tifffile dependency: version pin outdated?

[m-albert]

Hi, thanks a lot for your work which makes dealing with all the different file formats so much easier!

I wanted to report a dependency issue here:

I'm running into issues trying to install aicsimageio[all] together with newer versions of tifffile. Specifically,

pip install "tifffile>2022.7.28" "aicsimageio[all]==4.14.0" would yield

ERROR: Cannot install aicsimageio, aicsimageio[all]==4.14.0 and tifffile>2022.7.28 because these package versions have conflicting dependencies.

The conflict is caused by:
The user requested tifffile>2022.7.28
aicsimageio 4.14.0 depends on tifffile<2023.3.15 and >=2021.8.30
aicsimageio[all] 4.14.0 depends on tifffile<2023.3.15 and >=2021.8.30
aicsimageio[all] 4.14.0 depends on tifffile<2022.4.22; extra == "all"

I digged a bit into this and found that the tifffile pin in aicsimageio is attached to the bfio dependency and placed here:

aicsimageio/setup.py

Line 39 in e5197d1

"bfio": ["bfio==2.3.0", "tifffile<2022.4.22"],

However, bfio has different tifffile version requirements that are compatible with newer tifffile versions:

https://github.com/PolusAI/bfio/blob/v2.3.0/setup.py

Could it be that the tifffile pin by aicsimageio is outdated? Or is there maybe a reason for the tifffile pin that's independent of the bfio dependency with which it is listed together?

[toloudis]

Thanks for writing here. It's certainly possible that the tifffile pin is outdated. I wonder if you can write a pull request that unpins it and all tests still pass? We have seen incompatibilities with tifffile vs aicsimageio before, related to micromanager support. Also please consider trying out bioio which is the successor to aicsimageio. It uses a plugin model for the file format readers, so it's possible that you'd only have this conflict if you installed the bfio plugin.

[m-albert]

Cool, I wasn't aware that bioio is a more modular successor of aicsimageio. That's good to know and I'll try it out soon.

I'll open a PR here unpinning tifffile as you suggested.

Thanks for your help @toloudis.

[m-albert]

Just found there's already a PR with the exact same change #547.

The PR seems to already be approved! I commented there that it should solve this issue.

[m-albert]

Thanks @toloudis . Closing as #547 is merged.