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
eschnett · May 19, 2023 · 9c97be2 · 9c97be2
2 parents e31818f + 4423be4
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -43,7 +43,6 @@ A clear and concise description of what you expected to happen.
  - machine: [Are you running on a public cluster? It's likely we compute on it as well!]
  - name and version of Python implementation: [e.g. CPython 3.9]
  - version of HDF5: [e.g. 1.12.0]
- - version of ADIOS1: [e.g. 1.13.1]
  - version of ADIOS2: [e.g. 2.7.1]
  - name and version of MPI: [e.g. OpenMPI 4.1.1]
 

diff --git a/.github/ci/sanitizer/clang/Leak.supp b/.github/ci/sanitizer/clang/Leak.supp
@@ -9,9 +9,6 @@ leak:libevent*
 leak:*py*
 # 10 byte memleak in main of "make" 4.1
 leak:/usr/bin/make*
-# ADIOS 1.13.1
-leak:adios_read_bp_open_file
-leak:adios_inq_var
 # ADIOS2
 leak:adios2::core::engine::SstReader::*
 leak:adios2::core::engine::SstWriter::*

diff --git a/...clang14_py311_nompi_h5_ad1_ad2/spack.yaml → ...nvs/clang14_py311_nompi_h5_ad2/spack.yaml b/...clang14_py311_nompi_h5_ad1_ad2/spack.yaml → ...nvs/clang14_py311_nompi_h5_ad2/spack.yaml
@@ -6,15 +6,12 @@
 #
 spack:
   specs:
-  - adios
   - adios2
   - hdf5
 
   packages:
     hdf5:
       variants: ~mpi
-    adios:
-      variants: ~mpi ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~mpi ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:

diff --git a/...vs/clang6_nopy_nompi_h5_libcpp/spack.yaml → ...vs/clang7_nopy_nompi_h5_libcpp/spack.yaml b/...vs/clang6_nopy_nompi_h5_libcpp/spack.yaml → ...vs/clang7_nopy_nompi_h5_libcpp/spack.yaml
@@ -12,7 +12,7 @@ spack:
     all:
       target: [x86_64]
       variants: ~mpi ~fortran
-      compiler: [clang@6.0.0]
+      compiler: [clang@7.0.1]
 
   compilers:
   - compiler:
@@ -22,13 +22,13 @@ spack:
         cxxflags: -stdlib=libc++
         ldflags: -stdlib=libc++
       modules: []
-      operating_system: ubuntu18.04
+      operating_system: ubuntu20.04
       paths:
-        cc: /usr/lib/llvm-6.0/bin/clang
-        cxx: /usr/lib/llvm-6.0/bin/clang++
+        cc: /usr/bin/clang-7
+        cxx: /usr/bin/clang++-7
         f77: null
         fc: null
-      spec: clang@6.0.0
+      spec: clang@7.0.1
       target: x86_64
 
   config:

diff --git a/...vs/clang7_nopy_ompi_h5_ad1_ad2/spack.yaml → ...k-envs/clang7_nopy_ompi_h5_ad2/spack.yaml b/...vs/clang7_nopy_ompi_h5_ad1_ad2/spack.yaml → ...k-envs/clang7_nopy_ompi_h5_ad2/spack.yaml
@@ -6,14 +6,11 @@
 #
 spack:
   specs:
-  - adios
   - adios2
   - hdf5
   - openmpi
 
   packages:
-    adios:
-      variants: ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:

diff --git a/...opy_ompi_h5_ad1_ad2_bp3_libcpp/spack.yaml → ...clang7_nopy_ompi_h5_ad2_libcpp/spack.yaml b/...opy_ompi_h5_ad1_ad2_bp3_libcpp/spack.yaml → ...clang7_nopy_ompi_h5_ad2_libcpp/spack.yaml
@@ -6,14 +6,11 @@
 #
 spack:
   specs:
-  - adios
   - adios2
   - hdf5
   - openmpi
 
   packages:
-    adios:
-      variants: ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
@@ -41,7 +38,7 @@ spack:
       variants: ~fortran
       providers:
         mpi: [openmpi]
-      compiler: [clang@6.0.0]
+      compiler: [clang@7.0.1]
 
   compilers:
   - compiler:
@@ -51,13 +48,13 @@ spack:
         cxxflags: -stdlib=libc++
         ldflags: -stdlib=libc++
       modules: []
-      operating_system: ubuntu18.04
+      operating_system: ubuntu20.04
       paths:
-        cc: /usr/lib/llvm-6.0/bin/clang
-        cxx: /usr/lib/llvm-6.0/bin/clang++
+        cc: /usr/bin/clang-7
+        cxx: /usr/bin/clang++-7
         f77: /usr/bin/gfortran
         fc: /usr/bin/gfortran
-      spec: clang@6.0.0
+      spec: clang@7.0.1
       target: x86_64
 
   config:

diff --git a/...s/clang8_py38_mpich_h5_ad1_ad2/spack.yaml → ...-envs/clang8_py38_mpich_h5_ad2/spack.yaml b/...s/clang8_py38_mpich_h5_ad1_ad2/spack.yaml → ...-envs/clang8_py38_mpich_h5_ad2/spack.yaml
@@ -6,14 +6,11 @@
 #
 spack:
   specs:
-  - adios
   - [email protected]
   - hdf5
   - mpich
 
   packages:
-    adios:
-      variants: ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:

diff --git a/...clangtidy_nopy_ompi_h5_ad1_ad2/spack.yaml → ...nvs/clangtidy_nopy_ompi_h5_ad2/spack.yaml b/...clangtidy_nopy_ompi_h5_ad1_ad2/spack.yaml → ...nvs/clangtidy_nopy_ompi_h5_ad2/spack.yaml
@@ -6,14 +6,11 @@
 #
 spack:
   specs:
-  - adios
   - adios2
   - hdf5
   - openmpi
 
   packages:
-    adios:
-      variants: ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:

diff --git a/...envs/gcc7_py36_ompi_h5_ad1_ad2/spack.yaml → ...ack-envs/gcc7_py36_ompi_h5_ad2/spack.yaml b/...envs/gcc7_py36_ompi_h5_ad1_ad2/spack.yaml → ...ack-envs/gcc7_py36_ompi_h5_ad2/spack.yaml
@@ -6,14 +6,11 @@
 #
 spack:
   specs:
-  - adios
   - adios2
   - hdf5
   - openmpi
 
   packages:
-    adios:
-      variants: ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
@@ -47,7 +44,7 @@ spack:
       extra_rpaths: []
       flags: {}
       modules: []
-      operating_system: ubuntu18.04
+      operating_system: ubuntu20.04
       paths:
         cc: /usr/bin/gcc-7
         cxx: /usr/bin/g++-7

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -0,0 +1,67 @@
+name: 🔍 CodeQL
+
+on:
+  push:
+    branches: [ "dev" ]
+  pull_request:
+    branches: [ "dev" ]
+  schedule:
+    - cron: "14 6 * * 6"
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-codeql
+  cancel-in-progress: true
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ python, cpp ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Install Packages
+        run: |
+          sudo apt-get update
+          sudo apt-get install --yes cmake openmpi-bin libopenmpi-dev libhdf5-openmpi-dev
+
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade wheel
+          python -m pip install --upgrade cmake
+          export CMAKE="$HOME/.local/bin/cmake" && echo "CMAKE=$CMAKE" >> $GITHUB_ENV
+          python -m pip install --upgrade numpy
+          python -m pip install --upgrade mpi4py
+          python -m pip install --upgrade pytest
+
+      - name: Configure (C++)
+        if: ${{ matrix.language == 'cpp' }}
+        run: $CMAKE -S . -B build
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+
+      - name: Build (Py)
+        uses: github/codeql-action/autobuild@v2
+        if: ${{ matrix.language == 'python' }}
+
+      - name: Build (C++)
+        if: ${{ matrix.language == 'cpp' }}
+        run: $CMAKE --build build -j 2
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:${{ matrix.language }}"
diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Install
       run: |
         sudo .github/workflows/dependencies/install_icc
@@ -39,7 +39,7 @@ jobs:
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Install
       run: |
         sudo .github/workflows/dependencies/install_icx