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gnu: onnx: Update to 1.16.2.

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* gnu/packages/machine-learning.scm (onnx): Update to 1.16.2.
[source]: Remove patch.
[build-system]: Move to pyproject-build-system.
[arguments]<#:tests?>: Disable for systems where python-nbval is not
supported.
<#:phases>: Remove 'relax-requirements' phase.  Pass "-DONNX_BUILD_TESTS" to
CMake depending on tests?.
[native-inputs]: Add python-fb-re2 and python-parameterized-next.  Remove
python-nbval on unsupported systems.
* gnu/packages/patches/onnx-shared-libraries.patch: Adjust patch.
* gnu/packages/patches/onnx-skip-model-downloads.patch: Adjust patch.
* gnu/packages/patches/onnx-use-system-googletest.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Co-authored-by: Andy Tai <atai@atai.org>
This commit is contained in:
David Elsing 2024-08-04 22:15:54 +00:00 committed by Ludovic Courtès
parent 852c75a125
commit 595cc594b6
No known key found for this signature in database
GPG key ID: 090B11993D9AEBB5
5 changed files with 94 additions and 131 deletions
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1
gnu/local.mk
View file

@ -1821,7 +1821,6 @@ dist_patch_DATA = \
%D%/packages/patches/onionshare-cli-async-mode.patch \
%D%/packages/patches/online-judge-tools.patch \
%D%/packages/patches/onnx-optimizer-system-library.patch \
%D%/packages/patches/onnx-use-system-googletest.patch \
%D%/packages/patches/onnx-1.13.1-use-system-googletest.patch \
%D%/packages/patches/onnx-shared-libraries.patch \
%D%/packages/patches/onnx-skip-model-downloads.patch \

133
gnu/packages/machine-learning.scm
View file

@ -28,6 +28,7 @@
;;; Copyright © 2024 Timothee Mathieu <timothee.mathieu@inria.fr>
;;; Copyright © 2024 Spencer King <spencer.king@geneoscopy.com>
;;; Copyright © 2024 David Elsing <david.elsing@posteo.net>
;;; Copyright © 2024 Andy Tai <atai@atai.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -1331,7 +1332,7 @@ (define (delete-ifdefs file)
(define-public onnx
(package
(name "onnx")
(version "1.12.0")
(version "1.16.2")
(source (origin
(method git-fetch)
(uri (git-reference
@ -1339,70 +1340,88 @@ (define-public onnx
(commit (string-append "v" version))))
(sha256
(base32
"1g9f1hviksbn7gi6fnd0dsm7nf0w3yia0mjj33d9mggklrl0db6x"))
"0f5h204ksfz4ir3qq38ckxja1jfhf1vn5xzwrj83vkkbfjq6fv16"))
(file-name (git-file-name name version))
(patches (search-patches "onnx-use-system-googletest.patch"
"onnx-shared-libraries.patch"
"onnx-skip-model-downloads.patch"))
(patches (search-patches
"onnx-shared-libraries.patch"
"onnx-skip-model-downloads.patch"))
(modules '((guix build utils)))
(snippet '(delete-file-recursively "third_party"))))
(build-system python-build-system)
(build-system pyproject-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
(add-after 'unpack 'relax-requirements
(lambda _
;; Does this difference really matter?
(substitute* "requirements.txt"
(("3.20.1") "3.20.2"))))
(add-before 'build 'pass-cmake-arguments
(lambda* (#:key outputs #:allow-other-keys)
;; Pass options to the CMake-based build process.
(define out
(assoc-ref outputs "out"))
(list
;; python-nbval depends transitively on Rust.
#:tests?
(->bool (member (or (%current-target-system)
(%current-system))
(package-transitive-supported-systems python-nbval)))
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'pass-cmake-arguments
(lambda* (#:key outputs tests? #:allow-other-keys)
;; For derived package use
(substitute* "CMakeLists.txt"
(("set\\(ONNX_ROOT.*")
(string-append "set(ONNX_ROOT "#$(package-source this-package) ")\n"))
(("\\$\\{ROOT_DIR\\}(/tools.*)" _ rest)
(string-append "${PROJECT_SOURCE_DIR}" rest)))
;; Pass options to the CMake-based build process.
(define out
(assoc-ref outputs "out"))
(define args
;; Copy arguments from 'cmake-build-system', plus ask
;; for shared libraries.
(list "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
(string-append "-DCMAKE_INSTALL_PREFIX=" out)
"-DCMAKE_INSTALL_LIBDIR=lib"
"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE"
(string-append "-DCMAKE_INSTALL_RPATH=" out
"/lib")
"-DCMAKE_VERBOSE_MAKEFILE=ON"
(define args
;; Copy arguments from 'cmake-build-system', plus ask
;; for shared libraries.
(list "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
(string-append "-DCMAKE_INSTALL_PREFIX=" out)
"-DCMAKE_INSTALL_LIBDIR=lib"
"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE"
(string-append "-DCMAKE_INSTALL_RPATH=" out
"/lib")
"-DCMAKE_VERBOSE_MAKEFILE=ON"
(string-append "-DONNX_BUILD_TESTS="
(if tests? "ON" "OFF"))
"-DBUILD_SHARED_LIBS=ON"
"-DONNX_USE_PROTOBUF_SHARED_LIBS=ON"))
"-DBUILD_SHARED_LIBS=ON"))
;; This environment variable is honored by 'setup.py',
;; which passes it down to 'cmake'.
(setenv "CMAKE_ARGS" (string-join args))
;; This environment variable is honored by 'setup.py',
;; which passes it down to 'cmake'.
(setenv "CMAKE_ARGS" (string-join args))
;; This one is honored by 'setup.py' and passed to 'make
;; -j'.
(setenv "MAX_JOBS"
(number->string (parallel-job-count)))))
(add-before 'check 'make-test-directory-writable
(lambda _
;; Make things writable for tests.
(setenv "HOME" (getcwd))
(for-each make-file-writable
(find-files "onnx/examples" "."
#:directories? #t))))
(add-after 'install 'install-from-cmake
(lambda _
;; Run "make install" in the build tree 'setup.py'
;; created for CMake so that libonnx.so,
;; libonnx_proto.so, etc. are installed.
(invoke "make" "install"
"-C" ".setuptools-cmake-build"))))))
;; This one is honored by 'setup.py' and passed to 'make
;; -j'.
(setenv "MAX_JOBS"
(number->string (parallel-job-count)))))
(add-before 'check 'make-test-directory-writable
(lambda _
;; Make things writable for tests.
(setenv "HOME" (getcwd))
(for-each make-file-writable
(find-files "onnx/examples" "."
#:directories? #t))))
(add-after 'install 'install-from-cmake
(lambda _
;; Run "make install" in the build tree 'setup.py'
;; created for CMake so that libonnx.so,
;; libonnx_proto.so, etc. are installed.
(invoke "make" "install"
"-C" ".setuptools-cmake-build"))))))
(native-inputs
(list cmake
googletest
pybind11
python-coverage
python-nbval
python-pytest
python-pytest-runner))
(append
(list cmake-minimal
googletest
pybind11
python-coverage
python-fb-re2
python-parameterized-next
python-pytest
python-pytest-runner)
(filter
(lambda (pkg)
(member (or (%current-target-system)
(%current-system))
(package-transitive-supported-systems pkg)))
(list python-nbval))))
(inputs
(list protobuf))
(propagated-inputs

18
gnu/packages/patches/onnx-shared-libraries.patch
View file

@ -1,13 +1,12 @@
These linker options for the 'onnx_cpp2py_export.cpython-38-*-gnu.so'
(or similar) extension are meant to be used when building 'libonn.a',
a static archive. This patch adapts the link flags to linking with
'libonnx.so'.
These linker options for the 'onnx_cpp2py_export.cpython-310-*-gnu.so' (or
similar) extension are meant to be used when building 'libonn.a', a static
archive. This patch adapts the link flags to linking with 'libonnx.so'.
diff --git a/CMakeLists.txt b/CMakeLists.txt
index cede3073..52f846ed 100644
index b666eec4..1525b219 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -475,11 +475,10 @@ if(BUILD_ONNX_PYTHON)
@@ -585,16 +585,15 @@ if(BUILD_ONNX_PYTHON)
PRIVATE $<TARGET_OBJECTS:onnx>)
else()
# Assume everything else is like gcc
@ -15,10 +14,15 @@ index cede3073..52f846ed 100644
- PRIVATE "-Wl,--whole-archive" $<TARGET_FILE:onnx>
- "-Wl,--no-whole-archive")
+ target_link_libraries(onnx_cpp2py_export PRIVATE onnx)
# Prevent "undefined symbol: _ZNSt10filesystem7__cxx114path14_M_split_cmptsEv"
# (std::filesystem::__cxx11::path::_M_split_cmpts()) on gcc 8
if (CMAKE_CXX_STANDARD EQUAL 17 AND CMAKE_COMPILER_IS_GNUCC AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
target_link_libraries(onnx_cpp2py_export PRIVATE "-lstdc++fs")
endif()
set_target_properties(onnx_cpp2py_export
- PROPERTIES LINK_FLAGS "-Wl,--exclude-libs,ALL")
+ PROPERTIES LINK_FLAGS
+ "-Wl,-rpath=${CMAKE_INSTALL_PREFIX}/lib")
+ "-Wl,-rpath=${CMAKE_INSTALL_PREFIX}/lib")
endif()
target_link_libraries(onnx_cpp2py_export PRIVATE onnx)

16
gnu/packages/patches/onnx-skip-model-downloads.patch
View file

@ -1,16 +1,14 @@
A few tests require downloading models from URLs such as
<https://s3.amazonaws.com/download.onnx/models/opset_9/zfnet512.tar.gz>.
Skip those.
A few tests require downloading models. Skip those.
diff --git a/onnx/backend/test/runner/__init__.py b/onnx/backend/test/runner/__init__.py
index 049ed57b..f236f1bf 100644
index 5b60e7c0..838c7ba5 100644
--- a/onnx/backend/test/runner/__init__.py
+++ b/onnx/backend/test/runner/__init__.py
@@ -202,6 +202,7 @@ class Runner(object):
print('Start downloading model {} from {}'.format(
model_test.model_name,
model_test.url))
@@ -236,6 +236,7 @@ class Runner:
print(
f"Start downloading model {model_test.model_name} from {model_test.url}"
)
+ raise unittest.SkipTest('Skipping download')
urlretrieve(model_test.url, download_file.name)
print('Done')
print("Done")
with tarfile.open(download_file.name) as t:

57
gnu/packages/patches/onnx-use-system-googletest.patch
View file

@ -1,57 +0,0 @@
ONNX will build googletest from a Git checkout. Patch CMake to use our
googletest package and enable tests by default.
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0aa9fda2..a573170c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -22,7 +22,7 @@ option(BUILD_ONNX_PYTHON "Build Python binaries" OFF)
option(ONNX_GEN_PB_TYPE_STUBS "Generate protobuf python type stubs" ON)
option(ONNX_WERROR "Build with Werror" OFF)
option(ONNX_COVERAGE "Build with coverage instrumentation" OFF)
-option(ONNX_BUILD_TESTS "Build ONNX C++ APIs Tests" OFF)
+option(ONNX_BUILD_TESTS "Build ONNX C++ APIs Tests" ON)
option(ONNX_USE_LITE_PROTO "Use lite protobuf instead of full." OFF)
option(ONNXIFI_ENABLE_EXT "Enable onnxifi extensions." OFF)
if(NOT DEFINED ONNX_ML)
@@ -82,8 +82,10 @@ if(CMAKE_SYSTEM_NAME STREQUAL "AIX")
endif()
if(ONNX_BUILD_TESTS)
- list(APPEND CMAKE_MODULE_PATH ${ONNX_ROOT}/cmake/external)
- include(googletest)
+ find_package(GTest REQUIRED)
+ if(NOT GTest_FOUND)
+ message(FATAL_ERROR "cannot find googletest")
+ endif()
endif()
if((ONNX_USE_LITE_PROTO AND TARGET protobuf::libprotobuf-lite) OR ((NOT ONNX_USE_LITE_PROTO) AND TARGET protobuf::libprotobuf))
diff --git a/cmake/unittest.cmake b/cmake/unittest.cmake
index e29a93ff..ae146390 100644
--- a/cmake/unittest.cmake
+++ b/cmake/unittest.cmake
@@ -6,8 +6,8 @@ include(${ONNX_ROOT}/cmake/Utils.cmake)
find_package(Threads)
-set(${UT_NAME}_libs ${googletest_STATIC_LIBRARIES})
-set(${ONNXIFI_TEST_DRIVER}_libs ${googletest_STATIC_LIBRARIES})
+set(${UT_NAME}_libs ${GTEST_LIBRARIES})
+set(${ONNXIFI_TEST_DRIVER}_libs ${GTEST_LIBRARIES})
list(APPEND ${UT_NAME}_libs onnx)
list(APPEND ${UT_NAME}_libs onnx_proto)
@@ -31,10 +31,10 @@ function(AddTest)
list(REMOVE_DUPLICATES _UT_SOURCES)
add_executable(${_UT_TARGET} ${_UT_SOURCES})
- add_dependencies(${_UT_TARGET} onnx onnx_proto googletest)
+ add_dependencies(${_UT_TARGET} onnx onnx_proto)
target_include_directories(${_UT_TARGET}
- PUBLIC ${googletest_INCLUDE_DIRS}
+ PUBLIC ${GTEST_INCLUDE_DIRS}
${ONNX_INCLUDE_DIRS}
${PROTOBUF_INCLUDE_DIRS}
${ONNX_ROOT}