Review requirements.txt

MannLabs / scPortrait

https://mannlabs.github.io/scPortrait/

Apache License 2.0

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Review requirements.txt #53

Open namsaraeva opened 2 months ago

namsaraeva commented 2 months ago

The requierements.txt file is possibly not up to date.

sophiamaedler commented 2 months ago

we have added stitching functionality which requires additional dependencies.

Problematic dependencies:

[x] ashlar: requires a specific version of scikit-image that is not compatible with our package #63
[x] graph_tool: only available via Conda #61
[ ] java: needs to be installed for pynius to work properly #62
[ ] py-lmd: currently no pip release

sophiamaedler commented 2 months ago

py-lmd has been added as a GitHub requirement until a pip release is available see commit 499f3d9

sophiamaedler commented 2 months ago

@namsaraeva do you have any issues running from scportrait.tools.stitch import Stitcher, ParallelStitcher in a fresh install of scportrait without installing any additional dependencies?

namsaraeva commented 2 months ago

@sophiamaedler just tested, it runs through for me

sophiamaedler commented 2 months ago

I am not sure how best to deal with the java dependency. On my devices I already have java installed so pyjnius runs without any issues but I guess this doesn't apply to all setups. I have added some information on this in the install instructions but its not an ideal solution yet.