Depend on iohub

[talonchandler]

This PR makes recOrder depend on the new iohub readers/writers, and removes the dependency on WaveorderReader and WaveorderWriter.

The major changes are:

• recOrder acquisitions and metadata now save to ome.zarr v0.4
• recorder view now uses iohub and can open ome.zarr v0.4 (in addition to v0.1 and MM datasets). recorder view is also no longer "officially supported" (i.e. it does not appear on README figure) since we expect its behavior to change significantly and it should not block our 0.3 and 0.4 releases.
• recorder/examples scripts write to iohub
• recorder info and recorder convert are removed - improved alternatives live in iohub
• drops python 3.8 support and adds 3.11

[deprecated-napari-hub-preview-bot]

Preview page for your plugin is ready here:
https://preview.napari-hub.org/mehta-lab/recOrder/331
Updated: 2023-04-06T17:25:48.102864

[ziw-liu]

iohub requires python 3.9+. Should this be a separate issue or we just bump it here?

[talonchandler]

iohub requires python 3.9+. Should this be a separate issue or we just bump it here?

Thanks! I think we can bump it here.

[codecov-commenter]

Codecov Report

Merging #331 (60e6d1f) into main (6742be9) will decrease coverage by 2.17%.
The diff coverage is 0.00%.

@@           Coverage Diff            @@
##            main    #331      +/-   ##
========================================
- Coverage   4.23%   2.06%   -2.17%     
========================================
  Files         23      21       -2     
  Lines       5150    4888     -262     
========================================
- Hits         218     101     -117     
+ Misses      4932    4787     -145     

Impacted Files	Coverage Δ
recOrder/acq/acq_functions.py	0.00% <0.00%> (ø)
recOrder/acq/acquisition_workers.py	0.00% <0.00%> (ø)
recOrder/calib/calibration_workers.py	0.00% <0.00%> (ø)
recOrder/compute/phantoms.py	0.00% <0.00%> (ø)
recOrder/io/_reader.py	0.00% <0.00%> (ø)
recOrder/plugin/main_widget.py	0.00% <ø> (ø)
recOrder/scripts/cli.py	0.00% <0.00%> (ø)

... and 1 file with indirect coverage changes

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[talonchandler]

@ziw-liu thanks for your help here. I'm calling this "ready for review" because I need to keep driving this forward. I tested on hummingbird this morning and I'm planning to continue testing tomorrow. Can I request complete review and that you spend some time testing on hummingbird and/or automaton?

When this merges I think it's ready to be released as 0.3.0rc0 0.3.0rc1.

[talonchandler]

@ziw-liu following our discussion I've now removed recorder view from the README figure. I couldn't find an obvious way to hide the CLI docs with click, so I left it as is. Thanks for your help with testing.

[ziw-liu]

@talonchandler Should we do anything to the codecov workflow? Our test coverage is not ideal, but I don't think it has to fail for this PR. It's not blocking the merge though so we can also deal with it later.

[talonchandler]

@talonchandler Should we do anything to the codecov workflow? Our test coverage is not ideal, but I don't think it has to fail for this PR. It's not blocking the merge though so we can also deal with it later.

I agree that test coverage shouldn't block this merge. We can discuss more in the meeting.

[ziw-liu]

LGTM!

[ziw-liu]

Last minute request: can we remove these lines?

recOrder/README.md

Lines 56 to 60 in 6742be9

	View command-line help by running
	```sh
	recOrder.help
	```