TypeError using conda environment

[rocketeer1998]

Hi @jmuhlich, thanks for your great devotion to ASHLAR! I've created a new conda environment on my Windows10 computer and successfully installed ASHLAR. However, I can't run it on exemplar-001 data, where there was an error said,
TypeError: Invalid instance of ‘java/lang/Integer’ passed for a ‘java/lang/Boolean’.
What's the reason and how can I fix it? Thanks a lot!

[rocketeer1998]

I've also tested it on Centos. Unfortunately, the same error occurred.

[jmuhlich]

What version of Ashlar are you using? Can you provide the full stack trace so I can see which line of Ashlar code is causing that error? This looks like something we fixed back in Ashlar 1.15.1 (current version is 1.17.0).

[bpavie]

I have the same error too,I have installed it on Windows 11 Enterprise following the instruction found at https://labsyspharm.github.io/ashlar/instructions/installation.html:

mamba create -y -n ashlar python=3.7
mamba activate ashlar
mamba install -y -c conda-forge numpy scipy matplotlib networkx scikit-image=0.16.2 scikit-learn pyjnius
pip install ashlar

Unzipped the exemplar-001.zip and try to stitch the ashlar exemplar-001-cycle-06.ome.tiff

ashlar exemplar-001-cycle-06.ome.tiff --version
ashlar 1.14.1

ashlar exemplar-001-cycle-06.ome.tiff
Cycle 0:
    reading exemplar-001-cycle-06.ome.tiff
Traceback (most recent call last):
  File "C:\mambaforge\envs\ashlar\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "C:\mambaforge\envs\ashlar\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\mambaforge\envs\ashlar\Scripts\ashlar.exe\__main__.py", line 7, in <module>
  File "C:\mambaforge\envs\ashlar\lib\site-packages\ashlar\scripts\ashlar.py", line 184, in main
    args.quiet
  File "C:\mambaforge\envs\ashlar\lib\site-packages\ashlar\scripts\ashlar.py", line 212, in process_single
    reader = build_reader(filepaths[0], plate_well=plate_well)
  File "C:\mambaforge\envs\ashlar\lib\site-packages\ashlar\scripts\ashlar.py", line 338, in build_reader
    reader = reader_class(path, **kwargs)
  File "C:\GBW_MyPrograms\mambaforge\envs\ashlar\lib\site-packages\ashlar\reg.py", line 391, in __init__
    self.metadata = BioformatsMetadata(self.path)
  File "C:\mambaforge\envs\ashlar\lib\site-packages\ashlar\reg.py", line 207, in __init__
    self._init_metadata()
  File "C:\mambaforge\envs\ashlar\lib\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 71, 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'

[bpavie]

I answer to myself:

updating the python version to 3.8 and installing the last version of ashlar fixed it:

mamba create -y -n ashlar python=3.8
mamba activate ashlar
mamba install -y -c conda-forge numpy scipy matplotlib networkx scikit-image=0.19.3 scikit-learn pyjnius
pip install ashlar==1.17.0