Changelog

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Fixes in 1.2.4

1.2.3 - 2021-02-09

Added in 1.2.3

  • Add citation for paper published in Bioinformatics (doi)

Changes in 1.2.3

  • CI with Github Actions (Linux, macOS)

Fixes in 1.2.3

  • Fixes a bug where custom trained models would not use dropout correctly see #44

  • Fixes data usage in training with an iterable dataset without shuffling see #43

  • Fixes several non-critical warnings see #50

  • Several small fixes regarding updated libraries etc.

1.2.2 - 2020-12-10

Added in 1.2.2

  • Install from bioconda

  • Support for 109 taxonomic levels in eggNOG 5 (was three before) (e.g. deepnog infer -db eggnog5 -t 1239 for Firmicutes)

  • Support for COG2020 (use deepnog infer -db cog2020 -t 1)

Fixes/changes in 1.2.2

  • Requirement PyYAML

  • Test class imports

  • Exit on requesting unavailable device (instead of raising an error)

1.2.1 - 2020-08-28

Added in 1.2.1

  • Training custom models: Users can now train additional models for further tax. levels of eggNOG 5 or even different orthology databases

  • TensorBoard status reports: Follow training/validation loss online

  • Support for configuration file (deepnog_config.yml)

  • Model quality assessment

Changed in 1.2.1

  • The command line invocation now uses two subcommands:

    • deepnog train for training new models, and

    • deepnog infer for general orthologous group assignment (and model quality assessment)

Fixed in 1.2.1

  • Fixed packaging issue in 1.2.0 (which was subsequently removed altogether)

  • Several additional bug fixes and smaller changes

1.1.0 - 2020-02-28

Added

  • EggNOG5 root (tax 1) prediction

Changed

  • Package structure changed for higher modularity. This will require changes in downstream usages.

  • Remove network weights from the repository, because files are too large for github and/or PyPI. deepnog automatically downloads these from CUBE servers, and caches them locally.

  • More robust inter-process communication in data loading

Fixes

  • Fix error on very short amino acid sequences

  • Fix error on unrecognized symbols in sequences (stop codons etc.)

  • Fix multiprocess data loading from gzipped files

  • Fix type mismatch in deepencoding embedding layer (Windows only)

Maintenance

  • Continuous integration on

  • Codecov coverage reports

  • LGTM code quality/security reports

  • Documentation on ReadTheDocs

  • Upload to PyPI, thus enabling $ pip install deepnog.

1.0.0 - 2019-10-18

The first release of deepnog to appear in this changelog. It already contains the following features:

  • EggNOG5 bacteria (tax 2) prediction

  • DeepEncoding architecture

  • CPU and GPU support

  • Runs on all major platforms (Linux, MacOS, Windows)