maintenance: h5py.default_file_mode is deprecated

[sjanssen2]

When starting Qiita, the log reports about a deprecated use of h5py.get_config().default_file_mode = 'r'. This function was indeed deprecated with version 3.0.0. I therefore use the packaging lib to check if the used h5py version is older than that before trying to manually set to 'r'.

Should you feel we anyways would not use older h5py versions, we can delete these lines 15-20 in qiita_files/util.py altogether

[antgonza]

Thank you @sjanssen2. Do you think is worth supporting older versions of h5py or just support the latests? I vote to just support the latests - thus, not needing packaging and checking.

[sjanssen2]

Hi @antgonza I tend to agree that we don't have to support older versions, however I don't feel to competent to consider all edge cases. Thus, I chose the more conservative method. Your choice :-) But I'd be happy to get rid of this test altogether.

[antgonza]

In my experience, is better to just rip off the bandaid and then deal with any tentative issues if/when they arise. So, please remove that extra conditional and the need of packaging. Thanks.

[antgonza]

Just to confirm before merging, what version of h5py should we be using and are there any other updated dependencies for that?

[antgonza]

Also, I just realized that the actions are not testing against python 2.7 and while the plan is to stop supporting ASAP we still have at least 1 plugin that uses it.

[sjanssen2]

I fear that we need to keep this old stuff, due to qp-target-gene is still using py2.7.
But I am first testing h5py version now, instead of generally removing setting of default mode