Change Log

All notable changes to this project will be documented in this file.

The format is based on this sample changelog.

[0.2.5] - 2023-07-18

Update MLflow version
Fix data dir missing from src/graphmb
Add option to write bins to fasta files (--writebins)

[0.2.4] - 2023-03-31

Update Tensorflow and MLflow versions

[0.2.3] - 2023-02-03

Changed

vaepretrain parameter controls the number of epochs of VAE pre-training (default 500)

[0.2.2] - 2023-02-02

Fixed

Correct wheel file

[0.2.0] - 2023-02-01

Added

VAE, GCN, SAGE and GAT models based on tensorflow (VAEG code)
SCG-based loss to train VAE and GNNs
Output assembly stats while starting
Eliminate VAMB and DGL dependencies
PyPI installation

Changed

Code structure changed to load data outside of DGL and use DGL only for the GraphSAGE-LSTM model
Log dataloading steps
Write cache to numpy files

Fixed

Feature files are written to specific directories (fixes #17)

[0.1.3] - 2022-02-25

BioarXiv version

pip install . --upgrade

Added

Dockerfile and docker image link
Set seed option
Eval interval option

Changed

Change default file name

Fixed

Assembly dir option is no longer mandatory, so files can be in different directories
Logging also includes errors
DGL should no longer write a file to ~/