Merge branch 'next-run-id' into uuid-run-id

* next-run-id:
  Note removing support for HDF5 in changelog
  Better notation for indexing zShift
  Update note on zShift in grid-files section of manual
  Print error for HDF5 macros when running bout-v5-macro-upgrader.py
  Support macros being removed in bout-v5-macro-upgrader.py
  Remove HDF5 support

.github/workflows/clang-tidy-review.yml

@@ -18,8 +18,6 @@ jobs:
                  libnetcdf-dev
                  libnetcdf-c++4-dev
                  netcdf-bin
-                 hdf5-tools
-                 libhdf5-mpi-dev
                  openmpi-bin
                  libopenmpi-dev
                  petsc-dev
@@ -39,7 +37,6 @@ jobs:
                            -DBOUT_ENABLE_OPENMP=ON \
                            -DBOUT_USE_PETSC=ON \
                            -DBOUT_USE_SLEPC=ON \
-                           -DBOUT_USE_HDF5=ON \
                            -DBOUT_USE_SUNDIALS=ON \
                            -DBOUT_BUILD_EXAMPLES=ON \
                            -DCMAKE_EXPORT_COMPILE_COMMANDS=On
@@ -49,6 +46,6 @@ jobs:
         id: review
         with:
           build_dir: build
-          apt_packages: "libfftw3-dev,libnetcdf-c++4-dev,libhdf5-mpi-dev,libopenmpi-dev,petsc-dev,slepc-dev,liblapack-dev,libparpack2-dev,libsundials-dev"
+          apt_packages: "libfftw3-dev,libnetcdf-c++4-dev,libopenmpi-dev,petsc-dev,slepc-dev,liblapack-dev,libparpack2-dev,libsundials-dev"
           clang_tidy_checks: '-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers'
 

.github/workflows/tests.yml

@@ -30,7 +30,6 @@ jobs:
             os: ubuntu-18.04
             configure_options: "--with-petsc
                                 --with-slepc
-                                --with-hdf5
                                 --with-sundials=/home/runner/local"
             script_flags: "-uim"
 
@@ -44,7 +43,6 @@ jobs:
                                 --disable-backtrace
                                 --with-petsc
                                 --with-slepc
-                                --with-hdf5
                                 --with-sundials=/home/runner/local"
             script_flags: "-uim -t shared -t python"
 
@@ -54,7 +52,6 @@ jobs:
                                 --enable-sigfpe
                                 --enable-debug
                                 --enable-track
-                                --with-hdf5
                                 --with-petsc
                                 --with-slepc
                                 --with-sundials=/home/runner/local"
@@ -66,7 +63,6 @@ jobs:
                                 --enable-openmp
                                 --with-petsc
                                 --with-slepc
-                                --with-hdf5
                                 --with-sundials=/home/runner/local"
             script_flags: "-uim"
             omp_num_threads: 2
@@ -77,7 +73,6 @@ jobs:
                             -DBOUT_ENABLE_OPENMP=ON
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
-                            -DBOUT_USE_HDF5=ON
                             -DBOUT_USE_SUNDIALS=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
@@ -89,7 +84,6 @@ jobs:
                                 --enable-debug
                                 --enable-track
                                 --with-lapack
-                                --with-hdf5
                                 --with-petsc
                                 --with-slepc
                                 --with-sundials=/home/runner/local"
@@ -114,14 +108,12 @@ jobs:
                  libnetcdf-dev
                  libnetcdf-c++4-dev
                  netcdf-bin
-                 hdf5-tools
                  python3
                  python3-pip
                  python3-pytest
                  python3-numpy
                  python3-scipy
                  lcov
-                 libhdf5-mpi-dev
                  openmpi-bin
                  libopenmpi-dev
                  petsc-dev

.travis_fedora.sh

@@ -37,7 +37,7 @@ then
     cat /etc/os-release
     # Ignore weak depencies
     echo "install_weak_deps=False" >> /etc/dnf/dnf.conf
-    time dnf -y install dnf-plugins-core {petsc,hdf5}-${mpi}-devel /usr/lib/rpm/redhat/redhat-hardened-cc1 python3-h5py
+    time dnf -y install dnf-plugins-core petsc-${mpi}-devel /usr/lib/rpm/redhat/redhat-hardened-cc1 python3-h5py
     # Allow to override packages - see #2073
     time dnf copr enable -y davidsch/fixes4bout || :
     time dnf -y upgrade

CHANGELOG.md

@@ -46,6 +46,8 @@
 - `PhysicsModel` expects the options `datadir` and `dump_format` to
   have been set; this is only a problem if you don't call
   `BoutInitialise`. [\#2062](https://github.com/boutproject/BOUT-dev/pull/2062)
+- Support for reading/writing HDF5 files has been removed ahead of completely
+  refactoring the I/O systems. [\#2208](https://github.com/boutproject/BOUT-dev/pull/2208)
 
 
 ## [v4.3.2](https://github.com/boutproject/BOUT-dev/tree/v4.3.2) (2020-10-19)

CMakeLists.txt

@@ -166,8 +166,6 @@ set(BOUT_SOURCES
   ./src/fileio/formatfactory.cxx
   ./src/fileio/formatfactory.hxx
   ./src/fileio/impls/emptyformat.hxx
-  ./src/fileio/impls/hdf5/h5_format.cxx
-  ./src/fileio/impls/hdf5/h5_format.hxx
   ./src/fileio/impls/netcdf/nc_format.cxx
   ./src/fileio/impls/netcdf/nc_format.hxx
   ./src/fileio/impls/netcdf4/ncxx4.cxx
@@ -518,15 +516,6 @@ endif()
 message(STATUS "NetCDF support: ${BOUT_USE_NETCDF}")
 set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF})
 
-option(BOUT_USE_HDF5 "Enable support for HDF5 output" OFF)
-if (BOUT_USE_HDF5)
-  find_package(HDF5 REQUIRED COMPONENTS CXX)
-  target_link_libraries(bout++ PUBLIC "${HDF5_CXX_LIBRARIES}")
-  target_include_directories(bout++ PUBLIC "${HDF5_CXX_INCLUDE_DIRS}")
-endif()
-message(STATUS "HDF5 support: ${BOUT_USE_HDF5}")
-set(BOUT_HAS_HDF5 ${BOUT_USE_HDF5})
-
 option(BOUT_USE_FFTW "Enable support for FFTW" ON)
 if (BOUT_USE_FFTW)
   find_package(FFTW REQUIRED)
@@ -873,7 +862,6 @@ message("
    SLEPc support            : ${BOUT_HAS_SLEPC}
    SUNDIALS support         : ${BOUT_HAS_SUNDIALS}
    NetCDF support           : ${BOUT_HAS_NETCDF}
-   HDF5 support             : ${BOUT_HAS_HDF5}
    FFTW support             : ${BOUT_HAS_FFTW}
    LAPACK support           : ${BOUT_HAS_LAPACK}
    OpenMP support           : ${BOUT_USE_OPENMP}

README.md

@@ -62,9 +62,7 @@ BOUT++ needs the following:
 
 * A C++14 compiler
 * MPI
-* Either NetCDF or HDF5
-
-Note that some of the tests require NetCDF rather than HDF5
+* NetCDF
 
 BOUT++ has the following optional dependencies:
 

autoconf_build_defines.hxx.in

@@ -15,9 +15,6 @@
 /* NLS support */
 #undef BOUT_HAS_GETTEXT
 
-/* HDF5 support */
-#undef BOUT_HAS_HDF5
-
 /* IDA support */
 #undef BOUT_HAS_IDA
 

bin/bout-config.in

@@ -31,7 +31,6 @@ pythonpath="@PYTHONCONFIGPATH@"
 has_netcdf="@BOUT_HAS_NETCDF@"
 has_legacy_netcdf="@BOUT_HAS_LEGACY_NETCDF@"
 has_pnetcdf="@BOUT_HAS_PNETCDF@"
-has_hdf5="@BOUT_HAS_HDF5@"
 has_pvode="@BOUT_HAS_PVODE@"
 has_cvode="@BOUT_HAS_CVODE@"
 has_ida="@BOUT_HAS_IDA@"
@@ -71,7 +70,6 @@ Available values for OPTION include:
   --has-netcdf  NetCDF file support
   --has-legacy-netcdf  Legacy NetCDF file support
   --has-pnetcdf Parallel NetCDF file support
-  --has-hdf5    HDF5 file support
   --has-pvode   PVODE solver support
   --has-cvode   SUNDIALS CVODE solver support
   --has-ida     SUNDIALS IDA solver support
@@ -107,7 +105,6 @@ all()
         echo "  --has-netcdf  -> $has_netcdf"
         echo "  --has-legacy-netcdf  -> $has_legacy_netcdf"
         echo "  --has-pnetcdf -> $has_pnetcdf"
-        echo "  --has-hdf5    -> $has_hdf5"
         echo "  --has-pvode   -> $has_pvode"
         echo "  --has-cvode   -> $has_cvode"
         echo "  --has-ida     -> $has_ida"
@@ -200,10 +197,6 @@ while test $# -gt 0; do
         echo $has_pnetcdf
         ;;
 
-    --has-hdf5)
-        echo $has_hdf5
-        ;;
-
     --has-pvode)
         echo $has_pvode
         ;;

bin/bout-v5-macro-upgrader.py

@@ -9,7 +9,8 @@
 # List of macros, their replacements and what header to find them
 # in. Each element should be a dict with "old", "new" and "headers"
 # keys, with "old" and "new" values being strings, and "headers" being a
-# list of strings
+# list of strings. "new" can also be None if the macro has been removed, which
+# will cause an error to be printed if the macro is found.
 MACRO_REPLACEMENTS = [
     {
         "old": "REVISION",
@@ -63,8 +64,8 @@
     },
     {
         "old": "HAS_HDF5",
-        "new": "BOUT_HAS_HDF5",
-        "headers": "bout/build_config.hxx",
+        "new": None,
+        "headers": [],
         "macro": True,
         "always_defined": True,
     },
@@ -140,8 +141,8 @@
     },
     {
         "old": "HDF5",
-        "new": "BOUT_HAS_HDF5",
-        "headers": "bout/build_config.hxx",
+        "new": None,
+        "headers": [],
         "macro": True,
         "always_defined": True,
     },
@@ -297,6 +298,13 @@ def apply_fixes(replacements, source):
     modified = copy.deepcopy(source)
 
     for replacement in replacements:
+        if replacement["new"] is None:
+            print(
+                "'%s' has been removed, please delete from your code"
+                % replacement["old"]
+            )
+            continue
+
         modified = fix_include_version_header(
             replacement["old"], replacement["headers"], modified
         )

bout++Config.cmake.in

@@ -58,9 +58,6 @@ endif()
 if(EXISTS "@netCDFCxx_ROOT@")
   set(netCDFCxx_ROOT "@netCDFCxx_ROOT@")
 endif()
-if(EXISTS "@HDF5F_ROOT@")
-  set(HDF5F_ROOT "@HDF5F_ROOT@")
-endif()
 if(EXISTS "@PVODE_ROOT@")
   set(PVODE_ROOT "@PVODE_ROOT@")
 endif()
@@ -85,9 +82,6 @@ endif()
 if (BOUT_HAS_NETCDF)
   find_dependency(netCDFCxx @netCDFCxx_VERSION@)
 endif()
-if (BOUT_HAS_HDF5)
-  find_dependency(HDF5 @HDF5_VERSION@)
-endif()
 if (BOUT_HAS_PVODE)
   find_dependency(PVODE @PVODE_VERSION@)
 endif()

cmake_build_defines.hxx.in

@@ -9,7 +9,6 @@
 #cmakedefine01 BOUT_HAS_CVODE
 #cmakedefine01 BOUT_HAS_FFTW
 #cmakedefine01 BOUT_HAS_GETTEXT
-#cmakedefine01 BOUT_HAS_HDF5
 #cmakedefine01 BOUT_HAS_IDA
 #cmakedefine01 BOUT_HAS_LAPACK
 #cmakedefine01 BOUT_HAS_NETCDF