v3.7.0

Added

• SWAR (SIMD Within A Register) implementation of the connection scoring pre-filter for platforms lacking SSE or NEON support.
• Support for Pyodide/Emscripten builds (#73).
• source_separator argument to Genes.write_gff to support using the preferred GFF3 format (#77).

Fixed

• Detection of SIMD flags on non-MSVC compilers used on Windows.
• Incorrect metadata keys in pyproject.toml causing compilation issues with recent build versions.
• Miscellaneous broken links in documentation and README.md.
• Confusing documentation of the --no-stop-codon flag in CLI (#66, by @apcamargo).

Changed

• Internal type of strands encoded in SIMD pre-filter to uint8_t to only have to perform unsigned comparisons.

Removed

• Deprecated code for MMX detection and testing.

v3.6.3-post1

Fixed

• Extra key in pyproject.toml causing build issues with version 0.11.0 of scikit-build-core.

v3.6.3

Fixed

• Dynamic dispatch to NEON connection scorer on Aarch64 MacOS.

v3.6.2

Fixed

• pyrodigal console script not being installed.

v3.6.1

Added

• Compilation of the connection scoring code for AVX-512.

Fixed

• Import issue on platforms without AVX2 runtime support.
• Missing metadata in pyproject.toml.

v3.5.2

Added

• Warning in CLI when given sequences with empty identifiers.

Fixed

• FASTA parser used in CLI crashing on empty header lines (#61).

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• Outdated code in pyrodigal.cli breaking the CLI.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).