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CHANGELOG.md

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Changelog

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

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

Unreleased

v0.5.4 - 2021-09-18

Added

  • Prediction.confidence method to compute the confidence for a prediction like reported in Prodigal's GFF output.
  • Prediction.sequence method get the nucleotide sequence of a predicted gene (#4).

Changed

  • Replaced internal storage of input sequences to use a byte array instead of a bitmap.

Fixed

  • Extract Prediction.gc_cont number directly from the start node instead of the text representation to get full accuracy.
  • Prodigal bug causing nodes on the reverse strand to always receive a penalty instead of penalizing only small ORFs (hyattpd/Prodigal#88).

v0.5.3 - 2021-09-12

Fixed

  • Prediction.translate not translating the last unknown codon properly for genes on the direct strand.

v0.5.2 - 2021-09-11

Changed

  • Make Pyrodigal.train return a reference to the newly created TrainingInfo for inspection if needed.
  • Reimplement add_nodes and add_genes to use a growable array instead of counting and pre-allocating the C arrays.

Fixed

  • Inconsistent handling of unknown nucleotides in input sequences and gene translations.

v0.5.1 - 2021-09-04

Added

  • Additional Gene properties to access the score

Changed

  • Use more efficient PyUnicode macros when reading or creating a string containing a nucleotide or a protein sequence.
  • Release the GIL when creating a bitmap for an str given as input to Pyrodigal.find_genes.
  • Release the GIL when creating the protein sequence returned by Gene.translate.

Fixed

  • Pyrodigal.find_genes and Gene.translate not behaving like Prodigal when handling sequences with unknown nucleotides.

v0.5.0 - 2021-06-15

Added

  • pyrodigal.TrainingInfo class exposing variables obtained during training as an attribute to Pyrodigal, Gene and Genes instance.
  • Support for passing objects implementing the buffer protocol to Pyrodigal.find_genes and Pyrodigal.train instead of requiring str sequences.

Fixed

  • Potential data race on training info in case a Gene.translate with a non-default translation table was being translated at the same time as a Pyrodigal.find_genes call.
  • Spurious handling of Unicode strings causing potential issues on platform using a different base encoding.

v0.4.7 - 2021-04-09

Fixed

  • Pyrodigal.find_genes segfaulting on some sequences when called in single mode (#2).
  • MemoryError potentially not being properly raised on allocation issues for sequence bitmaps.

v0.4.6 - 2021-03-05

Changed

  • Tests are now in the pyrodigal.tests module and can be run after a site install.

Fixed

  • Pyrodigal.find_genes stalling on sequences shorter than 3 nucleotides.

v0.4.5 - 2021-03-03

Fixed

  • Compilation of OSX and Windows wheels.

v0.4.4 - 2021-03-03

Fixed

  • Mark package as OS-independent.

Added

  • Support for Python 3.5.
  • Compilation of PyPy wheels on OSX.

v0.4.3 - 2021-03-01

Fixed

  • Buffer overflow when running in meta mode on a sequence too small to have any dynamic programming nodes.

v0.4.2 - 2021-02-07

Fixed

  • Buffer overflow coming from the node array, caused by an incorrect estimation of the node count from the sequence length.

v0.4.1 - 2021-01-07

Removed

  • Python 3.5 from the project metadata (the code was only compatible with Python 3.6+ already because of f-strings).

Fixed

v0.4.0 - 2021-01-06

Changed

  • trans_table keyword argument to Pyrodigal.train has been renamed to translation_table.

Added

  • Option to change the translation table to any allowed number in Gene.translate (#1).

v0.3.2 - 2020-11-27

Fixed

  • Broken compilation of PyPy wheels in Travis-CI.

v0.3.1 - 2020-11-27

Added

  • Link to Zenodo record in README.md.
  • Typing :: Typed classifier to the PyPI metadata.
  • Explicit support for Python 3.9.

Changed

  • Streamlined compilation process when building from source distribution.

v0.3.0 - 2020-09-07

Added

  • Thread-safety for all Pyrodigal methods

Fixed

  • Reduced total amount of memory used to allocated dynamic programming nodes for a given sequence.

v0.2.4 - 2020-09-04

Added

  • Precompiled wheels for Windows x86-64 platform.

Changed

  • Compilation of large Prodigal/training.c file is now done in chunks and uses static const to reduce build time.

v0.2.3 - 2020-08-09

Fixed

  • Buffer overflow issue with Pyrodigal in closed=False mode.

v0.2.2 - 2020-07-14

Added

  • Access to the translation table of a Gene object.

v0.2.1 - 2020-05-29

Fixed

  • Memory issues causing PyPy to crash when using Pyrodigal in single mode.

v0.2.0 - 2020-05-28

Added

  • Support for Prodigal's single mode.

v0.1.1 - 2020-04-30

Added

  • Distribution of CPython wheels for ManyLinux2010 and OSX platforms.

v0.1.0 - 2020-04-27

Initial release.