Bpnet-lite

Latest version: v0.8.1

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0.8.1

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Highlights
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- Added robustness toward other characters in the nucleotide alphabet.
Anything not A, C, G, or T gets ignored. This robustness has been added to
PeakGenerator and the command line arguments.

0.8.0

==============

Highlights
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- When training ChromBPNet bias models from the command line and no loci
are provided for training the bias model, the default is changed to inherit
from `negatives` instead of `loci`. Colloquially, when the user provides a
set of negatives and peak loci to train ChromBPNet, the default is now that
the bias model will be trained on the negatives instead of incorrectly on
the peaks.
- When calculating the maximum number of reads a negative region can have
when training the bias model, changed from using the minimum number of reads
in the peaks to the 1st quantile of reads because it is more robust.

0.7.4

==============

Highlights
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- Re-added the `attribute.py` file back in with a `deep_lift_shap` function
that wraps tangermeme's function but passes in the layers that must be
registered.

0.7.3

==============

Highlights
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- Added `BasePairNet` in `bpnetlite.bpnet` which is an implementation of the
model from the official `basepairmodels`
- Added `BasePairNet.from_bpnet` to load TensorFlow-trained models from
`basepairmodels` into the PyTorch wrapper
- Removed a few dependencies that are no longer needed after using
tangermeme

0.7.2

==============

Highlights
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- Complete inclusion of tangermeme as the backend for operations
- Remove the `predict` method for models in favor of `tangermeme.predict`
- Remove attribute.py in favor of `tangermeme.deep_lift_shap`
- Remove marginalization functions in favor of `tangermeme.marginalize`
- Remove plotting functions in favor of `tangermeme.plot`
- Alter the `bpnet` and `chrombpnet` command-line tools to account for
these changes.
- Add in `_Log` and `_Exp` as layers for the ChromBPNet model so that they
can be registered as non-linear functions for `deep_lift_shap`.

0.7.1

==============

Highlights
----------

- Begin inclusion of tangermeme into the backend.

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