AttributeError: module 'bionty' has no attribute 'Gene'

[zhang0730]

I am running the bench_perturbseq_genie3_transp.ipynb in benGRN tutorial. when I used the "Preprocessor" function,
the error:

---

File ~/mambaforge/envs/benGRN/lib/python3.10/site-packages/scdataloader/utils.py:387, in load_genes(organisms)
385 organisms = [organisms]
386 for organism in organisms:
--> 387 genesdf = bt.Gene.filter(
388 organism_id=bt.Organism.filter(ontology_id=organism).first().id
...
391 genesdf.ensembl_gene_id.isna(), "stable_id"
392 ]
393 genesdf = genesdf.drop_duplicates(subset="ensembl_gene_id")

AttributeError: module 'bionty' has no attribute 'Gene'

---

and I found that the internal struture of bionty changed

import bionty as bt
print(dir(bt))
['__builtins__', '__cached__', '__doc__', '__file__', '__getattr__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '__version__', '_check_instance_setup', '_load_bionty_sources', 'base', 'ids']
print(dir(bt.base))
['BFXPipeline', 'BioSample', 'CellLine', 'CellMarker', 'CellType', 'DevelopmentalStage', 'Disease', 'Drug', 'Ethnicity', 'ExperimentalFactor', 'Gene', 'Ontology', 'Organism', 'Pathway', 'Phenotype', 'Protein', 'PublicOntology', 'PublicOntologyField', 'Tissue', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '_display_sources', '_ontology', '_public_ontology', '_settings', '_sync_sources', 'dev', 'display_available_sources', 'display_currently_used_sources', 'entities', 'reset_sources', 'settings', 'sync_sources']

and my package version:
scdataloader 2.0.0
bionty 1.0.0
lamindb 1.0.4

[jkobject]

Hello @zhang0730,

Yes I am sorry, this notebook is a bit old and I haven't run it in quite some time. I think it must be run with an older version of scPRINT and the corresponding scDataloader (like the ones listed in the scPRINT nature paper)

Another solution would be to look at more up-to-date notebooks, like the example cancer notebook and also to modify slightly some cells based on what newer package versions require

Cheers,