feat: remove git submodules, use CMake FetchContent for C++ deps

Replace git submodules (onnx, optimizer, pybind11, glog) with:
- FetchContent for ONNX v1.20.1 and onnx-optimizer v0.3.19
- find_package for pybind11 and glog (system-installed)

Also: update tests for PaddlePaddle 3.x, add uv.lock, update docs.

Author: Goldziher

.gitignore

@@ -20,6 +20,12 @@ paddle2onnx/*.so
 paddle2onnx/__pycache_*
 protobuf-*
 
+# Python / uv
+.venv
+__pycache__/
+*.egg-info/
+.hypothesis/
+
 # Temporary files automatically generated when executing Paddle2ONNX unit tests
 *.pdmodel
 *.pdiparams

.gitmodules

@@ -1,18 +1,15 @@
 cmake_minimum_required(VERSION 3.16)
 project(paddle2onnx C CXX)
-# ONNX 1.20 requires C++ 17
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
-# Build the libraries with - fPIC
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-# Always link with libstdc++ fs.a when using GCC 8.
 link_libraries(
   "$<$<AND:$<CXX_COMPILER_ID:GNU>,$<VERSION_LESS:$<CXX_COMPILER_VERSION>,9.0>>:-lstdc++fs>"
 )
 
-option(WITH_STATIC "Compile Paddle2ONNX with  STATIC" OFF)
+option(WITH_STATIC "Compile Paddle2ONNX with STATIC" OFF)
 option(PADDLE2ONNX_DEBUG "If open the debug log while converting model" OFF)
-option(MSVC_STATIC_CRT "Compile Paddle2ONNX with  MSVC STATIC CRT" OFF)
+option(MSVC_STATIC_CRT "Compile Paddle2ONNX with MSVC STATIC CRT" OFF)
 if(MSVC)
   set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>DLL")
   add_definitions(-DPADDLE_WITH_TESTING)
@@ -22,12 +19,9 @@ if(PADDLE2ONNX_DEBUG)
   add_definitions(-DPADDLE2ONNX_DEBUG)
 endif()
 
-# Set max opset version for onnx if you build from other version of onnx this
-# should be modified.
 add_definitions(-DMAX_ONNX_OPSET_VERSION=25)
 add_definitions(-DPADDLE2ONNX_LIB)
 
-# Internal flags for convert.h.in
 set(WITH_PADDLE2ONNX_STATIC_INTERNAL OFF)
 if(WITH_STATIC)
   set(WITH_PADDLE2ONNX_STATIC_INTERNAL
@@ -40,115 +34,135 @@ include(utils)
 configure_file(${PROJECT_SOURCE_DIR}/paddle2onnx/mappers_registry.h.in
                ${PROJECT_SOURCE_DIR}/paddle2onnx/mappers_registry.h)
 
-# Third dependency : onnx
-if(NOT TARGET onnx_proto)
-  if(NOT ONNX_NAMESPACE)
-    set(ONNX_NAMESPACE "onnx")
-  endif()
-  add_definitions("-DONNX_NAMESPACE=${ONNX_NAMESPACE}")
-  add_subdirectory(${PROJECT_SOURCE_DIR}/third_party/onnx)
+# --- Dependencies ---
+
+# Protobuf (system-installed, CONFIG mode for proper targets)
+find_package(Protobuf REQUIRED CONFIG)
+
+include(FetchContent)
+
+# ONNX (built from source for protobuf compatibility)
+if(NOT ONNX_NAMESPACE)
+  set(ONNX_NAMESPACE "onnx")
+endif()
+add_definitions("-DONNX_NAMESPACE=${ONNX_NAMESPACE}")
+
+set(ONNX_USE_LITE_PROTO OFF CACHE BOOL "" FORCE)
+set(ONNX_ML ON CACHE BOOL "" FORCE)
+set(ONNX_USE_PROTOBUF_SHARED_LIBS OFF CACHE BOOL "" FORCE)
+set(ONNX_BUILD_TESTS OFF CACHE BOOL "" FORCE)
+set(ONNX_BUILD_BENCHMARKS OFF CACHE BOOL "" FORCE)
+
+FetchContent_Declare(
+  onnx
+  GIT_REPOSITORY https://github.com/onnx/onnx.git
+  GIT_TAG v1.20.1
+  GIT_SHALLOW TRUE
+)
+FetchContent_MakeAvailable(onnx)
+
+# onnx-optimizer: fetch source only, compile directly
+FetchContent_Declare(
+  onnx_optimizer
+  GIT_REPOSITORY https://github.com/onnx/optimizer.git
+  GIT_TAG b3a4611861734e0731bbcc2bed1f080139e4988b # v0.3.19
+  GIT_SHALLOW FALSE
+  PATCH_COMMAND ${CMAKE_COMMAND} -P
+    ${CMAKE_CURRENT_SOURCE_DIR}/cmake/patch_optimizer.cmake
+)
+FetchContent_Populate(onnx_optimizer)
+
+# pybind11 (system-installed)
+find_package(pybind11 REQUIRED)
+
+# glog (system-installed)
+if(MSVC)
+  set(WITH_GFLAGS
+      OFF
+      CACHE BOOL "Disable gflags support in glog")
 endif()
+find_package(glog REQUIRED)
 
 # generate Paddle2ONNX proto files
 add_subdirectory(${PROJECT_SOURCE_DIR}/paddle2onnx/proto)
 
 include_directories(${PROJECT_SOURCE_DIR})
 include_directories(${CMAKE_CURRENT_BINARY_DIR})
-include_directories(${PROJECT_SOURCE_DIR}/third_party/optimizer)
+include_directories(${onnx_optimizer_SOURCE_DIR})
 
-file(GLOB_RECURSE ALL_SRCS ${PROJECT_SOURCE_DIR}/paddle2onnx/*.cc
-     ${PROJECT_SOURCE_DIR}/third_party/optimizer/onnx/optimizer/*.cc)
+# Collect sources: paddle2onnx + onnx-optimizer (compiled in)
+file(GLOB_RECURSE OPTIMIZER_SRCS
+     ${onnx_optimizer_SOURCE_DIR}/onnxoptimizer/*.cc)
+file(GLOB_RECURSE ALL_SRCS ${PROJECT_SOURCE_DIR}/paddle2onnx/*.cc)
+list(APPEND ALL_SRCS ${OPTIMIZER_SRCS})
 list(REMOVE_ITEM ALL_SRCS ${PROJECT_SOURCE_DIR}/paddle2onnx/cpp2py_export.cc)
+list(REMOVE_ITEM ALL_SRCS
+     ${onnx_optimizer_SOURCE_DIR}/onnxoptimizer/cpp2py_export.cc)
 
 file(READ "${PROJECT_SOURCE_DIR}/VERSION_NUMBER" PADDLE2ONNX_VERSION)
 string(STRIP "${PADDLE2ONNX_VERSION}" PADDLE2ONNX_VERSION)
 
+# find Python site-packages and PaddlePaddle
+set(PYTHON_SITE_PACKAGES "")
+execute_process(
+  COMMAND ${PYTHON_EXECUTABLE} -c
+          "import site; print(';'.join(site.getsitepackages()))"
+  OUTPUT_VARIABLE SITE_PACKAGES_LIST
+  OUTPUT_STRIP_TRAILING_WHITESPACE)
+string(REPLACE ";" " " SITE_PACKAGES_LIST "${SITE_PACKAGES_LIST}")
+separate_arguments(SITE_PACKAGES_LIST)
+foreach(SITE_PACKAGES IN LISTS SITE_PACKAGES_LIST)
+  if(EXISTS "${SITE_PACKAGES}" AND SITE_PACKAGES MATCHES "site-packages")
+    string(REPLACE "\\" "/" PYTHON_SITE_PACKAGES "${SITE_PACKAGES}")
+    message(STATUS "Found valid site-packages path: ${PYTHON_SITE_PACKAGES}.")
+    break()
+  endif()
+endforeach()
+if(NOT PYTHON_SITE_PACKAGES)
+  message(FATAL_ERROR "No valid site-packages path found.")
+endif()
+
+if(MSVC)
+  set(PADDLE_LIB "${PYTHON_SITE_PACKAGES}/paddle/base/libpaddle.lib")
+  set(COMMON_LIB "${PYTHON_SITE_PACKAGES}/paddle/libs/common.lib")
+else()
+  set(PADDLE_LIB "${PYTHON_SITE_PACKAGES}/paddle/base/libpaddle.so")
+endif()
+if(EXISTS ${PADDLE_LIB})
+  message(STATUS "Found libpaddle: ${PADDLE_LIB}.")
+else()
+  message(
+    FATAL_ERROR
+      "Can not find libpaddle at ${PYTHON_SITE_PACKAGES}/paddle/base!")
+endif()
+set(PADDLE_INCLUDE_DIR ${PYTHON_SITE_PACKAGES}/paddle/include/)
+include_directories(${PADDLE_INCLUDE_DIR})
+
+if(MSVC)
+  add_custom_target(
+    pir_patch ALL
+    COMMAND
+      ${CMAKE_COMMAND} -E copy_if_different
+      ${CMAKE_SOURCE_DIR}/patch/paddle/interface_support.h
+      ${PADDLE_INCLUDE_DIR}/paddle/pir/include/core/interface_support.h
+    COMMENT "PIR patch for MSVC")
+endif()
+
 if(WITH_STATIC)
-  # Here, we use a dummy target (paddle2onnx_dummy) to form a build dependency
-  # tree for paddle2onnx_static lib.
   add_library(paddle2onnx_dummy STATIC ${ALL_SRCS})
-
-  if(APPLE)
-    set_target_properties(paddle2onnx_dummy PROPERTIES COMPILE_FLAGS
-                                                       "-fvisibility=hidden")
-  elseif(MSVC)
-    message("------ BUILD WITH MSVC --------")
-  else()
+  if(NOT MSVC)
     set_target_properties(paddle2onnx_dummy PROPERTIES COMPILE_FLAGS
                                                        "-fvisibility=hidden")
   endif()
   target_link_libraries(paddle2onnx_dummy p2o_paddle_proto onnx)
-  # Bundle paddle2onnx static lib here
   bundle_static_library(paddle2onnx_dummy paddle2onnx_static bundle_paddle2onnx)
 else()
   add_library(paddle2onnx SHARED ${ALL_SRCS})
-
-  # add pybind11
-  add_subdirectory(third_party/pybind11)
-
-  # add glog
-  if(MSVC)
-    set(WITH_GFLAGS
-        OFF
-        CACHE BOOL "Disable gflags support in glog")
-  endif()
-  add_subdirectory(third_party/glog)
-
-  # find Python site-packages dir
-  set(PYTHON_SITE_PACKAGES "")
-  execute_process(
-    COMMAND ${PYTHON_EXECUTABLE} -c
-            "import site; print(';'.join(site.getsitepackages()))"
-    OUTPUT_VARIABLE SITE_PACKAGES_LIST
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-  string(REPLACE ";" " " SITE_PACKAGES_LIST "${SITE_PACKAGES_LIST}")
-  separate_arguments(SITE_PACKAGES_LIST)
-  foreach(SITE_PACKAGES IN LISTS SITE_PACKAGES_LIST)
-    if(EXISTS "${SITE_PACKAGES}" AND SITE_PACKAGES MATCHES "site-packages")
-      string(REPLACE "\\" "/" PYTHON_SITE_PACKAGES "${SITE_PACKAGES}")
-      message(STATUS "Found valid site-packages path: ${PYTHON_SITE_PACKAGES}.")
-      break()
-    endif()
-  endforeach()
-  if(NOT PYTHON_SITE_PACKAGES)
-    message(FATAL_ERROR "No valid site-packages path found.")
-  endif()
-
-  if(MSVC)
-    set(PADDLE_LIB "${PYTHON_SITE_PACKAGES}/paddle/base/libpaddle.lib")
-    set(COMMON_LIB "${PYTHON_SITE_PACKAGES}/paddle/libs/common.lib")
-  else()
-    set(PADDLE_LIB "${PYTHON_SITE_PACKAGES}/paddle/base/libpaddle.so")
-  endif()
-  if(EXISTS ${PADDLE_LIB})
-    message(STATUS "Found libpaddle: ${PADDLE_LIB}.")
-  else()
-    message(
-      FATAL_ERROR
-        "Can not find libpaddle at ${PYTHON_SITE_PACKAGES}/paddle/base!")
-  endif()
-  # add paddle include dir
-  set(PADDLE_INCLUDE_DIR ${PYTHON_SITE_PACKAGES}/paddle/include/)
-  include_directories(${PADDLE_INCLUDE_DIR})
-  if(MSVC)
-    # PIR patch
-    add_custom_target(
-      pir_patch ALL
-      COMMAND
-        ${CMAKE_COMMAND} -E copy_if_different
-        ${CMAKE_SOURCE_DIR}/patch/paddle/interface_support.h
-        ${PADDLE_INCLUDE_DIR}/paddle/pir/include/core/interface_support.h
-      COMMENT
-        "Replace file ${PADDLE_INCLUDE_DIR}/paddle/pir/include/core/interface_support.h with ${CMAKE_SOURCE_DIR}/patch/paddle/interface_support.h"
-    )
-  endif()
   if(APPLE)
     set_target_properties(paddle2onnx PROPERTIES LINK_FLAGS
                                                  "-undefined dynamic_lookup")
   elseif(MSVC)
     message("------ BUILD WITH MSVC --------")
-    # remove `interface` macro defined in MSVC
-    # target_compile_options(paddle2onnx PRIVATE /Uinterface)
   else()
     set_target_properties(paddle2onnx PROPERTIES COMPILE_FLAGS
                                                  "-fvisibility=hidden")
@@ -211,32 +225,20 @@ if(BUILD_PADDLE2ONNX_PYTHON)
                         PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
   target_include_directories(
     paddle2onnx_cpp2py_export
-    PRIVATE $<BUILD_INTERFACE:${ONNX_ROOT}>
-            $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>
+    PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>
             $<INSTALL_INTERFACE:include>
             ${PYTHON_INCLUDE_DIR}
             ${PADDLE_INCLUDE_DIR})
 
-  if(EXISTS
-     ${PROJECT_SOURCE_DIR}/third_party/pybind11/include/pybind11/pybind11.h)
-    target_include_directories(
-      paddle2onnx_cpp2py_export
-      PUBLIC ${PROJECT_SOURCE_DIR}/third_party/pybind11/include)
-  else()
-    message(FATAL_ERROR "cannot find pybind")
-  endif()
-
   if(APPLE)
     set_target_properties(paddle2onnx_cpp2py_export
                           PROPERTIES LINK_FLAGS "-undefined dynamic_lookup")
     target_link_libraries(paddle2onnx_cpp2py_export
                           PRIVATE -Wl,-force_load,$<TARGET_FILE:onnx>)
   elseif(MSVC)
-    # In MSVC, we will add whole archive in default
     target_link_libraries(paddle2onnx_cpp2py_export
                           PRIVATE -WHOLEARCHIVE:$<TARGET_FILE:onnx>)
   else()
-    # Assume everything else is like gcc
     target_link_libraries(
       paddle2onnx_cpp2py_export
       PRIVATE "-Wl,--whole-archive" $<TARGET_FILE:onnx>
@@ -253,20 +255,6 @@ if(BUILD_PADDLE2ONNX_PYTHON)
     target_link_libraries(paddle2onnx_cpp2py_export PRIVATE ${PYTHON_LIBRARIES})
     target_compile_options(
       paddle2onnx_cpp2py_export
-      PRIVATE /MP
-              /wd4244 # 'argument': conversion from 'google::protobuf::uint64'
-                      # to 'int', possible loss of data
-              /wd4267 # Conversion from 'size_t' to 'int', possible loss of data
-              /wd4996 # The second parameter is ignored.
-              ${EXTRA_FLAGS})
-    if(ONNX_USE_PROTOBUF_SHARED_LIBS)
-      target_compile_options(
-        onnx_cpp2py_export
-        PRIVATE /wd4251 # 'identifier' : class 'type1' needs to have
-                        # dll-interface to be used by clients of class 'type2'
-      )
-    endif()
-    add_msvc_runtime_flag(paddle2onnx_cpp2py_export)
-    add_onnx_global_defines(paddle2onnx_cpp2py_export)
+      PRIVATE /MP /wd4244 /wd4267 /wd4996 ${EXTRA_FLAGS})
   endif()
 endif()

CMakeLists.txt

@@ -8,9 +8,12 @@ Paddle2ONNX 支持将 **PaddlePaddle** 模型格式转化到 **ONNX** 模型格
 
 ## 2 Paddle2ONNX 环境依赖
 
-Paddle2ONNX 依赖PaddlePaddle3.0，我们建议您在以下环境下使用 Paddle2ONNX ：
+Paddle2ONNX 依赖 PaddlePaddle 3.3+，我们建议您在以下环境下使用 Paddle2ONNX ：
 
-- PaddlePaddle == 3.0.0
+- Python >= 3.10
+- PaddlePaddle >= 3.3
+- ONNX >= 1.20.1
+- protobuf >= 34.0
 - onnxruntime >= 1.10.0
 
 ## 3 安装 Paddle2ONNX

README.md

@@ -8,9 +8,12 @@ Paddle2ONNX supports the conversion of PaddlePaddle model format to ONNX model f
 
 ## 2 Paddle2ONNX Environment Dependencies
 
-Paddle2ONNX depends on paddle3.0, we recommend using Paddle2ONNX in the following environments:
+Paddle2ONNX depends on PaddlePaddle 3.3+, we recommend using Paddle2ONNX in the following environments:
 
-- PaddlePaddle == 3.0.0b2
+- Python >= 3.10
+- PaddlePaddle >= 3.3
+- ONNX >= 1.20.1
+- protobuf >= 34.0
 - onnxruntime >= 1.10.0
 
 ## 3 Install Paddle2ONNX

README_en.md

@@ -0,0 +1,9 @@
+# Patch onnx-optimizer for compatibility with ONNX 1.20.1
+# Dimension constructor is now explicit, so fix implicit conversions
+
+file(READ "onnxoptimizer/passes/fuse_add_bias_into_conv.h" content)
+string(REPLACE
+  "std::vector<Dimension> s = {1};"
+  "std::vector<Dimension> s = {Dimension(1)};"
+  content "${content}")
+file(WRITE "onnxoptimizer/passes/fuse_add_bias_into_conv.h" "${content}")