v2.3.0

Changed

• Bump Cython to v3.0.0.

v2.2.0

Changed

• Release GIL while masking sequence regions in Sequence.__init__.
• Use archspec instead of cpu_features for runtime feature detection.

Added

• CLI flag to run ORF detection in parallel when input contains several contigs.

Removed

• Support for Python 3.5.

v2.1.0

Changed

• Update Prodigal to v2.6.3+c1e2d36 to fix a bug with Shine-Dalgarno detection on reverse contig edge (hyattpd/Prodigal#100).

Added

• CLI flags to set the minimum gene size (#32, by @cjprybol).

Fixed

• ArchLinux User Repository package generation in CI.

v2.0.4

Fixed

• GC% computation and RBS scoring for reverse strand nodes close to the contig edge (#27).

v2.0.3

Fixed

• OrfFinder(mask=True) ignoring the minimum mask size when masking regions (#26).

Changed

• Use cibuildhweel for building wheel distributions.

Added

• Wheels for MacOS Aarch64 platforms.

v2.0.2

Fixed

• Syntax issue in Cython files failing build on Bioconda runner.

v2.0.1

Fixed

• Syntax issue in Cython files failing build on some environments.

v2.0.0

Added

• MMX implementation of the SIMD prefilter.
• Proper GFF headers and metadata section to GFF output.
• Sequence.gc_frame_plot method to compute the max GC frame profile from Python.
• metagenomic_bin property to TrainingInfo to support recovering the object corresponding to a pre-trained model.
• meta attribute to Genes to store whether genes were predicted in single or in meta mode.
• pyrodigal.PRODIGAL_VERSION constant storing the wrapped Prodigal version.
• pyrodigal.MIN_SINGLE_GENOME and pyrodigal.IDEAL_SINGLE_GENOME constants storing the minimum and recommended sequence sizes for training.

Changed

• Make all write methods of Genes objects require a sequence_id argument instead of using the internal sequence number.
• Rewrite SIMD prefilter using a generic template with C macros.
• Make Mask record coordinates in start-inclusive end-exclusive mode to follow Python conventions.
• Make connection scoring tests only score some randomly selected node pairs for faster runs.
• Rewrite tests to use importlib.resources for managing test data.

Removed

• from_bytes and from_string constructors of Sequence objects.

Fixed

• Duplicate extraction of start codons located on contig edges inside Nodes._extract (#21).
• Pickling and unpickling of TrainingInfo objects corresponding to pre-trained models.
• Implementation of calc_most_gc_frame being inconsistent with the Prodigal implementation.
• Implementation of the maximum search in score_connection_forward_start not following the (weird?) behaviour from Prodigal (#21).
• Gene identifier being used instead of the sequence identifier in the GFF output (#18).
• Out of bound access to sequence data in Sequence._shine_dalgarno_mm and Sequence._shine_dalgarno_exact.

v2.0.0-rc.4

Changed

• Make Mask record coordinates in start-inclusive end-exclusive mode to follow Python conventions.

Removed

• from_bytes and from_string constructors of Sequence objects.

v2.0.0-rc.3

Added

• Sequence.gc_frame_plot method to compute the max GC frame profile from Python.

Changed

• Rewrite tests to use importlib.resources for managing test data.
• Make connection scoring tests only score some randomly selected node pairs for faster runs.

Fixed

• Duplicate extraction of start codons located on contig edges inside Nodes._extract.