[med-svn] [Git][med-team/vbz-compression][master] 10 commits: Add B-D on libstreamvbyte-dev (currently in salsa)
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sat May 22 18:55:37 BST 2021
Nilesh Patra pushed to branch master at Debian Med / vbz-compression
Commits:
b23e9016 by Nilesh Patra at 2021-05-22T21:33:30+05:30
Add B-D on libstreamvbyte-dev (currently in salsa)
- - - - -
b701c416 by Nilesh Patra at 2021-05-22T21:34:30+05:30
Add patch to use packaged streamvbyte
- - - - -
1c8a6462 by Nilesh Patra at 2021-05-22T21:51:02+05:30
Fix install location for .so
- - - - -
40f41a90 by Nilesh Patra at 2021-05-22T16:56:25+00:00
Add SOVERSION
- - - - -
1699b988 by Nilesh Patra at 2021-05-22T16:56:53+00:00
Split binary for library style packaging
- - - - -
88f4737f by Nilesh Patra at 2021-05-22T22:30:05+05:30
Add "Rules-Requires-Root: no"
- - - - -
a2662c66 by Nilesh Patra at 2021-05-22T22:30:41+05:30
Add upstream/metadata
- - - - -
a814ff75 by Nilesh Patra at 2021-05-22T23:20:28+05:30
Fix copyright
- - - - -
5f970cc9 by Nilesh Patra at 2021-05-22T23:21:07+05:30
Add myself to uploaders
- - - - -
75542397 by Nilesh Patra at 2021-05-22T23:25:25+05:30
[skip ci] Interim changelog entry
- - - - -
10 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/libvbz-compression-dev.install
- + debian/libvbz-compression0.install
- + debian/patches/fix-install-location.patch
- + debian/patches/series
- + debian/patches/soversion.patch
- + debian/patches/use-packaged-streamvbyte.patch
- + debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
vbz-compression (1.0.1-1) UNRELEASED; urgency=medium
- * Initial release (Closes: #<bug>)
+ [ Andreas Tille, Nilesh Patra ]
+ * Initial release (Closes: #988993)
- -- Andreas Tille <tille at debian.org> Thu, 18 Jun 2020 16:03:26 +0200
+ -- Nilesh Patra <nilesh at debian.org> Sat, 22 May 2021 23:24:27 +0530
=====================================
debian/control
=====================================
@@ -1,19 +1,23 @@
Source: vbz-compression
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>, Nilesh Patra <nilesh at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
cmake,
libzstd-dev,
- libhdf5-dev
+ libhdf5-dev,
+ libstreamvbyte-dev,
+ dh-exec
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/vbz-compression
Vcs-Git: https://salsa.debian.org/med-team/vbz-compression.git
Homepage: https://github.com/nanoporetech/vbz_compression/
+Rules-Requires-Root: no
-Package: vbz-compression
+Package: libvbz-compression0
Architecture: any
+Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
Description: VBZ compression plugin for nanopore signal data
@@ -26,3 +30,23 @@ Description: VBZ compression plugin for nanopore signal data
be able to take advantage of the default VBZ settings for compression.
VBZ will be used as the default compression scheme in a future release
of MinKNOW.
+ .
+ This package contains the shared object library.
+
+Package: libvbz-compression-dev
+Architecture: any
+Depends: libvbz-compression0 (= ${binary:Version}),
+ ${shlibs:Depends},
+ ${misc:Depends}
+Description: VBZ compression plugin for nanopore signal data
+ VBZ Compression uses variable byte integer encoding to compress nanopore
+ signal data.
+ .
+ The performance of VBZ is achieved by taking advantage of the properties
+ of the raw signal and therefore is most effective when applied to the
+ signal dataset. Other datasets you may have in your Fast5 files will not
+ be able to take advantage of the default VBZ settings for compression.
+ VBZ will be used as the default compression scheme in a future release
+ of MinKNOW.
+ .
+ This package contains the header files.
=====================================
debian/copyright
=====================================
@@ -3,10 +3,252 @@ Upstream-Name: vbz-compression
Source: https://github.com/nanoporetech/vbz_compression/releases
Files: *
-Copyright: 20xx-20yy <upstream>
-License: nanopore_community
- FIXME
+Copyright: Oxford Nanopore Technologies
+License: MPL-2.0
+
+Files: third_party/gsl/*
+ third_party/gsl.h
+Copyright: 2015, Martin Moene
+ 2015, Microsoft Corporation.
+License: Expat
+
+Files: third_party/catch2/catch.hpp
+Copyright: 2018, Two Blue Cubes Ltd.
+License: Boost-1.0
+
+Files: third_party/catch2/fakeit.hpp
+Copyright: Eran Pe'er 2013
+License: Expat
+
+Files: third_party/hdf5/*
+Copyright: HDF Group <help at hdfgroup.org>
+License: BSD-3-clause
+Comment: Same copyright is also mentioned in src:hdf5
+
+Files: cmake/asan-wrapper
+ cmake/FindASan.cmake
+ cmake/FindMSan.cmake
+ cmake/FindSanitizers.cmake
+ cmake/FindTSan.cmake
+ cmake/FindUBSan.cmake
+ cmake/sanitize-helpers.cmake
+Copyright: 2013, Matthew Arsenault
+ 2015-2016 RWTH Aachen University, Federal Republic of Germany
+License: Expat
+
+Files: cmake/conan.cmake
+Copyright: 2018 JFrog
+License: Expat
Files: debian/*
Copyright: 2020 Andreas Tille <tille at debian.org>
-License: <license>
+ 2021 Nilesh Patra <nilesh at debian.org>
+License: MPL-2.0
+
+License: MPL-2.0
+ This Source Code Form is subject to the terms of the Mozilla Public
+ License, v. 2.0. If a copy of the MPL was not distributed with this
+ file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ .
+ On Debian systems, the complete text of the MPL-2.0 license can be found
+ in "/usr/share/common-licenses/MPL-2.0".
+
+License: Expat
+ 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.
+
+License: Boost-1.0
+ Boost Software License - Version 1.0 - August 17th, 2003
+ .
+ Permission is hereby granted, free of charge, to any person or organization
+ obtaining a copy of the software and accompanying documentation covered by
+ this license (the "Software") to use, reproduce, display, distribute,
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+ DEALINGS IN THE SOFTWARE.
+
+License: BSD-3-clause
+ Copyright Notice and License Terms for
+ HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+ -----------------------------------------------------------------------------
+ .
+ HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+ Copyright (c) 2006-2018, The HDF Group.
+ .
+ NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+ Copyright (c) 1998-2006, The Board of Trustees of the University of Illinois.
+ .
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+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted for any purpose (including commercial purposes)
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+ .
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+ .
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+ SHALL THE HDF GROUP OR THE CONTRIBUTORS BE LIABLE FOR ANY DAMAGES SUFFERED BY
+ THE USERS ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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+ available either publicly, or directly to The HDF Group, without imposing a
+ separate written license agreement for such Enhancements, then you hereby grant
+ the following license: a non-exclusive, royalty-free perpetual license to
+ install, use, modify, prepare derivative works, incorporate into other computer
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+ -----------------------------------------------------------------------------
+ -----------------------------------------------------------------------------
+ .
+ Limited portions of HDF5 were developed by Lawrence Berkeley National
+ Laboratory (LBNL). LBNL's Copyright Notice and Licensing Terms can be
+ found here: COPYING_LBNL_HDF5 file in this directory or at
+ http://support.hdfgroup.org/ftp/HDF5/releases/COPYING_LBNL_HDF5.
+ .
+ -----------------------------------------------------------------------------
+ -----------------------------------------------------------------------------
+ .
+ Contributors: National Center for Supercomputing Applications (NCSA) at
+ the University of Illinois, Fortner Software, Unidata Program Center (netCDF),
+ The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler (gzip), and
+ Digital Equipment Corporation (DEC).
+ .
+ -----------------------------------------------------------------------------
+ .
+ Portions of HDF5 were developed with support from the Lawrence Berkeley
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+ .
+ -----------------------------------------------------------------------------
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+ .
+ This work was partially produced at the University of California,
+ Lawrence Livermore National Laboratory (UC LLNL) under contract
+ no. W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy
+ (DOE) and The Regents of the University of California (University)
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+ -----------------------------------------------------------------------------
+ .
+ HDF5 is available with the SZIP compression library but SZIP is not part
+ of HDF5 and has separate copyright and license terms. See SZIP Compression
+ in HDF Products (www.hdfgroup.org/doc_resource/SZIP/) for further details.
+ .
+ -----------------------------------------------------------------------------
+ .
+ Copyright Notice and License Terms for
+ HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+ -----------------------------------------------------------------------------
+ .
+ HDF5 (Hierarchical Data Format 5)
+ Copyright (c) 2016, The Regents of the University of California, through
+ Lawrence Berkeley National Laboratory (subject to receipt of any required
+ approvals from the U.S. Dept. of Energy).
+ .
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+ .
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+ this list of conditions, and the following disclaimer.
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+ National Laboratory, U.S. Dept. of Energy nor the names of its contributors
+ may be used to endorse or promote products derived from this software without
+ specific prior written permission.
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+ 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 OWNER 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.
+ .
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+ or upgrades to the features, functionality or performance of the source
+ code ("Enhancements") to anyone; however, if you choose to make your
+ Enhancements available either publicly, or directly to Lawrence Berkeley
+ National Laboratory, without imposing a separate written license agreement
+ for such Enhancements, then you hereby grant the following license:
+ a non-exclusive, royalty-free perpetual license to install, use, modify,
+ prepare derivative works, incorporate into other computer software,
+ distribute, and sublicense such enhancements or derivative works thereof,
+ in binary and source code form.
=====================================
debian/libvbz-compression-dev.install
=====================================
@@ -0,0 +1,4 @@
+#!/usr/bin/dh-exec
+
+usr/lib/*/lib*.so
+vbz_plugin/*.h vbz/*.h vbz/v0/*.h obj-${DEB_HOST_MULTIARCH}/*/*/*.h usr/include/vbz-compression
=====================================
debian/libvbz-compression0.install
=====================================
@@ -0,0 +1 @@
+usr/lib/*/lib*.so.*
=====================================
debian/patches/fix-install-location.patch
=====================================
@@ -0,0 +1,15 @@
+Description: Fix install location for .so
+Author: Nilesh Patra <nilesh at debian.org>
+Forwarded: not-needed
+Last-Update: 2021-05-22
+--- a/vbz_plugin/CMakeLists.txt
++++ b/vbz_plugin/CMakeLists.txt
+@@ -62,7 +62,7 @@
+ set(VBZ_PLUGIN_COMPONENT COMPONENT hdf_plugin)
+ endif()
+
+-set(INSTALL_DESTINATION "hdf5/lib/plugin")
++set(INSTALL_DESTINATION "lib/$ENV{DEB_HOST_MULTIARCH}")
+ if (STANDARD_LIB_INSTALL)
+ set(VBZ_PLUGIN_COMPONENT COMPONENT vbz_hdf_plugin)
+ set_target_properties(vbz_hdf_plugin
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,3 @@
+use-packaged-streamvbyte.patch
+fix-install-location.patch
+soversion.patch
=====================================
debian/patches/soversion.patch
=====================================
@@ -0,0 +1,13 @@
+Description: Add a SOVERSION
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2021-05-22
+--- a/vbz_plugin/CMakeLists.txt
++++ b/vbz_plugin/CMakeLists.txt
+@@ -4,6 +4,7 @@
+ vbz_plugin.cpp
+ vbz_plugin.h
+ )
++set_target_properties(vbz_hdf_plugin PROPERTIES SOVERSION 0)
+ add_sanitizers(vbz_hdf_plugin)
+
+ generate_export_header(vbz_hdf_plugin EXPORT_FILE_NAME vbz_plugin/vbz_hdf_plugin_export.h)
=====================================
debian/patches/use-packaged-streamvbyte.patch
=====================================
@@ -0,0 +1,79 @@
+Description: Use packaged streamvbyte instead of third_party
+Author: Nilesh Patra <nilesh at debian.org>
+Forwarded: not-needed
+Last-Update: 2021-05-22
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -138,34 +138,8 @@
+ find_package(HDF5 1.8.16)
+ find_package(zstd 1.3.1 REQUIRED)
+ find_package(Sanitizers)
+-
+-get_filename_component(STREAMVBYTE_SOURCE_DIR
+- third_party/streamvbyte
+- ABSOLUTE
+-)
+-set(STREAMVBYTE_INSTALL_DIR "${CMAKE_BINARY_DIR}/streamvbyte_lib/")
+-set(STREAMVBYTE_PREFIX ${CMAKE_BINARY_DIR}/streamvbyte)
+-set(STREAMVBYTE_STATIC_LIB_NAME ${CMAKE_STATIC_LIBRARY_PREFIX}streamvbyte_static${CMAKE_STATIC_LIBRARY_SUFFIX})
+-set(STREAMVBYTE_STATIC_LIB_SUBDIR ".")
+-get_property(is_multi_config GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
+-if (is_multi_config)
+- set(STREAMVBYTE_STATIC_LIB_SUBDIR "$<CONFIG>")
+-endif()
+-ExternalProject_Add(
+- streamvbyte
+- SOURCE_DIR ${STREAMVBYTE_SOURCE_DIR}
+- UPDATE_DISCONNECTED TRUE
+- PREFIX ${STREAMVBYTE_PREFIX}
+- CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STREAMVBYTE_INSTALL_DIR} -DSTREAMVBYTE_DISABLE_NATIVE=ON -DSTD_FLAGS="-std=c99"
+- # We need to tell CMake about libraries we will link to, otherwise some generators (eg: Ninja)
+- # complain about how knowing how to build libstreamvbyte_static.a, for example.
+- # Ideally, we'd set a hypothetical INSTALL_BYPRODUCTS, and link to the installed file, but that
+- # doesn't seem to be an option.
+- BUILD_BYPRODUCTS "<BINARY_DIR>/${STREAMVBYTE_STATIC_LIB_NAME}"
+-)
+-ExternalProject_Get_Property(streamvbyte BINARY_DIR)
+-set(STREAMVBYTE_STATIC_LIB "${BINARY_DIR}/${STREAMVBYTE_STATIC_LIB_SUBDIR}/${STREAMVBYTE_STATIC_LIB_NAME}")
+-
++find_library(STREAMVBYTE_STATIC_LIB NAMES libstreamvbyte.a PATHS /usr/lib/$ENV{DEB_HOST_MULTIARCH})
++message("INFO: The library that was found is: ${STREAMVBYTE_STATIC_LIB}")
+
+ ########################################################################
+ #
+--- a/vbz/CMakeLists.txt
++++ b/vbz/CMakeLists.txt
+@@ -22,14 +22,16 @@
+ PUBLIC
+ ${CMAKE_CURRENT_SOURCE_DIR}
+ ${CMAKE_CURRENT_BINARY_DIR}
+- ${STREAMVBYTE_INSTALL_DIR}/include
++)
++
++target_link_libraries(vbz
++ PUBLIC
++ ${STREAMVBYTE_STATIC_LIB}
++ zstd::zstd
+ )
+
+ # This explicit dependency is required to make sure the header files are installed into the right
+ # location before we try building against them.
+-add_dependencies(vbz
+- streamvbyte
+-)
+
+ if (WIN32 OR APPLE OR "${CMAKE_SYSTEM_PROCESSOR}" MATCHES "x86_64")
+ if(NOT MSVC)
+@@ -37,12 +39,6 @@
+ endif()
+ endif()
+
+-target_link_libraries(vbz
+- PUBLIC
+- ${STREAMVBYTE_STATIC_LIB}
+- zstd::zstd
+-)
+-
+ if (BUILD_TESTING)
+ add_subdirectory(fuzzing)
+ add_subdirectory(test)
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,7 @@
+---
+Archive: GitHub
+Bug-Database: https://github.com/nanoporetech/vbz_compression/issues
+Bug-Submit: https://github.com/nanoporetech/vbz_compression/issues/new
+Changelog: https://github.com/nanoporetech/vbz_compression/tags
+Repository: https://github.com/nanoporetech/vbz_compression.git
+Repository-Browse: https://github.com/nanoporetech/vbz_compression
View it on GitLab: https://salsa.debian.org/med-team/vbz-compression/-/compare/acad57acb7a2cbb5a4ad0e575f05901d61b08068...75542397b019fdb60ca287af41d02f10a9f31a5c
--
View it on GitLab: https://salsa.debian.org/med-team/vbz-compression/-/compare/acad57acb7a2cbb5a4ad0e575f05901d61b08068...75542397b019fdb60ca287af41d02f10a9f31a5c
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