What's Changed

• Corrected index_info msg call to fix single quote confusion by @maca8e in #298
• Fixes #293 by @npalacioescat in #304
• Removing "*" fallback in organism_id for inputs.uniprot.UniProtQuery by @npalacioescat in #303

New Contributors

• @maca8e made their first contribution in #298

Full Changelog: v0.16.18...v0.16.20

Almost complete transition to the newly split off package pypath_common.
There might be still many minor issues, bug reports are very welcome.

Full Changelog: v0.16.0...v0.16.5

• Improved handling of possible ID pairs in ID translation
• Minor bug fixes in orthology.translate_df
• Many other bug fixes

• Refactored orthology translation
• OMA is the default source of orthology data

• New UniProt REST API instead of legacy UniProt API
• New UniProt ID Mapping API instead of legacy Uploadlists API
• Evidences carry dataset attribute
• New evidences column in web server interactions data frame contains JSON encoded detailed evidence and direction information

• Fixed minor issues in many inputs
• Fixed license related issues in CollecTRI
• Added a few missing dependencies

• New network resource: CollecTRI, a major and comprehensive gene regulatory network
• Fixed issues in the following input modules: corum, guide2pharma, kirouac2010, go, cosmic, wang, msigdb, kegg, interpro, matrisome, ramilowski2015, embopress, celltypist, mppi
• Minor improvements in ID translation
• New ID translation services for metabolites and other small molecules: ramp and hmdb
• New clients in inputs: RaMP and HMDB
• New sections in the Pypath Book

• Updated sphinx docs build
• Fixed: in rare cases, file names with forbidden characters resulted download failures under Windows

UniProt moved its uploadlists API to the legacy domain. This API is essential for the ID translation and orthology utilities, also used by many input modules, hence this update is critical to keep pypath working.