[bug#42650] [PATCH 1/2] gnu: python-protobuf: Update to 3.12.4.

[bug#42650] [PATCH 1/2] gnu: python-protobuf: Update to 3.12.4.

[Vinicius Monego]

* gnu/packages/protobuf.scm (python-protobuf): Update to 3.12.4.
---
 gnu/packages/protobuf.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 7c14ddbdfa..b8bd617eca 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -206,15 +207,17 @@ encoder in C++.  The developer using protozero has to manually translate the
 (define-public python-protobuf
   (package
     (name "python-protobuf")
-    (version "3.11.3")
+    (version "3.12.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "protobuf" version))
        (sha256
         (base32
-         "07qby3yc2a8a1vsxnc79j687q4r68k1d3npni7bldwmd3m6rfz67"))))
+         "0mj6z58aiw532s1mq48m9xdrm3gdyp2vv9cdinfb5wmnfpm5m7n9"))))
     (build-system python-build-system)
+    (native-inputs
+     `(("python-wheel" ,python-wheel)))
     (propagated-inputs
      `(("python-six" ,python-six)))
     (home-page "https://github.com/google/protobuf")
-- 
2.20.1

[bug#42650] [PATCH 2/2] gnu: Add python-onnx.

[Vinicius Monego]

* gnu/packages/machine-learning.scm (python-onnx): New variable.
---
 gnu/packages/machine-learning.scm             | 43 +++++++++++++++
 .../python-onnx-use-system-googletest.patch   | 54 +++++++++++++++++++
 2 files changed, 97 insertions(+)
 create mode 100644 gnu/packages/patches/python-onnx-use-system-googletest.patch

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 18a4ac9ef2..4ec3ed05c7 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -15,6 +15,7 @@
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
 ;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
 ;;; Copyright © 2020 Edouard Klein <edk@beaver-labs.com>
+;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -53,6 +54,7 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages cmake)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages dejagnu)
@@ -70,6 +72,7 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
@@ -576,6 +579,46 @@ tools.  This enables both rapid prototyping of data pipelines and extensibility
 in terms of new algorithms.")
     (license license:gpl3+)))
 
+(define-public python-onnx
+  (package
+    (name "python-onnx")
+    (version "1.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "onnx" version))
+       ;; ONNX will build googletest from a git checkout.  Patch CMake
+       ;; to use googletest from Guix and enable tests by default.
+       (patches (search-patches "python-onnx-use-system-googletest.patch"))
+       (sha256
+        (base32 "0j6rgfbhsw3a8id8pyg18y93k68lbjbj1kq6qia36h69f6pvlyjy"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("cmake" ,cmake)
+       ("googletest" ,googletest)
+       ("pybind11" ,pybind11)
+       ("python-coverage" ,python-coverage)
+       ("python-nbval" ,python-nbval)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-runner" ,python-pytest-runner)))
+    (inputs
+     `(("protobuf" ,protobuf)))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-protobuf" ,python-protobuf)
+       ("python-six" ,python-six)
+       ("python-tabulate" ,python-tabulate)
+       ("python-typing-extensions"
+        ,python-typing-extensions)))
+    (home-page "https://onnx.ai/")
+    (synopsis "Open Neural Network Exchange")
+    (description
+     "Open Neural Network Exchange (ONNX) provides an open source format for
+AI models, both deep learning and traditional ML.  It defines an extensible
+computation graph model, as well as definitions of built-in operators and
+standard data types.")
+    (license license:expat)))
+
 (define-public rxcpp
   (package
     (name "rxcpp")
diff --git a/gnu/packages/patches/python-onnx-use-system-googletest.patch b/gnu/packages/patches/python-onnx-use-system-googletest.patch
new file mode 100644
index 0000000000..33d2fa12de
--- /dev/null
+++ b/gnu/packages/patches/python-onnx-use-system-googletest.patch
@@ -0,0 +1,54 @@
+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}
-- 
2.20.1

bug#42650: [PATCH 2/2] gnu: Add python-onnx.

[Mathieu Othacehe]

Hello,

A few comments on this one.

> * gnu/packages/machine-learning.scm (python-onnx): New variable.

You need to mention the added file in the commit message and also add it
to gnu/local.mk.

> +       ;; ONNX will build googletest from a git checkout.  Patch CMake
> +       ;; to use googletest from Guix and enable tests by default.

That seems to be a recurrent issue. Did you fix it by yourself or is
there a patch out there? 

Otherwise both patches look fine. I fixed the patch registering thing
and pushed.

Thanks,

Mathieu

[bug#42650] [PATCH 2/2] gnu: Add python-onnx.

[Vinicius Monego]

Hello,

Mathieu Othacehe writes:

> You need to mention the added file in the commit message and also add it
> to gnu/local.mk.

Noted, thanks.

>> +       ;; ONNX will build googletest from a git checkout.  Patch CMake
>> +       ;; to use googletest from Guix and enable tests by default.
>
> That seems to be a recurrent issue. Did you fix it by yourself or is
> there a patch out there? 

I fixed it by myself.

Vinicius