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qiita-spots / qiita-files

File formats defined for Qiita and Qiita plugins internal use
BSD 3-Clause "New" or "Revised" License
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maintenance: h5py.default_file_mode is deprecated #12

Open sjanssen2 opened 5 months ago

sjanssen2 commented 5 months ago

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 commented 5 months ago

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 commented 5 months ago

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 commented 5 months ago

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 commented 5 months ago

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

antgonza commented 5 months ago

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.