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CHANGELOG.md

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Change Log

All notable changes to this project will be documented in this file, following the suggestions of Keep a CHANGELOG. This project adheres to Semantic Versioning.

v0.3.6 - 2019-01-18

  • New features
    • Added ref_genome parameter to g2sDataset.get_position_dataset

v0.3.5 - 2018-12-28

  • Changes
    • Replaced top level notebook example with new version using InteractionExtractor

v0.3.0 - 2018-12-26

  • Bug fixes

    • Removed hard-coded denominator value for decoding occupancy values

  • Changes

    • Upgraded pyspark to 2.3.2
    • Use pandas msgpack library instead of msgpack-python for decoding

  • New features

    • Added InteractionExtractor class using vectorized methods
    • Added new filter methods in InteractionFilter class using vectorized methods

v0.2.7 - 2018-11-24

  • Bug fixes

    • Fixed MMTF decoding error

  • New features

    • Added method to retrieve PTMs from dbPTM
    • Added method to retrieve PTMs from PDB
    • Added method to retrieve PDB to Uniprot chain and residue level mappings
    • Added support for ligandIds in advanced search results
    • Added method to create dataset for advanced search results
    • Added pyarrow 0.8.0 dependency
    • Added xlrd 1.1.0 dependency to support Excel spreadsheets with pandas

  • Changes

    • Use https instead of ftp to retrieve BlastClust data
    • Upgraded py3dmol to 0.8.0
    • Moved binder related files to binder directory

v0.2.6 - 2018-05-21

Upgrade to mmtf-python 1.1.2

  • use latest version of mmtf-python that uses msgpack 0.5.6
  • update to msgpack>=0.5.6 from msgpack-python (PyPi package name has changed!)
  • update py4j to 0.10.6 as required by pyspark 2.3.0

v0.2.5 - 2018-05-18

Remove SparkContext as parameter

  • remove sc from mmtfReader and mmtfWriter functions parameters
  • fix windows durgbank decoding issue

v0.2.4 - 2018-05-06

Final updates before MMTF Workshop 2018

  • Included all modules in init files

v0.2.2 - 2018-05-04

Using Wheel for better packaging

  • Using wheel to package

v0.2.1 - 2018-05-04

Update version for MMTF Workshop 2018

  • New functions, classes and demo notebooks

v0.2.0 - 2018-03-05

Alpha Version Released on PyPI

  • Finished all classes, functions and unit tests for alpha release

v0.1.0 - 2017-11-27

Development Version

  • Created setup.py for local pip install