Releases: draeger-lab/refinegems
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 frommodel.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 theanalysis_db
module to also obtain a mapping from the ModelSEED namespace to the BiGG namespace - Enhanced the
get_model_reacs_or_metabs
function in theentities
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 modulepolish
- 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