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@francois.mazen can you please review the actual changes? thanks!

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Try to build from scratch following the instruction, and it seems that the install command tries to build the h5py wheel which fails on my machine:

Building wheels for collected packages: animtovtkhdf, h5py, numpy

      /tmp/pip-install-ztxq_aw0/h5py_e1e5024013b2442289022418bafe71e1/h5py/defs.c: Dans la fonction « __Pyx_PyInt_As_long »:
      /tmp/pip-install-ztxq_aw0/h5py_e1e5024013b2442289022418bafe71e1/h5py/defs.c:62446:27: erreur: trop peu d'arguments pour la fonction « _PyLong_AsByteArray »
      62446 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,                 
            |                           ^~~~~~~~~~~~~~~~~~~       
      Dans le fichier inclus depuis /usr/include/python3.13/longobject.h:107, 
                       depuis /usr/include/python3.13/Python.h:81,
                       depuis /tmp/pip-install-ztxq_aw0/h5py_e1e5024013b2442289022418bafe71e1/h5py/defs.c:51:
      /usr/include/python3.13/cpython/longobject.h:111:17: note: déclaré ici
        111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,                             
            |                 ^~~~~~~~~~~~~~~~~~~
      /tmp/pip-install-ztxq_aw0/h5py_e1e5024013b2442289022418bafe71e1/h5py/defs.c: Dans la fonction « __Pyx_PyInt_As_int »:
      /tmp/pip-install-ztxq_aw0/h5py_e1e5024013b2442289022418bafe71e1/h5py/defs.c:62642:27: erreur: trop peu d'arguments pour la fonction « _PyLong_AsByteArray »
      62642 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
            |                           ^~~~~~~~~~~~~~~~~~~                                    
      /usr/include/python3.13/cpython/longobject.h:111:17: note: déclaré ici
        111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,                             
            |                 ^~~~~~~~~~~~~~~~~~~                 
      error: command '/usr/bin/gcc' failed with exit code 1                   
      [end of output]             

Why do we need to build this h5py wheel?

that looks like a python version mismatch to me, what version of Python are you using?

Python 3.13.1

I'm also getting compilation issues of h5py in python 3.13.1 because of Python C API changes. It should be fixed in h5py master branch, but Python 3.13.1 was released after the latest tag of h5py, so until h5py gets a new release it is only compatible with python <=3.12

and to answer your original question, h5py is shipped with a specific version of HDF5 and compiles it as part of its build process

let's open a dedicated issue for python 3.13 compat

marked this merge request as ready

mentioned in commit 7c87882e

merged