BPReveal 5.0.2

This minor bugfix release fixes a rare segfault that could occur with extremely large training data sets. This bug was introduced in 4.1.1. If you need this fixed in a 4.x release, copy over the new libslide.c file into src/internal and run make in src to re-build libslide with the segfault fix.

This release has no breaking changes.

BPReveal 5.0.1

Version 5.0 of BPReveal moves from the old Keras 2.0-based code to Keras 3.0 through most of the repository. All existing configurations should still be valid, but note that models are now saved with a .keras extension instead of .model. If you are using the BPReveal API, those calls should all work just as before, but if you were manually loading a model, that will probably need to change.

If your current BPReveal install is working fine, there's not much reason to upgrade to 5.0, but new features will not be backported.

Note that 5.0.0 should not be installed, since Tensorflow 2.18 has a regression that totally breaks the GPU on my machine and therefore I'm not able to test it. 5.0.1 (this release) locks the Tensorflow version to 2.17 and that should be used instead.

Happy training!

BPReveal 4.3.0

• Fixed a long-standing bug where it was impossible to interpret combined or transformation models. Fixing this required a slight change to the internals of how a transformation model works, but this should be transparent for most users.
• There's a motif curation program in the tools/ directory, and it will migrate to the main repository in the next release. It's called bestMotifsOnly.py.
• You can also now have interactive PISA plots, which is handy for exploring your data.
• You can render the documentation as man pages now.

Documentation is available as a PDF attached to this announcement, or online at https://bpreveal.readthedocs.io/en/v4.3.0/

Happy training!

BPReveal 4.2.0

This release brings the python version to 3.12 and Tensorflow to 2.16, but keeps using the old keras (TF_ENABLE_LEGACY_KERAS). If you're using Keras directly, you'll have to import tf_keras instead of keras on its own.
Once the deepshap code can use Keras 3, then the whole repo will migrate to keras 3, which will likely introduce more breaking changes.

This version introduces plotting.py, which can create handsome graphics like this:

As always, everything is documented to the nines, and you can read the documentation on readthedocs, or in the attached four-and-a-half megabyte, two hundred fifty-nine page PDF.

Happy training!

BPReveal 4.1.4

Locked the tensorflow version to 2.15, since the change in Keras version in 2.16 caused all sorts of breakage.
Due to the tensorflow update being a breaking change, old releases of BPReveal will no longer create a valid environment.

Added a tool to shift PISA data, mostly useful for mnase data.

Added a very performant metapeak calculator to bedUtils.

Lots of little bug fixes.

BPReveal 4.1.3

• You can specify quantile cutoffs for each pattern independently in motif scanning
• Motif seqlet cutoffs now extracts seqlet coordinate information and saves it
• Fixed the tensorflow version to 2.15 since 2.16 breaks everything.

BPReveal 4.1.1

Parallelized the PISA code so it now runs quite a bit faster if you specify num-threads.

Combined makePredictionsBed and makePredictionsFasta into a single makePredictions script. The old names will be retired in 6.0.0.

Added documentation for motif scanning. (Melanie Weilert)

Made the generator used during training a lot faster at generating new batches.

Made non-links be non-blue in the documentation. (Patrick Moeller)

Documentation is now online at https://mmtrebuchet.github.io/bpreveal/4.1.1/index.html

BPReveal 4.1.0

Re-wrote the logging system for training from scratch, you can now use a fancy TUI to watch your model's progress as it trains.

Extracted logging into a separate logUtils module

Several performance improvements in bed file processing.