diff options
30 files changed, 722 insertions, 0 deletions
diff --git a/debian/TODO.Debian b/debian/TODO.Debian new file mode 100644 index 00000000..630425b6 --- /dev/null +++ b/debian/TODO.Debian @@ -0,0 +1,8 @@ +- Man pages for gudhi-utilities, preferably from upstream. + +- Upstream more patches. + +- Integrate upstream's extensive tests, adapting them to test + installed code. + +- Generate Sphinx documentation for the Python package.
\ No newline at end of file diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 00000000..b9d3ebd5 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,52 @@ +gudhi (2.2.0+dfsg-3) unstable; urgency=medium + + * Fix build of bindings for multiple Python versions when building just + binary-arch. + * Test all supported Python (3) versions. + + -- Gard Spreemann <gspreemann@gmail.com> Tue, 14 Aug 2018 13:45:43 +0200 + +gudhi (2.2.0+dfsg-2) unstable; urgency=medium + + * Build Python bindings for all supported Python (3) versions. + * Drop patch forcing Python 3 detection. Upstream has cmake option for + selecting Python version. + * Standards-version 4.2.0. No changes needed. + + -- Gard Spreemann <gspreemann@gmail.com> Tue, 07 Aug 2018 13:47:38 +0200 + +gudhi (2.2.0+dfsg-1) unstable; urgency=medium + + * New upstream release. + - Čech complex. + - New functionality for the Rips complex. + * Refresh patches: + - Drop floating point precision workaround patch (fixed upstream). + - Drop CGAL 4.12 compatibility patch (fixed upstream). + * Streamline the copyright information a bit. + * Bump CMake build-dep to 3.1. + * New upstream utilities in gudhi-utils. + + -- Gard Spreemann <gspreemann@gmail.com> Fri, 22 Jun 2018 10:12:19 +0200 + +gudhi (2.1.0+dfsg-3) unstable; urgency=medium + + * Add patch for floating point rounding problem on some architectures. + * Add patch that forces linking against libatomic. This hopefully fixes + building on MIPS et al. + * Install utilities (gudhi-utils). + + -- Gard Spreemann <gspreemann@gmail.com> Thu, 14 Jun 2018 20:07:51 +0200 + +gudhi (2.1.0+dfsg-2) unstable; urgency=medium + + * Add patches for CGAL 4.12 compatibility. + * Bump standards-version to 4.1.4. No changes needed. + + -- Gard Spreemann <gspreemann@gmail.com> Thu, 24 May 2018 11:46:12 +0200 + +gudhi (2.1.0+dfsg-1) unstable; urgency=medium + + * Initial packaging. (Closes: #840686) + + -- Gard Spreemann <gspreemann@gmail.com> Sun, 25 Mar 2018 23:52:14 +0200
\ No newline at end of file diff --git a/debian/clean b/debian/clean new file mode 100644 index 00000000..1258531f --- /dev/null +++ b/debian/clean @@ -0,0 +1,2 @@ +GUDHIVersion.cmake +doc/html/ diff --git a/debian/compat b/debian/compat new file mode 100644 index 00000000..b4de3947 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +11 diff --git a/debian/control b/debian/control new file mode 100644 index 00000000..c2a02e8c --- /dev/null +++ b/debian/control @@ -0,0 +1,150 @@ +Source: gudhi +Maintainer: Gard Spreemann <gspreemann@gmail.com> +Section: math +Priority: optional +Standards-Version: 4.2.0 +Build-Depends: cmake (>= 3.1), + cython3, + debhelper (>= 11), + dh-python, + libboost-chrono-dev, + libboost-filesystem-dev, + libboost-program-options-dev, + libboost-system-dev, + libboost-test-dev, + libboost-timer-dev, + libcgal-dev (>> 4.11.0), + libcgal-qt5-dev (>> 4.11.0), + libeigen3-dev, + libgmp-dev, + libqglviewer-dev-qt5, + libtbb-dev, + python3-all-dev, + python3-matplotlib, + python3-pytest, + python3-tk, + qtbase5-dev +Build-Depends-Indep: doxygen, + graphviz +Homepage: http://gudhi.gforge.inria.fr/ +Vcs-Browser: https://git.nonempty.org/debian-gudhi +Vcs-Git: https://git.nonempty.org/debian-gudhi -b debian/sid + +Package: libgudhi-dev +Section: libdevel +Architecture: all +Multi-Arch: foreign +Depends: libboost-chrono-dev (>= 1.48), + libboost-filesystem-dev (>= 1.48), + libboost-program-options-dev (>= 1.48), + libboost-system-dev (>= 1.48), + libboost-test-dev (>= 1.48), + libboost-timer-dev (>= 1.48), + libcgal-dev (>> 4.11.0), + libeigen3-dev (>= 3.1.0), + libgmp-dev (>= 4.2), + libtbb-dev, + ${misc:Depends} +Suggests: libgudhi-doc, libgudhi-examples +Description: Generic open source C++ library for topological data analysis + The GUDHI library is a generic open source C++ library for + Topological Data Analysis (TDA) and Higher Dimensional Geometry + Understanding. The library offers state-of-the-art data structures + and algorithms to construct simplicial complexes and compute + persistent homology. + . + The GUDHI library is developed as part of the GUDHI project supported + by the European Research Council. + . + This package contains the header files. See the libgudhi-examples + package for example programs using the library. + +Package: libgudhi-examples +Section: misc +Architecture: all +Multi-Arch: foreign +Depends: ${misc:Depends} +Suggests: libgudhi-dev, libgudhi-doc +Description: Example programs for the GUDHI library + The GUDHI library is a generic open source C++ library for + Topological Data Analysis (TDA) and Higher Dimensional Geometry + Understanding. The library offers state-of-the-art data structures + and algorithms to construct simplicial complexes and compute + persistent homology. + . + The GUDHI library is developed as part of the GUDHI project supported + by the European Research Council. + . + This package contains some source code examples. + +Package: libgudhi-doc +Section: doc +Architecture: all +Multi-Arch: foreign +Depends: libjs-mathjax, ${misc:Depends} +Description: Documentation for the GUDHI library + The GUDHI library is a generic open source C++ library for + Topological Data Analysis (TDA) and Higher Dimensional Geometry + Understanding. The library offers state-of-the-art data structures + and algorithms to construct simplicial complexes and compute + persistent homology. + . + The GUDHI library is developed as part of the GUDHI project supported + by the European Research Council. + . + This package contains documentation. + +Package: python3-gudhi +Section: python +Architecture: any +Multi-Arch: same +Depends: python3-matplotlib, + python3-tk, + ${misc:Depends}, + ${python3:Depends}, + ${shlibs:Depends} +Description: Python 3 interface to the GUDHI library + The GUDHI library is a generic open source C++ library for + Topological Data Analysis (TDA) and Higher Dimensional Geometry + Understanding. The library offers state-of-the-art data structures + and algorithms to construct simplicial complexes and compute + persistent homology. + . + The GUDHI library is developed as part of the GUDHI project supported + by the European Research Council. + . + This package contains GUDHI's Python (3) interface. + +Package: gudhui +Section: math +Architecture: any +Depends: ${misc:Depends}, ${shlibs:Depends} +Description: GUI for some of the functionality of the GUDHI library + The GUDHI library is a generic open source C++ library for + Topological Data Analysis (TDA) and Higher Dimensional Geometry + Understanding. The library offers state-of-the-art data structures + and algorithms to construct simplicial complexes and compute + persistent homology. + . + The GUDHI library is developed as part of the GUDHI project supported + by the European Research Council. + . + This package contains GudhUI, a graphical interface to a few of GUDHI's + features. Be aware that it is quite rough around the edges. + +Package: gudhi-utils +Section: math +Architecture: any +Depends: ${misc:Depends}, ${shlibs:Depends} +Description: Utilities from the GUDHI library + The GUDHI library is a generic open source C++ library for + Topological Data Analysis (TDA) and Higher Dimensional Geometry + Understanding. The library offers state-of-the-art data structures + and algorithms to construct simplicial complexes and compute + persistent homology. + . + The GUDHI library is developed as part of the GUDHI project supported + by the European Research Council. + . + This package contains some utilities built with the GUDHI library. +
\ No newline at end of file diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 00000000..9619ce4a --- /dev/null +++ b/debian/copyright @@ -0,0 +1,131 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: gudhi +Files-Excluded: GudhUI/utils/homsimpl data/filtered_simplicial_complex/bunny_5000_complex.fsc data/points/COIL_database data/points/SO3* data/points/bunny* doc/common/MathJax.* include/gudhi_patches/CGAL/* +Source: http://gudhi.gforge.inria.fr + Deleted unnecessary precompiled binary and upstream data files of unclear licensing status. Deleted also bundled MathJax. + +Files: * +Copyright: 2014-2018 Inria +License: GPL-3+ + +Files: include/gudhi/Miniball* +Copyright: 1999-2013 Bernd Gärtner +License: GPL-3+ + +Files: cmake/modules/FindEigen3.cmake +Copyright: 2006, 2007 Montel Laurent <montel@kde.org> + 2008, 2009 Gael Guennebaud <g.gael@free.fr> + 2009 Benoit Jacob <jacob.benoit.1@gmail.com> +License: BSD-2-clause + +Files: cmake/modules/FindTBB.cmake +Copyright: Hannes Hofmann +License: MIT + +Files: cmake/modules/FindCython.cmake +Copyright: 2011 Kitware, Inc. +License: Apache-2.0 + +Files: utilities/Nerve_GIC/km.py* +Copyright: 2015 Triskelion - HJ van Veen <info@mlwave.com> +License: MIT + +Files: include/gudhi/Contraction/CGAL_queue/Modifiable_priority_queue.h +Copyright: 2006-2011 GeometryFactory +License: LGPL-3+ + This file is part of CGAL (www.cgal.org); you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public License as + published by the Free Software Foundation; either version 3 of the License, + or (at your option) any later version. + . + Licensees holding a valid commercial license may use this file in + accordance with the commercial license agreement provided with the software. + . + This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE + WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. + . + On Debian systems, the complete text of the GNU Lesser General Public + License version 3 can be found in "/usr/share/common-licenses/LGPL-3". + +Files: debian/* +Copyright: 2016-2018 Gard Spreemann <gspreemann@gmail.com> +License: GPL-3+ + +License: GPL-3+ + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + . + This package is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <https://www.gnu.org/licenses/>. + . + On Debian systems, the complete text of the GNU General + Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". + +License: BSD-2-clause + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + . + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + . + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + . + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS + OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED + AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT + LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY + WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE + POSSIBILITY OF SUCH DAMAGE. + +License: Apache-2.0 + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + . + http://www.apache.org/licenses/LICENSE-2.0 + . + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + . + On Debian systems, the complete text of the Apache License version 2.0 + can be found in "/usr/share/common-licenses/Apache-2.0". + +License: MIT + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + . + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. diff --git a/debian/gudhi-utils.install b/debian/gudhi-utils.install new file mode 100644 index 00000000..71e8eb9f --- /dev/null +++ b/debian/gudhi-utils.install @@ -0,0 +1 @@ +debian/tmp/usr/bin/gudhi-* usr/bin/ diff --git a/debian/gudhui.1 b/debian/gudhui.1 new file mode 100644 index 00000000..53ce0867 --- /dev/null +++ b/debian/gudhui.1 @@ -0,0 +1,12 @@ +.TH GUDHUI 1 "" "" "" +.SH NAME +GudhUI \- graphical interface for some of the GUDHI library's features +.SH SYNOPSIS +.B gudhui +[\fIQt options\fR] +.SH DESCRIPTION +.B gudhui +is a graphical interface for some of the GUDHI library's features. It +can aid the exploratory steps of topological data analysis. +.SH OPTIONS +The program accepts only standard Qt options. diff --git a/debian/gudhui.install b/debian/gudhui.install new file mode 100644 index 00000000..9f140378 --- /dev/null +++ b/debian/gudhui.install @@ -0,0 +1 @@ +debian/tmp/usr/bin/gudhui diff --git a/debian/gudhui.manpages b/debian/gudhui.manpages new file mode 100644 index 00000000..4ffbdc9f --- /dev/null +++ b/debian/gudhui.manpages @@ -0,0 +1 @@ +debian/gudhui.1
\ No newline at end of file diff --git a/debian/libgudhi-dev.docs b/debian/libgudhi-dev.docs new file mode 100644 index 00000000..3d523db3 --- /dev/null +++ b/debian/libgudhi-dev.docs @@ -0,0 +1 @@ +biblio diff --git a/debian/libgudhi-dev.install b/debian/libgudhi-dev.install new file mode 100644 index 00000000..3035131d --- /dev/null +++ b/debian/libgudhi-dev.install @@ -0,0 +1,2 @@ +debian/tmp/usr/include/gudhi/ usr/include/ +debian/tmp/usr/share/gudhi/*.cmake usr/lib/cmake/gudhi/ diff --git a/debian/libgudhi-doc.doc-base b/debian/libgudhi-doc.doc-base new file mode 100644 index 00000000..f8175ee1 --- /dev/null +++ b/debian/libgudhi-doc.doc-base @@ -0,0 +1,8 @@ +Document: libgudhi-doc +Title: GUDHI C++ library manual +Abstract: This Doxygen manual describes the GUDHI C++ API +Section: Science/Mathematics + +Format: HTML +Index: /usr/share/doc/libgudhi/html/index.html +Files: /usr/share/doc/libgudhi/html/*.html diff --git a/debian/libgudhi-doc.install b/debian/libgudhi-doc.install new file mode 100644 index 00000000..ceccbc47 --- /dev/null +++ b/debian/libgudhi-doc.install @@ -0,0 +1 @@ +doc/html/* usr/share/doc/libgudhi/html/ diff --git a/debian/libgudhi-examples.docs b/debian/libgudhi-examples.docs new file mode 100644 index 00000000..253d5377 --- /dev/null +++ b/debian/libgudhi-examples.docs @@ -0,0 +1 @@ +debian/tmp/usr/share/doc/libgudhi-examples/* diff --git a/debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch b/debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch new file mode 100644 index 00000000..abf2a450 --- /dev/null +++ b/debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch @@ -0,0 +1,23 @@ +From: Gard Spreemann <gspreemann@gmail.com> +Date: Fri, 15 Jun 2018 13:18:26 +0200 +Subject: Disable Sphinx test since we're not currently using. + +--- + cython/CMakeLists.txt | 5 ----- + 1 file changed, 5 deletions(-) + +diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt +index 17d440e..9194e45 100644 +--- a/cython/CMakeLists.txt ++++ b/cython/CMakeLists.txt +@@ -280,10 +280,5 @@ if(CYTHON_FOUND) + DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" + COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM) + +- add_test(NAME sphinx_py_test +- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} +- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" +- ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest) +- + endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + endif(CYTHON_FOUND) diff --git a/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch b/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch new file mode 100644 index 00000000..d58b56a9 --- /dev/null +++ b/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch @@ -0,0 +1,79 @@ +From: Gard Spreemann <gspreemann@gmail.com> +Date: Fri, 15 Jun 2018 13:19:42 +0200 +Subject: Disable tests that use DFSG-deleted data files. + +--- + example/Nerve_GIC/CMakeLists.txt | 6 ------ + example/Persistent_cohomology/CMakeLists.txt | 4 ---- + example/Simplex_tree/CMakeLists.txt | 2 -- + utilities/Nerve_GIC/CMakeLists.txt | 8 -------- + 4 files changed, 20 deletions(-) + +diff --git a/example/Nerve_GIC/CMakeLists.txt b/example/Nerve_GIC/CMakeLists.txt +index fdecf86..f63e08e 100644 +--- a/example/Nerve_GIC/CMakeLists.txt ++++ b/example/Nerve_GIC/CMakeLists.txt +@@ -12,16 +12,10 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + + # Copy files for not to pollute sources when testing + file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +- file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +- file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + + add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC> + "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") + +- add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC> +- "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" +- "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") +- + install(TARGETS CoordGIC DESTINATION bin) + install(TARGETS FuncGIC DESTINATION bin) + +diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt +index 0f73151..4cac586 100644 +--- a/example/Persistent_cohomology/CMakeLists.txt ++++ b/example/Persistent_cohomology/CMakeLists.txt +@@ -28,10 +28,6 @@ add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D CO + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") + add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $<TARGET_FILE:rips_persistence_via_boundary_matrix> + "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") +-add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $<TARGET_FILE:persistence_from_file> +- "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0") +-add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $<TARGET_FILE:persistence_from_file> +- "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") + + install(TARGETS plain_homology DESTINATION bin) + install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin) +diff --git a/example/Simplex_tree/CMakeLists.txt b/example/Simplex_tree/CMakeLists.txt +index 857e851..48bb069 100644 +--- a/example/Simplex_tree/CMakeLists.txt ++++ b/example/Simplex_tree/CMakeLists.txt +@@ -29,8 +29,6 @@ if(GMP_FOUND AND CGAL_FOUND) + if (TBB_FOUND) + target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${TBB_LIBRARIES}) + endif() +- add_test(NAME Simplex_tree_example_alpha_shapes_3_from_off COMMAND $<TARGET_FILE:Simplex_tree_example_alpha_shapes_3_from_off> +- "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off") + + install(TARGETS Simplex_tree_example_alpha_shapes_3_from_off DESTINATION bin) + +diff --git a/utilities/Nerve_GIC/CMakeLists.txt b/utilities/Nerve_GIC/CMakeLists.txt +index 215f9df..20aeb8e 100644 +--- a/utilities/Nerve_GIC/CMakeLists.txt ++++ b/utilities/Nerve_GIC/CMakeLists.txt +@@ -11,14 +11,6 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + endif() + + file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +- # Copy files for not to pollute sources when testing +- file(COPY "${CMAKE_SOURCE_DIR}/data/points/human.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +- +- add_test(NAME Nerve_GIC_utilities_nerve COMMAND $<TARGET_FILE:Nerve> +- "human.off" "2" "10" "0.3") +- +- add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC> +- "human.off" "100") + + install(TARGETS Nerve DESTINATION bin) + install(TARGETS VoronoiGIC DESTINATION bin) diff --git a/debian/patches/0004-Use-system-MathJax.patch b/debian/patches/0004-Use-system-MathJax.patch new file mode 100644 index 00000000..ecd7b0d3 --- /dev/null +++ b/debian/patches/0004-Use-system-MathJax.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann <gspreemann@gmail.com> +Date: Fri, 15 Jun 2018 13:20:33 +0200 +Subject: Use system MathJax. + +--- + Doxyfile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Doxyfile b/Doxyfile +index 020667e..88ce932 100644 +--- a/Doxyfile ++++ b/Doxyfile +@@ -1454,7 +1454,7 @@ MATHJAX_FORMAT = HTML-CSS + # The default value is: http://cdn.mathjax.org/mathjax/latest. + # This tag requires that the tag USE_MATHJAX is set to YES. + +-MATHJAX_RELPATH = ../common ++MATHJAX_RELPATH = /usr/share/javascript/mathjax + + # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax + # extension names that should be enabled during MathJax rendering. For example diff --git a/debian/patches/0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch b/debian/patches/0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch new file mode 100644 index 00000000..5ab944f7 --- /dev/null +++ b/debian/patches/0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann <gspreemann@gmail.com> +Date: Fri, 15 Jun 2018 13:21:25 +0200 +Subject: Don't set runtime library dirs for Python extensions. + +--- + cython/setup.py.in | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/cython/setup.py.in b/cython/setup.py.in +index ee381a1..3c8e0c4 100644 +--- a/cython/setup.py.in ++++ b/cython/setup.py.in +@@ -36,7 +36,7 @@ gudhi = Extension( + libraries=[@GUDHI_CYTHON_LIBRARIES@], + library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@], + include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@], +- runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@], ++ runtime_library_dirs=[], + ) + + setup( diff --git a/debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch b/debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch new file mode 100644 index 00000000..cea5de9d --- /dev/null +++ b/debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann <gspreemann@gmail.com> +Date: Fri, 15 Jun 2018 13:23:55 +0200 +Subject: Force linking of Python module with CGAL. + +--- + cython/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt +index 9194e45..90ca2b7 100644 +--- a/cython/CMakeLists.txt ++++ b/cython/CMakeLists.txt +@@ -78,7 +78,7 @@ if(CYTHON_FOUND) + if(CGAL_HEADER_ONLY) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") + else(CGAL_HEADER_ONLY) +- add_gudhi_cython_lib(${CGAL_LIBRARY}) ++ add_gudhi_cython_lib("${CGAL_LIBRARIES_DIR}/libCGAL.so") + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") + # If CGAL is not header only, CGAL library may link with boost system, + add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY}) diff --git a/debian/patches/0007-Force-linking-against-libatomic-for-parts-that-use-T.patch b/debian/patches/0007-Force-linking-against-libatomic-for-parts-that-use-T.patch new file mode 100644 index 00000000..7d69e5ce --- /dev/null +++ b/debian/patches/0007-Force-linking-against-libatomic-for-parts-that-use-T.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann <gspreemann@gmail.com> +Date: Fri, 15 Jun 2018 13:25:37 +0200 +Subject: Force linking against libatomic for parts that use TBB. + +--- + cmake/modules/FindTBB.cmake | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/cmake/modules/FindTBB.cmake b/cmake/modules/FindTBB.cmake +index 13f4d92..6baa8d7 100644 +--- a/cmake/modules/FindTBB.cmake ++++ b/cmake/modules/FindTBB.cmake +@@ -375,6 +375,8 @@ if (TBB_INCLUDE_DIR) + endif(NOT TBB_without_pthread) + endif(UNIX AND NOT APPLE) + ++ list(APPEND ALL_TBB_LIBRARIES atomic) ++ + set (TBB_LIBRARIES ${ALL_TBB_LIBRARIES} + CACHE PATH "TBB libraries" FORCE) + diff --git a/debian/patches/0008-Offline-header-to-avoid-loading-remote-resources-in-.patch b/debian/patches/0008-Offline-header-to-avoid-loading-remote-resources-in-.patch new file mode 100644 index 00000000..3c93cecd --- /dev/null +++ b/debian/patches/0008-Offline-header-to-avoid-loading-remote-resources-in-.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann <gspreemann@gmail.com> +Date: Fri, 15 Jun 2018 13:42:45 +0200 +Subject: Offline header to avoid loading remote resources in HTML docs. + +--- + Doxyfile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Doxyfile b/Doxyfile +index 88ce932..eb565bc 100644 +--- a/Doxyfile ++++ b/Doxyfile +@@ -1059,7 +1059,7 @@ HTML_FILE_EXTENSION = .html + # of the possible markers and block names see the documentation. + # This tag requires that the tag GENERATE_HTML is set to YES. + +-HTML_HEADER = doc/common/header.html ++HTML_HEADER = doc/common/offline_header.html + + # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each + # generated HTML page. If the tag is left blank doxygen will generate a standard diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 00000000..81114a30 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,7 @@ +0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch +0003-Disable-tests-that-use-DFSG-deleted-data-files.patch +0004-Use-system-MathJax.patch +0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch +0006-Force-linking-of-Python-module-with-CGAL.patch +0007-Force-linking-against-libatomic-for-parts-that-use-T.patch +0008-Offline-header-to-avoid-loading-remote-resources-in-.patch diff --git a/debian/python3-gudhi.install b/debian/python3-gudhi.install new file mode 100644 index 00000000..be9e3f27 --- /dev/null +++ b/debian/python3-gudhi.install @@ -0,0 +1 @@ +debian/tmp/usr/lib/python3/dist-packages/cython/gudhi.cpython*.so usr/lib/python3/dist-packages/
\ No newline at end of file diff --git a/debian/rules b/debian/rules new file mode 100755 index 00000000..3cd05121 --- /dev/null +++ b/debian/rules @@ -0,0 +1,100 @@ +#!/usr/bin/make -f + +export DEB_BUILD_MAINT_OPTIONS = hardening=+all +CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) +CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) +LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) + +TMPBIN:=debian/tmp/usr/bin + +PY3VERS:=$(shell py3versions -vs) +DEFAULT_PY3VER=$(shell py3versions -vd) +REMAINING_PY3VERS:=$(filter-out $(DEFAULT_PY3VER), $(PY3VERS)) + +%: +# The --buildirectory=build is there so that we can easily get a hold +# of documentation and examples, which are not installed by upstream. + dh $@ --with=python3 --builddirectory=build + for py3ver in $(REMAINING_PY3VERS) ; do \ + dh $@ --with=python3 --builddirectory=build$$py3ver ; \ + done + +override_dh_auto_configure: + dh_auto_configure -- -DWITH_GUDHI_BENCHMARK=true -DWITH_GUDHI_EXAMPLE=true -DWITH_GUDHI_PYTHON=true -DWITH_GUDHI_TEST=true -DWITH_GUDHI_UTILITIES=true -DPython_ADDITIONAL_VERSIONS=$(DEFAULT_PY3VER) + for py3ver in $(REMAINING_PY3VERS) ; do \ + dh_auto_configure --builddirectory=build$$py3ver -- -DWITH_GUDHI_BENCHMARK=false -DWITH_GUDHI_EXAMPLE=false -DWITH_GUDHI_PYTHON=true -DWITH_GUDHI_TEST=true -DWITH_GUDHI_UTILITIES=false -DPython_ADDITIONAL_VERSIONS=$$py3ver ; \ + done + +override_dh_auto_build-arch: + dh_auto_build --builddirectory=build + for py3ver in $(REMAINING_PY3VERS) ; do \ + dh_auto_build --builddirectory=build$$py3ver ; \ + done + +override_dh_auto_build-indep: + make -C build doxygen + dh_auto_build --builddirectory=build + +override_dh_auto_test-indep: + +override_dh_auto_test-arch: + dh_auto_test --no-parallel --builddirectory=build + for py3ver in $(REMAINING_PY3VERS) ; do \ + dh_auto_test --no-parallel --builddirectory=build$$py3ver ; \ + done + +override_dh_auto_install: + find example -type f \( -name '*.cpp' -o \( -name '*.txt' -a ! -iname 'cmake*' \) \) -exec sh -c 'install -D -m 644 $$0 debian/tmp/usr/share/doc/libgudhi-examples/$$0' {} \; + + dh_auto_install --builddirectory=build + for py3ver in $(REMAINING_PY3VERS) ; do \ + dh_auto_install --builddirectory=build$$py3ver ; \ + done + + # Remove installed information about Miniball header. + rm debian/tmp/usr/include/gudhi/Miniball.COPYRIGHT + rm debian/tmp/usr/include/gudhi/Miniball.README + + mv $(TMPBIN)/Nerve \ + $(TMPBIN)/gudhi-nerve + mv $(TMPBIN)/VoronoiGIC \ + $(TMPBIN)/gudhi-voronoi-gic + mv $(TMPBIN)/Witness_complex_strong_witness_persistence \ + $(TMPBIN)/gudhi-witness-complex-strong-witness-persistence + mv $(TMPBIN)/Witness_complex_weak_witness_persistence \ + $(TMPBIN)/gudhi-witness-complex-weak-witness-persistence + mv $(TMPBIN)/alpha_complex_3d_persistence \ + $(TMPBIN)/gudhi-alpha-complex-3d-persistence + mv $(TMPBIN)/alpha_complex_persistence \ + $(TMPBIN)/gudhi-alpha-complex-persistence + mv $(TMPBIN)/bottleneck_distance \ + $(TMPBIN)/gudhi-bottleneck-distance + mv $(TMPBIN)/cech_persistence \ + $(TMPBIN)/gudhi-cech-persistence + mv $(TMPBIN)/cubical_complex_persistence \ + $(TMPBIN)/gudhi-cubical-complex-persistence + mv $(TMPBIN)/exact_alpha_complex_3d_persistence \ + $(TMPBIN)/gudhi-exact-alpha-complex-3d-persistence + mv $(TMPBIN)/off_file_from_shape_generator \ + $(TMPBIN)/gudhi-off-file-from-shape-generator + mv $(TMPBIN)/periodic_alpha_complex_3d_persistence \ + $(TMPBIN)/gudhi-periodic-alpha-complex-3d-persistence + mv $(TMPBIN)/periodic_cubical_complex_persistence \ + $(TMPBIN)/gudhi-periodic-cubical-complex-persistence + mv $(TMPBIN)/rips_correlation_matrix_persistence \ + $(TMPBIN)/gudhi-rips-correlation-matrix-persistence + mv $(TMPBIN)/rips_distance_matrix_persistence \ + $(TMPBIN)/gudhi-rips-distance-matrix-persistence + mv $(TMPBIN)/rips_persistence \ + $(TMPBIN)/gudhi-rips-persistence + mv $(TMPBIN)/sparse_rips_persistence \ + $(TMPBIN)/gudhi-sparse-rips-persistence + mv $(TMPBIN)/weighted_alpha_complex_3d_persistence \ + $(TMPBIN)/gudhi-weighted-alpha-complex-3d-persistence + mv $(TMPBIN)/weighted_periodic_alpha_complex_3d_persistence \ + $(TMPBIN)/gudhi-weighted-periodic-alpha-complex-3d-persistence + + install -D build/GudhUI/GudhUI $(TMPBIN)/gudhui + +override_dh_compress: + dh_compress -X.cpp diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 00000000..163aaf8d --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/tests/control b/debian/tests/control new file mode 100644 index 00000000..65510cef --- /dev/null +++ b/debian/tests/control @@ -0,0 +1,3 @@ +Tests: python-upstream.sh +Depends: python3-all, python3-gudhi, python3-pytest + diff --git a/debian/tests/python-upstream.py b/debian/tests/python-upstream.py new file mode 100644 index 00000000..098701aa --- /dev/null +++ b/debian/tests/python-upstream.py @@ -0,0 +1,17 @@ +import pytest +import os + +tmpdir = os.getenv("AUTOPKGTEST_TMP") + +if tmpdir is None: + print("Need the environment variable AUTOPKGTEST_TMP.") + exit(1) + +cwd = os.getcwd() +test_path = cwd + "/cython/test" + +os.chdir(tmpdir) + +print("Running tests from %s with cwd %s." %(test_path, os.getcwd())) + +exit(pytest.main([test_path])) diff --git a/debian/tests/python-upstream.sh b/debian/tests/python-upstream.sh new file mode 100755 index 00000000..e292ab76 --- /dev/null +++ b/debian/tests/python-upstream.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +set -e + +for py3ver in $(py3versions -vs) +do + echo "Running tests with Python ${py3ver}." + /usr/bin/python${py3ver} -B debian/tests/python-upstream.py +done diff --git a/debian/watch b/debian/watch new file mode 100644 index 00000000..d518384a --- /dev/null +++ b/debian/watch @@ -0,0 +1,5 @@ +version=3 + +opts="dversionmangle=s/\+dfsg(\.\d+)?$//,filenamemangle=s/\S+\/v?(\S+)\.tar\.gz/gudhi-$1\.tar\.gz/" \ + https://gforge.inria.fr/frs/?group_id=3865 \ + .*\/.*GUDHI_(\d[\d.-]*)\.tar\.gz |