Merge branch 'development' into BenWibking/fix-fextract-mpi

BenWibking · web-flow · commit 98af303e8b30 · 2025-12-04T23:30:35.000-05:00
diff --git a/.github/workflows/check_changes.yml b/.github/workflows/check_changes.yml
@@ -1,4 +1,4 @@
-name: Check Changes
+name: 🔍 Check Changes
 
 on:
   workflow_call:
diff --git a/.github/workflows/checkpoint-restart-refine.yml b/.github/workflows/checkpoint-restart-refine.yml
@@ -1,4 +1,4 @@
-name: CheckpointRestartRefine
+name: 🔄 CheckpointRestartRefine
 
 on:
   push:
diff --git a/.github/workflows/checkpoint-restart.yml b/.github/workflows/checkpoint-restart.yml
@@ -1,4 +1,4 @@
-name: CheckpointRestart
+name: 🔄 CheckpointRestart
 
 on:
   push:
diff --git a/.github/workflows/clang-tidy-comments.yml b/.github/workflows/clang-tidy-comments.yml
@@ -1,4 +1,4 @@
-name: Post clang-tidy-review comments
+name: 💬 Post clang-tidy-review comments
 
 on:
   workflow_run:
diff --git a/.github/workflows/clang-tidy.yml b/.github/workflows/clang-tidy.yml
@@ -1,4 +1,4 @@
-name: clang-tidy-review
+name: 🧹 clang-tidy-review
 
 # You can be more specific, but it currently only works on pull requests
 # Fiewer paths are ignored because some folders (e.g. scripts) are not relavent to code build but should be linted
diff --git a/.github/workflows/claude-code-review.yml b/.github/workflows/claude-code-review.yml
@@ -1,4 +1,4 @@
-name: Claude Code Review
+name: 🤖 Claude Code Review
 
 on:
   # Manual trigger
diff --git a/.github/workflows/claude.yml b/.github/workflows/claude.yml
@@ -1,4 +1,4 @@
-name: Claude Code
+name: 🤖 Claude Code
 
 on:
   issue_comment:
diff --git a/.github/workflows/cmake-arm64-debug.yml b/.github/workflows/cmake-arm64-debug.yml
@@ -1,4 +1,4 @@
-name: linux-arm64-debug
+name: 🐛 linux-arm64-debug
 
 on:
   push:
diff --git a/.github/workflows/cmake-arm64-hwasan.yml b/.github/workflows/cmake-arm64-hwasan.yml
@@ -1,4 +1,4 @@
-name: linux-arm64-hwasan
+name: 🛡️ linux-arm64-hwasan
 
 on:
   push:
diff --git a/.github/workflows/cmake-arm64-release.yml b/.github/workflows/cmake-arm64-release.yml
@@ -1,4 +1,4 @@
-name: linux-arm64-release
+name: 🚀 linux-arm64-release
 
 on:
   push:
diff --git a/.github/workflows/cmake-macos.yml b/.github/workflows/cmake-macos.yml
@@ -1,4 +1,4 @@
-name: CMake (macOS)
+name: 🍎 CMake (macOS)
 
 on:
   push:
diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
@@ -1,4 +1,4 @@
-name: CMake
+name: ⚙️ CMake
 
 on:
   push:
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -1,4 +1,4 @@
-name: CodeQL
+name: 🔒 CodeQL
 
 on:
   push:
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -1,4 +1,4 @@
-name: codespell
+name: ✍️ codespell
 
 on:
   push:
diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
@@ -1,4 +1,4 @@
-name: cuda
+name: 🎮 cuda
 
 on:
   push:
diff --git a/.github/workflows/docs-toctree.yml b/.github/workflows/docs-toctree.yml
@@ -1,4 +1,4 @@
-name: Docs toctree coverage
+name: 📚 Docs toctree coverage
 
 on:
   push:
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -1,4 +1,4 @@
-name: Build and Deploy Docs
+name: 📖 Build and Deploy Docs
 
 on:
   push:
diff --git a/.github/workflows/hip.yml b/.github/workflows/hip.yml
@@ -1,4 +1,4 @@
-name: hip
+name: 🔥 hip
 
 on:
   push:
diff --git a/.github/workflows/hydro-wave-convergence.yml b/.github/workflows/hydro-wave-convergence.yml
@@ -1,4 +1,4 @@
-name: Hydro Wave Convergence
+name: 🌊 Hydro Wave Convergence
 
 on:
   workflow_dispatch:
diff --git a/.github/workflows/mhd-asan.yml b/.github/workflows/mhd-asan.yml
@@ -1,4 +1,4 @@
-name: MHD-WaveTests-ASAN
+name: 🧲 MHD-WaveTests-ASAN
 
 on:
   push:
diff --git a/.github/workflows/mhd.yml b/.github/workflows/mhd.yml
@@ -1,4 +1,4 @@
-name: MHD-WaveTests
+name: 🧲 MHD-WaveTests
 
 on:
   push:
diff --git a/.github/workflows/openpmd.yml b/.github/workflows/openpmd.yml
@@ -1,4 +1,4 @@
-name: OpenPMD
+name: 📊 OpenPMD
 
 on:
   push:
diff --git a/.github/workflows/sonarcloud.yml b/.github/workflows/sonarcloud.yml
@@ -1,4 +1,4 @@
-name: SonarCloud
+name: ☁️ SonarCloud
 on:
   push:
     branches:
diff --git a/.github/workflows/warnings.yml b/.github/workflows/warnings.yml
@@ -1,4 +1,4 @@
-name: warnings
+name: ⚠️ warnings
 
 on:
   push:
diff --git a/src/.clang-tidy b/src/.clang-tidy
@@ -1,5 +1,5 @@
 ---
-Checks:          'clang-diagnostic-*,clang-analyzer-*,*,-fuchsia-*,-llvmlibc-*,-altera-*,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-non-private-member-variables-in-classes,-google-runtime-references,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-bugprone-easily-swappable-parameters,-readability-identifier-length,-cppcoreguidelines-pro-bounds-constant-array-index,-readability-function-cognitive-complexity,-llvm-header-guard,-performance-enum-size,-misc-include-cleaner,-cppcoreguidelines-misleading-capture-default-by-value,-readability-math-missing-parentheses,-misc-use-internal-linkage,-boost-*,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-abseil-*'
+Checks:          'clang-diagnostic-*,clang-analyzer-*,*,-fuchsia-*,-llvmlibc-*,-altera-*,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-non-private-member-variables-in-classes,-google-runtime-references,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-bugprone-easily-swappable-parameters,-readability-identifier-length,-cppcoreguidelines-pro-bounds-constant-array-index,-readability-function-cognitive-complexity,-llvm-header-guard,-performance-enum-size,-misc-include-cleaner,-cppcoreguidelines-misleading-capture-default-by-value,-readability-math-missing-parentheses,-misc-use-internal-linkage,-boost-*,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-abseil-*,-llvm-*'
 WarningsAsErrors: ''
 HeaderFilterRegex: ''
 FormatStyle:     none
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -30,8 +30,11 @@ else()
   set(openPMDSources "")
 endif()
 
-# HDF5
-find_package(HDF5 REQUIRED)
+# HDF5 (use library list instead of imported target to avoid NOTFOUND device-link deps)
+find_package(HDF5 REQUIRED COMPONENTS C)
+if(HDF5_LIBRARIES MATCHES "NOTFOUND")
+  message(FATAL_ERROR "HDF5 libraries were not fully found: ${HDF5_LIBRARIES}")
+endif()
 
 # std::filesystem (required for GCC < 9)
 if (NOT ((CMAKE_SYSTEM_NAME MATCHES "Darwin") AND ((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))))
@@ -115,7 +118,7 @@ endif(WARNINGS_AS_ERRORS)
 
 include_directories(${amrex_INCLUDE_DIRS_RET})
 include_directories(${fmt_INCLUDE_DIRS_RET})
-include_directories(${HDF5_INCLUDE_DIRS_RET})
+include_directories(${HDF5_INCLUDE_DIRS})
 include_directories(${Boost_INCLUDE_DIRS_RET})
 include_directories(${CMAKE_SOURCE_DIR}/src)
 
@@ -128,7 +131,7 @@ include_directories(${gamma_law_dirs} ${CMAKE_CURRENT_BINARY_DIR} "includes/exte
 
 link_libraries(AMReX::amrex)
 link_libraries(fmt::fmt)
-link_libraries(hdf5::hdf5)
+link_libraries(${HDF5_LIBRARIES})
 link_libraries(yaml-cpp::yaml-cpp)
 
 include(CTest)

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: Check Changes`
	`1`	`+name: 🔍 Check Changes`
`2`	`2`
`3`	`3`	`on:`
`4`	`4`	`workflow_call:`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: CheckpointRestartRefine`
	`1`	`+name: 🔄 CheckpointRestartRefine`
`2`	`2`
`3`	`3`	`on:`
`4`	`4`	`push:`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: CheckpointRestart`
	`1`	`+name: 🔄 CheckpointRestart`
`2`	`2`
`3`	`3`	`on:`
`4`	`4`	`push:`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: Post clang-tidy-review comments`
	`1`	`+name: 💬 Post clang-tidy-review comments`
`2`	`2`
`3`	`3`	`on:`
`4`	`4`	`workflow_run:`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: clang-tidy-review`
	`1`	`+name: 🧹 clang-tidy-review`
`2`	`2`
`3`	`3`	`# You can be more specific, but it currently only works on pull requests`
`4`	`4`	`# Fiewer paths are ignored because some folders (e.g. scripts) are not relavent to code build but should be linted`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: Claude Code Review`
	`1`	`+name: 🤖 Claude Code Review`
`2`	`2`
`3`	`3`	`on:`
`4`	`4`	`# Manual trigger`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: Claude Code`
	`1`	`+name: 🤖 Claude Code`
`2`	`2`
`3`	`3`	`on:`
`4`	`4`	`issue_comment:`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: linux-arm64-debug`
	`1`	`+name: 🐛 linux-arm64-debug`
`2`	`2`
`3`	`3`	`on:`
`4`	`4`	`push:`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: linux-arm64-hwasan`
	`1`	`+name: 🛡️ linux-arm64-hwasan`
`2`	`2`
`3`	`3`	`on:`
`4`	`4`	`push:`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: linux-arm64-release`
	`1`	`+name: 🚀 linux-arm64-release`
`2`	`2`
`3`	`3`	`on:`
`4`	`4`	`push:`