[med-svn] [Git][med-team/vbz-compression][upstream] New upstream version 1.0.1
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sat May 22 15:50:00 BST 2021
Nilesh Patra pushed to branch upstream at Debian Med / vbz-compression
Commits:
0ab35a67 by Nilesh Patra at 2021-05-22T19:23:35+05:30
New upstream version 1.0.1
- - - - -
20 changed files:
- CMakeLists.txt
- + LICENCE.txt
- README.md
- − cmake/FindHDF5.cmake
- + cmake/SignFile.cmake
- + cmake/SigningUtils.cmake
- cmake/conan.cmake
- − conanfile.txt
- − license.txt
- packaging/hdf_plugin_packaging.cmake
- + python/fast5compress/fast5vbz.py
- python/pyvbz/setup.py
- python/test/test_vbz_filter.py
- vbz/v0/vbz_streamvbyte_impl_sse3.h
- vbz_plugin/CMakeLists.txt
- vbz_plugin/hdf_test_utils/CMakeLists.txt
- vbz_plugin/perf/CMakeLists.txt
- vbz_plugin/test/CMakeLists.txt
- vbz_plugin/vbz_plugin.cpp
- vbz_plugin/vbz_plugin_user_utils.h
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.11.0)
execute_process(
COMMAND git describe --tags
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
OUTPUT_VARIABLE GIT_VERSION
OUTPUT_STRIP_TRAILING_WHITESPACE
)
@@ -13,14 +13,18 @@ set(GIT_VERSION "${CMAKE_MATCH_1}")
message(STATUS "Building version ${GIT_VERSION}")
project(hdf_plugins
VERSION ${GIT_VERSION}
- LANGUAGES CXX
+ LANGUAGES CXX C
)
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
include(ExternalProject)
include(GenerateExportHeader)
-include(CTest)
+# If we're including hdf_plugins as a subdir then we might not be able
+# to override BUILD_TESTING from CTest's default ON value.
+if (NOT DEFINED BUILD_TESTING OR BUILD_TESTING)
+ include(CTest)
+endif()
if (NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE)
message(STATUS "No CMAKE_BUILD_TYPE set - defaulting to Debug")
@@ -31,6 +35,7 @@ if (NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Debug" CACHE STRING "${_bt_docstring}" FORCE)
endif()
+set(HDF_PLUGIN_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
if (NOT DEFINED VBZ_BUILD_ARCHIVE)
@@ -53,6 +58,17 @@ if (NOT DEFINED ENABLE_CONAN)
option(ENABLE_CONAN "Enable conan for dependency installation" ON)
endif()
+if (NOT DEFINED STANDARD_LIB_INSTALL)
+ set(STD_LIB_INSTALL_DEFAULT OFF)
+ if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_DIR)
+ set(STD_LIB_INSTALL_DEFAULT ON)
+ endif()
+ option(STANDARD_LIB_INSTALL
+ "Install library to standard lib / bin paths"
+ ${STD_LIB_INSTALL_DEFAULT}
+ )
+endif()
+
if (NOT VBZ_BUILD_ARCHIVE)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
@@ -70,8 +86,21 @@ if (ENABLE_CONAN)
else()
include(conan)
+ set(_requirements
+ "zstd/1.3.4 at nanopore/stable")
+ set(_generators
+ cmake
+ json)
+ set(_imports
+ "bin, *.dll -> ../bin"
+ "lib, *.dylib* -> ../bin")
set(_extra_args)
+ if (ENABLE_PERF_TESTING)
+ list(APPEND _requirements
+ "google-benchmark/1.5 at nanopore/stable"
+ )
+ endif()
if (CMAKE_BUILD_TYPE)
set(_build_type_DEBUG Debug)
set(_build_type_RELEASE Release)
@@ -82,8 +111,18 @@ if (ENABLE_CONAN)
list(APPEND _extra_args BUILD_TYPE "${_build_type_${_build_type}}")
endif()
endif()
+ if (CONAN_EXTRA_SETTINGS)
+ list(APPEND _extra_args
+ SETTINGS
+ ${CONAN_EXTRA_SETTINGS}
+ )
+ endif()
- conan_cmake_run(CONANFILE conanfile.txt ${_extra_args})
+ conan_cmake_run(
+ GENERATORS ${_generators}
+ REQUIRES ${_requirements}
+ IMPORTS ${_imports}
+ ${_extra_args})
endif()
conan_check_compiler()
conan_define_targets()
@@ -94,10 +133,10 @@ if (ENABLE_PACKAGING)
include(packaging/hdf_plugin_packaging.cmake)
endif()
-include_directories("${CMAKE_SOURCE_DIR}/third_party")
+include_directories("${CMAKE_CURRENT_SOURCE_DIR}/third_party")
find_package(HDF5 1.8.16)
-find_package(zstd 1.3.3 REQUIRED)
+find_package(zstd 1.3.1 REQUIRED)
find_package(Sanitizers)
get_filename_component(STREAMVBYTE_SOURCE_DIR
@@ -117,7 +156,7 @@ ExternalProject_Add(
SOURCE_DIR ${STREAMVBYTE_SOURCE_DIR}
UPDATE_DISCONNECTED TRUE
PREFIX ${STREAMVBYTE_PREFIX}
- CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STREAMVBYTE_INSTALL_DIR} -DSTREAMVBYTE_DISABLE_NATIVE=ON
+ 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
@@ -199,6 +238,8 @@ elseif (CMAKE_CXX_COMPILER_ID MATCHES "Clang") # AppleClang and Clang
)
endif()
+include(SigningUtils)
+
if (ENABLE_PYTHON)
add_subdirectory(python)
endif()
=====================================
LICENCE.txt
=====================================
@@ -0,0 +1,374 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+ means each individual or legal entity that creates, contributes to
+ the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+ means the combination of the Contributions of others (if any) used
+ by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+ means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+ means Source Code Form to which the initial Contributor has attached
+ the notice in Exhibit A, the Executable Form of such Source Code
+ Form, and Modifications of such Source Code Form, in each case
+ including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+ means
+
+ (a) that the initial Contributor has attached the notice described
+ in Exhibit B to the Covered Software; or
+
+ (b) that the Covered Software was made available under the terms of
+ version 1.1 or earlier of the License, but not also under the
+ terms of a Secondary License.
+
+1.6. "Executable Form"
+ means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+ means a work that combines Covered Software with other material, in
+ a separate file or files, that is not Covered Software.
+
+1.8. "License"
+ means this document.
+
+1.9. "Licensable"
+ means having the right to grant, to the maximum extent possible,
+ whether at the time of the initial grant or subsequently, any and
+ all of the rights conveyed by this License.
+
+1.10. "Modifications"
+ means any of the following:
+
+ (a) any file in Source Code Form that results from an addition to,
+ deletion from, or modification of the contents of Covered
+ Software; or
+
+ (b) any new file in Source Code Form that contains any Covered
+ Software.
+
+1.11. "Patent Claims" of a Contributor
+ means any patent claim(s), including without limitation, method,
+ process, and apparatus claims, in any patent Licensable by such
+ Contributor that would be infringed, but for the grant of the
+ License, by the making, using, selling, offering for sale, having
+ made, import, or transfer of either its Contributions or its
+ Contributor Version.
+
+1.12. "Secondary License"
+ means either the GNU General Public License, Version 2.0, the GNU
+ Lesser General Public License, Version 2.1, the GNU Affero General
+ Public License, Version 3.0, or any later versions of those
+ licenses.
+
+1.13. "Source Code Form"
+ means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+ means an individual or a legal entity exercising rights under this
+ License. For legal entities, "You" includes any entity that
+ controls, is controlled by, or is under common control with You. For
+ purposes of this definition, "control" means (a) the power, direct
+ or indirect, to cause the direction or management of such entity,
+ whether by contract or otherwise, or (b) ownership of more than
+ fifty percent (50%) of the outstanding shares or beneficial
+ ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+ Licensable by such Contributor to use, reproduce, make available,
+ modify, display, perform, distribute, and otherwise exploit its
+ Contributions, either on an unmodified basis, with Modifications, or
+ as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+ for sale, have made, import, and otherwise transfer either its
+ Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+ or
+
+(b) for infringements caused by: (i) Your and any other third party's
+ modifications of Covered Software, or (ii) the combination of its
+ Contributions with other software (except as part of its Contributor
+ Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+ its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+ Form, as described in Section 3.1, and You must inform recipients of
+ the Executable Form how they can obtain a copy of such Source Code
+ Form by reasonable means in a timely manner, at a charge no more
+ than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+ License, or sublicense it under different terms, provided that the
+ license for the Executable Form does not attempt to limit or alter
+ the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+* *
+* 6. Disclaimer of Warranty *
+* ------------------------- *
+* *
+* Covered Software is provided under this License on an "as is" *
+* basis, without warranty of any kind, either expressed, implied, or *
+* statutory, including, without limitation, warranties that the *
+* Covered Software is free of defects, merchantable, fit for a *
+* particular purpose or non-infringing. The entire risk as to the *
+* quality and performance of the Covered Software is with You. *
+* Should any Covered Software prove defective in any respect, You *
+* (not any Contributor) assume the cost of any necessary servicing, *
+* repair, or correction. This disclaimer of warranty constitutes an *
+* essential part of this License. No use of any Covered Software is *
+* authorized under this License except under this disclaimer. *
+* *
+************************************************************************
+
+************************************************************************
+* *
+* 7. Limitation of Liability *
+* -------------------------- *
+* *
+* Under no circumstances and under no legal theory, whether tort *
+* (including negligence), contract, or otherwise, shall any *
+* Contributor, or anyone who distributes Covered Software as *
+* permitted above, be liable to You for any direct, indirect, *
+* special, incidental, or consequential damages of any character *
+* including, without limitation, damages for lost profits, loss of *
+* goodwill, work stoppage, computer failure or malfunction, or any *
+* and all other commercial damages or losses, even if such party *
+* shall have been informed of the possibility of such damages. This *
+* limitation of liability shall not apply to liability for death or *
+* personal injury resulting from such party's negligence to the *
+* extent applicable law prohibits such limitation. Some *
+* jurisdictions do not allow the exclusion or limitation of *
+* incidental or consequential damages, so this exclusion and *
+* limitation may not apply to You. *
+* *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+ 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/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+ This Source Code Form is "Incompatible With Secondary Licenses", as
+ defined by the Mozilla Public License, v. 2.0.
+
=====================================
README.md
=====================================
@@ -72,6 +72,6 @@ Then configure the project using:
> git submodule update --init
> mkdir build
> cd build
-> cmake -D ENABLE_CONAN=OFF ..
+> cmake -D CMAKE_BUILD_TYPE=Release -D ENABLE_CONAN=OFF -D ENABLE_PERF_TESTING=OFF -D ENABLE_PYTHON=OFF ..
> make -j
-```
\ No newline at end of file
+```
=====================================
cmake/FindHDF5.cmake deleted
=====================================
@@ -1,88 +0,0 @@
-include(ONTFindModuleHelpers)
-
-set(HDF5_known_components
- Z
- C
- CXX
- HL
- HL_CXX
- Tools
-)
-foreach(_comp ${HDF5_known_components})
- set(HDF5_${_comp}_compile_opts "-DH5_BUILT_AS_DYNAMIC_LIB=1")
-endforeach()
-
-set(HDF5_Z_compile_opts "")
-set(HDF5_Z_lib_names_debug "zlibd;zd")
-set(HDF5_Z_lib_names_release "zlib;z")
-set(HDF5_Z_component_deps)
-
-set(HDF5_C_lib_names_release "hdf5")
-set(HDF5_C_header_names "hdf5.h")
-set(HDF5_C_component_deps Z)
-
-set(HDF5_CXX_lib_names_release "hdf5_cpp")
-set(HDF5_CXX_header_names "H5Cpp.h")
-set(HDF5_CXX_component_deps C)
-
-set(HDF5_HL_lib_names_release "hdf5_hl")
-set(HDF5_HL_header_names "hdf5_hl.h")
-set(HDF5_HL_component_deps C)
-
-set(HDF5_HL_CXX_lib_names_release "hdf5_hl_cpp")
-set(HDF5_HL_CXX_header_names "H5PacketTable.h")
-set(HDF5_HL_CXX_component_deps HL CXX)
-
-set(HDF5_Tools_lib_names_release "hdf5_tools")
-set(HDF5_Tools_header_names "h5tools.h")
-set(HDF5_Tools_component_deps C)
-
-foreach(_comp ${HDF5_known_components})
- if(NOT _comp STREQUAL "Z")
- set(HDF5_${_comp}_lib_names_debug)
- foreach(_name ${HDF5_${_comp}_lib_names_release})
- list(APPEND HDF5_${_comp}_lib_names_debug "${_name}_D")
- endforeach()
- endif()
-endforeach()
-
-ont_find_package_parse_components(HDF5
- RESULT_VAR HDF5_components
- KNOWN_COMPONENTS ${HDF5_known_components}
-)
-ont_find_package_handle_library_components(HDF5
- COMPONENTS ${HDF5_components}
- DEBUG_AND_RELEASE
- SKIP_PKG_CONFIG
-)
-
-find_path(HDF5_INCLUDE_DIR
- NAMES H5public.h
- HINTS ${PKG_HDF5_C_INCLUDE_DIRS}
-)
-mark_as_advanced(HDF5_INCLUDE_DIR)
-if(HDF5_INCLUDE_DIR AND EXISTS "${HDF5_INCLUDE_DIR}/H5public.h")
- set(HDF5_PUBLIC_HEADER "${HDF5_INCLUDE_DIR}/H5public.h")
- file(STRINGS ${HDF5_PUBLIC_HEADER} _hdf5_version_lines
- REGEX "^#define[ \t]+H5_VERS")
- string(REGEX MATCH "H5_VERS_MAJOR[\t ]+([0-9]+)" _dummy ${_hdf5_version_lines})
- set(_hdf5_version_major "${CMAKE_MATCH_1}")
- string(REGEX MATCH "H5_VERS_MINOR[\t ]+([0-9]+)" _dummy ${_hdf5_version_lines})
- set(_hdf5_version_minor "${CMAKE_MATCH_1}")
- string(REGEX MATCH "H5_VERS_RELEASE[\t ]+([0-9]+)" _dummy ${_hdf5_version_lines})
- set(_hdf5_version_release "${CMAKE_MATCH_1}")
- unset(_hdf5_version_lines)
- set(HDF5_VERSION "${_hdf5_version_major}.${_hdf5_version_minor}.${_hdf5_version_release}")
-endif()
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(HDF5
- FOUND_VAR
- HDF5_FOUND
- REQUIRED_VARS
- HDF5_LIBRARIES
- HDF5_INCLUDE_DIR
- VERSION_VAR
- HDF5_VERSION
- HANDLE_COMPONENTS
-)
=====================================
cmake/SignFile.cmake
=====================================
@@ -0,0 +1,47 @@
+set(file_to_sign ${CMAKE_ARGV3})
+
+# Pull from command line by default - otherwise require an environment variable.
+if (NOT MINKNOW_CODE_SIGN_IDENTITY)
+ if ("$ENV{MINKNOW_CODE_SIGN_IDENTITY}" STREQUAL "")
+ message(FATAL_ERROR "Caller must specify code sign identiyy in environment variable 'MINKNOW_CODE_SIGN_IDENTITY'")
+ endif()
+
+ set(MINKNOW_CODE_SIGN_IDENTITY "$ENV{MINKNOW_CODE_SIGN_IDENTITY}")
+endif()
+
+if (APPLE)
+ message("Signing file... ${file_to_sign}${keychain_comment}")
+ set(SIGN_COMMAND
+ codesign -s ${MINKNOW_CODE_SIGN_IDENTITY} ${keychain_arg} --force --deep -vvvv ${file_to_sign})
+elseif(WIN32)
+ find_program(
+ SIGNTOOL_EXE "Signtool.exe"
+ PATHS "C:\\Program Files (x86)\\Windows Kits\\10\\App Certification Kit")
+
+ if (NOT SIGNTOOL_EXE)
+ message(FATAL_ERROR "Failed to find signtool executable")
+ endif()
+
+ message("Signing file... ${file_to_sign}${comment}")
+ set(SIGN_COMMAND ${SIGNTOOL_EXE} sign "/v" "/sha1" "${MINKNOW_CODE_SIGN_IDENTITY}"
+ "/t" "http://timestamp.globalsign.com/scripts/"
+ ${file_to_sign}
+ )
+
+else()
+ message(FATAL_ERROR "Cannot sign code on this platform.")
+endif()
+
+message("Running sign command: ${SIGN_COMMAND}")
+execute_process(
+ COMMAND ${SIGN_COMMAND}
+ RESULT_VARIABLE result
+ OUTPUT_VARIABLE output
+ ERROR_VARIABLE output
+)
+
+if (NOT result EQUAL 0)
+ message(FATAL_ERROR "Could not sign file: ${result}: ${output}")
+else()
+ message("Signed file: ${output}")
+endif()
\ No newline at end of file
=====================================
cmake/SigningUtils.cmake
=====================================
@@ -0,0 +1,25 @@
+function(hdf_add_signing_command target)
+ set(options)
+ set(oneValArgs FILE)
+ set(multiValArgs)
+ cmake_parse_arguments(ARG "${options}" "${oneValArgs}" "${multiValArgs}" ${ARGN})
+
+ if (ARG_UNPARSED_ARGUMENTS)
+ message(FATAL_ERROR "Unexpected arguments to hdf_add_signing_command: ${ARG_UNPARSED_ARGUMENTS}")
+ endif()
+
+ if (NOT APPLE AND NOT WIN32)
+ message(FATAL_ERROR "hdf_add_signing_command called on unsupported platform - platform=${CMAKE_SYSTEM_NAME}, target=${target}")
+ endif()
+
+ if (NOT ARG_FILE)
+ set(ARG_FILE $<TARGET_FILE:${target}>)
+ endif()
+
+ add_custom_command(
+ TARGET ${target}
+ POST_BUILD
+ COMMAND ${CMAKE_COMMAND} -P ${HDF_PLUGIN_SOURCE_DIR}/cmake/SignFile.cmake ${ARG_FILE}
+ COMMENT "Signing ${target}"
+ )
+endfunction()
=====================================
cmake/conan.cmake
=====================================
@@ -195,6 +195,19 @@ function(conan_cmake_settings result)
elseif(CMAKE_VS_PLATFORM_TOOLSET AND (CMAKE_GENERATOR STREQUAL "Ninja"))
set(_SETTINGS ${_SETTINGS} -s compiler.toolset=${CMAKE_VS_PLATFORM_TOOLSET})
endif()
+ # Temp fix due to https://github.com/conan-io/cmake-conan/issues/166
+ elseif (${CMAKE_${LANGUAGE}_COMPILER_ID} STREQUAL Intel)
+ string(REPLACE "." ";" VERSION_LIST ${CMAKE_${LANGUAGE}_COMPILER_VERSION})
+ list(GET VERSION_LIST 0 MAJOR)
+ list(GET VERSION_LIST 1 MINOR)
+ set(COMPILER_VERSION ${MAJOR}.${MINOR})
+ set(_CONAN_SETTING_COMPILER icc)
+ set(_CONAN_SETTING_COMPILER_VERSION ${COMPILER_VERSION})
+ set(_SETTINGS ${_SETTINGS} -s compiler=icc -s compiler.version=${COMPILER_VERSION})
+ if (USING_CXX)
+ conan_cmake_detect_gnu_libcxx(_LIBCXX)
+ set(_CONAN_SETTING_COMPILER_LIBCXX ${_LIBCXX})
+ endif ()
else()
message(FATAL_ERROR "Conan: compiler setup not recognized")
endif()
=====================================
conanfile.txt deleted
=====================================
@@ -1,12 +0,0 @@
-[requires]
-zstd/1.3.4 at nanopore/stable
-google-benchmark/1.5 at nanopore/stable
-
-[generators]
-cmake
-json
-
-[imports]
-# Copy runtime files to the bin folder
-bin, *.dll -> ../bin
-lib, *.dylib* -> ../bin
=====================================
license.txt deleted
=====================================
@@ -1,4 +0,0 @@
-The vbz-plugin software is provided under the Terms and Conditions of the Nanopore Community.
-
-These are available on the Oxford Nanopore Technologies website (https://nanoporetech.com) and
-also inthe included pdf file, "Nanopore Community TCs 09 September 2016.pdf".
=====================================
packaging/hdf_plugin_packaging.cmake
=====================================
@@ -7,7 +7,7 @@ set(CPACK_PACKAGE_VERSION "${PROJECT_VERSION}")
if (NOT VBZ_BUILD_ARCHIVE)
set(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_SOURCE_DIR}/packaging/readme.txt")
set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/packaging/readme.txt")
- set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/license.txt")
+ set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENCE.txt")
cpack_add_component(
hdf_plugin
=====================================
python/fast5compress/fast5vbz.py
=====================================
@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Fast5 compression filter for demonstrating vbz compression
+"""
+
+import os
+import h5py
+import argparse
+from shutil import copy2
+
+__version__ = "0.1.1"
+
+
+def compress_fast5(filename, output_suffix, vbz_version=0, decompress=False):
+ """
+ (De)compress the raw signal in the fast5
+ """
+ # create a copy of the input file for compressing
+ filename = os.path.abspath(filename)
+ out_filename = filename + output_suffix
+ copy2(filename, out_filename)
+
+ # open the copy and compress the signal datasets only
+ with h5py.File(out_filename, 'r+') as fast5:
+
+ if decompress:
+ compression_opts = {
+ "compression": "gzip", "compression_opts": 1
+ }
+ else:
+ compression_opts = {
+ "compression": 32020,
+ # 2 byte integers with zig zag + level 1 zstd
+ "compression_opts": (vbz_version, 2, 1, 1)
+ }
+
+ # multi read files
+ for read in fast5:
+ if not read.startswith("read_"):
+ continue
+
+ # read the signal dataset
+ group = '%s/Raw/' % read
+ raw = fast5[group]["Signal"][:]
+
+ # remove the dataset
+ del fast5[group]["Signal"]
+
+ # store the dataset with the new compression
+ fast5[group].create_dataset(
+ "Signal",
+ data=raw,
+ **compression_opts,
+ chunks=(len(raw),)
+ )
+
+ return out_filename
+
+
+def main(args, print_help):
+ for filename in args.files:
+ print(compress_fast5(filename, args.output_suffix, args.vbz_version, args.decompress))
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser("fast5compress")
+ parser.add_argument('files', nargs='*', help='input files')
+ parser.add_argument("-d", "--decompress", action="store_true", default=False)
+ parser.add_argument("-s", "--output-suffix", default=".tmp")
+ parser.add_argument('-v', '--version', action='version', version=__version__)
+ parser.add_argument('--vbz-version', type=int, default=1)
+ main(parser.parse_args(), parser.print_help)
=====================================
python/pyvbz/setup.py
=====================================
@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
setup(
name='pyvbz',
- version='1.0.0',
+ version='1.0.1',
url='https://nanoporetech.com',
author='Oxford Nanopore Technologies, Limited',
author_email="support at nanoporetech.com",
@@ -16,7 +16,7 @@ setup(
'Environment :: Console',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
- 'License :: Other/Proprietary License',
+ 'License :: OSI Approved :: Mozilla Public License 2.0',
'Natural Language :: English',
'Operating System :: POSIX :: Linux',
'Programming Language :: Python :: 2',
=====================================
python/test/test_vbz_filter.py
=====================================
@@ -10,7 +10,7 @@ class TestVbzFilter(unittest.TestCase):
VBZ_VERISON = 0
def test_simple_range(self):
- original_data = numpy.array(range(1, 100), dtype="i2")
+ original_data = numpy.arange(1, 100, dtype="i2")
with h5py.File("test_file.h5", "w") as f:
f.create_dataset("bar", compression=32020, compression_opts=(self.VBZ_VERISON, 2, 1, 1), data=original_data)
=====================================
vbz/v0/vbz_streamvbyte_impl_sse3.h
=====================================
@@ -3,7 +3,11 @@
#include <cstring>
#include <iostream>
+#if (defined __INTEL_COMPILER) && (defined WIN32)
+#include <intrin.h>
+#else
#include <x86intrin.h>
+#endif
// See: https://github.com/lemire/streamvbyte
static const uint8_t encode_shuf_lut[64*16] = {
=====================================
vbz_plugin/CMakeLists.txt
=====================================
@@ -24,6 +24,19 @@ target_link_libraries(vbz_hdf_plugin
vbz
)
+if (${CMAKE_CXX_COMPILER_ID} MATCHES "Intel" AND NOT WIN32)
+ target_link_libraries(vbz_hdf_plugin
+ PRIVATE
+ $<$<CXX_COMPILER_ID:Intel>:-static-intel>
+ $<$<CXX_COMPILER_ID:Intel>:-mkl=sequential>
+ $<$<CXX_COMPILER_ID:Intel>:-wd10237>
+ )
+endif()
+
+if (ENABLE_CODE_SIGNING)
+ hdf_add_signing_command(vbz_hdf_plugin)
+endif()
+
if (WIN32)
target_compile_definitions(vbz_hdf_plugin
PRIVATE
@@ -49,9 +62,26 @@ if (NOT VBZ_BUILD_ARCHIVE)
set(VBZ_PLUGIN_COMPONENT COMPONENT hdf_plugin)
endif()
+set(INSTALL_DESTINATION "hdf5/lib/plugin")
+if (STANDARD_LIB_INSTALL)
+ set(VBZ_PLUGIN_COMPONENT COMPONENT vbz_hdf_plugin)
+ set_target_properties(vbz_hdf_plugin
+ PROPERTIES
+ VERSION ${PROJECT_VERSION}
+ SOVERSION ${PROJECT_VERSION_MAJOR}
+ )
+ if(WIN32)
+ set(INSTALL_DESTINATION "bin")
+ else()
+ set(INSTALL_DESTINATION "lib")
+ endif()
+elseif (VBZ_BUILD_ARCHIVE)
+ set(INSTALL_DESTINATION "bin")
+endif()
+
install(
TARGETS vbz_hdf_plugin
- DESTINATION "hdf5/lib/plugin"
+ DESTINATION ${INSTALL_DESTINATION}
${VBZ_PLUGIN_COMPONENT}
)
=====================================
vbz_plugin/hdf_test_utils/CMakeLists.txt
=====================================
@@ -7,10 +7,11 @@ set_property(TARGET hdf_test_utils PROPERTY CXX_STANDARD 11)
target_include_directories(hdf_test_utils
PUBLIC
- ${CMAKE_CURRENT_SOURCE_DIR}
+ ${CMAKE_CURRENT_SOURCE_DIR}
+ ${HDF5_C_INCLUDE_DIRS}
)
target_link_libraries(hdf_test_utils
PRIVATE
- HDF5::C
-)
\ No newline at end of file
+ ${HDF5_C_LIBRARIES}
+)
=====================================
vbz_plugin/perf/CMakeLists.txt
=====================================
@@ -8,7 +8,7 @@ add_sanitizers(vbz_hdf_perf_test)
target_link_libraries(vbz_hdf_perf_test
PRIVATE
google::benchmark
- HDF5::C
+ ${HDF5_C_LIBRARIES}
hdf_test_utils
vbz_hdf_plugin
)
@@ -19,4 +19,4 @@ add_test(
NAME vbz_hdf_perf_test
COMMAND vbz_hdf_perf_test
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-)
\ No newline at end of file
+)
=====================================
vbz_plugin/test/CMakeLists.txt
=====================================
@@ -9,7 +9,7 @@ set_property(TARGET vbz_hdf_plugin_test PROPERTY CXX_STANDARD 11)
target_link_libraries(vbz_hdf_plugin_test
PUBLIC
vbz_hdf_plugin
- HDF5::C
+ ${HDF5_C_LIBRARIES}
hdf_test_utils
)
@@ -17,4 +17,4 @@ add_test(
NAME vbz_hdf_plugin_test
COMMAND vbz_hdf_plugin_test "${CMAKE_SOURCE_DIR}/test_data"
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-)
\ No newline at end of file
+)
=====================================
vbz_plugin/vbz_plugin.cpp
=====================================
@@ -108,7 +108,7 @@ size_t vbz_filter(
if (cd_nelmts < 3)
{
- return -1;
+ return 0;
}
unsigned int vbz_version = cd_values[FILTER_VBZ_VERSION_OPTION];
@@ -139,7 +139,7 @@ size_t vbz_filter(
if (input_span.size() > std::numeric_limits<vbz_size_t>::max())
{
std::cerr << "vbz_filter: Chunk size too large." << std::endl;
- return -1;
+ return 0;
}
#if VBZ_DEBUG
@@ -153,7 +153,7 @@ size_t vbz_filter(
if (vbz_is_error(expected_uncompressed_size))
{
std::cerr << "vbz_filter: size error" << std::endl;
- return -1;
+ return 0;
}
outbuf.reset(h5_malloc(expected_uncompressed_size));
@@ -166,13 +166,13 @@ size_t vbz_filter(
if (vbz_is_error(outbuf_used_size))
{
std::cerr << "vbz_filter: compression error" << std::endl;
- return -1;
+ return 0;
}
if (outbuf_used_size != expected_uncompressed_size)
{
std::cerr << "vbz_filter: decompressed size error" << std::endl;
- return -1;
+ return 0;
}
#if VBZ_DEBUG
@@ -188,14 +188,14 @@ size_t vbz_filter(
if (*buf_size > std::numeric_limits<vbz_size_t>::max())
{
std::cerr << "vbz_filter: Chunk size too large." << std::endl;
- return -1;
+ return 0;
}
auto const byte_remainder = *buf_size % integer_size;
if (byte_remainder != 0)
{
std::cerr << "vbz_filter: Invalid integer_size specified" << std::endl;
- return -1;
+ return 0;
}
outbuf_size = vbz_max_compressed_size(vbz_size_t(*buf_size), &options);
@@ -214,7 +214,7 @@ size_t vbz_filter(
if (vbz_is_error(outbuf_used_size))
{
std::cerr << "vbz_filter: compression error" << std::endl;;
- return -1;
+ return 0;
}
#if VBZ_DEBUG
=====================================
vbz_plugin/vbz_plugin_user_utils.h
=====================================
@@ -1,6 +1,7 @@
#pragma once
#include <hdf5.h>
+#include "vbz_plugin.h"
#define FILTER_VBZ_VERSION 1
View it on GitLab: https://salsa.debian.org/med-team/vbz-compression/-/commit/0ab35a67f05333a77dde9dba973a7672433b3a84
--
View it on GitLab: https://salsa.debian.org/med-team/vbz-compression/-/commit/0ab35a67f05333a77dde9dba973a7672433b3a84
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