kipoi / models

Model zoo for genomics
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`kipoi test-source dir --all` not finding parent_subpath #354

Open zeitlingerlab opened 1 year ago

zeitlingerlab commented 1 year ago

I'm trying to upload a set of 4 models, identical architecture, trained on different datasets. The individual kipoi test commands work for each model, I have the model-template.yaml and the models.tsv drafted. But when I try to run kipoi test-source dir --all, it returns the following error:

(chrombpnet) bash-4.4$ kipoi test-source dir --all
Traceback (most recent call last):
  File "/home/mw2098/anaconda3/envs/chrombpnet/bin/kipoi", line 8, in <module>
    sys.exit(main())
  File "/home/mw2098/anaconda3/envs/chrombpnet/lib/python3.6/site-packages/kipoi/__main__.py", line 107, in main
    command_fn(args.command, sys.argv[2:])
  File "/home/mw2098/anaconda3/envs/chrombpnet/lib/python3.6/site-packages/kipoi/cli/source_test.py", line 312, in cli_test_source
    all_models = all_models_to_test(source)
  File "/home/mw2098/anaconda3/envs/chrombpnet/lib/python3.6/site-packages/kipoi/cli/source_test.py", line 89, in all_models_to_test
    models = src.list_models().model
  File "/home/mw2098/anaconda3/envs/chrombpnet/lib/python3.6/site-packages/kipoi/sources.py", line 372, in list_models
    for model in self._list_components("model")])
  File "/home/mw2098/anaconda3/envs/chrombpnet/lib/python3.6/site-packages/kipoi/sources.py", line 372, in <listcomp>
    for model in self._list_components("model")])
  File "/home/mw2098/anaconda3/envs/chrombpnet/lib/python3.6/site-packages/kipoi/sources.py", line 422, in get_model_descr
    return self._get_component_descr(model, which="model")
  File "/home/mw2098/anaconda3/envs/chrombpnet/lib/python3.6/site-packages/kipoi/sources.py", line 599, in _get_component_descr
    return self.component_group_list[which][k]._get_component_descr(relative_path(component, k))
  File "/home/mw2098/anaconda3/envs/chrombpnet/lib/python3.6/site-packages/kipoi_utils/utils.py", line 656, in relative_path
    assert parent_subpath != ""
AssertionError

I traced back and it seems like the kipoi source.get_component_descr returns an empty string, not a None. There seems to be an issue with the groups. I'm following the instructions exactly based on (https://kipoi.org/docs/contributing/01_Getting_started/) with a few custom model import changes in a model.py. Any advice for getting this to work?

k = src.get_group_name(component, which)
k
''