Merge branch 'development' into add_IPAC_3DSC_benchmarks

.clang-tidy

@@ -1,6 +1,85 @@
-# Future consideration: cppcoreguidelines-*,clang-analyzer-*,google-*,hicpp-*,llvm-*,misc-*,readability-*,-clang-diagnostic-unused-command-line-argument,-*-namespace-comment*,-*-braces-around-statements,-google-readability-todo,-readability-inconsistent-declaration-parameter-name,-readability-named-parameter
-# FIXME: all performance-* reports
-# FIXME: all cert-* reports
-# FIXME: all bugprone-* reports
-Checks: -*,bugprone-*,-bugprone-unhandled-self-assignment,-bugprone-parent-virtual-call,-bugprone-narrowing-conversions,-bugprone-exception-escape,-bugprone-string-literal-with-embedded-nul,cppcoreguidelines-slicing,mpi-*,readability-non-const-parameter,performance-for-range-copy,modernize-*,-modernize-use-trailing-return-type,-modernize-use-bool-literals,-modernize-avoid-c-arrays,-modernize-use-auto,-modernize-return-braced-init-list
-HeaderFilterRegex: '((^(?!\/fetchedamrex-src\/).*)$)'
+Checks: '-*,
+    bugprone-*
+        -bugprone-easily-swappable-parameters,
+        -bugprone-implicit-widening-of-multiplication-result,
+        -bugprone-misplaced-widening-cast,
+        -bugprone-unchecked-optional-access,
+    cert-*
+        -cert-err58-cpp,
+    cppcoreguidelines-avoid-goto,
+    cppcoreguidelines-interfaces-global-init,
+        -cppcoreguidelines-avoid-non-const-global-variables,
+        -cppcoreguidelines-init-variables,
+        -cppcoreguidelines-macro-usage,
+        -cppcoreguidelines-narrowing-conversions,
+        -cppcoreguidelines-no-malloc,
+        -cppcoreguidelines-owning-memory,
+    misc-const-correctness,
+    misc-misleading-bidirectional,
+    misc-misleading-identifier,
+    misc-misplaced-const,
+    misc-uniqueptr-reset-release,
+    misc-unused-alias-decls,
+    misc-unused-parameters,
+    misc-unused-using-decls,
+        -misc-definitions-in-headers,
+    modernize-avoid-bind,
+    modernize-concat-nested-namespaces,
+    modernize-deprecated-headers,
+    modernize-deprecated-ios-base-aliases,
+    modernize-loop-convert,
+    modernize-make-shared,
+    modernize-make-unique,
+    modernize-pass-by-value,
+    modernize-raw-string-literal,
+    modernize-redundant-void-arg,
+    modernize-replace-auto-ptr,
+    modernize-replace-disallow-copy-and-assign-macro,
+    modernize-replace-random-shuffle,
+    modernize-return-braced-init-list,
+    modernize-shrink-to-fit,
+    modernize-unary-static-assert,
+    modernize-use-nullptr,
+    mpi-*,
+    performance-faster-string-find,
+    performance-for-range-copy,
+    performance-implicit-conversion-in-loop,
+    performance-inefficient-algorithm,
+    performance-inefficient-string-concatenation,
+    performance-inefficient-vector-operation,
+    performance-move-const-arg,
+    performance-move-constructor-init,
+    performance-no-automatic-move,
+    performance-no-int-to-ptr,
+    performance-unnecessary-copy-initialization,
+    performance-unnecessary-value-param,
+    readability-avoid-const-params-in-decls,
+    readability-const-return-type,
+    readability-container-contains,
+    readability-container-data-pointer,
+    readability-container-size-empty,
+    readability-non-const-parameter,
+    readability-redundant-control-flow,
+    readability-redundant-declaration,
+    readability-redundant-function-ptr-dereference,
+    readability-redundant-member-init,
+    readability-redundant-preprocessor,
+    readability-redundant-smartptr-get,
+    readability-redundant-string-cstr,
+    readability-redundant-string-init,
+    readability-simplify-boolean-expr,
+    readability-simplify-subscript-expr,
+    readability-static-accessed-through-instance,
+    readability-static-definition-in-anonymous-namespace,
+    readability-string-compare,
+    readability-suspicious-call-argument,
+    readability-uniqueptr-delete-release,
+    readability-use-anyofallof,
+        -readability-uppercase-literal-suffix
+    '
+
+CheckOptions:
+- key:          modernize-pass-by-value.ValuesOnly
+  value:        'true'
+
+HeaderFilterRegex: 'src[a-z_A-Z0-9\/]+\.H$'

.github/workflows/dependencies/clang-san-openmpi.sh

@@ -26,10 +26,11 @@ sudo apt-get install -y \
     python3-pip         \
     wget
 
-python3 -m pip install -U pip setuptools wheel
+python3 -m pip install -U pip
+python3 -m pip install -U build packaging setuptools wheel
 python3 -m pip install -U cmake pytest
-python3 -m pip install -r requirements_mpi.txt
-python3 -m pip install -r examples/requirements.txt
+python3 -m pip install -U -r requirements_mpi.txt
+python3 -m pip install -U -r examples/requirements.txt
 
 # cmake-easyinstall
 #

.github/workflows/dependencies/clang-tidy.sh

@@ -25,10 +25,11 @@ sudo apt-get install -y \
     python3-pip         \
     wget
 
-python3 -m pip install -U pip setuptools wheel
+python3 -m pip install -U pip
+python3 -m pip install -U build packaging setuptools wheel
 python3 -m pip install -U cmake pytest
-python3 -m pip install -r requirements_mpi.txt
-python3 -m pip install -r examples/requirements.txt
+python3 -m pip install -U -r requirements_mpi.txt
+python3 -m pip install -U -r examples/requirements.txt
 
 # cmake-easyinstall
 #

.github/workflows/dependencies/gcc-openmpi.sh

@@ -22,9 +22,10 @@ sudo apt-get install -y \
     python3-pip         \
     wget
 
-python3 -m pip install -U pip setuptools wheel
+python3 -m pip install -U pip
+python3 -m pip install -U build packaging setuptools wheel
 python3 -m pip install -U cmake pytest
-python3 -m pip install -r requirements_mpi.txt
-python3 -m pip install -r examples/requirements.txt
+python3 -m pip install -U -r requirements_mpi.txt
+python3 -m pip install -U -r examples/requirements.txt
 
 python3 -m pip install -U openPMD-validator

.github/workflows/dependencies/gcc.sh

@@ -21,8 +21,9 @@ sudo apt-get install -y \
     python3-pip         \
     wget
 
-python3 -m pip install -U pip setuptools wheel
+python3 -m pip install -U pip
+python3 -m pip install -U build packaging setuptools wheel
 python3 -m pip install -U cmake pytest
-python3 -m pip install -r examples/requirements.txt
+python3 -m pip install -U -r examples/requirements.txt
 
 python3 -m pip install -U openPMD-validator

.github/workflows/macos.yml

@@ -13,12 +13,7 @@ jobs:
     if: github.event.pull_request.draft == false
     env:
       CXXFLAGS: "-Werror -Wno-error=pass-failed"
-      # For macOS, Ninja is slower than the default:
-      #CMAKE_GENERATOR: Ninja
-      # setuptools/mp4py work-around, see
-      #   https://github.com/mpi4py/mpi4py/pull/159
-      #   https://github.com/mpi4py/mpi4py/issues/157#issuecomment-1001022274
-      SETUPTOOLS_USE_DISTUTILS: stdlib
+      HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: TRUE
     steps:
     - uses: actions/checkout@v3
     - name: Brew Cache
@@ -46,14 +41,21 @@ jobs:
         brew install cmake
         brew install hdf5-mpi
         brew install libomp
-        brew link --force libomp
+        brew link --overwrite --force libomp
         brew install ninja
         brew install open-mpi
         brew install pkg-config
-        python3 -m pip install --upgrade pip setuptools wheel pytest
+
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade virtualenv
+
+        python3 -m venv py-venv
+        source py-venv/bin/activate
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade build packaging setuptools wheel pytest
         python3 -m pip install --upgrade pytest
-        python3 -m pip install -r requirements_mpi.txt
-        python3 -m pip install -r examples/requirements.txt
+        python3 -m pip install --upgrade -r requirements_mpi.txt
+        python3 -m pip install --upgrade -r examples/requirements.txt
         python3 -m pip install --upgrade openPMD-validator
         set -e
     - name: CCache Cache
@@ -68,6 +70,8 @@ jobs:
           ccache-macos-appleclang-
     - name: build ImpactX
       run: |
+        source py-venv/bin/activate
+
         cmake -S . -B build            \
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
           -DImpactX_PYTHON=ON          \
@@ -76,12 +80,15 @@ jobs:
 
     - name: run tests
       run: |
+        source py-venv/bin/activate
+
         ctest --test-dir build --output-on-failure -E pytest.AMReX
 
     - name: run installed python module
       run: |
         cmake --build build --target pip_install
 
+        source py-venv/bin/activate
         python3 examples/fodo/run_fodo.py
 
     - name: run installed app

.github/workflows/windows.yml

@@ -52,9 +52,10 @@ jobs:
         $env:HDF5_DIR = "C:/Program Files/HDF_Group/HDF5/1.12.2/cmake/"
         $env:HDF5_USE_STATIC_LIBRARIES = "ON"
 
-        python3 -m pip install -U pip setuptools wheel pytest
-        python3 -m pip install -r requirements.txt
-        python3 -m pip install -r examples/requirements.txt
+        python3 -m pip install -U pip
+        python3 -m pip install -U build packaging setuptools wheel pytest
+        python3 -m pip install -U -r requirements.txt
+        python3 -m pip install -U -r examples/requirements.txt
         python3 -m pip install -U openPMD-validator
     - name: Build
       run: |
@@ -137,9 +138,10 @@ jobs:
         set "HDF5_DIR=C:/Program Files/HDF_Group/HDF5/1.12.2/cmake/"
         set "HDF5_USE_STATIC_LIBRARIES=ON"
 
-        python3 -m pip install -U pip setuptools wheel pytest
-        python3 -m pip install -r requirements.txt
-        python3 -m pip install -r examples/requirements.txt
+        python3 -m pip install -U pip
+        python3 -m pip install -U build packaging setuptools wheel pytest
+        python3 -m pip install -U -r requirements.txt
+        python3 -m pip install -U -r examples/requirements.txt
         python3 -m pip install -U openPMD-validator
     - name: Build
       shell: cmd

.pre-commit-config.yaml

@@ -15,7 +15,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     - id: trailing-whitespace
       args: [--markdown-linebreak-ext=md]
@@ -65,7 +65,7 @@ repos:
 
 # Autoremoves unused Python imports
 - repo: https://github.com/hadialqattan/pycln
-  rev: v2.2.2
+  rev: v2.4.0
   hooks:
   - id: pycln
     name: pycln (python)
@@ -91,15 +91,15 @@ repos:
 
 # Python Formatting
 - repo: https://github.com/psf/black
-  rev: 23.7.0 # Keep in sync with blacken-docs
+  rev: 23.11.0 # Keep in sync with blacken-docs
   hooks:
   - id: black
 - repo: https://github.com/asottile/blacken-docs
   rev: 1.16.0
   hooks:
   - id: blacken-docs
     additional_dependencies:
-    - black==23.7.0 # keep in sync with black hook
+    - black==23.11.0 # keep in sync with black hook
   # TODO: black-jupyter
 
 # Jupyter Notebooks: clean up all cell outputs

CMakeLists.txt

@@ -1,7 +1,7 @@
 # Preamble ####################################################################
 #
 cmake_minimum_required(VERSION 3.20.0)
-project(ImpactX VERSION 23.08)
+project(ImpactX VERSION 23.11)
 
 include(${ImpactX_SOURCE_DIR}/cmake/ImpactXFunctions.cmake)
 
@@ -81,7 +81,7 @@ option(ImpactX_openpmd_internal                  "Download & build openPMD-api"
 option(ImpactX_pyamrex_internal                  "Download & build pyAMReX" ON)
 
 set(pyImpactX_VERSION_INFO "" CACHE STRING
-    "PEP-440 conformant version (set by distutils)")
+    "PEP-440 conformant version (set by setup.py)")
 
 # change the default build type to Release (or RelWithDebInfo) instead of Debug
 set_default_build_type("Release")
@@ -407,6 +407,17 @@ if(ImpactX_PYTHON)
             ${ImpactX_CUSTOM_TARGET_PREFIX}pip_wheel ${ImpactX_CUSTOM_TARGET_PREFIX}pip_install_requirements
             ${_EXTRA_INSTALL_DEPENDS}
     )
+
+    # this is for package managers only
+    add_custom_target(${ImpactX_CUSTOM_TARGET_PREFIX}pip_install_nodeps
+        ${CMAKE_COMMAND} -E env IMPACTX_MPI=${ImpactX_MPI}
+            ${Python_EXECUTABLE} -m pip install --force-reinstall --no-index --no-deps ${PYINSTALLOPTIONS} --find-links=impactx-whl impactx
+        WORKING_DIRECTORY
+            ${ImpactX_BINARY_DIR}
+        DEPENDS
+            pyImpactX
+            ${ImpactX_CUSTOM_TARGET_PREFIX}pip_wheel
+    )
 endif()