Move changes from structure update to dev-2 #119
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- restructured media documentation - added new description for database
extended load_model_cobra to allow entering all types of model files readable by cobrapy
update reannotate SBO
analysis_biocyc.py: 1. chemical formula error catching 2. check if input paths exists because PICNIC analysis_db: 1. added multiprocessing for BiGG db requests, currently splitted in 5 threads, more might overwhelm db? 1. TODO: progress bar is not working 2. TODO: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_index,col_indexer] = value instead in line 165, 170 -> however .loc is used, I dont see the issue here... gapfill.py: 1. avoid conflicts while converting None ChEBI values to floats
fixed the progress bar & accidentally enhanced the run time of gap_analysis added to analysis db: pd.options.mode.chained_assignment = None # suppresses the pandas SettingWithCopyWarning; comment out before developing!!
- Added logo to Zenodo DOI & changed appearance of badge - Added DOI for publication in Frontiers
This reverts commit 5a5e8eb.
…inegems into structure-update
- Addition of DiReM - Minor fixes for incorrect substance names
- Added better description of boolean 'update_entries' - Changed FLOAT_REGEX.match to FLOAT_REGEX.fullmatch
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Apr 12, 2024
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The structure update is done so far. Moving the changes to dev-2 to move forward to a new release.