Update packages (pybind11 and catch2) and do not use nvidia-docker command

cpp/cmake/deps/catch2.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::catch2)
     FetchContent_Declare(
             deps-catch2
             GIT_REPOSITORY https://github.com/catchorg/Catch2.git
-            GIT_TAG v2.13.1
+            GIT_TAG v3.4.0
             GIT_SHALLOW TRUE
     )
     FetchContent_GetProperties(deps-catch2)
@@ -29,8 +29,9 @@ if (NOT TARGET deps::catch2)
 
     add_subdirectory(${deps-catch2_SOURCE_DIR} ${deps-catch2_BINARY_DIR} EXCLUDE_FROM_ALL)
 
-    # Include Append catch2's cmake module path so that we can use `include(ParseAndAddCatchTests)`.
-    list(APPEND CMAKE_MODULE_PATH "${deps-catch2_SOURCE_DIR}/contrib")
+    # Include Append catch2's cmake module path so that we can use `include(Catch)`.
+    # https://github.com/catchorg/Catch2/blob/devel/docs/cmake-integration.md#catchcmake-and-catchaddtestscmake
+    list(APPEND CMAKE_MODULE_PATH "${deps-catch2_SOURCE_DIR}/extras")
     set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} PARENT_SCOPE)
 
     add_library(deps::catch2 INTERFACE IMPORTED GLOBAL)

cpp/cmake/deps/pybind11.cmake

@@ -17,8 +17,9 @@ if (NOT TARGET deps::pybind11)
     FetchContent_Declare(
             deps-pybind11
             GIT_REPOSITORY https://github.com/pybind/pybind11.git
-            GIT_TAG v2.10.3
+            GIT_TAG v2.11.1
             GIT_SHALLOW TRUE
+            PATCH_COMMAND git apply "${CMAKE_CURRENT_LIST_DIR}/pybind11_pr4857_4877.patch" || true
     )
     FetchContent_GetProperties(deps-pybind11)
     if (NOT deps-pybind11_POPULATED)

cpp/cmake/deps/pybind11_pr4857_4877.patch

@@ -0,0 +1,247 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 87ec103..f2f1d19 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -132,6 +132,7 @@ set(PYBIND11_HEADERS
+     include/pybind11/embed.h
+     include/pybind11/eval.h
+     include/pybind11/gil.h
++    include/pybind11/gil_safe_call_once.h
+     include/pybind11/iostream.h
+     include/pybind11/functional.h
+     include/pybind11/numpy.h
+diff --git a/include/pybind11/detail/common.h b/include/pybind11/detail/common.h
+index 31a54c7..8906c1f 100644
+--- a/include/pybind11/detail/common.h
++++ b/include/pybind11/detail/common.h
+@@ -118,6 +118,14 @@
+ #    endif
+ #endif
+
++#if defined(PYBIND11_CPP20)
++#    define PYBIND11_CONSTINIT constinit
++#    define PYBIND11_DTOR_CONSTEXPR constexpr
++#else
++#    define PYBIND11_CONSTINIT
++#    define PYBIND11_DTOR_CONSTEXPR
++#endif
++
+ // Compiler version assertions
+ #if defined(__INTEL_COMPILER)
+ #    if __INTEL_COMPILER < 1800
+diff --git a/include/pybind11/gil.h b/include/pybind11/gil.h
+index 570a558..da22f48 100644
+--- a/include/pybind11/gil.h
++++ b/include/pybind11/gil.h
+@@ -11,6 +11,8 @@
+
+ #include "detail/common.h"
+
++#include <cassert>
++
+ #if defined(WITH_THREAD) && !defined(PYBIND11_SIMPLE_GIL_MANAGEMENT)
+ #    include "detail/internals.h"
+ #endif
+@@ -137,7 +139,9 @@ private:
+
+ class gil_scoped_release {
+ public:
++    // PRECONDITION: The GIL must be held when this constructor is called.
+     explicit gil_scoped_release(bool disassoc = false) : disassoc(disassoc) {
++        assert(PyGILState_Check());
+         // `get_internals()` must be called here unconditionally in order to initialize
+         // `internals.tstate` for subsequent `gil_scoped_acquire` calls. Otherwise, an
+         // initialization race could occur as multiple threads try `gil_scoped_acquire`.
+@@ -201,7 +205,11 @@ class gil_scoped_release {
+     PyThreadState *state;
+
+ public:
+-    gil_scoped_release() : state{PyEval_SaveThread()} {}
++    // PRECONDITION: The GIL must be held when this constructor is called.
++    gil_scoped_release() {
++        assert(PyGILState_Check());
++        state = PyEval_SaveThread();
++    }
+     gil_scoped_release(const gil_scoped_release &) = delete;
+     gil_scoped_release &operator=(const gil_scoped_release &) = delete;
+     ~gil_scoped_release() { PyEval_RestoreThread(state); }
+diff --git a/include/pybind11/gil_safe_call_once.h b/include/pybind11/gil_safe_call_once.h
+new file mode 100644
+index 0000000..58b90b8
+--- /dev/null
++++ b/include/pybind11/gil_safe_call_once.h
+@@ -0,0 +1,90 @@
++// Copyright (c) 2023 The pybind Community.
++
++
++#include "detail/common.h"
++#include "gil.h"
++
++#include <cassert>
++#include <mutex>
++
++PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE)
++
++// Use the `gil_safe_call_once_and_store` class below instead of the naive
++//
++//   static auto imported_obj = py::module_::import("module_name"); // BAD, DO NOT USE!
++//
++// which has two serious issues:
++//
++//     1. Py_DECREF() calls potentially after the Python interpreter was finalized already, and
++//     2. deadlocks in multi-threaded processes (because of missing lock ordering).
++//
++// The following alternative avoids both problems:
++//
++//   PYBIND11_CONSTINIT static py::gil_safe_call_once_and_store<py::object> storage;
++//   auto &imported_obj = storage // Do NOT make this `static`!
++//       .call_once_and_store_result([]() {
++//           return py::module_::import("module_name");
++//       })
++//       .get_stored();
++//
++// The parameter of `call_once_and_store_result()` must be callable. It can make
++// CPython API calls, and in particular, it can temporarily release the GIL.
++//
++// `T` can be any C++ type, it does not have to involve CPython API types.
++//
++// The behavior with regard to signals, e.g. `SIGINT` (`KeyboardInterrupt`),
++// is not ideal. If the main thread is the one to actually run the `Callable`,
++// then a `KeyboardInterrupt` will interrupt it if it is running normal Python
++// code. The situation is different if a non-main thread runs the
++// `Callable`, and then the main thread starts waiting for it to complete:
++// a `KeyboardInterrupt` will not interrupt the non-main thread, but it will
++// get processed only when it is the main thread's turn again and it is running
++// normal Python code. However, this will be unnoticeable for quick call-once
++// functions, which is usually the case.
++template <typename T>
++class gil_safe_call_once_and_store {
++public:
++    // PRECONDITION: The GIL must be held when `call_once_and_store_result()` is called.
++    template <typename Callable>
++    gil_safe_call_once_and_store &call_once_and_store_result(Callable &&fn) {
++        if (!is_initialized_) { // This read is guarded by the GIL.
++            // Multiple threads may enter here, because the GIL is released in the next line and
++            // CPython API calls in the `fn()` call below may release and reacquire the GIL.
++            gil_scoped_release gil_rel; // Needed to establish lock ordering.
++            std::call_once(once_flag_, [&] {
++                // Only one thread will ever enter here.
++                gil_scoped_acquire gil_acq;
++                ::new (storage_) T(fn()); // fn may release, but will reacquire, the GIL.
++                is_initialized_ = true;   // This write is guarded by the GIL.
++            });
++            // All threads will observe `is_initialized_` as true here.
++        }
++        // Intentionally not returning `T &` to ensure the calling code is self-documenting.
++        return *this;
++    }
++
++    // This must only be called after `call_once_and_store_result()` was called.
++    T &get_stored() {
++        assert(is_initialized_);
++        PYBIND11_WARNING_PUSH
++#if !defined(__clang__) && defined(__GNUC__) && __GNUC__ < 5
++        // Needed for gcc 4.8.5
++        PYBIND11_WARNING_DISABLE_GCC("-Wstrict-aliasing")
++#endif
++        return *reinterpret_cast<T *>(storage_);
++        PYBIND11_WARNING_POP
++    }
++
++    constexpr gil_safe_call_once_and_store() = default;
++    PYBIND11_DTOR_CONSTEXPR ~gil_safe_call_once_and_store() = default;
++
++private:
++    alignas(T) char storage_[sizeof(T)] = {};
++    std::once_flag once_flag_ = {};
++    bool is_initialized_ = false;
++    // The `is_initialized_`-`storage_` pair is very similar to `std::optional`,
++    // but the latter does not have the triviality properties of former,
++    // therefore `std::optional` is not a viable alternative here.
++};
++
++PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE)
+diff --git a/include/pybind11/numpy.h b/include/pybind11/numpy.h
+index 36077ec..1217c8d 100644
+--- a/include/pybind11/numpy.h
++++ b/include/pybind11/numpy.h
+@@ -10,7 +10,10 @@
+ #pragma once
+
+ #include "pybind11.h"
++#include "detail/common.h"
+ #include "complex.h"
++#include "gil_safe_call_once.h"
++#include "pytypes.h"
+
+ #include <algorithm>
+ #include <array>
+@@ -120,6 +123,20 @@ inline numpy_internals &get_numpy_internals() {
+     return *ptr;
+ }
+
++PYBIND11_NOINLINE module_ import_numpy_core_submodule(const char *submodule_name) {
++    module_ numpy = module_::import("numpy");
++    str version_string = numpy.attr("__version__");
++
++    module_ numpy_lib = module_::import("numpy.lib");
++    object numpy_version = numpy_lib.attr("NumpyVersion")(version_string);
++    int major_version = numpy_version.attr("major").cast<int>();
++
++    /* `numpy.core` was renamed to `numpy._core` in NumPy 2.0 as it officially
++        became a private module. */
++    std::string numpy_core_path = major_version >= 2 ? "numpy._core" : "numpy.core";
++    return module_::import((numpy_core_path + "." + submodule_name).c_str());
++}
++
+ template <typename T>
+ struct same_size {
+     template <typename U>
+@@ -192,8 +209,8 @@ struct npy_api {
+     };
+
+     static npy_api &get() {
+-        static npy_api api = lookup();
+-        return api;
++        PYBIND11_CONSTINIT static gil_safe_call_once_and_store<npy_api> storage;
++        return storage.call_once_and_store_result(lookup).get_stored();
+     }
+
+     bool PyArray_Check_(PyObject *obj) const {
+@@ -263,9 +280,13 @@ private:
+     };
+
+     static npy_api lookup() {
+-        module_ m = module_::import("numpy.core.multiarray");
++        module_ m = detail::import_numpy_core_submodule("multiarray");
+         auto c = m.attr("_ARRAY_API");
+         void **api_ptr = (void **) PyCapsule_GetPointer(c.ptr(), nullptr);
++        if (api_ptr == nullptr) {
++            raise_from(PyExc_SystemError, "FAILURE obtaining numpy _ARRAY_API pointer.");
++            throw error_already_set();
++        }
+         npy_api api;
+ #define DECL_NPY_API(Func) api.Func##_ = (decltype(api.Func##_)) api_ptr[API_##Func];
+         DECL_NPY_API(PyArray_GetNDArrayCFeatureVersion);
+@@ -625,13 +646,14 @@ public:
+     char flags() const { return detail::array_descriptor_proxy(m_ptr)->flags; }
+
+ private:
+-    static object _dtype_from_pep3118() {
+-        static PyObject *obj = module_::import("numpy.core._internal")
+-                                   .attr("_dtype_from_pep3118")
+-                                   .cast<object>()
+-                                   .release()
+-                                   .ptr();
+-        return reinterpret_borrow<object>(obj);
++    static object &_dtype_from_pep3118() {
++        PYBIND11_CONSTINIT static gil_safe_call_once_and_store<object> storage;
++        return storage
++            .call_once_and_store_result([]() {
++                return detail::import_numpy_core_submodule("_internal")
++                    .attr("_dtype_from_pep3118");
++            })
++            .get_stored();
+     }
+
+     dtype strip_padding(ssize_t itemsize) {

cpp/plugins/cucim.kit.cumed/cmake/deps/catch2.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::catch2)
     FetchContent_Declare(
             deps-catch2
             GIT_REPOSITORY https://github.com/catchorg/Catch2.git
-            GIT_TAG v2.13.1
+            GIT_TAG v3.4.0
             GIT_SHALLOW TRUE
     )
     FetchContent_GetProperties(deps-catch2)
@@ -29,8 +29,9 @@ if (NOT TARGET deps::catch2)
 
     add_subdirectory(${deps-catch2_SOURCE_DIR} ${deps-catch2_BINARY_DIR} EXCLUDE_FROM_ALL)
 
-    # Include Append catch2's cmake module path so that we can use `include(ParseAndAddCatchTests)`.
-    list(APPEND CMAKE_MODULE_PATH "${deps-catch2_SOURCE_DIR}/contrib")
+    # Include Append catch2's cmake module path so that we can use `include(Catch)`.
+    # https://github.com/catchorg/Catch2/blob/devel/docs/cmake-integration.md#catchcmake-and-catchaddtestscmake
+    list(APPEND CMAKE_MODULE_PATH "${deps-catch2_SOURCE_DIR}/extras")
     set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} PARENT_SCOPE)
 
     add_library(deps::catch2 INTERFACE IMPORTED GLOBAL)

cpp/plugins/cucim.kit.cumed/tests/CMakeLists.txt

@@ -57,6 +57,6 @@ target_include_directories(cumed_tests
             $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../src>
         )
 
-include(ParseAndAddCatchTests)
-# See https://github.com/catchorg/Catch2/blob/master/docs/cmake-integration.md#parseandaddcatchtestscmake for other options
-ParseAndAddCatchTests(cumed_tests)
+include(Catch)
+# See https://github.com/catchorg/Catch2/blob/devel/docs/cmake-integration.md#catchcmake-and-catchaddtestscmake for other options
+catch_discover_tests(cumed_tests)

cpp/plugins/cucim.kit.cumed/tests/main.cpp

@@ -14,15 +14,16 @@
  * limitations under the License.
  */
 
-//#define CATCH_CONFIG_MAIN
-//#include <catch2/catch.hpp>
+// #define CATCH_CONFIG_MAIN
+// #include <catch2/catch_test_macros.hpp>
 
 // Implement main explicitly to handle additional parameters.
 #define CATCH_CONFIG_RUNNER
 #include "config.h"
 #include "cucim/core/framework.h"
 
-#include <catch2/catch.hpp>
+#include <catch2/catch_test_macros.hpp>
+#include <catch2/catch_session.hpp>
 #include <string>
 #include <fmt/format.h>
 

cpp/plugins/cucim.kit.cumed/tests/test_basic.cpp

@@ -16,7 +16,7 @@
 
 #include "config.h"
 
-#include <catch2/catch.hpp>
+#include <catch2/catch_test_macros.hpp>
 #include <chrono>
 
 TEST_CASE("Verify file", "[test_basic.cpp]")

cpp/plugins/cucim.kit.cuslide/cmake/deps/catch2.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::catch2)
     FetchContent_Declare(
             deps-catch2
             GIT_REPOSITORY https://github.com/catchorg/Catch2.git
-            GIT_TAG v2.13.1
+            GIT_TAG v3.4.0
             GIT_SHALLOW TRUE
     )
     FetchContent_GetProperties(deps-catch2)
@@ -29,8 +29,9 @@ if (NOT TARGET deps::catch2)
 
     add_subdirectory(${deps-catch2_SOURCE_DIR} ${deps-catch2_BINARY_DIR} EXCLUDE_FROM_ALL)
 
-    # Include Append catch2's cmake module path so that we can use `include(ParseAndAddCatchTests)`.
-    list(APPEND CMAKE_MODULE_PATH "${deps-catch2_SOURCE_DIR}/contrib")
+    # Include Append catch2's cmake module path so that we can use `include(Catch)`.
+    # https://github.com/catchorg/Catch2/blob/devel/docs/cmake-integration.md#catchcmake-and-catchaddtestscmake
+    list(APPEND CMAKE_MODULE_PATH "${deps-catch2_SOURCE_DIR}/extras")
     set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} PARENT_SCOPE)
 
     add_library(deps::catch2 INTERFACE IMPORTED GLOBAL)

cpp/plugins/cucim.kit.cuslide/tests/CMakeLists.txt

@@ -60,6 +60,6 @@ target_include_directories(cuslide_tests
             $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../src>
         )
 
-include(ParseAndAddCatchTests)
-# See https://github.com/catchorg/Catch2/blob/master/docs/cmake-integration.md#parseandaddcatchtestscmake for other options
-ParseAndAddCatchTests(cuslide_tests)
+include(Catch)
+# See https://github.com/catchorg/Catch2/blob/devel/docs/cmake-integration.md#catchcmake-and-catchaddtestscmake for other options
+catch_discover_tests(cuslide_tests)

cpp/plugins/cucim.kit.cuslide/tests/main.cpp

@@ -14,15 +14,16 @@
  * limitations under the License.
  */
 
-//#define CATCH_CONFIG_MAIN
-//#include <catch2/catch.hpp>
+// #define CATCH_CONFIG_MAIN
+// #include <catch2/catch_test_macros.hpp>
 
 // Implement main explicitly to handle additional parameters.
 #define CATCH_CONFIG_RUNNER
 #include "config.h"
 #include "cucim/core/framework.h"
 
-#include <catch2/catch.hpp>
+#include <catch2/catch_test_macros.hpp>
+#include <catch2/catch_session.hpp>
 #include <string>
 #include <fmt/format.h>
 

cpp/plugins/cucim.kit.cuslide/tests/test_philips_tiff.cpp

@@ -19,7 +19,7 @@
 #include "cuslide/tiff/tiff.h"
 #include "config.h"
 
-#include <catch2/catch.hpp>
+#include <catch2/catch_test_macros.hpp>
 #include <chrono>
 
 TEST_CASE("Verify philips tiff file", "[test_philips_tiff.cpp]")