Merge branch 'dev' into eschnett/julia-bindings

* dev: (70 commits) Docs: Recommend Static Build for Superbuilds (openPMD#1325) Python 3.11 (openPMD#1323) pybind11: v2.10.1+ (openPMD#1322) Add Attribute::getOptional<T>() and use to add some more dynamic datatype conversions at read time (openPMD#1278) Mapping between ADIOS steps and openPMD iterations (openPMD#949) Deprecate shareRaw (openPMD#1229) Fix append mode double attributes (openPMD#1302) Constant scalars: Don't flush double (openPMD#1315) Remove caching cmake vars (openPMD#1313) [pre-commit.ci] pre-commit autoupdate (openPMD#1311) storeChunk: Add an overload for shared_ptr<T[]> (openPMD#1296) Fix `operationAsString` Export (openPMD#1309) ADIOS2: more fine-grained control for file endings (openPMD#1218) [pre-commit.ci] pre-commit autoupdate (openPMD#1307) Fix file existence check in parallel tests (openPMD#1303) ADIOS2: Flush to disk within a step (openPMD#1207) [pre-commit.ci] pre-commit autoupdate (openPMD#1304) [pre-commit.ci] pre-commit autoupdate (openPMD#1295) Update catch2 to v2.13.9 (openPMD#1299) [pre-commit.ci] pre-commit autoupdate (openPMD#1292) ... # Conflicts: # .github/workflows/linux.yml
eschnett · Nov 11, 2022 · e6a18e7 · e6a18e7
2 parents 84bce33 + 97890ee
commit e6a18e7
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Showing 213 changed files with 16,159 additions and 7,197 deletions.
diff --git a/.clang-format b/.clang-format
@@ -1,3 +1,4 @@
+---
 Language:  Cpp
 
 BasedOnStyle:  LLVM
@@ -64,3 +65,8 @@ SpacesInParentheses: false
 SpacesInSquareBrackets: false
 Standard: Auto
 StatementMacros: ["OPENPMD_private", "OPENPMD_protected"]
+
+---
+Language: Json
+BasedOnStyle: llvm
+...
diff --git a/.github/ci/sanitizer/clang/Leak.supp b/.github/ci/sanitizer/clang/Leak.supp
@@ -15,3 +15,4 @@ leak:adios_inq_var
 # ADIOS2
 leak:adios2::core::engine::SstReader::*
 leak:adios2::core::engine::SstWriter::*
+leak:ps_make_timer_name_
diff --git a/.../clang12_py38_nompi_h5_ad1_ad2/spack.yaml → ...clang14_py311_nompi_h5_ad1_ad2/spack.yaml b/.../clang12_py38_nompi_h5_ad1_ad2/spack.yaml → ...clang14_py311_nompi_h5_ad1_ad2/spack.yaml
@@ -19,40 +19,43 @@ spack:
       variants: ~mpi ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
       externals:
-      - spec: "cmake"
+      - spec: cmake@3.22.1
         prefix: /usr
       buildable: False
     perl:
       externals:
-      - spec: "perl"
+      - spec: perl@5.34.0
         prefix: /usr
       buildable: False
     python:
       externals:
-      - spec: "python"
+      - spec: python@3.11.0
         prefix: /usr
       buildable: False
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~fortran
       providers:
         mpi: [openmpi]
-      compiler: [clang@12.0.0]
+      compiler: [clang@14.0.0]
 
   compilers:
   - compiler:
       environment: {}
       extra_rpaths: []
       flags: {}
       modules: []
-      operating_system: ubuntu20.04
+      operating_system: ubuntu22.04
       paths:
-        cc: /usr/lib/llvm-12/bin/clang
-        cxx: /usr/lib/llvm-12/bin/clang++
+        cc: /usr/lib/llvm-14/bin/clang
+        cxx: /usr/lib/llvm-14/bin/clang++
         f77: /usr/bin/gfortran
         fc: /usr/bin/gfortran
-      spec: clang@12.0.0
+      spec: clang@14.0.0
       target: x86_64
 
   config:
     build_jobs: 2
+
+  mirrors:
+    E4S: https://cache.e4s.io
diff --git a/.github/ci/spack-envs/clang6_nopy_nompi_h5_libcpp/spack.yaml b/.github/ci/spack-envs/clang6_nopy_nompi_h5_libcpp/spack.yaml
@@ -10,7 +10,7 @@ spack:
 
   packages:
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~mpi ~fortran
       compiler: [[email protected]]
 
@@ -33,3 +33,6 @@ spack:
 
   config:
     build_jobs: 2
+
+  mirrors:
+    E4S: https://cache.e4s.io
diff --git a/.github/ci/spack-envs/clang6_nopy_ompi_h5_ad1_ad2_bp3_libcpp/spack.yaml b/.github/ci/spack-envs/clang6_nopy_ompi_h5_ad1_ad2_bp3_libcpp/spack.yaml
@@ -18,26 +18,26 @@ spack:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
       externals:
-      - spec: "cmake"
+      - spec: cmake@3.23.0
         prefix: /usr
       buildable: False
     openmpi:
       externals:
-      - spec: "openmpi"
+      - spec: openmpi@2.1.1
         prefix: /usr
       buildable: False
     perl:
       externals:
-      - spec: "perl"
+      - spec: perl@5.26.1
         prefix: /usr
       buildable: False
     python:
       externals:
-      - spec: "python"
+      - spec: python@3.8.0
         prefix: /usr
       buildable: False
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~fortran
       providers:
         mpi: [openmpi]
@@ -62,3 +62,6 @@ spack:
 
   config:
     build_jobs: 2
+
+  mirrors:
+    E4S: https://cache.e4s.io
diff --git a/.github/ci/spack-envs/clang7_nopy_ompi_h5_ad1_ad2/spack.yaml b/.github/ci/spack-envs/clang7_nopy_ompi_h5_ad1_ad2/spack.yaml
@@ -18,26 +18,26 @@ spack:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
       externals:
-      - spec: "cmake"
+      - spec: cmake@3.23.0
         prefix: /usr
       buildable: False
     openmpi:
       externals:
-      - spec: "openmpi"
+      - spec: openmpi@2.1.1
         prefix: /usr
       buildable: False
     perl:
       externals:
-      - spec: "perl"
+      - spec: perl@5.26.1
         prefix: /usr
       buildable: False
     python:
       externals:
-      - spec: "python"
+      - spec: python@3.8.0
         prefix: /usr
       buildable: False
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~fortran
       providers:
         mpi: [openmpi]
@@ -60,3 +60,6 @@ spack:
 
   config:
     build_jobs: 2
+
+  mirrors:
+    E4S: https://cache.e4s.io
diff --git a/.github/ci/spack-envs/clang8_py38_mpich_h5_ad1_ad2/spack.yaml b/.github/ci/spack-envs/clang8_py38_mpich_h5_ad1_ad2/spack.yaml
@@ -7,7 +7,7 @@
 spack:
   specs:
   - adios
-  - adios2
+  - adios2@2.7.1
   - hdf5
   - mpich
 
@@ -18,26 +18,26 @@ spack:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
       externals:
-      - spec: "cmake"
+      - spec: cmake@3.23.0
         prefix: /usr
       buildable: False
     mpich:
       externals:
-      - spec: "mpich"
+      - spec: mpich@3.3
         prefix: /usr
       buildable: False
     perl:
       externals:
-      - spec: "perl"
+      - spec: perl@5.26.1
         prefix: /usr
       buildable: False
     python:
       externals:
-      - spec: "python"
+      - spec: python@3.8.0
         prefix: /usr
       buildable: False
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~fortran
       providers:
         mpi: [mpich]
@@ -60,3 +60,6 @@ spack:
 
   config:
     build_jobs: 2
+
+  mirrors:
+    E4S: https://cache.e4s.io
diff --git a/.github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad1_ad2/spack.yaml b/.github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad1_ad2/spack.yaml
@@ -18,26 +18,26 @@ spack:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
       externals:
-      - spec: "cmake"
+      - spec: cmake@3.23.0
         prefix: /usr
       buildable: False
     openmpi:
       externals:
-      - spec: "openmpi"
+      - spec: openmpi@2.1.1
         prefix: /usr
       buildable: False
     perl:
       externals:
-      - spec: "perl"
+      - spec: perl@5.26.1
         prefix: /usr
       buildable: False
     python:
       externals:
-      - spec: "python"
+      - spec: python@3.8.0
         prefix: /usr
       buildable: False
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~fortran
       providers:
         mpi: [openmpi]
@@ -60,3 +60,6 @@ spack:
 
   config:
     build_jobs: 2
+
+  mirrors:
+    E4S: https://cache.e4s.io
diff --git a/.github/ci/spack-envs/gcc7_py36_ompi_h5_ad1_ad2/spack.yaml b/.github/ci/spack-envs/gcc7_py36_ompi_h5_ad1_ad2/spack.yaml
@@ -18,26 +18,26 @@ spack:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
       externals:
-      - spec: "cmake"
+      - spec: cmake@3.23.0
         prefix: /usr
       buildable: False
     openmpi:
       externals:
-      - spec: "openmpi"
+      - spec: openmpi@2.1.1
         prefix: /usr
       buildable: False
     perl:
       externals:
-      - spec: "perl"
+      - spec: perl@5.26.1
         prefix: /usr
       buildable: False
     python:
       externals:
-      - spec: "python"
+      - spec: python@3.6.3
         prefix: /usr
       buildable: False
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~fortran
       compiler: [[email protected]]
 
@@ -58,3 +58,6 @@ spack:
 
   config:
     build_jobs: 2
+
+  mirrors:
+    E4S: https://cache.e4s.io