v2.0.0-rc.2

Added

• 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.

Fixed

• 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.

v2.0.0-rc.1

Added

• MMX implementation of the SIMD prefilter.
• Propert GFF headers and metadata section to GFF output.

Fixed

• Out of bound access to sequence data in Sequence._shine_dalgarno_mm and Sequence._shine_dalgarno_exact.
• Gene identifier being used instead of the sequence identifier in the GFF output (#18).

Changed

• Rewrite SIMD prefilter using a generic template with C macros.
• Make all write methods of Genes objects require a sequence_id argument instead of using the internal sequence number.

v1.1.2

Changed

• Use the vbicq Arm intrinsic in the NEON implementation to combine vandq and vmvnq.

Fixed

• Prevent direct instantiation of Node and Gene objects from Python code.
• Configuration of platform-specific NEON flags in setup.py not being applied to the linker.

v1.1.1

Fixed

• Some cpu_features source files not being included in source distribution.

v1.1.0

Changed

• OrfFinder.train can now be given more than one sequence argument to train on contigs from an unclosed genome.
• Updated cpu_features to v0.7.0 and added hardware detection of NEON features on Linux Aarch64 platforms.

v1.0.2

Fixed

• Detection of Arm64 platform in setup.py (#16).

v1.0.1

Changed

• pyrodigal.cli now concatenates training sequences the same way as Prodigal does.

v1.0.0

Stable version, to be published in the Journal of Open-Source Software.

Added

• pickle protocol implementation for Nodes, TrainingInfo, OrfFinder, Sequence, Masks and Genes objects.
• Buffer protocol implementation for Sequence, allowing access to raw digits.
• __eq__ and __repr__ magic methods to Mask objects.

Changed

• Optimized code used for region masking to avoid searching for the same mask repeatedly.
• TRANSLATION_TABLES and METAGENOMIC_BINS are now exposed as constants in the top pyrodigal module.
• Refactored connection scoring into different functions based on the type (start/stop) and strand (direct/reverse) of the node being scored.
• Changed the growth factor for dynamic arrays to be the same as the one used in CPython list buffers.

v0.7.3

Added

• Gene.score property to get the gene score as reported in the score data string.

Fixed

• OrfFinder.find_genes not producing consistent results across runs in meta mode (#13).
• OrfFinder.find_genes returning Nodes with incomplete score information.

v0.7.2

Changed

• Improve performance of mer_ndx and score_connection using dedicated implementations with better branch prediction.
• Mark arguments as const in C code where possible.

Fixed

• Signatures of Cython classes not displaying properly because of the embedsignature directive.
• _sequence.h functions not being inlined as expected.