Merge pull request #135 from hklion/HSdevmerge_231128

Harris sheet merge to development
RevathiJambunathan · Nov 29, 2023 · f4be661 · f4be661
2 parents 5854ea5 + f11623e
commit f4be661
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diff --git a/.clang-tidy b/.clang-tidy
@@ -1,48 +1,33 @@
-Checks: '-*,
-    bugprone-*
+Checks: '
+    -*,
+    bugprone-*,
         -bugprone-easily-swappable-parameters,
         -bugprone-implicit-widening-of-multiplication-result,
         -bugprone-misplaced-widening-cast,
         -bugprone-unchecked-optional-access,
-    cert-*
+    cert-*,
         -cert-err58-cpp,
-    cppcoreguidelines-avoid-goto,
-    cppcoreguidelines-interfaces-global-init,
+    cppcoreguidelines-*,
+        -cppcoreguidelines-avoid-c-arrays,
+        -cppcoreguidelines-avoid-magic-numbers,
         -cppcoreguidelines-avoid-non-const-global-variables,
         -cppcoreguidelines-init-variables,
         -cppcoreguidelines-macro-usage,
-        -cppcoreguidelines-narrowing-conversions,
         -cppcoreguidelines-no-malloc,
+        -cppcoreguidelines-narrowing-conversions,
+        -cppcoreguidelines-non-private-member-variables-in-classes,
         -cppcoreguidelines-owning-memory,
+        -cppcoreguidelines-pro-*,
     google-build-explicit-make-pair,
     google-build-namespaces,
     google-global-names-in-headers,
-    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,
+    misc-*,
+        -misc-no-recursion,
+        -misc-non-private-member-variables-in-classes,
+    modernize-*,
+        -modernize-avoid-c-arrays,
+        -modernize-return-braced-init-list,
+        -modernize-use-trailing-return-type,
     mpi-*,
     performance-faster-string-find,
     performance-for-range-copy,
@@ -80,7 +65,12 @@ Checks: '-*,
     '
 
 CheckOptions:
+- key:          bugprone-narrowing-conversions.WarnOnIntegerToFloatingPointNarrowingConversion
+  value:        "false"
+- key:          misc-definitions-in-headers.HeaderFileExtensions
+  value:        "H,"
 - key:          modernize-pass-by-value.ValuesOnly
-  value:        'true'
+  value:        "true"
+
 
 HeaderFilterRegex: 'Source[a-z_A-Z0-9\/]+\.H$'
diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
@@ -18,10 +18,6 @@ jobs:
     env:
       CXXFLAGS: "-Werror"
       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
     steps:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
@@ -75,7 +71,8 @@ jobs:
           -DAMReX_CUDA_ERROR_CAPTURE_THIS=ON
         cmake --build build_sp -j 2
 
-        python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade build packaging setuptools wheel
         export WARPX_MPI=ON
         export PYWARPX_LIB_DIR=$PWD/build_sp/lib/site-packages/pywarpx/
         python3 -m pip wheel .
@@ -111,20 +108,16 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach 23.09 && cd -
+        cd ../amrex && git checkout --detach 9e35dc19489dc5d312e92781cb0471d282cf8370 && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_PSATD=TRUE USE_CCACHE=TRUE -j 2
 
   build_nvhpc21-11-nvcc:
     name: [email protected] NVCC/NVC++ Release [tests]
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false
-    env:
-      # For NVHPC, 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
+    #env:
+    #  # For NVHPC, Ninja is slower than the default:
+    #  CMAKE_GENERATOR: Ninja
     steps:
     - uses: actions/checkout@v3
     - name: Dependencies
@@ -175,7 +168,8 @@ jobs:
         #   https://github.com/mpi4py/mpi4py/issues/114
         #export CFLAGS="-noswitcherror"
 
-        #python3 -m pip install --upgrade pip setuptools wheel
+        #python3 -m pip install --upgrade pip
+        #python3 -m pip install --upgrade build packaging setuptools wheel
         #export WARPX_MPI=ON
         #export PYWARPX_LIB_DIR=$PWD/build/lib/site-packages/pywarpx/
         #python3 -m pip wheel .

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
@@ -41,7 +41,8 @@ jobs:
         export CXX=$(which icpc)
         export CC=$(which icc)
 
-        python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade build packaging setuptools wheel
 
         cmake -S . -B build_dp \
           -DCMAKE_VERBOSE_MAKEFILE=ON \
@@ -104,7 +105,7 @@ jobs:
         export CC=$(which icx)
 
         python3 -m pip install --upgrade pip
-        python3 -m pip install --upgrade setuptools wheel
+        python3 -m pip install --upgrade build packaging setuptools wheel
 
         cmake -S . -B build_sp         \
           -DCMAKE_CXX_FLAGS_RELEASE="-O1 -DNDEBUG" \
@@ -178,6 +179,6 @@ jobs:
 
      # Skip this as it will copy the binary artifacts and we are tight on disk space
      #   python3 -m pip install --upgrade pip
-     #   python3 -m pip install --upgrade setuptools wheel
+     #   python3 -m pip install --upgrade build packaging setuptools wheel
      #   PYWARPX_LIB_DIR=$PWD/build_sp/lib/site-packages/pywarpx/ python3 -m pip wheel .
      #   python3 -m pip install *.whl
diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -16,10 +16,6 @@ jobs:
       HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: TRUE
       # 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
     steps:
     - uses: actions/checkout@v3
     - name: Brew Cache
@@ -45,13 +41,22 @@ jobs:
         brew install ccache
         brew install fftw
         brew install libomp
-        brew link --force libomp
+        brew link --overwrite --force libomp
         brew install ninja
         brew install open-mpi
         brew install pkg-config
         set -e
         brew tap openpmd/openpmd
         brew install openpmd-api
+
+        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
+        python3 -m pip install --upgrade mpi4py
     - name: CCache Cache
       uses: actions/cache@v3
       # - once stored under a key, they become immutable (even if local cache path content changes)
@@ -64,8 +69,7 @@ jobs:
           ccache-macos-appleclang-
     - name: build WarpX
       run: |
-        python3 -m pip install --upgrade pip
-        python3 -m pip install --upgrade pip setuptools wheel
+        source py-venv/bin/activate
 
         cmake -S . -B build_dp         \
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
@@ -87,5 +91,7 @@ jobs:
 
     - name: run pywarpx
       run: |
+        source py-venv/bin/activate
         export OMP_NUM_THREADS=1
+
         mpirun -n 2 Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
@@ -167,10 +167,6 @@ jobs:
       CXX: clang++
       # On CI for this test, 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
     steps:
     - uses: actions/checkout@v3
     - name: install dependencies
@@ -190,7 +186,8 @@ jobs:
           ccache-openmp-pyfull-
     - name: build WarpX
       run: |
-        python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade build packaging setuptools wheel
 
         export CXXFLAGS="-Werror -Wno-error=pass-failed"
 

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -41,7 +41,9 @@ jobs:
         cmake --build build --config Debug --parallel 2
         if(!$?) { Exit $LASTEXITCODE }
 
-        python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade pip
+        if(!$?) { Exit $LASTEXITCODE }
+        python3 -m pip install --upgrade build packaging setuptools wheel
         if(!$?) { Exit $LASTEXITCODE }
         cmake --build build --config Debug --target install
         if(!$?) { Exit $LASTEXITCODE }
@@ -64,7 +66,7 @@ jobs:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
       with:
-        python-version: '3.x'
+        python-version: '3.8'
     - uses: seanmiddleditch/gha-setup-ninja@master
     - name: CCache Cache
       uses: actions/cache@v3
@@ -100,7 +102,9 @@ jobs:
         cmake --build build --config Release --target install
         if errorlevel 1 exit 1
 
-        python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade pip
+        if errorlevel 1 exit 1
+        python3 -m pip install --upgrade build packaging setuptools wheel
         if errorlevel 1 exit 1
         python3 -m pip install --upgrade -r requirements.txt
         if errorlevel 1 exit 1

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -18,7 +18,7 @@ exclude: '^share/openPMD/thirdParty'
 # 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]
@@ -68,7 +68,7 @@ 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)