Openpmd-api: Python: Read the Write Example

[ax3l]

The 0.3.1-alpha python write example HDF5 files lack the geometry attribute. Reading them in fileBased again fails.

Python: adding

    del series


    s = openPMD.Series("../samples/3_write_serial_py.h5",
        openPMD.Access_Type.read_only)

to 3_write_serial.py fails on missing geometry attribute.

Expected behavior
Do not fail :-)

Software Environment:

• version of openPMD-api: 0.3.1-alpha
• installed openPMD-api via: conda-forge
• operating system: OSX
• machine: [Are you running on a public cluster? It's likely we compute on it as well!]
• name and version of Python implementation: [e.g. CPython 3.6]
• version of HDF5: [e.g. 1.10.1]
• version of ADIOS1: [e.g. 1.13.1]
• name and version of MPI: [e.g. OpenMPI 3.0.0]

Additional context

This bug is already fixed in dev, tested with 1e9c2200069a4767058e2ca4aedfa3f31e3cdde3.

[C0nsultant]

The symptom of the bug report is not the actual cause. The behaviour was a side-effect of https://github.com/openPMD/openPMD-api/pull/156. File-based handles were incorrectly over-written and files were thus only partially complete.
~(I am unsure which commit this was fixed in.)~ See https://github.com/openPMD/openPMD-api/pull/193.

[ax3l]

But aren't both linked PRs already in 0.3.1-alpha? I would guess that actually #297 might have fixed it?

[C0nsultant]

Both are involved, actually. #193 restores the hierarchy-relationship that was broken by #156 (here), and #297 writes it to disk at the correct point in time (here).