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eschnetteschnett
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Merge branch 'dev' into eschnett/julia-bindings
* dev: (82 commits) Docs: Linking to C++ Projects (openPMD#1445) CI: macOS-11 Update (openPMD#1446) [pre-commit.ci] pre-commit autoupdate (openPMD#1437) Fix deprecated storeChunk APIs in first read/write examples (openPMD#1435) Update .readthedocs.yml (openPMD#1438) Doc: Fix Bib Authors (openPMD#1434) [pre-commit.ci] pre-commit autoupdate (openPMD#1425) More careful documentation of streaming API (openPMD#1430) Fix gcc9 warning (openPMD#1429) Python bindings: Release GIL during IO wait operations (openPMD#1381) RecordComponent: Properly handle uninitialized datasets (openPMD#1316) Remove ADIOS1 - Long Live ADIOS2 (openPMD#1419) Post 0.15.0 Changelog Template (openPMD#1420) GitHub Actions: macOS has 3 Cores (openPMD#1421) `version.hpp`: 0.15.1 (openPMD#1417) [pre-commit.ci] pre-commit autoupdate (openPMD#1416) Release 0.15.1 (openPMD#1414) Doc: More HTML Updates (CSS) (openPMD#1413) Enable clang-format also for .tpp files by using a regex instead of a predefined filter (openPMD#1403) Docs: Update Funding (openPMD#1412) ... # Conflicts: # .github/workflows/linux.yml # CMakeLists.txt
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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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- machine: [Are you running on a public cluster? It's likely we compute on it as well!]
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- name and version of Python implementation: [e.g. CPython 3.9]
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- version of HDF5: [e.g. 1.12.0]
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- version of ADIOS1: [e.g. 1.13.1]
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- version of ADIOS2: [e.g. 2.7.1]
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- name and version of MPI: [e.g. OpenMPI 4.1.1]
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‎.github/ci/sanitizer/clang/Leak.supp‎

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leak:*py*
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# 10 byte memleak in main of "make" 4.1
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leak:/usr/bin/make*
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# ADIOS 1.13.1
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leak:adios_read_bp_open_file
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leak:adios_inq_var
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# ADIOS2
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leak:adios2::core::engine::SstReader::*
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leak:adios2::core::engine::SstWriter::*

.github/ci/spack-envs/clang14_py311_nompi_h5_ad1_ad2/spack.yaml renamed to .github/ci/spack-envs/clang14_py311_nompi_h5_ad2/spack.yaml

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#
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spack:
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specs:
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- adios2
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- hdf5
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packages:
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hdf5:
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variants: ~mpi
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adios:
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variants: ~mpi ~zfp ~sz ~lz4 ~blosc
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adios2:
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variants: ~mpi ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
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cmake:

.github/ci/spack-envs/clang6_nopy_nompi_h5_libcpp/spack.yaml renamed to .github/ci/spack-envs/clang7_nopy_nompi_h5_libcpp/spack.yaml

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all:
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target: [x86_64]
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variants: ~mpi ~fortran
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compiler: [clang@6.0.0]
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compiler: [clang@7.0.1]
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compilers:
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- compiler:
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cxxflags: -stdlib=libc++
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ldflags: -stdlib=libc++
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modules: []
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operating_system: ubuntu18.04
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operating_system: ubuntu20.04
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paths:
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cc: /usr/lib/llvm-6.0/bin/clang
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cxx: /usr/lib/llvm-6.0/bin/clang++
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cc: /usr/bin/clang-7
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cxx: /usr/bin/clang++-7
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f77: null
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fc: null
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spec: clang@6.0.0
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spec: clang@7.0.1
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target: x86_64
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config:

.github/ci/spack-envs/clang7_nopy_ompi_h5_ad1_ad2/spack.yaml renamed to .github/ci/spack-envs/clang7_nopy_ompi_h5_ad2/spack.yaml

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specs:
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- hdf5
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- openmpi
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packages:
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adios:
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variants: ~zfp ~sz ~lz4 ~blosc
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adios2:
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variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
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cmake:

.github/ci/spack-envs/clang6_nopy_ompi_h5_ad1_ad2_bp3_libcpp/spack.yaml renamed to .github/ci/spack-envs/clang7_nopy_ompi_h5_ad2_libcpp/spack.yaml

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specs:
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packages:
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adios2:
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variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
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cmake:
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variants: ~fortran
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providers:
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mpi: [openmpi]
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compiler: [clang@6.0.0]
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compiler: [clang@7.0.1]
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cxxflags: -stdlib=libc++
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modules: []
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operating_system: ubuntu18.04
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operating_system: ubuntu20.04
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paths:
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cc: /usr/lib/llvm-6.0/bin/clang
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cxx: /usr/lib/llvm-6.0/bin/clang++
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cc: /usr/bin/clang-7
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cxx: /usr/bin/clang++-7
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spec: clang@6.0.0
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spec: clang@7.0.1
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.github/ci/spack-envs/clang8_py38_mpich_h5_ad1_ad2/spack.yaml renamed to .github/ci/spack-envs/clang8_py38_mpich_h5_ad2/spack.yaml

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- [email protected]
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- mpich
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variants: ~zfp ~sz ~lz4 ~blosc
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adios2:
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variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
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.github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad1_ad2/spack.yaml renamed to .github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad2/spack.yaml

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- adios2
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- hdf5
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- openmpi
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packages:
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adios:
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variants: ~zfp ~sz ~lz4 ~blosc
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adios2:
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variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
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cmake:

.github/ci/spack-envs/gcc7_py36_ompi_h5_ad1_ad2/spack.yaml renamed to .github/ci/spack-envs/gcc7_py36_ompi_h5_ad2/spack.yaml

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- hdf5
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- openmpi
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adios:
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variants: ~zfp ~sz ~lz4 ~blosc
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adios2:
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variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
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cmake:
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extra_rpaths: []
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flags: {}
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modules: []
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operating_system: ubuntu18.04
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operating_system: ubuntu20.04
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‎.github/workflows/codeql.yml‎

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name: 🔍 CodeQL
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on:
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push:
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branches: [ "dev" ]
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pull_request:
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branches: [ "dev" ]
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schedule:
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- cron: "14 6 * * 6"
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concurrency:
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group: ${{ github.ref }}-${{ github.head_ref }}-codeql
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cancel-in-progress: true
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jobs:
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analyze:
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name: Analyze
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runs-on: ubuntu-latest
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permissions:
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actions: read
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contents: read
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security-events: write
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strategy:
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fail-fast: false
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matrix:
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language: [ python, cpp ]
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Install Packages
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run: |
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sudo apt-get update
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sudo apt-get install --yes cmake openmpi-bin libopenmpi-dev libhdf5-openmpi-dev
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python -m pip install --upgrade pip
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python -m pip install --upgrade wheel
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python -m pip install --upgrade cmake
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export CMAKE="$HOME/.local/bin/cmake" && echo "CMAKE=$CMAKE" >> $GITHUB_ENV
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python -m pip install --upgrade numpy
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python -m pip install --upgrade mpi4py
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python -m pip install --upgrade pytest
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- name: Configure (C++)
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if: ${{ matrix.language == 'cpp' }}
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run: $CMAKE -S . -B build
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- name: Initialize CodeQL
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uses: github/codeql-action/init@v2
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with:
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languages: ${{ matrix.language }}
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queries: +security-and-quality
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- name: Build (Py)
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uses: github/codeql-action/autobuild@v2
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if: ${{ matrix.language == 'python' }}
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- name: Build (C++)
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if: ${{ matrix.language == 'cpp' }}
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run: $CMAKE --build build -j 2
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- name: Perform CodeQL Analysis
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uses: github/codeql-action/analyze@v2
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with:
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category: "/language:${{ matrix.language }}"

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