v2.0.0a1 - Hot fixes in gapfill, growth & docs

What's Changed

• Fixed issues in .classes.gapfill.GapFiller.fill_model -> BioCycGapFiller is now usable.
• Fixed issues in .analysis.growth.test_auxotrophies -> Infeasible result from model.optimize is now handled as 0.0.
• Added a tutorial Python notebook
• Removed now obsolete deprecation warning from index.html

• Hot fixes for 2.0.0a0 pre-release by @GwennyGit in #135

Full Changelog: v2.0.0a0...v2.0.0a1

v2.0.0a0 - Pre-release of refactored & extended version

What's Changed

• For details see what @cb-Hades + @GwennyGit did in #121
• Polish update - Enable more GeneProduct annotations by @GwennyGit in #88
• Refactoring of the complete program structure
  • Move changes from structure update to dev-2 by @GwennyGit in #119
  • Merge dev-2 into dev to get refactoring ready for main by @GwennyGit in #133
• Pre-release of version 2.0.0 by @GwennyGit in #134

Full Changelog: v1.5.0...v2.0.0a0

v1.5.0

What's Changed

Due to changes in the planned-to-release version 2.0.0, which will lead to backward incompatibility for all functions, deprecation warnings for the end user were added to all modules and the documentation.

• Dev by @GwennyGit in #132

Full Changelog: v1.4.2...v1.5.0

Hotfix to enable download from PyPI again

The latest version did not import after it was downloaded from PyPI. This hotfix resolves the issue.

Minor bug fixes & Fixed documentation

With this release, the following files are updated:

• README
• Makefile and make.bat
• requirements.txt
• main.py

For the documentation to work, a requirements.in file was created to automatically update the requirements.txt to make it more reproducible. Furthermore, the documentation for the ‘Notes for developers’ section is updated, and minor bugs in the main.py file are fixed.

Publication badge, how to cite and more

With this release:

• a badge for the Frontiers publication mentioning/ introducing refineGEMs,
• a How to cite section within the documentation main page and the README of this repository,
• a CITATION.cff enabling a citation button on the main page of this repository,
• some bug fixes,
• a new module called util and
• some computational time changes are added.

In addition, the Pipfile, Pipfile.lock & MANIFEST.in files are removed.
Moreover, the media definitions within the database data. db are updated.

The bug fixes are for the module polish.
The computational time changes are for the module gapfill.

New features: database access & more general functions

• Made internal database in refineGEMs available to be used in user-specific scripts
• Enhanced the get_bigg2other_db function in the analysis_db module to also obtain a mapping from the ModelSEED namespace to the BiGG namespace
• Enhanced the get_model_reacs_or_metabs function in the entities module to create a pandas.DataFrame with a user-specific column name for the extracted reactions/metabolites (The default column name stayed the same to keep backwards compatibility.)

Fixed bugs in the `polish` module related to BioCyc annotations and Nones

• Adjusted handling of BioCyc identifiers within the polish_annotations function of the module polish
• Added requirement for importlib_resources=5.13.0 to Pipfile
• Added code to cope with missing sub-database prefixes for BioCyc identifiers
• Changed NaN identifier handling
• Fixed issue with None prefix identifier pairs being listed in invalid_curies.tsv

Removed bug from documentation for polish module

The documentation displayed the functions of the polish module incorrectly. This is fixed now.

Enhacements in polish module

With this release, the polish module is now connected to the API of bioregistry.io.

New additions to the polish module:

• Check for invalid CURIEs with bioregistry
• Addition of MIRIAM compliant URIs/IRIs with bioregistry
• Invalid URIs & CURIEs are reported back with file(s) for better manual curation
• NaN identifiers are removed, reported with invalid URIs & CURIEs and removed
• If 'id_db' is set to 'VMH' the BiGG identifiers retrieved from the VMH ones are checked for validity