Codebase list ciftilib / 762900a
Initial debianization. Ghislain Antony Vaillant 7 years ago
21 changed file(s) with 713 addition(s) and 0 deletion(s). Raw diff Collapse all Expand all
0 ciftilib (1.5.1-1) UNRELEASED; urgency=low
1
2 * Initial release. (Closes: #818983)
3
4 -- Ghislain Antony Vaillant <ghisvail@gmail.com> Sat, 05 Nov 2016 17:21:51 +0000
0 Source: ciftilib
1 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
2 Uploaders: Ghislain Antony Vaillant <ghisvail@gmail.com>
3 Section: libs
4 Priority: optional
5 Build-Depends: cmake,
6 debhelper (>= 10),
7 libboost-dev,
8 libboost-filesystem-dev,
9 libxml++2.6-dev,
10 zlib1g-dev
11 Build-Depends-Indep: doxygen
12 Standards-Version: 3.9.8
13 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ciftilib.git
14 Vcs-Git: https://anonscm.debian.org/git/debian-med/ciftilib.git
15 Homepage: https://github.com/Washington-University/CiftiLib
16
17 Package: libcifti0
18 Architecture: any
19 Multi-Arch: same
20 Depends: ${misc:Depends},
21 ${shlibs:Depends}
22 Description: library for manipulating CIFTI files
23 CIFTI (Connectivity Informatics Technology Initiative) standardizes the file
24 formats for storage of connectivity data. These formats are developed by the
25 Human Connectome Project and other interested parties.
26 .
27 CiftiLib is a C++ library for CIFTI-1 and CIFTI-2 file I/O, supporting both
28 on-disk and in-memory access. It also provides facilities for reading and
29 writing generic NIfTI-1 and NIfTI-2 files.
30 .
31 This package provides the shared libraries.
32
33 Package: libcifti-dev
34 Architecture: any
35 Multi-Arch: same
36 Section: libdevel
37 Depends: ${misc:Depends},
38 libboost-dev,
39 libcifti0 (= ${binary:Version}),
40 libxml++2.6-dev
41 Suggests: libcifti-doc
42 Description: development files for CiftiLib
43 CIFTI (Connectivity Informatics Technology Initiative) standardizes the file
44 formats for storage of connectivity data. These formats are developed by the
45 Human Connectome Project and other interested parties.
46 .
47 CiftiLib is a C++ library for CIFTI-1 and CIFTI-2 file I/O, supporting both
48 on-disk and in-memory access. It also provides facilities for reading and
49 writing generic NIfTI-1 and NIfTI-2 files.
50 .
51 This package provides the development files.
52
53 Package: libcifti-doc
54 Architecture: all
55 Multi-Arch: foreign
56 Section: doc
57 Depends: ${misc:Depends}
58 Description: documentation for CiftiLib
59 CIFTI (Connectivity Informatics Technology Initiative) standardizes the file
60 formats for storage of connectivity data. These formats are developed by the
61 Human Connectome Project and other interested parties.
62 .
63 CiftiLib is a C++ library for CIFTI-1 and CIFTI-2 file I/O, supporting both
64 on-disk and in-memory access. It also provides facilities for reading and
65 writing generic NIfTI-1 and NIfTI-2 files.
66 .
67 This package provides the documentation.
0 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
1 Upstream-Name: CiftiLib
2 Upstream-Contact: Tim Coalson <tsc5yc@mst.edu>
3 Source: https://github.com/Washington-University/CiftiLib
4
5 Files: *
6 Copyright: 2014 Washington University School of Medicine
7 License: BSD-2-Clause
8
9 Files: cmake/Modules/UseDoxygen/*
10 Copyright: 2009-2011 Tobias Rautenkranz <tobias@rautenkranz.ch>
11 License: BSD-3-Clause
12
13 Files: debian/*
14 Copyright: 2016 Ghislain Antony Vaillant <ghisvail@gmail.com>
15 License: BSD-2-Clause
16
17 Files: example/data/*
18 Copyright: Public Domain
19 License: ODC-PDDL-1.0
20
21 License: BSD-2-Clause
22 Redistribution and use in source and binary forms, with or without
23 modification, are permitted provided that the following conditions are met:
24 .
25 1. Redistributions of source code must retain the above copyright notice, this
26 list of conditions and the following disclaimer.
27 .
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29 this list of conditions and the following disclaimer in the documentation
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37 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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39 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
40 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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43 License: BSD-3-Clause
44 Redistribution and use in source and binary forms, with or without
45 modification, are permitted provided that the following conditions are met:
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(New empty file)
0 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
1 Upstream-Name: CiftiLib
2 Upstream-Contact: Tim Coalson
3 Source: https://github.com/Washington-University/CiftiLib
4
5 Files: *
6 Copyright 2014 Washington University School of Medicine
7 License: BSD-2-Clause
8
9 Files: debian/*
10 Copyright: 2016 Ghislain Antony Vaillant <ghisvail@gmail.com>
11 License: BSD-2-Clause
12
13 License: BSD-2-Clause
14 Redistribution and use in source and binary forms, with or without
15 modification, are permitted provided that the following conditions are met:
16 .
17 1. Redistributions of source code must retain the above copyright notice, this
18 list of conditions and the following disclaimer.
19 .
20 2. Redistributions in binary form must reproduce the above copyright notice,
21 this list of conditions and the following disclaimer in the documentation
22 and/or other materials provided with the distribution.
23 .
24 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
25 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
26 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
27 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
28 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
29 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
30 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
31 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
32 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
33 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
0 [DEFAULT]
1 upstream-branch = upstream/latest
2 debian-branch = debian/master
3 upstream-tag = upstream/%(version)s
4 debian-tag = debian/%(version)s
5 pristine-tar = True
6
7 [pq]
8 patch-numbers = False
0 usr/include
1 usr/lib/*/*.so
2 usr/lib/*/pkgconfig
0 Document: libcifti-doc
1 Title: API documentation for CiftiLib
2 Author: Washington University School of Medicine
3 Abstract: This is the reference documentation for CiftiLib.
4 Section: Programming
5
6 Format: HTML
7 Index: /usr/share/doc/libcifti-doc/html/index.html
8 Files: /usr/share/doc/libcifti-doc/html/*.html
0 */doc/html
1 USAGE
0 usr/lib/*/*.so.*
0 From: Ghislain Antony Vaillant <ghisvail@gmail.com>
1 Date: Tue, 8 Nov 2016 11:28:10 +0000
2 Subject: Enable parallel execution of tests.
3
4 ---
5 example/CMakeLists.txt | 2 ++
6 1 file changed, 2 insertions(+)
7
8 diff --git a/example/CMakeLists.txt b/example/CMakeLists.txt
9 index 71f4b0a..bc34779 100644
10 --- a/example/CMakeLists.txt
11 +++ b/example/CMakeLists.txt
12 @@ -76,8 +76,10 @@ FOREACH(index RANGE ${loop_end})
13 ADD_TEST(rewrite-little-${testfile} rewrite ${CMAKE_SOURCE_DIR}/example/data/${testfile} little-${testfile} LITTLE)
14 LIST(GET cifti_le_md5s ${index} goodsum)
15 ADD_TEST(rewrite-little-md5-${testfile} ${CMAKE_COMMAND} -Dgood_sum=${goodsum} -Dcheck_file=little-${testfile} -P ${CMAKE_SOURCE_DIR}/cmake/scripts/testmd5.cmake)
16 + SET_TESTS_PROPERTIES(rewrite-little-md5-${testfile} PROPERTIES DEPENDS rewrite-little-${testfile})
17
18 ADD_TEST(rewrite-big-${testfile} rewrite ${CMAKE_SOURCE_DIR}/example/data/${testfile} big-${testfile} BIG)
19 LIST(GET cifti_be_md5s ${index} goodsum)
20 ADD_TEST(rewrite-big-md5-${testfile} ${CMAKE_COMMAND} -Dgood_sum=${goodsum} -Dcheck_file=big-${testfile} -P ${CMAKE_SOURCE_DIR}/cmake/scripts/testmd5.cmake)
21 + SET_TESTS_PROPERTIES(rewrite-big-md5-${testfile} PROPERTIES DEPENDS rewrite-big-${testfile})
22 ENDFOREACH(index RANGE ${loop_end})
0 From: Ghislain Antony Vaillant <ghisvail@gmail.com>
1 Date: Tue, 8 Nov 2016 12:41:01 +0000
2 Subject: Fix spelling errors reported by Lintian.
3
4 ---
5 src/Cifti/CiftiBrainModelsMap.cxx | 8 ++++----
6 src/CiftiFile.cxx | 6 +++---
7 2 files changed, 7 insertions(+), 7 deletions(-)
8
9 diff --git a/src/Cifti/CiftiBrainModelsMap.cxx b/src/Cifti/CiftiBrainModelsMap.cxx
10 index 39e65c6..d8c1e54 100644
11 --- a/src/Cifti/CiftiBrainModelsMap.cxx
12 +++ b/src/Cifti/CiftiBrainModelsMap.cxx
13 @@ -262,7 +262,7 @@ const vector<int64_t>& CiftiBrainModelsMap::getNodeList(const StructureEnum::Enu
14 map<StructureEnum::Enum, int>::const_iterator iter = m_surfUsed.find(structure);
15 if (iter == m_surfUsed.end())
16 {
17 - throw CiftiException("getNodeList called for nonexistant structure");//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this
18 + throw CiftiException("getNodeList called for nonexistent structure");//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this
19 }
20 CiftiAssertVectorIndex(m_modelsInfo, iter->second);
21 return m_modelsInfo[iter->second].m_nodeIndices;
22 @@ -274,7 +274,7 @@ vector<CiftiBrainModelsMap::SurfaceMap> CiftiBrainModelsMap::getSurfaceMap(const
23 map<StructureEnum::Enum, int>::const_iterator iter = m_surfUsed.find(structure);
24 if (iter == m_surfUsed.end())
25 {
26 - throw CiftiException("getSurfaceMap called for nonexistant structure");//also throw, for consistency
27 + throw CiftiException("getSurfaceMap called for nonexistent structure");//also throw, for consistency
28 }
29 CiftiAssertVectorIndex(m_modelsInfo, iter->second);
30 const BrainModelPriv& myModel = m_modelsInfo[iter->second];
31 @@ -380,7 +380,7 @@ vector<CiftiBrainModelsMap::VolumeMap> CiftiBrainModelsMap::getVolumeStructureMa
32 map<StructureEnum::Enum, int>::const_iterator iter = m_volUsed.find(structure);
33 if (iter == m_volUsed.end())
34 {
35 - throw CiftiException("getVolumeStructureMap called for nonexistant structure");//also throw, for consistency
36 + throw CiftiException("getVolumeStructureMap called for nonexistent structure");//also throw, for consistency
37 }
38 CiftiAssertVectorIndex(m_modelsInfo, iter->second);
39 const BrainModelPriv& myModel = m_modelsInfo[iter->second];
40 @@ -404,7 +404,7 @@ const vector<int64_t>& CiftiBrainModelsMap::getVoxelList(const StructureEnum::En
41 map<StructureEnum::Enum, int>::const_iterator iter = m_volUsed.find(structure);
42 if (iter == m_volUsed.end())
43 {
44 - throw CiftiException("getVoxelList called for nonexistant structure");//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this
45 + throw CiftiException("getVoxelList called for nonexistent structure");//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this
46 }
47 CiftiAssertVectorIndex(m_modelsInfo, iter->second);
48 return m_modelsInfo[iter->second].m_voxelIndicesIJK;
49 diff --git a/src/CiftiFile.cxx b/src/CiftiFile.cxx
50 index 99dd512..6e768d7 100644
51 --- a/src/CiftiFile.cxx
52 +++ b/src/CiftiFile.cxx
53 @@ -165,11 +165,11 @@ void CiftiFile::writeFile(const AString& fileName, const CiftiVersion& writingVe
54 {
55 if (m_readingImpl == NULL || m_dims.empty()) throw CiftiException("writeFile called on uninitialized CiftiFile");
56 bool writeSwapped = shouldSwap(endian);
57 - AString canonicalFilename = pathToCanonical(fileName);//NOTE: returns EMPTY STRING for nonexistant file
58 + AString canonicalFilename = pathToCanonical(fileName);//NOTE: returns EMPTY STRING for nonexistent file
59 const CiftiOnDiskImpl* testImpl = dynamic_cast<CiftiOnDiskImpl*>(m_readingImpl.get());
60 bool collision = false, hadWriter = (m_writingImpl != NULL);
61 if (testImpl != NULL && canonicalFilename != "" && pathToCanonical(testImpl->getFilename()) == canonicalFilename)
62 - {//empty string test is so that we don't say collision if both are nonexistant - could happen if file is removed/unlinked while reading on some filesystems
63 + {//empty string test is so that we don't say collision if both are nonexistent - could happen if file is removed/unlinked while reading on some filesystems
64 if (m_onDiskVersion == writingVersion && (dontRewrite(endian) || writeSwapped == testImpl->isSwapped())) return;//don't need to copy to itself
65 collision = true;//we need to copy to memory temporarily
66 boost::shared_ptr<WriteImplInterface> tempMemory(new CiftiMemoryImpl(m_xml));//because tempRead is a ReadImpl, can't be used to copy to
67 @@ -300,7 +300,7 @@ void CiftiFile::verifyWriteImpl()
68 CiftiOnDiskImpl* testImpl = dynamic_cast<CiftiOnDiskImpl*>(m_readingImpl.get());
69 if (testImpl != NULL)
70 {
71 - AString canonicalCurrent = pathToCanonical(testImpl->getFilename());//returns "" if nonexistant, if unlinked while open
72 + AString canonicalCurrent = pathToCanonical(testImpl->getFilename());//returns "" if nonexistent, if unlinked while open
73 if (canonicalCurrent != "" && canonicalCurrent == pathToCanonical(m_writingFile))//these were already absolute
74 {
75 convertToInMemory();//save existing data in memory before we clobber file
0 Enable-parallel-execution-of-tests.patch
1 Fix-spelling-errors-reported-by-Lintian.patch
0 #!/usr/bin/make -f
1
2 # Uncomment this to turn on verbose mode.
3 #export DH_VERBOSE = 1
4
5 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
6 # Prevent overlinkage with libsigc++-2.0.
7 export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
8
9 %:
10 dh $@
11
12 override_dh_auto_configure:
13 dh_auto_configure -- -DBUILD_SHARED_LIBS=ON -DIGNORE_QT=ON
14
15 override_dh_auto_build-indep:
16 dh_auto_build -- doc
17
18 override_dh_installdocs-indep:
19 dh_installdocs --indep
20 dh_doxygen --indep
21
22 override_dh_compress-indep:
23 dh_compress --indep --exclude=examples
0 3.0 (quilt)
0 #!/bin/sh
1 # Copyright 2016 Ghislain Antony Vaillant
2 #
3 # This file is part of the packaging testsuite for ciftilib.
4
5 set -e
6
7 # Prepare the testsuite.
8 cp -a /usr/share/doc/libcifti-doc/examples/* "$AUTOPKGTEST_TMP"
9 cp ./cmake/scripts/testmd5.cmake "$AUTOPKGTEST_TMP"
10 cd "$AUTOPKGTEST_TMP"
11
12 # Setup the CMake project.
13 rm -f CMakeLists.txt
14 cat << EOF > CMakeLists.txt
15 cmake_minimum_required(VERSION 2.8.12)
16 project(ciftilib-tests)
17
18 enable_testing()
19
20 find_package(PkgConfig)
21 pkg_check_modules(PC_CIFTI REQUIRED CiftiLib)
22 add_library(PkgConfig::Cifti INTERFACE IMPORTED)
23 set_target_properties(PkgConfig::Cifti PROPERTIES
24 INTERFACE_INCLUDE_DIRECTORIES "\${PC_CIFTI_INCLUDE_DIRS}"
25 INTERFACE_LINK_LIBRARIES "\${PC_CIFTI_LIBRARIES}"
26 INTERFACE_COMPILE_OPTIONS "\${PC_CIFTI_CFLAGS_OTHER}")
27
28 add_executable(rewrite rewrite.cxx)
29 target_link_libraries(rewrite PkgConfig::Cifti)
30
31 add_executable(xmlinfo xmlinfo.cxx)
32 target_link_libraries(xmlinfo PkgConfig::Cifti)
33
34 set(cifti_files Conte69.MyelinAndCorrThickness.32k_fs_LR.dscalar.nii
35 Conte69.MyelinAndCorrThickness.32k_fs_LR.dtseries.nii
36 Conte69.MyelinAndCorrThickness.32k_fs_LR.ptseries.nii
37 Conte69.parcellations_VGD11b.32k_fs_LR.dlabel.nii
38 ones.dscalar.nii)
39
40 list(LENGTH cifti_files num_cifti_files)
41 math(EXPR loop_end "\${num_cifti_files} - 1")
42
43 foreach(index RANGE \${loop_end})
44 list(GET cifti_files \${index} testfile)
45 add_test(info-\${testfile} xmlinfo \${CMAKE_CURRENT_SOURCE_DIR}/data/\${testfile})
46 add_test(rewrite-little-\${testfile} rewrite \${CMAKE_SOURCE_DIR}/data/\${testfile} little-\${testfile} LITTLE)
47 add_test(rewrite-big-\${testfile} rewrite \${CMAKE_SOURCE_DIR}/data/\${testfile} big-\${testfile} BIG)
48 endforeach(index RANGE \${loop_end})
49
50 EOF
51
52 # Configure, build and execute.
53 mkdir build && cd build
54 cmake .. && make && make test
0 Tests: ciftilib-tests
1 Depends: @, cmake, g++ | c++-compiler, pkg-config
0 Bug-Database: https://github.com/Washington-University/CiftiLib/issues
1 Bug-Submit: https://github.com/Washington-University/CiftiLib/issues/new
2 Name: CiftiLib
3 Repository: git@github.com:Washington-University/CiftiLib
4 Repository-Browse: https://github.com/Washington-University/CiftiLib
0 version=3
1 opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/CiftiLib-$1\.tar\.gz/ \
2 https://github.com/Washington-University/CiftiLib/tags .*/v?(\d\S*)\.tar\.gz