Release: 0.16.1

.github/workflows/linux.yml

@@ -328,8 +328,7 @@ jobs:
           -DopenPMD_USE_MPI=ON    \
           -DopenPMD_USE_HDF5=ON   \
           -DopenPMD_USE_ADIOS2=ON \
-          -DopenPMD_USE_INVASIVE_TESTS=ON \
-          -DMPIEXEC_EXECUTABLE=".github/workflows/mpirun_workaround.sh"
+          -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build build --parallel 2
         cd build
         ctest --output-on-failure

.github/workflows/macos.yml

@@ -40,13 +40,12 @@ jobs:
           -DopenPMD_USE_MPI=ON    \
           -DopenPMD_USE_HDF5=ON   \
           -DopenPMD_USE_ADIOS2=ON \
-          -DopenPMD_USE_INVASIVE_TESTS=ON \
-          -DMPIEXEC_EXECUTABLE=".github/workflows/mpirun_workaround.sh"
+          -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build build --parallel 3
         ctest --test-dir build --verbose
 
   appleclang14_py:
-    runs-on: macos-12
+    runs-on: macos-13
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v4

.github/workflows/windows.yml

@@ -42,7 +42,7 @@ jobs:
 
         python3.exe -m pip wheel .
         if(!$?) { Exit $LASTEXITCODE }
-        python3.exe -m pip install openPMD_api-0.16.0.dev0-cp39-cp39-win_amd64.whl
+        python3.exe -m pip install openPMD_api-0.16.1-cp39-cp39-win_amd64.whl
         if(!$?) { Exit $LASTEXITCODE }
 
         python3.exe -c "import openpmd_api as api; print(api.variants)"

CHANGELOG.rst

@@ -3,6 +3,41 @@
 Changelog
 =========
 
+0.16.1
+------
+**Date:** 2025-01-15
+
+New Backends, Extension, Perf. & Memory
+
+This is the 0.16.0 release but with internal version bumps where they were missing.
+
+Changes to "0.16.0"
+^^^^^^^^^^^^^^^^^^^
+
+Bug Fixes
+"""""""""
+
+- HDF5: Delete and re-create attribute when overwriting with diff. type #1697
+- TOUCH IOTask: Avoid setting files as dirty in non-write modes #1704
+- Fix CMake variables for controlling internal dependencies #1678
+- Bump toml11 dependency to ``v4.2.0`` by default #1679
+- Set ``PYBIND11_FINDPYTHON=ON`` #1684
+- Properly check for empty ``HDF5_VERSION`` in CMake #1702
+- Fix ICX build #1690
+- Explicitly specify ADIOS2 components in openPMDConfig.cmake #1693
+- Example 12: Use ``ULONG`` for particle patches #1710
+
+Other
+"""""
+
+- Replace deprecated Python unittest API call #1681
+- Remove ``mpirun_workaround.sh`` #1698
+- CI: Upgrade appleclang14 build to MacOS 13 #1703
+- Docs:
+
+  - Fix Shipped Internally #1682
+  - Fix leftover ADIOS2 mentions #1683
+
 0.16.0
 ------
 **Date:** 2024-10-07

CITATION.cff

@@ -37,7 +37,7 @@ contact:
   orcid: https://orcid.org/0000-0003-1943-7141
   email: [email protected]
 title: "openPMD-api: C++ & Python API for Scientific I/O with openPMD"
-version: 0.16.0-dev
+version: 0.16.1
 repository-code: https://github.com/openPMD/openPMD-api
 doi: 10.14278/rodare.27
 license: LGPL-3.0-or-later

CMakeLists.txt

@@ -2,7 +2,7 @@
 #
 cmake_minimum_required(VERSION 3.22.0)
 
-project(openPMD VERSION 0.16.0) # LANGUAGES CXX
+project(openPMD VERSION 0.16.1) # LANGUAGES CXX
 
 # the openPMD "markup"/"schema" standard version
 set(openPMD_STANDARD_VERSION 1.1.0)
@@ -314,7 +314,7 @@ endif()
 string(CONCAT openPMD_HDF5_STATUS "")
 # version: lower limit
 if(openPMD_HAVE_HDF5)
-    if(HDF5_VERSION STREQUAL "")
+    if("${HDF5_VERSION}" STREQUAL "")
         message(WARNING "HDF5_VERSION is empty. Now assuming it is 1.8.13 or newer.")
     else()
         if(HDF5_VERSION VERSION_LESS 1.8.13)
@@ -360,20 +360,24 @@ if(openPMD_HDF5_STATUS)
 endif()
 
 # external library: ADIOS2 (optional)
+set(openPMD_REQUIRED_ADIOS2_COMPONENTS CXX)
+if(openPMD_HAVE_MPI)
+    list(APPEND openPMD_REQUIRED_ADIOS2_COMPONENTS MPI)
+endif()
 if(openPMD_USE_ADIOS2 STREQUAL AUTO)
-    find_package(ADIOS2 2.7.0 CONFIG)
+    find_package(ADIOS2 2.7.0 CONFIG COMPONENTS ${openPMD_REQUIRED_ADIOS2_COMPONENTS})
     if(ADIOS2_FOUND)
         set(openPMD_HAVE_ADIOS2 TRUE)
     else()
         set(openPMD_HAVE_ADIOS2 FALSE)
     endif()
 elseif(openPMD_USE_ADIOS2)
-    find_package(ADIOS2 2.7.0 REQUIRED CONFIG)
+    find_package(ADIOS2 2.7.0 REQUIRED CONFIG COMPONENTS ${openPMD_REQUIRED_ADIOS2_COMPONENTS})
     set(openPMD_HAVE_ADIOS2 TRUE)
 else()
     set(openPMD_HAVE_ADIOS2 FALSE)
 endif()
-# TODO: Check if ADIOS2 is parallel when openPMD_HAVE_MPI is ON
+unset(openPMD_REQUIRED_ADIOS2_COMPONENTS)
 
 # external library: pybind11 (optional)
 include(${openPMD_SOURCE_DIR}/cmake/dependencies/pybind11.cmake)

README.md

@@ -99,7 +99,7 @@ Required:
 * CMake 3.22.0+
 * C++17 capable compiler, e.g., g++ 7+, clang 7+, MSVC 19.15+, icpc 19+, icpx
 
-Shipped internally in `share/openPMD/thirdParty/`:
+Shipped internally (downloaded by CMake unless `openPMD_SUPERBUILD=OFF` is set):
 * [Catch2](https://github.com/catchorg/Catch2) 2.13.10+ ([BSL-1.0](https://github.com/catchorg/Catch2/blob/master/LICENSE.txt))
 * [pybind11](https://github.com/pybind/pybind11) 2.13.0+ ([new BSD](https://github.com/pybind/pybind11/blob/master/LICENSE))
 * [NLohmann-JSON](https://github.com/nlohmann/json) 3.9.1+ ([MIT](https://github.com/nlohmann/json/blob/develop/LICENSE.MIT))
@@ -304,7 +304,7 @@ export CMAKE_PREFIX_PATH=$HOME/somepath:$CMAKE_PREFIX_PATH
 Use the following lines in your project's `CMakeLists.txt`:
 ```cmake
 # supports:                       COMPONENTS MPI NOMPI HDF5 ADIOS2
-find_package(openPMD 0.16.0 CONFIG)
+find_package(openPMD 0.16.1 CONFIG)
 
 if(openPMD_FOUND)
     target_link_libraries(YourTarget PRIVATE openPMD::openPMD)
@@ -332,7 +332,7 @@ set(openPMD_INSTALL OFF)            # or instead use:
 set(openPMD_USE_PYTHON OFF)
 FetchContent_Declare(openPMD
   GIT_REPOSITORY "https://github.com/openPMD/openPMD-api.git"
-  GIT_TAG        "0.16.0")
+  GIT_TAG        "0.16.1")
 FetchContent_MakeAvailable(openPMD)
 ```
 

cmake/dependencies/catch.cmake

@@ -1,49 +1,49 @@
 function(find_catch2)
     if(TARGET Catch2::Catch2)
         message(STATUS "Catch2::Catch2 target already imported")
-    elseif(openPMD_catch_src)
-        message(STATUS "Compiling local Catch2 ...")
-        message(STATUS "Catch2 source path: ${openPMD_catch_src}")
-        if(NOT IS_DIRECTORY ${openPMD_catch_src})
-            message(FATAL_ERROR "Specified directory openPMD_catch_src='${openPMD_catch_src}' does not exist!")
-        endif()
-    elseif(openPMD_catch_tar)
-        message(STATUS "Downloading Catch2 ...")
-        message(STATUS "Catch2 source: ${openPMD_catch_tar}")
     elseif(openPMD_USE_INTERNAL_CATCH)
-        message(STATUS "Downloading Catch2 ...")
-        message(STATUS "Catch2 repository: ${openPMD_catch_repo} (${openPMD_catch_branch})")
+        if(openPMD_catch_src)
+            message(STATUS "Compiling local Catch2 ...")
+            message(STATUS "Catch2 source path: ${openPMD_catch_src}")
+            if(NOT IS_DIRECTORY ${openPMD_catch_src})
+                message(FATAL_ERROR "Specified directory openPMD_catch_src='${openPMD_catch_src}' does not exist!")
+            endif()
+        elseif(openPMD_catch_tar)
+            message(STATUS "Downloading Catch2 ...")
+            message(STATUS "Catch2 source: ${openPMD_catch_tar}")
+        elseif(openPMD_catch_branch)
+            message(STATUS "Downloading Catch2 ...")
+            message(STATUS "Catch2 repository: ${openPMD_catch_repo} (${openPMD_catch_branch})")
+        endif()
     endif()
     if(TARGET Catch2::Catch2)
         # nothing to do, target already exists in the superbuild
-    elseif(openPMD_USE_INTERNAL_CATCH OR openPMD_catch_src OR openPMD_catch_tar)
-        if(openPMD_catch_src)
-            add_subdirectory(${openPMD_catch_src} _deps/localCatch2-build/)
+    elseif(openPMD_USE_INTERNAL_CATCH AND openPMD_catch_src)
+        add_subdirectory(${openPMD_catch_src} _deps/localCatch2-build/)
+    elseif(openPMD_USE_INTERNAL_CATCH AND (openPMD_catch_tar OR openPMD_catch_branch))
+        include(FetchContent)
+        if(openPMD_catch_tar)
+            FetchContent_Declare(fetchedCatch2
+                URL             ${openPMD_catch_tar}
+                URL_HASH        ${openPMD_catch_tar_hash}
+                BUILD_IN_SOURCE OFF
+            )
         else()
-            include(FetchContent)
-            if(openPMD_catch_tar)
-                FetchContent_Declare(fetchedCatch2
-                    URL             ${openPMD_catch_tar}
-                    URL_HASH        ${openPMD_catch_tar_hash}
-                    BUILD_IN_SOURCE OFF
-                )
-            else()
-                FetchContent_Declare(fetchedCatch2
-                    GIT_REPOSITORY ${openPMD_catch_repo}
-                    GIT_TAG        ${openPMD_catch_branch}
-                    BUILD_IN_SOURCE OFF
-                )
-            endif()
-            FetchContent_MakeAvailable(fetchedCatch2)
-
-            # advanced fetch options
-            mark_as_advanced(FETCHCONTENT_BASE_DIR)
-            mark_as_advanced(FETCHCONTENT_FULLY_DISCONNECTED)
-            mark_as_advanced(FETCHCONTENT_QUIET)
-            #mark_as_advanced(FETCHCONTENT_SOURCE_DIR_FETCHEDCatch2)
-            mark_as_advanced(FETCHCONTENT_UPDATES_DISCONNECTED)
-            #mark_as_advanced(FETCHCONTENT_UPDATES_DISCONNECTED_FETCHEDCatch2)
+            FetchContent_Declare(fetchedCatch2
+                GIT_REPOSITORY ${openPMD_catch_repo}
+                GIT_TAG        ${openPMD_catch_branch}
+                BUILD_IN_SOURCE OFF
+            )
         endif()
+        FetchContent_MakeAvailable(fetchedCatch2)
+
+        # advanced fetch options
+        mark_as_advanced(FETCHCONTENT_BASE_DIR)
+        mark_as_advanced(FETCHCONTENT_FULLY_DISCONNECTED)
+        mark_as_advanced(FETCHCONTENT_QUIET)
+        #mark_as_advanced(FETCHCONTENT_SOURCE_DIR_FETCHEDCatch2)
+        mark_as_advanced(FETCHCONTENT_UPDATES_DISCONNECTED)
+        #mark_as_advanced(FETCHCONTENT_UPDATES_DISCONNECTED_FETCHEDCatch2)
     elseif(NOT openPMD_USE_INTERNAL_CATCH)
         find_package(Catch2 2.13.10 CONFIG REQUIRED)
         message(STATUS "Catch2: Found version '${Catch2_VERSION}'")

cmake/dependencies/json.cmake

@@ -1,49 +1,49 @@
 function(find_json)
     if(TARGET nlohmann_json::nlohmann_json)
         message(STATUS "nlohmann_json::nlohmann_json target already imported")
-    elseif(openPMD_json_src)
-        message(STATUS "Compiling local nlohmann_json ...")
-        message(STATUS "nlohmann_json source path: ${openPMD_json_src}")
-        if(NOT IS_DIRECTORY ${openPMD_json_src})
-            message(FATAL_ERROR "Specified directory openPMD_json_src='${openPMD_json_src}' does not exist!")
-        endif()
-    elseif(openPMD_json_tar)
-        message(STATUS "Downloading nlohmann_json ...")
-        message(STATUS "nlohmann_json source: ${openPMD_json_tar}")
     elseif(openPMD_USE_INTERNAL_JSON)
-        message(STATUS "Downloading nlohmann_json ...")
-        message(STATUS "nlohmann_json repository: ${openPMD_json_repo} (${openPMD_json_branch})")
+        if(openPMD_json_src)
+            message(STATUS "Compiling local nlohmann_json ...")
+            message(STATUS "nlohmann_json source path: ${openPMD_json_src}")
+            if(NOT IS_DIRECTORY ${openPMD_json_src})
+                message(FATAL_ERROR "Specified directory openPMD_json_src='${openPMD_json_src}' does not exist!")
+            endif()
+        elseif(openPMD_json_tar)
+            message(STATUS "Downloading nlohmann_json ...")
+            message(STATUS "nlohmann_json source: ${openPMD_json_tar}")
+        elseif(openPMD_json_branch)
+            message(STATUS "Downloading nlohmann_json ...")
+            message(STATUS "nlohmann_json repository: ${openPMD_json_repo} (${openPMD_json_branch})")
+        endif()
     endif()
     if(TARGET nlohmann_json::nlohmann_json)
         # nothing to do, target already exists in the superbuild
-    elseif(openPMD_USE_INTERNAL_JSON OR openPMD_json_src OR openPMD_json_tar)
-        if(openPMD_json_src)
-            add_subdirectory(${openPMD_json_src} _deps/localnlohmann_json-build/)
+    elseif(openPMD_USE_INTERNAL_JSON AND openPMD_json_src)
+        add_subdirectory(${openPMD_json_src} _deps/localnlohmann_json-build/)
+    elseif(openPMD_USE_INTERNAL_JSON AND (openPMD_json_tar OR openPMD_json_branch))
+        include(FetchContent)
+        if(openPMD_json_tar)
+            FetchContent_Declare(fetchednlohmann_json
+                URL             ${openPMD_json_tar}
+                URL_HASH        ${openPMD_json_tar_hash}
+                BUILD_IN_SOURCE OFF
+            )
         else()
-            include(FetchContent)
-            if(openPMD_json_tar)
-                FetchContent_Declare(fetchednlohmann_json
-                    URL             ${openPMD_json_tar}
-                    URL_HASH        ${openPMD_json_tar_hash}
-                    BUILD_IN_SOURCE OFF
-                )
-            else()
-                FetchContent_Declare(fetchednlohmann_json
-                    GIT_REPOSITORY ${openPMD_json_repo}
-                    GIT_TAG        ${openPMD_json_branch}
-                    BUILD_IN_SOURCE OFF
-                )
-            endif()
-            FetchContent_MakeAvailable(fetchednlohmann_json)
-
-            # advanced fetch options
-            mark_as_advanced(FETCHCONTENT_BASE_DIR)
-            mark_as_advanced(FETCHCONTENT_FULLY_DISCONNECTED)
-            mark_as_advanced(FETCHCONTENT_QUIET)
-            #mark_as_advanced(FETCHCONTENT_SOURCE_DIR_FETCHEDnlohmann_json)
-            mark_as_advanced(FETCHCONTENT_UPDATES_DISCONNECTED)
-            #mark_as_advanced(FETCHCONTENT_UPDATES_DISCONNECTED_FETCHEDnlohmann_json)
+            FetchContent_Declare(fetchednlohmann_json
+                GIT_REPOSITORY ${openPMD_json_repo}
+                GIT_TAG        ${openPMD_json_branch}
+                BUILD_IN_SOURCE OFF
+            )
         endif()
+        FetchContent_MakeAvailable(fetchednlohmann_json)
+
+        # advanced fetch options
+        mark_as_advanced(FETCHCONTENT_BASE_DIR)
+        mark_as_advanced(FETCHCONTENT_FULLY_DISCONNECTED)
+        mark_as_advanced(FETCHCONTENT_QUIET)
+        #mark_as_advanced(FETCHCONTENT_SOURCE_DIR_FETCHEDnlohmann_json)
+        mark_as_advanced(FETCHCONTENT_UPDATES_DISCONNECTED)
+        #mark_as_advanced(FETCHCONTENT_UPDATES_DISCONNECTED_FETCHEDnlohmann_json)
     elseif(NOT openPMD_USE_INTERNAL_JSON)
         find_package(nlohmann_json 3.9.1 CONFIG REQUIRED)
         message(STATUS "nlohmann_json: Found version '${nlohmann_json_VERSION}'")