOOL=ON \ + -D CMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=OFF \ + -D INSTALL_LIB_DIR:PATH=lib/$(DEB_BUILD_MULTIARCH) \ + -D CMAKE_CXX_FLAGS:STRING="-fpermissive $(shell dpkg-buildflags --get CXXFLAGS | sed 's/-g //' )" \ + $(MSHR_HOME) + +ifeq (,$(DISTRIBUTION)) + DISTRIBUTION := $(shell dpkg-parsechangelog --format rfc822 | sed -ne "s/^Distribution: //p") +endif + +ifneq ($(DISTRIBUTION),$(findstring $(DISTRIBUTION),"squeeze wheezy lucid maverick natty oneiric precise quantal raring saucy trusty")) + DISTRIBUTION := sid +endif + +%: + dh $@ --buildsystem=cmake \ + --with python3 + +override_dh_auto_clean: + dh_auto_clean + rm -rf python/build* + +override_dh_auto_configure: + dh_auto_configure -- $(CMAKE_OPTS) ;\ + +override_dh_auto_install: + dh_auto_install + set -e; \ + for v in $(PYVERS); do \ + cd python; \ + CMAKE_PREFIX_PATH=$(CURDIR)/debian/tmp/usr $$v setup.py build --build-base=$(CURDIR)/python/build-$$v install --root=$(CURDIR)/debian/tmp --install-layout=deb; \ + cd ..; \ + done + dh_numpy3 + +override_dh_gencontrol: + dh_gencontrol -- -Vfenics:Upstream-Version=$(FENICS_VERSION) \ + -Vpybind11:Upstream-Version=$(PYBIND11_UPSTREAM_VERSION) -Vpybind11:Next-Upstream-Version=$(PYBIND11_NEXT_UPSTREAM_VERSION) + +# debug symbols (-g) have been switched off in CMAKE_OPTS, so no point building dbgsym packages +override_dh_strip: + dh_strip --no-automatic-dbgsym + +#override_dh_shlibdeps: +# dh_shlibdeps --dpkg-shlibdeps-params=--ignore-missing-info + +.PHONY: get-orig-source +get-orig-source: + uscan --force-download --verbose --destdir $(USCAN_DESTDIR) diff --git a/source/format b/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/tests/control b/tests/control new file mode 100644 index 0000000..ecdbff4 --- /dev/null +++ b/tests/control @@ -0,0 +1,3 @@ +Tests: test-mshr-python +Depends: python3-mshr, + python3-pytest diff --git a/tests/test-mshr-python b/tests/test-mshr-python new file mode 100644 index 0000000..5635b88 --- /dev/null +++ b/tests/test-mshr-python @@ -0,0 +1,7 @@ +echo "=== python unit tests ===" +python3 -m pytest -v test/test.py + +echo "=== python demo tests ===" +DEMO_TEST_DIR=test-mshr-demos +cp -r /usr/share/doc/python3-mshr/examples ${DEMO_TEST_DIR} +python3 -m pytest -v ${DEMO_TEST_DIR}/test.py diff --git a/watch b/watch new file mode 100644 index 0000000..0bfb33d --- /dev/null +++ b/watch @@ -0,0 +1,3 @@ +version=3 +opts=dversionmangle=s/\+dfsg\d*$//,repacksuffix=+dfsg1 \ +https://bitbucket.org/fenics-project/mshr/downloads/mshr-(.*)\.tar\.gz -- 2.30.2