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Release history

This is a summary of the changelog.

0.1.0

  • First release of PyPath, for initial testing.

0.2.0

  • 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.

0.3.0

  • First version with partial Python 3 support.

0.4.0

  • 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.

0.5.0

  • 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.

0.5.32

  • chembl, unichem, mysql and mysql_connect modules are Python3 compatible

0.6.31

  • 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

0.7.0

  • TF-target, miRNA-mRNA and TF-miRNA interactions from many databases

0.7.74

  • 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

0.7.93

  • New dataio methods for Gene Ontology

0.7.110

  • Many new docstrings

0.8

  • 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

0.9

  • 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

0.10.0

  • A complete reorganization of the module structure: submodules sorted into a few major groups: core, inputs, internals, omnipath, share, utils

0.11.0

  • A complete redesign of the intercellular communication database
  • License support

0.12.0

  • Reorganization of the inputs module: each resource has its own submodule

0.13.0

  • A large part of the input methods has been tested and updated

0.14.0

  • Reorganized repository tree: the contents of the former src directory have been moved to the root
  • Settings are stored in a YML file

Upcoming

  • 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)