Deprecated version 0.0.44 installed

[MDHowe4]

Hello,

Fantastic tool that I am certain will be of use for our group as we try to improve our spatial pipeline qc, however, we had quite a few issues with installing and running on the example data. Following the installation guide https://labsyspharm.github.io/cylinter/installation/ here installs version 0.0.44 which throws errors and causes other issues with the Example data syn52859560 and ultimately doesn't work as expected. I believe there are also deprecated config options from 0.0.44 that are incompatible with the example datas config.yml. Our short term solution was to install cellcutter from labsyspharm and install cylinter from pyproject.toml. Steps for reproduction:

mamba create -n cylinter -c labsyspharm python=3.11 cellcutter
mamba activate cylinter
pip install -e . with these specific packages commented out and matplotlib = "*" commented in.

Which installed v0.0.47 which worked perfectly with the Example data. I believe the channels will need to be updated with the newest version for compatibility with the example docs.

[jmuhlich]

Could you please run conda config --show > conda-config.txt and upload the resulting conda-config.txt file here? Thanks.

[gjbaker]

To avoid confusion with older versions, the CyLinter installation command (found here: https://labsyspharm.github.io/cylinter/installation/) now explicitly specifies the current version (v0.0.47) for download.