v3.5.1

Fixed

• Outdated code in pyrodigal.cli breaking the CLI.

v3.5.0

Added

• Support for reading from stdin in CLI (#35).
• Flag for changing parallel computation to use Pool instead of ThreadPool (#57).
• Better documentation of command line interface (#56).
• Allow changing the formatter class in pyrodigal.cli.argument_parser.

Changed

• Migrate documentation to pydata-sphinx-theme.

Fixed

• Cython warnings with unused except * statements in MetagenomicBins.
• Signatures of __init__ methods missing from all Cython types after the v3.0 update.
• Small typos in documentation.

v3.4.1

Changed

• Refactor SIMD code to reduce number of required registers, and improve SSE2 performance.
• Refactor Prodigal initialization functions into sparse initializer code to reduce library size.

v3.4.0

Added

• strict argument to Gene.translate to control translation of ambiguous codons with unambiguous translation (#54).
• strict_translation argument to Genes.write_genbank and Genes.write_translation.
• Support for translation tables 26 to 33 in Gene.translate.
• Support for translation tables 26, 29, 30, 32 and 33 in GeneFinder.train.
• Genes.score property to count the total score of all extracted genes.
• full_id parameter to Genes.write_gff, Genes.write_translation and Genes.write_genes to control the ID field written for each gene (#53).

Changed

• Gene.translate now raises a warning when called with a translation table incompatible with the training info.

Fixed

• Bug in code for masking trailing nucleotides (#55).

v3.3.0

Added

• CLI option to disable translation of stop codons (#51, by @zclaas).

Changed

• Scorer internal API to separate connection scoring and overlap disentangling.

Fixed

• Bug with computation of minimum node in connection scoring loop (hyattpd/Prodigal#108).
• Out-of-bounds sequence access in _shine_dalgarno_exact and _shine_dalgarno_mm methods of Sequence.
• Memory leak in Nodes.__setstate__ caused by incorrect reallocation.

v3.2.2

Fixed

• Always mark SSE2 support on x86-64 CPUs independently of archspec-detected features (#49).

v3.2.1

Added

• Option to change argument parser in pyrodigal.cli.main.

v3.2.0

Added

• AVX-512 implementation of the SIMD pre-filter.
• Additional support for reading lz4 and xz and zstd-compressed input in the CLI.
• Option to change gene finder type in pyrodigal.cli.main.

v3.1.1

Fixed

• Incorrect unpickling of GeneFinder causing crashes with multiprocessing (#46).

v3.1.0

Added

• Support for Python 3.12.
• min_mask argument to GeneFinder to control the minimum lenght of masked regions on mask=True.