--- /dev/null
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+
+reprotest:
+ allow_failure: true
+
+blhc:
+ allow_failure: true
+
+piuparts:
+ allow_failure: true
--- /dev/null
+64-bit Mshr/Dolfin
+-------------
+
+64-bit support is provided by python3-mshr64-real and libmshr64-dev.
+
+64-bit here refers to 64-bit indexing provided by a 64-bit build of
+PETSc, allowing handling of larger systems (larger meshes) with more
+than 2 billion degress of freedom. It is provided in Dolfin by the
+python3-dolfin64-real and libdolfin64-dev packages (libdolfin64.so).
+
+This is activated by setting PETSC_DIR and SLEPC_DIR to appropriate paths,
+e.g.
+ PETSC_DIR=/usr/lib/petsc64
+ SLEPC_DIR=/usr/lib/slepc64
+
+Depending on usage you may also need to specific the dolfin libname
+extension ("64") to link to libdolfin64.so rather than libdolfin.so.
+This is controlled via DOLFIN_LIB_NAME_EXT. Likewise, linking with
+libmshr64.so is facilitated via MSHR_LIB_NAME_EXT.
+For cmake (C++ applications), set the cmake variable
+ cmake -DMSHR_LIB_NAME_EXT=64 -DDOLFIN_LIB_NAME_EXT=64
+For python, set it as an environment variable
+ MSHR_LIB_NAME_EXT=64 DOLFIN_LIB_NAME_EXT=64 python3
+
+Each of PETSC_DIR (SLEPC_DIR), MSHR_LIB_NAME_EXT and
+DOLFIN_LIB_NAME_EXT need to be set to ensure the program links to
+libpetsc64_*.so, libmshr64.so and libdolfin64.so, and not their 32-bit
+counterparts.
+
+python3-mshr is now a base package providing a mshr.pth pointing by
+default at the preferred PETSc installation provided by
+python3-mshr-real (for PETSC_DIR=/usr/lib/petsc
+SLEPC_DIR=/usr/lib/slepc).
--- /dev/null
+mshr (2019.2.0~git20200924.c27eb18+dfsg1-7+rpi1) bookworm-staging; urgency=medium
+
+ * Link with libatomic.
+
+ -- Peter Michael Green <plugwash@raspbian.org> Sun, 24 Apr 2022 21:08:59 +0000
+
+mshr (2019.2.0~git20200924.c27eb18+dfsg1-7) unstable; urgency=medium
+
+ * drop PETSC_ARCH from mshr.pth. It is only used for local build
+ dirs, not in full installation, and interferes with python
+ initialization when PETSc is in the middle of an ABI upgrade.
+
+ -- Drew Parsons <dparsons@debian.org> Fri, 12 Nov 2021 22:37:14 +0100
+
+mshr (2019.2.0~git20200924.c27eb18+dfsg1-6) unstable; urgency=medium
+
+ * Standards-Version: 4.6.0
+
+ -- Drew Parsons <dparsons@debian.org> Sat, 23 Oct 2021 21:09:15 +0200
+
+mshr (2019.2.0~git20200924.c27eb18+dfsg1-5) unstable; urgency=medium
+
+ * include PETSC_ARCH in mshr.pth to prevent mshr from interfering
+ with new PETSc builds. mshr.pth checks
+ $PETSC_DIR/$PETSC_ARCH/include/petscconf.h
+ * fix parenthesis in python3-mshr description. Closes: #976011.
+ * Standards-Version: 4.5.1
+
+ -- Drew Parsons <dparsons@debian.org> Wed, 13 Jan 2021 10:55:53 +1100
+
+mshr (2019.2.0~git20200924.c27eb18+dfsg1-4) unstable; urgency=medium
+
+ * fix quotes in i386 test condition.
+
+ -- Drew Parsons <dparsons@debian.org> Wed, 18 Nov 2020 03:46:38 +0800
+
+mshr (2019.2.0~git20200924.c27eb18+dfsg1-3) unstable; urgency=medium
+
+ * skip python unit test test-meshes on i386.
+ mshr.UnitSphereMesh() hangs on i386. Use mshr.Sphere() instead
+ (cf. deathstar demo). Closes: #974561.
+
+ -- Drew Parsons <dparsons@debian.org> Tue, 17 Nov 2020 17:37:30 +0800
+
+mshr (2019.2.0~git20200924.c27eb18+dfsg1-2) unstable; urgency=medium
+
+ * install python modules in /usr/lib/mshr or /usr/lib/mshr64, not
+ under PETSC_DIR. mshr does not use PETSc directly, but mshr.pth
+ uses $PETSC_DIR/include/petscconf.h to select standard or 64-bit
+ build.
+
+ -- Drew Parsons <dparsons@debian.org> Sun, 15 Nov 2020 13:37:22 +0800
+
+mshr (2019.2.0~git20200924.c27eb18+dfsg1-1) unstable; urgency=medium
+
+ * New upstream snapshot.
+ * mark libmshr-dev-common and libmshr64-dev as Multi-Arch: same
+
+ -- Drew Parsons <dparsons@debian.org> Mon, 05 Oct 2020 00:15:24 +0800
+
+mshr (2019.2.0~git20200213.8895485+dfsg1-4) unstable; urgency=medium
+
+ * build against latest dolfin in unstable. Closes: #969635.
+ * libmshr-dev-common Replaces, Breaks: libmshr-dev (<< ...-3).
+ Closes: #970141.
+
+ -- Drew Parsons <dparsons@debian.org> Sun, 13 Sep 2020 02:10:27 +0800
+
+mshr (2019.2.0~git20200213.8895485+dfsg1-3) experimental; urgency=medium
+
+ * build 64 bit packages (supporting 64-bit dolfin)
+ python3-mshr64, libmshr64-dev, libmshr64-2019.2
+ - debian patch lib_rename.patch enables setting of soname to
+ mshr64 rather than mshr (setting LIB_NAME_EXT in cmake,
+ and MSHR_LIB_NAME_EXT in mshrConfig.cmake for client programs,
+ cmake -DMSHR_LIB_NAME_EXT=64 to invoke libmshr64)
+ Also uses DOLFIN_LIB_NAME_EXT=64 to link libdolfin64.so
+ - place common header files in libmshr-dev-common
+ - Build-Depends: libdolfin64-dev (>= 2019.2.0~git20200218.027d9cc-15)
+ (to ensure DOLFIN_LIB_NAME_EXT is available)
+ - activate 64-bit build with environment variables (see README.Debian)
+ PETSC_DIR=/usr/lib/petsc64 SLEPC_DIR=/usr/lib/slepc64
+ MSHR_LIB_NAME_EXT=64 DOLFIN_LIB_NAME_EXT=64
+
+ -- Drew Parsons <dparsons@debian.org> Sun, 30 Aug 2020 07:44:11 +0800
+
+mshr (2019.2.0~git20200213.8895485+dfsg1-2) unstable; urgency=medium
+
+ * python3-mshr Depends: python3-dolfin-real
+ (rather than common python3-dolfin)
+ * debhelper compatibility level 13
+
+ -- Drew Parsons <dparsons@debian.org> Tue, 04 Aug 2020 01:21:17 +0800
+
+mshr (2019.2.0~git20200213.8895485+dfsg1-1) unstable; urgency=medium
+
+ * New upstream snapshot.
+ - applies debian patches:
+ build_CGAL_4.14.patch
+ build_python.patch
+ cmake_config_in_lib.patch
+ demos_update.patch
+ depython_main_build.patch
+ pybind11_register.patch
+
+ -- Drew Parsons <dparsons@debian.org> Tue, 21 Apr 2020 14:41:30 +0800
+
+mshr (2019.2.0~git20190418.010d802+dfsg1-1) experimental; urgency=medium
+
+ * new upstream snapshot (2019.2)
+ * Standards-Version: 4.5.0
+ * add debian patches:
+ - enable_CGAL5_CXX14.patch enables build with CGAL 5
+ and builds with C++14 since std::enable_if is required by CGAL 5
+ - build_CGAL5.patch updates to CGAL 5 API
+ - pybind11_register.patch registers CSGCGALDomain3D::num_holes for
+ python module, enabling test-fuzzypointmap.py to pass
+ (update test_controls.patch)
+
+ -- Drew Parsons <dparsons@debian.org> Sat, 01 Feb 2020 16:44:38 +0800
+
+mshr (2019.1.0+dfsg1-7) unstable; urgency=medium
+
+ * Standards-Version: 4.5.0
+ * add debian patches:
+ - enable_CGAL5_CXX14.patch enables build with CGAL 5
+ and builds with C++14 since std::enable_if is required by CGAL 5
+ - build_CGAL5.patch updates to CGAL 5 API
+ - pybind11_register.patch registers CSGCGALDomain3D::num_holes for
+ python module, enabling test-fuzzypointmap.py to pass
+ (update test_controls.patch)
+
+ -- Drew Parsons <dparsons@debian.org> Sat, 01 Feb 2020 17:14:19 +0800
+
+mshr (2019.1.0+dfsg1-6) unstable; urgency=medium
+
+ * stop building mips64el, mipsel with debug symbols.
+ They are too fragile, often failing to build from source.
+
+ -- Drew Parsons <dparsons@debian.org> Mon, 21 Oct 2019 18:46:59 +0800
+
+mshr (2019.1.0+dfsg1-5) unstable; urgency=medium
+
+ * Standards-Version: 4.4.1
+ * relax pybind11 dependency. pybind11 follows semantic versioning,
+ so should be backwards compatible with minor and patch version
+ updates.
+
+ -- Drew Parsons <dparsons@debian.org> Sun, 20 Oct 2019 19:23:41 +0800
+
+mshr (2019.1.0+dfsg1-4) unstable; urgency=medium
+
+ * build with dh --no-parallel to reduce memory requirements
+ (to aid builds on mips,mipsel,ubuntu). Closes: #934244.
+
+ -- Drew Parsons <dparsons@debian.org> Sat, 10 Aug 2019 11:14:22 +0800
+
+mshr (2019.1.0+dfsg1-3) unstable; urgency=medium
+
+ * Standards-Version: 4.4.0
+ * debian patch build_CGAL_4.14.patch enables build against CGAL 4.14
+ * debian/control: remove ancient-python-version-field 3.5
+
+ -- Drew Parsons <dparsons@debian.org> Mon, 05 Aug 2019 17:50:52 +0800
+
+mshr (2019.1.0+dfsg1-2) experimental; urgency=medium
+
+ * update debian/copyright
+ - Benjamin Kehlet's dates are 2012-2017
+ - acknowledge Joachim B Haga and Lars Magnus Valnes
+ - list contributing authors under Files: *
+ - mark files licensed under LGPL-3+
+
+ -- Drew Parsons <dparsons@debian.org> Tue, 21 May 2019 14:11:59 +0800
+
+mshr (2019.1.0+dfsg1-1) experimental; urgency=medium
+
+ * New upstream release (official).
+
+ -- Drew Parsons <dparsons@debian.org> Thu, 25 Apr 2019 23:33:14 +0800
+
+mshr (2019.1.0+dfsg1~2018.1.0-1) experimental; urgency=medium
+
+ * Dummy upstream release using 2018.1.0 code to build against
+ dolfin 2019.1.
+ * Standards-Version: 4.3.0
+ * debhelper compatibility level 12
+ - skip dh_dwz since debug symbols have been switched off
+ (since 2018.1.0+dfsg1-5)
+ * Include debug symbols if build will be successful, only omit -g for
+ arches blacklisted in ARCH_NO_DEBUG_SYMBOLS
+
+ -- Drew Parsons <dparsons@debian.org> Thu, 28 Mar 2019 18:25:51 +0800
+
+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 <dparsons@debian.org> 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 <dparsons@debian.org> 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 <dparsons@debian.org> 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 <dparsons@debian.org> 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 <dparsons@debian.org> 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 <dparsons@debian.org> 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 <dparsons@debian.org> 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 <dparsons@debian.org> 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 <dparsons@debian.org> 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 <dparsons@debian.org> 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 <johannr@simula.no> 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 <johannr@simula.no> 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 <johannr@simula.no> 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 <dparsons@debian.org> Fri, 20 May 2016 08:23:26 +0800
--- /dev/null
+Source: mshr
+Section: math
+Priority: optional
+Maintainer: Debian Science Team <debian-science-maintainers@lists.alioth.debian.org>
+Uploaders: Johannes Ring <johannr@simula.no>, Drew Parsons <dparsons@debian.org>
+Build-Depends: debhelper-compat (= 13),
+ 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 (>= 2019.2),
+ libdolfin64-dev (>= 2019.2.0~git20200218.027d9cc-16),
+ python3-ffc (>= 2019.2),
+ python3-numpy,
+ python3-petsc4py,
+ python3-slepc4py,
+ python3-petsc4py-real,
+ python3-slepc4py-real,
+ python3-petsc4py-64-real,
+ python3-slepc4py-64-real,
+ libproj-dev
+Standards-Version: 4.6.0
+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: libmshr2019.2
+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: libmshr2019.2 (= ${binary:Version}),
+ libmshr-dev-common (= ${binary:Version}),
+ libdolfin-dev (>= ${fenics:Upstream-Version}),
+ ${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, and also the
+ utility program mshrable.
+
+Package: libmshr-dev-common
+Section: libdevel
+Architecture: any
+Multi-Arch: same
+Depends: python3-ffc (>= ${fenics:Upstream-Version}),
+ cmake (>= 2.8.0),
+ libproj-dev,
+ ${misc:Depends}
+Recommends: libmshr-dev (= ${binary:Version}) | libmshr64-dev (= ${binary:Version})
+Replaces: libmshr-dev (<< 2019.2.0~git20200213.8895485+dfsg1-3)
+Breaks: libmshr-dev (<< 2019.2.0~git20200213.8895485+dfsg1-3)
+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 common headers and development files.
+
+Package: python3-mshr
+Section: python
+Architecture: all
+Depends: libmshr-dev (>= ${source:Version}),
+ python3-mshr-real | python3-mshr64-real,
+ python3-dolfin (>= ${fenics:Upstream-Version}),
+ dolfin-bin (>= ${fenics:Upstream-Version}),
+ python3,
+ ${python3: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 common Python 3 interface for mshr, and examples
+ and demo programs.
+ .
+ This is the base package depending on specific mshr builds. By
+ default mshr is built against dolfin using the preferred version of PETSc in
+ /usr/lib/petsc (with 32-bit indexing), but the alternative version
+ (64-bit PETSc) can be selected by setting the environment variable PETSC_DIR.
+
+Package: python3-mshr-real
+Section: python
+Architecture: any
+Depends: libmshr2019.2 (= ${binary:Version}),
+ python3-dolfin-real (>= ${fenics:Upstream-Version}),
+ python3-pybind11 (>= ${pybind11:Upstream-Version}), python3-pybind11 (<< ${pybind11:Next-Upstream-Version}),
+ ${python3:Depends},
+ ${shlibs:Depends},
+ ${misc:Depends}
+Recommends: python3-mshr
+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.
+
+Package: libmshr64-2019.2
+Section: libs
+Architecture: any
+Multi-Arch: same
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Shared libraries for mshr with 64-bit indexing
+ 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 with support for
+ 64-bit indexing (libdolfin64 and PETSc-64).
+
+Package: libmshr64-dev
+Section: libdevel
+Architecture: any
+Multi-Arch: same
+Depends: libmshr64-2019.2 (= ${binary:Version}),
+ libmshr-dev-common (= ${binary:Version}),
+ libdolfin64-dev (>= ${fenics:Upstream-Version}),
+ ${shlibs:Depends},
+ ${misc:Depends}
+Description: Shared links and header files for mshr with 64-bit indexing
+ 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 with support for
+ 64-bit indexing (libdolfin64 and PETSc-64).
+
+Package: python3-mshr64-real
+Section: python
+Architecture: any
+Depends: libmshr64-2019.2 (= ${binary:Version}),
+ python3-dolfin64-real (>= ${fenics:Upstream-Version}),
+ python3-pybind11 (>= ${pybind11:Upstream-Version}), python3-pybind11 (<< ${pybind11:Next-Upstream-Version}),
+ ${python3:Depends},
+ ${shlibs:Depends},
+ ${misc:Depends}
+Recommends: python3-mshr
+Description: Python 3 interface for mshr with 64-bit indexing
+ mshr generates simplicial DOLFIN meshes in 2D and 3D from geometries
+ described by Constructive Solid Geometry (CSG) or from surface files,
+ utilizing CGAL and Tetgen as mesh generation backends.
+ .
+ This package contains the Python 3 interface for mshr with support for
+ 64-bit indexing (libdolfin64 and PETSc-64).
--- /dev/null
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: mshr
+Source: https://bitbucket.org/fenics-project/mshr
+Comment: Lead Author: Benjamin Kehlet <benjamik@simula.no>
+Contributors:
+ Anders Logg <logg@chalmers.se>
+ Joachim B Haga
+ Johannes Ring <johannr@simula.no>
+ Lars Magnus Valnes
+ Garth N. Wells <gnw20@cam.ac.uk>
+Files-Excluded: 3rdparty/CGAL 3rdparty/tetgen1.5.0
+
+Files: *
+Copyright: © 2012-2017 Benjamin Kehlet <benjamik@simula.no>
+ 2012-2015 Anders Logg <logg@chalmers.se>
+ 2012 Johannes Ring <johannr@simula.no>
+ 2012 Joachim B Haga
+ 2016 Lars Magnus Valnes
+License: GPL-3+
+
+Files: test/test.cpp test/test2.cpp test/test-csggeometries.cpp
+ demo/python/icecream.py
+Copyright: 2012-2017 Benjamin Kehlet <benjamik@simula.no>
+ 2012 Anders Logg, Johannes Ring, Joachim B Haga
+License: LGPL-3+
+
+License: GPL-3+
+ /usr/share/common-licenses/GPL-3
+
+License: LGPL-3+
+ /usr/share/common-licenses/LGPL-3
+
+Files: debian/*
+Copyright: © 2015 Johannes Ring <johannr@simula.no>,
+ 2016 Drew Parsons <dparsons@debian.org>
+License: GPL-2+
+ /usr/share/common-licenses/GPL-2
--- /dev/null
+README.rst
--- /dev/null
+usr/include/mshr
+usr/include/mshr.h
+usr/lib/*/cmake/mshr
--- /dev/null
+usr/lib/**/*.so
+usr/bin/mshrable
--- /dev/null
+debian/mshrable.1
--- /dev/null
+usr/lib/**/lib*.so.*
--- /dev/null
+#!/bin/sh
+echo "debian/tmp64/usr/lib/**/libmshr64*.so.* usr/lib/${DEB_HOST_MULTIARCH}"
--- /dev/null
+debian/README.Debian
--- /dev/null
+#!/bin/sh
+echo "debian/tmp64/usr/lib/**/libmshr64*.so usr/lib/${DEB_HOST_MULTIARCH}"
--- /dev/null
+# access mshr module from either /usr/lib/mshr or /usr/lib/mshr64 depending on whether petsc or petsc64 is used (controlled by PETSC_DIR).
+# petsc64 build identified by "#define PETSC_USE_64BIT_INDICES 1" in $PETSC_DIR/include/petscconf.h
+import sys, os, pathlib; petsc_dir = '/usr/lib/petsc'; petsc_dir = os.getenv('PETSC_DIR') or petsc_dir; petsc_conf=os.path.join(petsc_dir,'include/petscconf.h'); bit64='64' if '#define PETSC_USE_64BIT_INDICES 1' in open(petsc_conf).read() else ''; mshr_dir='/usr/lib/mshr{}/python3/dist-packages'.format(bit64); mshr_dir in sys.path or sys.path.append(mshr_dir);
--- /dev/null
+.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
--- /dev/null
+<!doctype refentry PUBLIC "-//Davenport//DTD DocBook V3.0//EN" [
+ <!ENTITY dhfirstname "<firstname>Drew</firstname>">
+ <!ENTITY dhsurname "<surname>Parsons</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>19 May, 2016</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>dparsons@debian.org</email>">
+ <!ENTITY dhusername "Drew Parsons">
+ <!ENTITY dhucpackage "<refentrytitle>MSHRABLE</refentrytitle>">
+ <!ENTITY dhpackage "mshrable">
+
+ <!ENTITY debian "<productname>Debian GNU/Linux</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+]>
+
+<!-- generate the man page with "docbook-to-man mshrable.sgml > mshrable.1" -->
+
+<refentry>
+ <docinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2001</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </docinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>Generate mesh from surface file</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg>-f <replaceable>FILE</replaceable></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para><command>&dhpackage;</command> 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.
+ </para>
+</refsect1>
+
+<refsect1>
+ <title>OPTIONS</title>
+<para>
+ <variablelist>
+ <varlistentry>
+ <term>-o [--outfile] <replaceable>arg</replaceable></term>
+ <listitem>
+ <para>
+ Filename of generated Dolfin mesh.
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>-r [--resolution] <replaceable>arg (=15)</replaceable></term>
+ <listitem>
+ <para>
+ Resolution of result mesh.
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>-s [--stats]</term>
+ <listitem>
+ <para>
+ Write some statistics of the mesh to stdout.
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>--polyout <replaceable>arg</replaceable></term>
+ <listitem>
+ <para>
+ Write the polyhedron to .poly which Tetgen can read
+ (and do not create a mesh).
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>--polystats</term>
+ <listitem>
+ <para>
+ Write statistics of polyhedron (and do not create a
+ mesh).
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>-b [--backend] <replaceable>arg (=cgal)</replaceable></term>
+ <listitem>
+ <para>
+ Use 3D mesh generation backend [tetgen|cgal].
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>--degenerate_tolerance <replaceable>arg (=9.9999999999999998e-13)</replaceable></term>
+ <listitem>
+ <para>
+ Tolerance for considering a facet as degenerate. Set
+ to 0 to not remove degenerate facets.
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>--check-mesh</term>
+ <listitem>
+ <para>
+ Check consistency of output mesh (most for debugging/testing.
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>-v [--verbose]</term>
+ <listitem>
+ <para>
+ Output more information about what is going on.
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>-h [--help]</term>
+ <listitem>
+ <para>
+ write help message.
+ </para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+</para>
+</refsect1>
+
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para>dolfin-convert (1), dolfin-order (1)</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+ <para><command>&dhpackage;</command> was written by Benjamin
+ Kehlet <email>benjamik@simula.no</email>. This man page was written by
+ &dhusername; &dhemail;.
+ </para>
+
+
+ <!-- <para>Permission is granted to copy, distribute and/or modify
+ this document under the terms of the <acronym>GNU</acronym> Free
+ Documentation License, Version 1.1 or any later version
+ published by the Free Software Foundation; with no Invariant
+ Sections, no Front-Cover Texts and no Back-Cover Texts. A copy
+ of the license can be found under
+ <filename>/usr/share/common-licenses/FDL</filename>.</para> -->
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
--- /dev/null
+--- a/src/SurfaceReconstruction.cpp
++++ b/src/SurfaceReconstruction.cpp
+@@ -21,7 +21,7 @@
+ #include <dolfin/common/constants.h>
+
+ #define CGAL_EIGEN3_ENABLED true
+-#include <CGAL/trace.h>
++#include <CGAL/IO/trace.h>
+ #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+ #include <CGAL/Surface_mesh_default_triangulation_3.h>
+ #include <CGAL/make_surface_mesh.h>
+@@ -230,7 +230,7 @@
+ }
+ // Computes average spacing
+ log(dolfin::TRACE, "Compute average spacing");
+- FT average_spacing = CGAL::compute_average_spacing<CGAL::Sequential_tag>(points.begin(), points.end(),
++ FT average_spacing = CGAL::compute_average_spacing<CGAL::Sequential_tag>(points,
+ 6 /* knn = 1 ring */);
+ // Gets one point inside the implicit surface
+ // and computes implicit function bounding sphere radius.
--- /dev/null
+Index: mshr/CMakeLists.txt
+===================================================================
+--- mshr.orig/CMakeLists.txt 2020-10-05 00:06:49.545312095 +0800
++++ mshr/CMakeLists.txt 2020-10-05 00:06:49.541312138 +0800
+@@ -14,7 +14,7 @@
+ # CGAL setup
+ option(USE_SYSTEM_CGAL "Do not build CGAL, but use an existing build instead." OFF)
+ if (USE_SYSTEM_CGAL)
+- find_package(CGAL 4.12 CONFIG REQUIRED)
++ find_package(CGAL CONFIG REQUIRED)
+ endif()
+
+ # Borrow some cmake modules from cgal
+@@ -43,8 +43,8 @@
+ ENDFOREACH (value2)
+ ENDMACRO(LIST_CONTAINS)
+
+-# Use C++11
+-SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x -Wall")
++# Use C++14 to support std:enable_if used by CGAL 5
++set(CMAKE_CXX_STANDARD 14)
+
+ # Boost
+ # This is workaround to avoid that find_package(Boost)
+@@ -158,6 +158,9 @@
+ ${Boost_MSHR_LIBRARIES}
+ )
+
++# CMAKE_CXX_STANDARD is ignored ;( Need to set standard manually here.
++set_property(TARGET mshr PROPERTY CXX_STANDARD 14)
++
+ # install library
+ install(TARGETS mshr
+ RUNTIME DESTINATION ${INSTALL_BIN_DIR}
+@@ -175,6 +178,9 @@
+ ${Boost_MSHR_LIBRARIES}
+ )
+
++# CMAKE_CXX_STANDARD is ignored ;( Need to set standard manually here.
++set_property(TARGET mshrable PROPERTY CXX_STANDARD 14)
++
+ # install app
+ install(TARGETS mshrable
+ RUNTIME DESTINATION ${INSTALL_BIN_DIR}
+Index: mshr/python/setup.py
+===================================================================
+--- mshr.orig/python/setup.py 2020-10-05 00:06:49.545312095 +0800
++++ mshr/python/setup.py 2020-10-05 00:06:49.541312138 +0800
+@@ -27,8 +27,8 @@
+ include_dirs=include_dirs,
+ library_dirs=config['mshr']['lib_dirs'].split(";"),
+ libraries=config['mshr']['libs'].split(";"),
+- extra_compile_args=['-std=c++11'],
+- language='c++11')
++ extra_compile_args=['-std=c++14'],
++ language='c++14')
+
+
+ setup(name = 'mshr',
--- /dev/null
+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<MeshDomain>::value > () (c3t3,
++ CGAL::Mesh_3::internal::has_Has_features<MeshDomain>::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
--- /dev/null
+Index: mshr/CMakeLists.txt
+===================================================================
+--- mshr.orig/CMakeLists.txt 2020-10-05 00:07:03.341164950 +0800
++++ mshr/CMakeLists.txt 2020-10-05 00:09:55.459354628 +0800
+@@ -90,6 +90,7 @@
+ include_directories(BEFORE ${EXTERNAL_INCLUDE_DIRS})
+ add_definitions("${EXTERNAL_DEFINITIONS}")
+
++set(DOLFIN_LIB_NAME_EXT ${LIB_NAME_EXT})
+ find_package(DOLFIN REQUIRED)
+ include(${DOLFIN_USE_FILE})
+
+@@ -127,6 +128,7 @@
+ set(MSHR_LIBRARY_PROPERTIES ${MSHR_LIBRARY_PROPERTIES}
+ VERSION ${MSHR_LIBRARY_VERSION}
+ SOVERSION ${MSHR_VERSION_MAJOR}.${MSHR_VERSION_MINOR}
++ OUTPUT_NAME "mshr${LIB_NAME_EXT}"
+ )
+ endif()
+ set_target_properties(mshr PROPERTIES ${MSHR_LIBRARY_PROPERTIES})
+Index: mshr/mshrConfig.cmake.in
+===================================================================
+--- mshr.orig/mshrConfig.cmake.in 2020-10-05 00:07:03.341164950 +0800
++++ mshr/mshrConfig.cmake.in 2020-10-05 00:07:03.337164993 +0800
+@@ -12,4 +12,4 @@
+ set(mshr_EXTERNAL_LIBRARIES "@CONF_EXTERNAL_LIBRARIES@")
+ set(mshr_CXX_DEFINITIONS "@CONF_CXX_DEFINITIONS@")
+ set(mshr_CXX_FLAGS "@CONF_CXX_FLAGS@")
+-set(mshr_LIBRARIES mshr)
++set(mshr_LIBRARIES mshr${MSHR_LIB_NAME_EXT})
+Index: mshr/python/setup.py
+===================================================================
+--- mshr.orig/python/setup.py 2020-10-05 00:07:03.341164950 +0800
++++ mshr/python/setup.py 2020-10-05 00:07:03.337164993 +0800
+@@ -6,15 +6,24 @@
+
+
+ # Call cmake to generate json file with include and link information about dolfin and pybind11
+-if not os.path.isfile(os.path.join("build", "config.json")) :
+- if not os.path.exists("build") :
+- os.mkdir("build")
++MSHR_LIB_NAME_EXT = os.environ.get('MSHR_LIB_NAME_EXT') or ''
++DOLFIN_LIB_NAME_EXT = os.environ.get('DOLFIN_LIB_NAME_EXT') or ''
++config_dir="build" + MSHR_LIB_NAME_EXT
++if not os.path.isfile(os.path.join(config_dir, "config.json")) :
++ if not os.path.exists(config_dir) :
++ os.mkdir(config_dir)
+ 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"))
++ if MSHR_LIB_NAME_EXT:
++ cmake_command.extend(['-DMSHR_LIB_NAME_EXT={}'.format(MSHR_LIB_NAME_EXT)])
++ if DOLFIN_LIB_NAME_EXT:
++ cmake_command.extend(['-DDOLFIN_LIB_NAME_EXT={}'.format(DOLFIN_LIB_NAME_EXT)])
++ elif MSHR_LIB_NAME_EXT:
++ cmake_command.extend(['-DDOLFIN_LIB_NAME_EXT={}'.format(MSHR_LIB_NAME_EXT)])
++ subprocess.check_call(cmake_command, cwd=os.path.abspath(config_dir))
+
+-with open(os.path.join("build", "config.json"), 'r') as infile :
++with open(os.path.join(config_dir, "config.json"), 'r') as infile :
+ config = json.load(infile)
+
+ include_dirs = config["pybind11"]["include_dirs"].split(";") + \
+Index: mshr/python/cmake/Findmshr.cmake
+===================================================================
+--- mshr.orig/python/cmake/Findmshr.cmake 2020-10-05 00:07:03.341164950 +0800
++++ mshr/python/cmake/Findmshr.cmake 2020-10-05 00:07:03.337164993 +0800
+@@ -20,7 +20,7 @@
+ find_path(mshr_INCLUDE_DIR mshr.h
+ DOC "The mshr include directory")
+
+-set(mshr_NAMES ${mshr_NAMES} libmshr mshr)
++set(mshr_NAMES ${mshr_NAMES} libmshr${MSHR_LIB_NAME_EXT} mshr${MSHR_LIB_NAME_EXT})
+ find_library(mshr_LIBRARY NAMES ${mshr_NAMES}
+ DOC "The mshr library")
+
+@@ -39,7 +39,7 @@
+ set( mshr_FOUND 1 )
+ # use by setuptools.Extension, mshr_LIBRARIES must be in a form that appends to -l
+ # i.e. mshr not libmshr.so
+- set( mshr_LIBRARIES "mshr" )
++ set( mshr_LIBRARIES "mshr${MSHR_LIB_NAME_EXT}" )
+ get_filename_component( mshr_LIBRARIES_DIRS ${mshr_LIBRARY} DIRECTORY )
+ set( mshr_INCLUDE_DIRS ${mshr_INCLUDE_DIR} )
+ else()
+Index: mshr/mshr-config.cmake.in
+===================================================================
+--- mshr.orig/mshr-config.cmake.in 2020-10-05 00:07:03.341164950 +0800
++++ mshr/mshr-config.cmake.in 2020-10-05 00:07:03.337164993 +0800
+@@ -12,6 +12,6 @@
+ set(MSHR_EXTERNAL_LIBRARIES "@CONF_EXTERNAL_LIBRARIES@")
+ set(MSHR_CXX_DEFINITIONS "@CONF_CXX_DEFINITIONS@")
+ set(MSHR_CXX_FLAGS "@CONF_CXX_FLAGS@")
+-set(MSHR_LIBRARIES mshr)
++set(MSHR_LIBRARIES mshr${MSHR_LIB_NAME_EXT})
+
+ set(MSHR_USE_FILE "${MSHR_CMAKE_DIR}/use-mshr.cmake")
+\ No newline at end of file
--- /dev/null
+Description: Link with libatomic.
+Author: Peter Michael Green <plugwash@raspbian.org>
+
+--- mshr-2019.2.0~git20200924.c27eb18+dfsg1.orig/CMakeLists.txt
++++ mshr-2019.2.0~git20200924.c27eb18+dfsg1/CMakeLists.txt
+@@ -119,6 +119,8 @@ if (NOT USE_SYSTEM_CGAL)
+ add_dependencies( mshr CGAL )
+ endif()
+
++target_link_libraries(mshr atomic)
++
+ # Append the library version information to the library target properties
+ option(MSHR_WITH_LIBRARY_VERSION "Build with library version information." ON)
+ if (MSHR_WITH_LIBRARY_VERSION)
--- /dev/null
+test_controls.diff
+fix_mesh3_internal.patch
+enable_CGAL5_CXX14.patch
+build_CGAL5.patch
+lib_rename.patch
+link-with-libatomic.patch
--- /dev/null
+--- /dev/null
++++ b/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)
+--- /dev/null
++++ b/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] not in '']
++
++
++@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)
--- /dev/null
+usr/lib/python3*/*-packages/*
--- /dev/null
+demo/python/*
--- /dev/null
+debian/mshr.pth usr/lib/python3/dist-packages/
--- /dev/null
+debian/README.Debian
--- /dev/null
+#!/bin/sh
+echo "debian/tmp64/usr/lib/python3*/dist-packages/* usr/lib/python3/dist-packages"
--- /dev/null
+#!/usr/bin/make -f
+
+include /usr/share/dpkg/architecture.mk
+
+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/^\([^.]*\)\.\([^.]*\)\..*$$/\2/")
+FENICS_VERSION=$(FENICS_MAJOR_VERSION).$(FENICS_MINOR_VERSION)
+FENICS_NEXT_VERSION=$(FENICS_MAJOR_VERSION).$(shell echo $$(( $(FENICS_MINOR_VERSION) + 1 )) )
+
+# dolfin depends on the pybind11 version it was built against,
+# if pybind11.h will be used in C++ code fragments in python scripts.
+# But pybind11 follows semantic versioning, so should have backwards compatibility
+# with minor and patch version updates.
+# Extract pybind11 version from pybind11-dev
+PYBIND11_DEB_VERSION=$(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_VERSION=$(shell echo $(PYBIND11_UPSTREAM_VERSION) | sed "s/^\([^.]*\).*/\1/")
+PYBIND11_X_Y_VERSION=$(shell echo $(PYBIND11_UPSTREAM_VERSION) | sed "s/^\(.*\)\.\([^.]*\)$$/\1/")
+PYBIND11_VERSION=$(PYBIND11_X_Y_VERSION)
+PYBIND11_NEXT_VERSION=$(shell echo $$(( $(PYBIND11_X_VERSION) + 1 )) )
+
+# extract PETSc version from petsc-dev
+PETSC_DEB_VERSION=$(shell dpkg -s petsc-dev | awk '/Version:/ {print $2}')
+# extract the current PETSc version
+PETSC_UPSTREAM_VERSION=$(shell pkg-config --modversion PETSc)
+# "Major" version is the first number in the upstream version (major.minor.release)
+PETSC_MAJOR_VERSION=$(shell echo $(PETSC_UPSTREAM_VERSION) | sed "s/^\([^.]*\)\..*$$/\1/")
+# "Minor" version is the second number in the upstream version (major.minor.release)
+PETSC_MINOR_VERSION=$(shell echo $(PETSC_UPSTREAM_VERSION) | sed "s/^\([^.]*\)\.\([^.]*\)\..*$$/\2/")
+PETSC_VERSION=$(PETSC_MAJOR_VERSION).$(PETSC_MINOR_VERSION)
+PETSC_VERSION_NEXT=$(shell echo $(PETSC_MAJOR_VERSION).$$(($(PETSC_MINOR_VERSION)+1)))
+
+SLEPC_UPSTREAM_VERSION=$(shell pkg-config --modversion SLEPc)
+# SLEPc version must match PETSc
+SLEPC_VERSION=$(PETSC_VERSION)
+SLEPC_VERSION_NEXT=$(PETSC_VERSION_NEXT)
+
+PETSC_DIR=/usr/lib/petscdir/petsc$(PETSC_VERSION)/$(DEB_HOST_MULTIARCH)-real
+SLEPC_DIR=/usr/lib/slepcdir/slepc$(SLEPC_VERSION)/$(DEB_HOST_MULTIARCH)-real
+
+PETSC64_DIR=/usr/lib/petscdir/petsc64-$(PETSC_VERSION)/$(DEB_HOST_MULTIARCH)-real
+SLEPC64_DIR=/usr/lib/slepcdir/slepc64-$(SLEPC_VERSION)/$(DEB_HOST_MULTIARCH)-real
+
+BUILDDIR = obj-$(DEB_HOST_GNU_TYPE)
+BUILDDIR_64 = obj-$(DEB_HOST_GNU_TYPE)-64
+
+MSHR_LIBDIR = /usr/lib/mshr
+MSHR64_LIBDIR = /usr/lib/mshr64
+
+# some arches (mostly 32 bit) don't provide enough memory to build with debug symbols
+ARCH_NO_DEBUG_SYMBOLS := armhf i386 mips64el mipsel hppa m68k powerpc x32
+ifeq ($(findstring $(DEB_BUILD_ARCH),$(ARCH_NO_DEBUG_SYMBOLS)),)
+ MSHR_BUILDFLAGS := $(shell dpkg-buildflags --get CXXFLAGS )
+else
+# remove -g from build flags on weak arches
+ MSHR_BUILDFLAGS := $(shell dpkg-buildflags --get CXXFLAGS | sed 's/-g //' )
+endif
+
+CMAKE_OPTS := \
+ -D CMAKE_BUILD_TYPE:STRING=Release \
+ -D BUILD_SHARED_LIBS:BOOL=ON \
+ -D USE_SYSTEM_CGAL:BOOL=ON \
+ -D USE_SYSTEM_TETGEN:BOOL=ON \
+ -D ENABLE_MSHRABLE:BOOL=ON \
+ -D CMAKE_SKIP_RPATH:BOOL=ON \
+ -D CMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=OFF \
+ -D INSTALL_LIB_DIR:PATH=lib/$(DEB_BUILD_MULTIARCH) \
+ -D CMAKE_CXX_FLAGS:STRING="-fpermissive $(MSHR_BUILDFLAGS)" \
+ $(MSHR_HOME)
+
+ifeq (,$(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 \
+ --no-parallel
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -rf python/build*
+ rm -rf python/mshr.egg-info
+ rm -rf debian/tmp64
+ rm -rf $(BUILDDIR) $(BUILDDIR_64)
+
+override_dh_auto_configure:
+ PETSC_DIR=$(PETSC_DIR) SLEPC_DIR=$(SLEPC_DIR) dh_auto_configure --builddir=$(BUILDDIR) -- $(CMAKE_OPTS)
+ PETSC_DIR=$(PETSC64_DIR) SLEPC_DIR=$(SLEPC64_DIR) dh_auto_configure --builddir=$(BUILDDIR_64) -- $(CMAKE_OPTS) -DLIB_NAME_EXT="64" -DDOLFIN_LIB_NAME_EXT="64"
+
+override_dh_auto_build:
+ PETSC_DIR=$(PETSC_DIR) SLEPC_DIR=$(SLEPC_DIR) dh_auto_build --builddir=$(BUILDDIR)
+ PETSC_DIR=$(PETSC64_DIR) SLEPC_DIR=$(SLEPC64_DIR) dh_auto_build --builddir=$(BUILDDIR_64)
+
+override_dh_auto_install:
+ dh_auto_install --builddir=$(BUILDDIR) --destdir=debian/tmp
+ dh_auto_install --builddir=$(BUILDDIR_64) --destdir=debian/tmp64
+ set -e; \
+ for v in $(PYVERS); do \
+ cd python; \
+ PETSC_DIR=$(PETSC_DIR) SLEPC_DIR=$(SLEPC_DIR) \
+ CMAKE_PREFIX_PATH=$(CURDIR)/debian/tmp/usr \
+ $$v setup.py build --build-base=$(CURDIR)/python/build-$$v install --root=$(CURDIR)/debian/tmp --install-layout=deb; \
+ PETSC_DIR=$(PETSC64_DIR) SLEPC_DIR=$(SLEPC64_DIR) \
+ CMAKE_PREFIX_PATH=$(CURDIR)/debian/tmp64/usr MSHR_LIB_NAME_EXT="64" DOLFIN_LIB_NAME_EXT="64" \
+ $$v setup.py build --build-base=$(CURDIR)/python/build64-$$v install --root=$(CURDIR)/debian/tmp64 --install-layout=deb; \
+ cd ..; \
+ done
+ dh_numpy3
+
+override_dh_python3-arch:
+ dh_python3 -a
+ dh_numpy3 -a
+ mkdir -p debian/python3-mshr-real/$(MSHR_LIBDIR)
+ mv debian/python3-mshr-real/usr/lib/python3 debian/python3-mshr-real/$(MSHR_LIBDIR)
+ mkdir -p debian/python3-mshr64-real/$(MSHR64_LIBDIR)
+ mv debian/python3-mshr64-real/usr/lib/python3 debian/python3-mshr64-real/$(MSHR64_LIBDIR)
+
+override_dh_gencontrol:
+ dh_gencontrol -- -Vfenics:Upstream-Version=$(FENICS_VERSION) \
+ -Vpybind11:Upstream-Version=$(PYBIND11_VERSION) -Vpybind11:Next-Upstream-Version=$(PYBIND11_NEXT_VERSION)
+
+# debug symbols (-g) have been switched off in CMAKE_OPTS for some arches, so no point building dbgsym packages
+override_dh_strip:
+ case " $(ARCH_NO_DEBUG_SYMBOLS) " in \
+ *\ $(DEB_HOST_ARCH)\ *) dh_strip --no-automatic-dbgsym;; \
+ *) dh_strip;; \
+ esac
+
+override_dh_dwz:
+ case " $(ARCH_NO_DEBUG_SYMBOLS) " in \
+ *\ $(DEB_HOST_ARCH)\ *) echo "skipping dh_dwz since debug symbols (-g) have been switched off for $(DEB_HOST_ARCH)";; \
+ *) dh_dwz;; \
+ esac
+
+#override_dh_shlibdeps:
+# dh_shlibdeps --dpkg-shlibdeps-params=--ignore-missing-info
+
+.PHONY: get-orig-source
+get-orig-source:
+ uscan --force-download --verbose --destdir $(USCAN_DESTDIR)
--- /dev/null
+3.0 (quilt)
--- /dev/null
+Tests: test-mshr-python
+Depends: python3-mshr,
+ python3-pytest
+
+Tests: test-mshr64-python,
+Depends: python3-mshr64-real,
+ python3-mshr,
+ python3-pytest
--- /dev/null
+DEB_HOST_ARCH=$( dpkg-architecture --query DEB_HOST_ARCH )
+if [ "${DEB_HOST_ARCH}" = "i386" ]; then
+ # skip test-meshes, which hangs on i386
+ PYTEST_KEY="-k 'not test-meshes'"
+fi
+
+echo "=== python unit tests ==="
+eval python3 -m pytest -v "${PYTEST_KEY}" test/test.py
+
+echo "=== python demo tests ==="
+DEMO_TEST_DIR=$AUTOPKGTEST_TMP
+cp -r /usr/share/doc/python3-mshr/examples ${DEMO_TEST_DIR}
+python3 -m pytest -v ${DEMO_TEST_DIR}/examples/test.py
--- /dev/null
+export PETSC_DIR=/usr/lib/petsc64
+export SLEPC_DIR=/usr/lib/slepc64
+
+export MSHR_LIB_NAME_EXT=64
+export DOLFIN_LIB_NAME_EXT=64
+
+DEB_HOST_ARCH=$( dpkg-architecture --query DEB_HOST_ARCH )
+if [ "${DEB_HOST_ARCH}" = "i386" ]; then
+ # skip test-meshes, which hangs on i386
+ PYTEST_KEY="-k 'not test-meshes'"
+fi
+
+echo "=== python unit tests for 64-bit build ==="
+eval python3 -m pytest -v "${PYTEST_KEY}" test/test.py
+
+echo "=== python demo tests for 64-bit build ==="
+DEMO_TEST_DIR=$AUTOPKGTEST_TMP
+cp -r /usr/share/doc/python3-mshr/examples ${DEMO_TEST_DIR}
+python3 -m pytest -v ${DEMO_TEST_DIR}/examples/test.py
--- /dev/null
+version=3
+opts=dversionmangle=s/\+dfsg\d*$//,repacksuffix=+dfsg1 \
+https://bitbucket.org/fenics-project/mshr/downloads/mshr-(.*)\.tar\.gz
projects / mshr.git / commitdiff