Review requirements.txt

[namsaraeva]

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

[sophiamaedler]

we have added stitching functionality which requires additional dependencies.

Problematic dependencies:

• ashlar: requires a specific version of scikit-image that is not compatible with our package ashlar requires scikit-image < 0.20  #63
• graph_tool: only available via Conda graph_tool dependency #61
• java: needs to be installed for pynius to work properly java dependency from pynius #62
• py-lmd: currently no pip release

[sophiamaedler]

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

[sophiamaedler]

@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]

@sophiamaedler just tested, it runs through for me

[sophiamaedler]

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.

[sophiamaedler]

we've addressed this issue by making the documentation more explicit and providing clear and precise install instructions for scportrait if the stitching capabilities want to be used. I don't think there is any workaround for having a working java installation for the stitching as we require the use of the Bioformats library to be able to work with a multitude of different imaging formats. If we create a conda release we could address this issue by providing java within the conda specs.