science/hdf5 should be upgraded to 1.12, but some ports are not compatible with this version, and it has been suggested to repocopy the actual port to science/hdf5-110.
PR 251894 proposes a patch to do that, and an exp-run has been launched to detect the incompatibilities.
Unfortunately, your port science/py-h5py failed: see
Could you please propose a patch, either to fix it with 1.12 or to switch to hdf5-110?
Update to 3.1.0 in r562832 which builds fine with hdf5 1.12.0. Thanks!