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CHANGELOG.md

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Version History


All notable changes to this project will be documented in this file.

Added

  • CHANGELOG.md for documenting changes

  • DEVELOPER.md developer notes

  • environment.yml conda environment specification

  • Included versioneer for managing version strings through git tags

Changed

  • Depends on python >= 3.7, ensure dict objects maintain insertion-order. See What’s New In Python 3.7
  • Removed bulk and sc subcommands since the single-cell stellarscope project has moved into its own repository.

Fixed

  • Error where numpy.int is deprecated

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Previous versions

Prior to this CHANGELOG, changes were tracked in README.md. The previous version history is relocated here:

v1.0.3.1

  • Checks that GTF feature type is "exon"
  • Skips GTF lines missing attribute (with warning)

v1.0.3

  • Added cimport statements to calignment.pyx (MacOS bug fix)
  • Fixed warning about deprecated PyYAML yaml.load
  • Compatibility with intervaltree v3.0.2

v1.0.2

  • Temporary files are written as BAM

v1.0.1

  • Changed default theta_prior to 200,000

v1.0

  • Removed dependency on git
  • Release version

v0.6.5

  • Support for sorted BAM files
  • Parallel reading of sorted BAM files
  • Improved performance of EM
  • Improved memory-efficiency of spare matrix

v0.5.4.1

  • Fixed bug where random seed is out of range

v0.5.4

  • Added MIT license
  • Changes to logging/reporting

v0.5.3

  • Improvements to telescope resume

v0.5.2

  • Implemented checkpoint and telescope resume

v0.5.1

  • Refactoring Telescope class with TelescopeLikelihood
  • Improved memory usage

v0.4.2

  • Subcommand option parsing class
  • Cython for alignment parsing
  • HTSeq as alternate alignment parser

v0.3.2

  • Python3 compatibility

v0.3

  • Implemented IntervalTree for Annotation data structure
  • Added support for annotation files where a locus may be non-contiguous.
  • Overlapping annotations with the same key value (locus) are merged
  • User can set minimum overlap criteria for assigning read to locus, default = 0.1

v0.2

  • Implemented checkpointing
  • Output tables as pickled objects
  • Changes to report format and output