jupyter investigation to close any open h5 file handles so not to reuse old data

[PhilipDeegan]

add exit registers closing any still existing h5file handles

[PhilipDeegan]

if you feel like testing this @nicolasaunai maybe it will resolve #526

[lgtm-com]

This pull request introduces 1 alert when merging 6304e5e into 4e7c94b - view on LGTM.com

new alerts:

• 1 for Unused import

[nicolasaunai]

after reading the PR I wonder: isn't the problem actually that we never close the files explicitly? when reading with hierarchy_fromh5, there is never a data_file.close()

[nicolasaunai]

probably not indented correclty?

[PhilipDeegan]

It's been some time since looking at this, and I'm pretty sure I had another later branch with modifications which I never added so it's quite likely

[nicolasaunai]

after reading the PR I wonder: isn't the problem actually that we never close the files explicitly? when reading with hierarchy_fromh5, there is never a data_file.close()

ok probably not a good idea.
calling data_file.close() will make all our dataset become <Closed HDF5 dataset> and the only way to keep our data would then be to really read it, i.e. not storing the dataset like here but storing the dataset[:] which may loose the nice if/when h5 offers us... (not sure I'm clear?)

[PhilipDeegan]

after reading the PR I wonder: isn't the problem actually that we never close the files explicitly? when reading with hierarchy_fromh5, there is never a data_file.close()

instead of closing the object, we could try to just reset it with a new handle = h5open(...)

and if that doesn't work we should probably ask the h5py people

[nicolasaunai]

converted to draft since not sure it's needed, see #526