Update LIMS2 modules to use Py3

AllenInstitute / AllenSDK

code for reading and processing Allen Institute for Brain Science data

https://allensdk.readthedocs.io/en/latest/

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Update LIMS2 modules to use Py3 #853

Open wbwakeman opened 5 years ago

wbwakeman commented 5 years ago

breaking: "MORPHOLOGY_UPRIGHT_TRANSFORM_QUEUE" "TISSUECYTE_PROJECTION_THUMBNAIL_QUEUE" "NEURON_GLOBAL_FEATURES_QUEUE" "TISSUECYTE_UNIONIZE_CAV_QUEUE" "TISSUECYTE_UNIONIZE_CLASSIC_QUEUE" "EPHYS_NWB_CONVERTER_QUEUE" "CONNECTIVITY_CORTICAL_PROJECTION_QUEUE"

not breaking: "OPHYS_MOTION_CORRECTION_QUEUE" "ISI_NWB_QUEUE" "NIKON_ND2_DECONVOLUTION_QUEUE" "DEWARPING_QUEUE"

Fixed: "NEUROPIL_CORRECTION_QUEUE" "ANNOTATED_REGION_METRICS_QUEUE"

wbwakeman commented 5 years ago

For Morphology Upright Transform, it is missing a package that is added to the PYTHONPATH by that run_python.sh script

import neuron_morphology.swc as swc

ModuleNotFoundError: No module named 'neuron_morphology'

/shared/bioapps/infoapps/lims2_modules/lib/python/run_python.sh export PYTHONPATH=/shared/bioapps/infoapps/lims2_modules/lib/neuron_morphology:${PYTHONPATH}