pip installation pulls v3.3.0 prerelease by default (+ error on inference)

[lkwhite]

When installing Remora via pip, the default package pulled is 3.3.0, which appears to still be a prerelease version?

My brief, unintended testing of v3.3.0 appears to produce this error when performing inference on a pre-trained model. This was resolved with rollback to 3.2.0.

Example command:

remora infer from_pod5_and_bam \
  data/myfile.pod5 data/myfile.bam \
  --model train_results/model_best.pt \
  --out-bam out/myfile_infer.bam \
  --log-filename out/myfile_infer.log \
  --reference-anchored --device 0

Error produced:
UNEXPECTED_ERROR in PrepBatches worker: ''base_pred''. KeyError: 'base_pred'
This further produced an empty output bam.

[marcus1487]

Hi Laura,

I would indeed recommend rolling back to v3.2. The features in v3.3 were mostly experimental aside from the release of the NCM 2024 modified base models.

If your model comes from v3.3.0 you should be able to run the model with v3.3.0 code. I'm having trouble tracking down where this error might be coming from. The last time the base_pred values was used was in <v3 (v2.1.2 was the last release). So it seems like your model might have been trained from an older dataset. The latest datasets structure should be much easier to work with if you can upgrade and remake the datasets.