Can't run on Ubuntu 20.04 and 18.04

[xixixihaha]

Tried the ashlar on both Ubuntu 18.04 and 20.04 both failed with the exception

Cycle 0:
reading 1.jpg
Traceback (most recent call last):
File "/home/simon/.local/bin/ashlar", line 8, in
sys.exit(main())
File "/home/simon/.local/lib/python3.8/site-packages/ashlar/scripts/ashlar.py", line 171, in main
return process_single(
File "/home/simon/.local/lib/python3.8/site-packages/ashlar/scripts/ashlar.py", line 202, in process_single
reader = build_reader(filepaths[0], plate_well=plate_well)
File "/home/simon/.local/lib/python3.8/site-packages/ashlar/scripts/ashlar.py", line 328, in build_reader
reader = reader_class(path, **kwargs)
File "/home/simon/.local/lib/python3.8/site-packages/ashlar/reg.py", line 391, in init
self.metadata = BioformatsMetadata(self.path)
File "/home/simon/.local/lib/python3.8/site-packages/ashlar/reg.py", line 207, in init
self._init_metadata()
File "/home/simon/.local/lib/python3.8/site-packages/ashlar/reg.py", line 228, in _init_metadata
options.setBoolean('zeissczi.autostitch', False)
File "jnius/jnius_export_class.pxi", line 879, in jnius.JavaMethod.call
File "jnius/jnius_conversion.pxi", line 72, in jnius.populate_args
File "jnius/jnius_utils.pxi", line 205, in jnius.check_assignable_from_str
TypeError: Invalid instance of 'java/lang/Integer' passed for a 'java/lang/Boolean'

Testing command:
ashlar 1.jpg 2.jpg --align-channel 0 --maximum-shift 50 --filter-sigma 1 -f ashlar_output_cycle{cycle}_channel{channel}.ome.tiff

Any clue to fix this?

[jmuhlich]

I think this is caused by kivy/pyjnius#602 so downgrading pyjnius should fix it. Pyjnius v1.2.1 or v1.3.0 should work. We will investigate how to work around this issue in ashlar so newer pyjnius versions will work too, or adjust our minimum compatible version if they fix the bug.

[xixixihaha]

@jmuhlich thanks so much! After downgrading pyjnius to 1.3.0 the issue solved.