0.5.2

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.

0.5.1

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.

0.5.0

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.

0.4.7

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.

0.4.6

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.

0.4.5

Fixed

• Compilation of OSX and Windows wheels.

0.4.4

Fixed

• Mark package as OS-independent.

Added

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

0.4.3

Fixed

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

0.4.2

Fixed

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

0.4.1

Removed

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

Fixed

• Broken linking of static libprodigal against the _pyrodigal extension
  on some OSX environments (bioconda/bioconda-recipes#25568).