imagej / pyimagej

Use ImageJ from Python
https://pyimagej.readthedocs.io/
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Update ImageJ2/Fiji version in the docs and improve toc layout #276

Closed elevans closed 1 year ago

elevans commented 1 year ago

This PR is in response to https://github.com/imagej/pyimagej/issues/271 and updates the version of ImageJ2/Fiji we use from 2.5.0 to 2.13.1. I also applied the following changes:

codecov[bot] commented 1 year ago

Codecov Report

Patch and project coverage have no change.

Comparison is base (d99fcf0) 77.60% compared to head (c5214a0) 77.60%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #276 +/- ## ======================================= Coverage 77.60% 77.60% ======================================= Files 16 16 Lines 1947 1947 ======================================= Hits 1511 1511 Misses 436 436 ```

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hinerm commented 1 year ago

@elevans @gselzer what do you think about changing the verbosity in the affected notebooks to avoid these printouts? Is that a possibility?

elevans commented 1 year ago

I think this might be confusing for people and might generate erroneous bug reports. If someone sees our notebooks with the clean output but theirs is duplicating they might reach out to us.

elevans commented 1 year ago

@elevans I like all of the changes - in fact, most of my comments probably aren't related to your changes.

One final question - can you build the documentation? I ran make docs && firefox doc/_build/html/index.html, but it errors.

I wasn't able to reproduce this. This command works fine on my end. I did make setup first which created the pyimagej-dev environment and then the make docs command without any issues.