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

@@ -17,7 +17,7 @@ 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
     )
     FetchContent_GetProperties(deps-pybind11)

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]")

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

@@ -19,7 +19,7 @@
 #include "config.h"
 
 #include <cuda_runtime.h>
-#include <catch2/catch.hpp>
+#include <catch2/catch_test_macros.hpp>
 #include <fmt/format.h>
 #include <cucim/filesystem/cufile_driver.h>
 #include <cstdlib>

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

@@ -16,7 +16,8 @@
 
 #include <chrono>
 
-#include <catch2/catch.hpp>
+#include <catch2/catch_test_macros.hpp>
+#include <catch2/generators/catch_generators.hpp>
 #include <openslide/openslide.h>
 
 #include <cucim/memory/memory_manager.h>

cpp/tests/CMakeLists.txt

@@ -60,6 +60,6 @@ target_link_libraries(cucim_tests
             Threads::Threads # -lpthread
         )
 
-include(ParseAndAddCatchTests)
-# See https://github.com/catchorg/Catch2/blob/master/docs/cmake-integration.md#parseandaddcatchtestscmake for other options
-ParseAndAddCatchTests(cucim_tests)
+include(Catch)
+# See https://github.com/catchorg/Catch2/blob/devel/docs/cmake-integration.md#catchcmake-and-catchaddtestscmake for other options
+catch_discover_tests(cucim_tests)

cpp/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/tests/test_cufile.cpp

@@ -17,7 +17,7 @@
 #include "cucim/logger/timer.h"
 #include "config.h"
 
-#include <catch2/catch.hpp>
+#include <catch2/catch_test_macros.hpp>
 #include <fmt/format.h>
 #include <cucim/filesystem/cufile_driver.h>
 #include <chrono>

cpp/tests/test_metadata.cpp

@@ -20,7 +20,7 @@
 #include "cucim/core/framework.h"
 #include "cucim/io/format/image_format.h"
 
-#include <catch2/catch.hpp>
+#include <catch2/catch_test_macros.hpp>
 #include <fmt/format.h>
 #include <chrono>
 #include <cstdlib>

cpp/tests/test_read_region.cpp

@@ -17,7 +17,7 @@
 #include <chrono>
 #include <iostream>
 
-#include <catch2/catch.hpp>
+#include <catch2/catch_test_macros.hpp>
 #include <cuda_runtime.h>
 #include <openslide/openslide.h>
 

dockcross-manylinux2014-x64

@@ -233,7 +233,7 @@ fi
 TTY_ARGS=
 tty -s && [ -z "$MSYS" ] && TTY_ARGS=-ti
 CONTAINER_NAME=dockcross_$RANDOM
-nvidia-docker run $TTY_ARGS --name $CONTAINER_NAME \
+docker run --runtime nvidia $TTY_ARGS --name $CONTAINER_NAME \
     -v "$HOST_PWD":/work \
     $HOST_VOLUMES \
     "${USER_IDS[@]}" \

notebooks/File-access_Experiments_on_TIFF.ipynb

@@ -199,7 +199,7 @@
     "#include \"cuslide/tiff/tiff.h\"\n",
     "#include \"config.h\"\n",
     "\n",
-    "#include <catch2/catch.hpp>\n",
+    "#include <catch2/catch_test_macros.hpp>\n",
     "#include <fmt/format.h>\n",
     "#include <cucim/filesystem/cufile_driver.h>\n",
     "#include <cstdlib>\n",

python/cmake/deps/pybind11.cmake

@@ -17,7 +17,7 @@ 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
     )
     FetchContent_GetProperties(deps-pybind11)

python/cucim/docs/getting_started/index.md

@@ -99,7 +99,7 @@ After executing the command, type a password for the instance and open a web bro
 ```bash
 ...
 Port 10001 would be used...(http://172.26.120.129:10001)
-2021-02-13 01:12:44 $ nvidia-docker run --gpus all -it --rm -v /home/repo/cucim/notebooks:/notebooks -p 10001:10001 cucim-jupyter -c echo -n 'Enter New Password: '; jupyter lab --ServerApp.password="$(python3 -u -c "from jupyter_server.auth import passwd;pw=input();print(passwd(pw));" | egrep 'sha|argon')" --ServerApp.root_dir=/notebooks --allow-root --port=10001 --ip=0.0.0.0 --no-browser
+2021-02-13 01:12:44 $ docker run --runtime nvidia --gpus all -it --rm -v /home/repo/cucim/notebooks:/notebooks -p 10001:10001 cucim-jupyter -c echo -n 'Enter New Password: '; jupyter lab --ServerApp.password="$(python3 -u -c "from jupyter_server.auth import passwd;pw=input();print(passwd(pw));" | egrep 'sha|argon')" --ServerApp.root_dir=/notebooks --allow-root --port=10001 --ip=0.0.0.0 --no-browser
 Enter New Password: <password>
 [I 2021-02-13 01:12:47.981 ServerApp] dask_labextension | extension was successfully linked.
 [I 2021-02-13 01:12:47.981 ServerApp] jupyter_server_proxy | extension was successfully linked.

run

@@ -984,14 +984,14 @@ launch_notebooks() {
 
     run_command cp ${TOP}/dist/*.whl ${TOP}/notebooks
 
-    run_command nvidia-docker build -t cucim-jupyter${gds_postfix} -f ${TOP}/docker/Dockerfile-jupyter${gds_postfix}-dev ${TOP}
+    run_command docker build --runtime nvidia -t cucim-jupyter${gds_postfix} -f ${TOP}/docker/Dockerfile-jupyter${gds_postfix}-dev ${TOP}
 
     [ $? -ne 0 ] && return 1
 
     c_echo W "Port " G "$port" W " would be used...(" B "http://$(hostname -I | cut -d' ' -f 1):${port}" W ")"
 
     if [ -z "${gds_postfix}" ]; then
-        run_command nvidia-docker run --gpus all -it --rm \
+        run_command docker run --runtime nvidia --gpus all -it --rm \
             -v ${TOP}/notebooks:/notebooks \
             -p ${port}:${port} \
             cucim-jupyter \

scripts/run-dist

@@ -307,14 +307,14 @@ launch_notebooks() {
 
     run_command cp ${TOP}/*.whl ${TOP}/notebooks
 
-    run_command nvidia-docker build -t cucim-jupyter${gds_postfix} -f ${TOP}/docker/Dockerfile-jupyter${gds_postfix} ${TOP}
+    run_command docker build --runtime nvidia -t cucim-jupyter${gds_postfix} -f ${TOP}/docker/Dockerfile-jupyter${gds_postfix} ${TOP}
 
     [ $? -ne 0 ] && return 1
 
     c_echo W "Port " G "$port" W " would be used...(" B "http://$(hostname -I | cut -d' ' -f 1):${port}" W ")"
 
     if [ -z "${gds_postfix}" ]; then
-        run_command nvidia-docker run --gpus all -it --rm \
+        run_command docker run --runtime nvidia --gpus all -it --rm \
             -v ${TOP}/notebooks:/notebooks \
             -p ${port}:${port} \
             cucim-jupyter \