2.0.0

Enrich2 now runs on Python 3 and is installable via PyPI.

Major changes:

• Updated to work on Python 3. The code has been most extensively tested on Python 3.12 but other versions should also work.

Minor changes:

• Fixes a long-standing bug with empty counts CSV files being generated for Experiment objects.
• Uses [fqfa](https://github.com/countess-project/fqfa} to handle FASTQ files instead of its own internal code.
• Many small changes due to the Python 2 to 3 conversion.

1.3.1

Minor changes:

• Fixed #34
• enrich_cmd --version now outputs only the version number.

1.3.0

After careful consideration of community feedback, Enrich2 will now be distributed under the permissive BSD 3-clause license.

Major changes:

• Relicensed from GPLv3 to BSD 3-clause.
• Overhauled logging to ensure compatibility with messages generated by other modules.
• Updated installation requirements so a fresh install is possible with the current version of conda.

Minor changes:

• Made some minor code changes to keep pace with updates to pandas and matplotlib.
• Numerous changes to tidy up the code, such as fixing whitespace and removing unused imports.
• Small updates to installation documentation.

1.2.1

Minor changes:

• Fixed bugs that prevented the use of custom amino acid groupings.
• Set matplotlib backend to "Agg" when running inside a Docker container. Previously, generating plots from inside a Docker container would throw an error.
• Updated version requirements to ensure Python2 versions of dependencies are used.

1.2.0

This version fixes an error that caused combined standard errors to be overestimated for most experiments. Existing users with replicate data should update and re-run their analyses. See the documentation for details on how to do this with least impact.

Major changes:

• Fix standard error calculation for combined replicates.

Minor changes:

• Update manuscript link in documentation.

1.1.1

First post-publication update.

Minor changes:

• Updated Enrich2 citation to point to the Genome Biology paper instead of bioRxiv.
• Updated dependencies to specify pandas 0.18 or 0.19 due to incompatibility with 0.20.
• Added a Conda environment file to simplify setup for Anaconda users.
• Version number is now displayed in the GUI main window title.
• When running on MacOS, the program now sets the matplotlib backend to 'TkAgg' to avoid the NSInvalidArgumentException that occurs when running in GUI mode with no backend set. Advanced users who want to use a different matplotlib backend under MacOS in command line mode will need to edit the matplotlib.use() statement in main.py.

1.1.0a

The version number is now correct throughout the code and documentation.

1.1.0

New features:

• Added count mode. This allows the user to specify a file containing counts for each element instead of a FASTQ file.
• Added identifier-only sequencing libraries.
• Users can now change the amino acid groupings used for sequence-function maps and diversity maps.

Minor changes:

• Basic SeqLibs now have read trimming options.
• Added a --version command line option.
• Identifier scoring now supports wild type normalization if the special wild type variant "_wt" is present.
• Multiple plotting updates to better support plotting in notebooks.
• Default amino acid groupings for sequence-function maps updated.
• Improved variant validation.
• Fixed an error when maximum N's was set to 0.
• Numerous linting and code cleanup changes.

1.0.0

Initial public release. Corresponds to the version used in the Enrich2 preprint.