This is a summary of the changelog.
- First release of PyPath, for initial testing.
- Lots of small improvements in almost every module
- Networks can be read from local files, remote files, lists or provided by any function
- Almost all redistributed data have been removed, every source downloaded from the original provider.
- First version with partial Python 3 support.
- pyreact module with BioPaxReader and PyReact classes
- Process description databases, BioPax and PathwayCommons SIF conversion rules are supported
- Format definitions for 6 process description databases included.
- Many new classes in the plot module
- All figures and tables in the manuscript can be generated automatically
- This is supported by a new module, analysis, which implements a generic workflow in its Workflow class.
- chembl, unichem, mysql and mysql_connect modules are Python3 compatible
- Orthology translation of network
- Homologene UniProt dict to translate between different organisms UniProt-to-UniProt
- Orthology translation of PTMs
- Better processing of PhosphoSite regulatory sites
- TF-target, miRNA-mRNA and TF-miRNA interactions from many databases
- New web server based on pandas data frames
- New module export for generating data frames of interactions or enzyme-substrate interactions
- New module websrvtab for exporting data frames for the web server
- TF-target interactions from DoRothEA
- New dataio methods for Gene Ontology
- Many new docstrings
- New module `complex`: a comprehensive database of complexes
- New module `annot`: database of protein annotations (function, location)
- New module `intercell`: special methods for data integration focusing on intercellular communication
- New module `bel`: BEL integration
- Module go and all the connected dataio methods have been rewritten offering a workaround for data access despite GO's terrible web services and providing much more versatile query methods
- Removed MySQL support (e.g. loading mapping tables from MySQL)
- Modules mapping, reflists, complex, ptm, annot, go became services: these modules build databases and provide query methods, sometimes they even automatically delete data to free memory
- New interaction category in `data_formats`: ligand_receptor
- Improved logging and control over verbosity
- Better control over paremeters by the settings module
- Many methods in dataio have been improved or fixed, docs and code style largely improved
- Started to add tests especially for methods in dataio
- The network database is not dependent any more on python-igraph hence it has been removed from the mandatory dependencies
- New API for the network, interactions, evidences, molecular entities
- A complete reorganization of the module structure: submodules sorted into a few major groups: core, inputs, internals, omnipath, share, utils
- A complete redesign of the intercellular communication database
- License support
- Reorganization of the inputs module: each resource has its own submodule
- A large part of the input methods has been tested and updated
- Reorganized repository tree: the contents of the former src directory have been moved to the root
- Settings are stored in a YML file
- Full support for multi-species molecular interaction networks (e.g. pathogene-host)
- Better support for not protein only molecular interaction networks (metabolites, drug compounds, RNA)
- Graph database (Neo4j) backend (biocypher)
- Split into separate modules (core, inputs, utils, dlmanager, etc)