gnu: onnx: Update to 1.16.2.

* 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>

3 files changed, 18 insertions, 73 deletions

diff --git a/gnu/packages/patches/onnx-shared-libraries.patch b/gnu/packages/patches/onnx-shared-libraries.patch
index 00583b35da..5a3fd658d0 100644
--- a/gnu/packages/patches/onnx-shared-libraries.patch
+++ b/gnu/packages/patches/onnx-shared-libraries.patch
@@ -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)
diff --git a/gnu/packages/patches/onnx-skip-model-downloads.patch b/gnu/packages/patches/onnx-skip-model-downloads.patch
index 4ab55b4ceb..55925a3ebf 100644
--- a/gnu/packages/patches/onnx-skip-model-downloads.patch
+++ b/gnu/packages/patches/onnx-skip-model-downloads.patch
@@ -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:
diff --git a/gnu/packages/patches/onnx-use-system-googletest.patch b/gnu/packages/patches/onnx-use-system-googletest.patch
deleted file mode 100644
index 5dfcbc6dc3..0000000000
--- a/gnu/packages/patches/onnx-use-system-googletest.patch
+++ /dev/null
@@ -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}