Documentation and clean up

[Thoemi09]

This PR is very similar to the one from itertools and mpi. The following things have been done:

• formatted .clang-tidy file
• added c++ documentation
• split object.hpp into multiple headers
• removed all sphinx and added doxygen related files
• updated the github action workflow
• fixed a bug in the h5::file constructor (-e option was not working)

I think we should consider either restricting or improving the h5::array_interface. Right now, it is kept quite general but only works for specific cases, e.g. contiguous data/views, hyperslabs with blocks of size (1, 1, ..., 1) and so on. It probably would be good to only support our specific use cases and otherwise throw an exception.

[Wentzell]

Thank you @Thoemi09 for this huge improvement! I pushed some minor changes, and this all looks good now!

[hmenke]

I'm getting lots of compiler errors when compiling 1.3.0 and it points to this change.

This is the first error, but there are more of the same kind

/home/abuild/rpmbuild/BUILD/triqs-3.3.0/_build/deps/h5_src/c++/h5/array_interface.cpp: In function 'h5::dataspace h5::array_interface::{anonymous}::make_mem_dspace(const h5::array_interface::array_view&)':
/home/abuild/rpmbuild/BUILD/triqs-3.3.0/_build/deps/h5_src/c++/h5/array_interface.cpp:46:77: error: invalid conversion from 'const long long unsigned int*' to 'const hsize_t*' {aka 'const long unsigned int*'} [-fpermissive]
   46 |       dataspace dspace = H5Screate_simple(v.slab.rank(), v.parent_shape.data(), nullptr);
      |                                                          ~~~~~~~~~~~~~~~~~~~^~
      |                                                                             |
      |                                                                             const long long unsigned int*
In file included from /mpcdf/soft/SLE_15/packages/haswell/hdf5/gcc_13-13.1.0/1.14.1/include/H5Ppublic.h:32,
                 from /mpcdf/soft/SLE_15/packages/haswell/hdf5/gcc_13-13.1.0/1.14.1/include/hdf5.h:35,
                 from /home/abuild/rpmbuild/BUILD/triqs-3.3.0/_build/deps/h5_src/c++/h5/array_interface.cpp:26:
/mpcdf/soft/SLE_15/packages/haswell/hdf5/gcc_13-13.1.0/1.14.1/include/H5Spublic.h:303:55: note:   initializing argument 2 of 'hid_t H5Screate_simple(int, const hsize_t*, const hsize_t*)'
  303 | H5_DLL hid_t H5Screate_simple(int rank, const hsize_t dims[], const hsize_t maxdims[]);
      |                                         ~~~~~~~~~~~~~~^~~~~~

My guess is that this doesn't surface in CI, because that still uses GCC 12.

[hmenke]

Hm, I'm also getting other errors llike the following. It looks like h5 relies on an old and deprecated API of HDF5.

https://docs.hdfgroup.org/hdf5/v1_14/group___h5_o.html#ga96ce408ffda805210844246904da2842

Deprecated:
As of HDF5-1.12 this function has been deprecated in favor of the function H5Oget_info_by_name2() or the macro H5Oget_info_by_name.

/home/abuild/rpmbuild/BUILD/triqs-3.3.0/_build/deps/h5_src/c++/h5/group.cpp: In function 'herr_t h5::get_group_elements_name_ds(hid_t, const char*, const H5L_info2_t*, void*)':
/home/abuild/rpmbuild/BUILD/triqs-3.3.0/_build/deps/h5_src/c++/h5/group.cpp:167:37: error: too few arguments to function 'herr_t H5Oget_info_by_name3(hid_t, const char*, H5O_info2_t*, unsigned int, hid_t)'
  167 |     herr_t err = H5Oget_info_by_name(loc_id, name, &object_info, H5P_DEFAULT);
      |                                     ^
In file included from /mpcdf/soft/SLE_15/packages/haswell/hdf5/gcc_13-13.1.0/1.14.1/include/H5Apublic.h:21,
                 from /mpcdf/soft/SLE_15/packages/haswell/hdf5/gcc_13-13.1.0/1.14.1/include/hdf5.h:22,
                 from /home/abuild/rpmbuild/BUILD/triqs-3.3.0/_build/deps/h5_src/c++/h5/group.cpp:24:
/mpcdf/soft/SLE_15/packages/haswell/hdf5/gcc_13-13.1.0/1.14.1/include/H5Opublic.h:544:15: note: declared here
  544 | H5_DLL herr_t H5Oget_info_by_name3(hid_t loc_id, const char *name, H5O_info2_t *oinfo, unsigned fields,
      |               ^~~~~~~~~~~~~~~~~~~~
/home/abuild/rpmbuild/BUILD/triqs-3.3.0/_build/deps/h5_src/c++/h5/group.cpp: In function 'herr_t h5::get_group_elements_name_grp(hid_t, const char*, const H5L_info2_t*, void*)':
/home/abuild/rpmbuild/BUILD/triqs-3.3.0/_build/deps/h5_src/c++/h5/group.cpp:175:37: error: too few arguments to function 'herr_t H5Oget_info_by_name3(hid_t, const char*, H5O_info2_t*, unsigned int, hid_t)'
  175 |     herr_t err = H5Oget_info_by_name(loc_id, name, &object_info, H5P_DEFAULT);
      |                                     ^
/mpcdf/soft/SLE_15/packages/haswell/hdf5/gcc_13-13.1.0/1.14.1/include/H5Opublic.h:544:15: note: declared here
  544 | H5_DLL herr_t H5Oget_info_by_name3(hid_t loc_id, const char *name, H5O_info2_t *oinfo, unsigned fields,
      |               ^~~~~~~~~~~~~~~~~~~~
/home/abuild/rpmbuild/BUILD/triqs-3.3.0/_build/deps/h5_src/c++/h5/group.cpp: In function 'herr_t h5::get_group_elements_name_ds_grp(hid_t, const char*, const H5L_info2_t*, void*)':
/home/abuild/rpmbuild/BUILD/triqs-3.3.0/_build/deps/h5_src/c++/h5/group.cpp:183:37: error: too few arguments to function 'herr_t H5Oget_info_by_name3(hid_t, const char*, H5O_info2_t*, unsigned int, hid_t)'
  183 |     herr_t err = H5Oget_info_by_name(loc_id, name, &object_info, H5P_DEFAULT);
      |                                     ^
/mpcdf/soft/SLE_15/packages/haswell/hdf5/gcc_13-13.1.0/1.14.1/include/H5Opublic.h:544:15: note: declared here
  544 | H5_DLL herr_t H5Oget_info_by_name3(hid_t loc_id, const char *name, H5O_info2_t *oinfo, unsigned fields,
      |               ^~~~~~~~~~~~~~~~~~~~

[Thoemi09]

I don't get any errors with gcc 13.2 and and HDF5 1.14.3 but this looks like an HDF5 version problem.

You can try to compile with H5_USE_110_API. This might fix the second issue.

I am not sure about the first issue. We define h5::hsize_t to be uint64_t which should be the same as in the HDF5 header. Could you check in H5Public.h how they define it there?

Anyway, it would definitely be a good idea to get rid of deprecated function calls.

[Thoemi09]

Oh sorry, I just saw that we already define H5_USE_110_API in the h5 CMakeLists.txt file. It should be using H5Oget_info_by_name1 and not H5Oget_info_by_name3.