Release v3.0.0

CHANGELOG.md

@@ -6,72 +6,76 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pyrodigal/compare/v3.0.0-alpha4...HEAD
+[Unreleased]: https://github.com/althonos/pyrodigal/compare/v3.0.0...HEAD
 
 
-## [v3.0.0-alpha4] - 2023-09-16
-[v3.0.0-alpha4]: https://github.com/althonos/pyrodigal/compare/v3.0.0-alpha3...v3.0.0-alpha4
+## [v3.0.0] - 2023-09-16
+[v3.0.0]: https://github.com/althonos/pyrodigal/compare/v2.3.0...v3.0.0
 
 ### Added
+- `MetagenomicBins` collection to store a dense array of `MetagenomicBin` objects.
+- `metagenomic_bins` keyword argument to `GeneFinder` allowing to control which models are used when running gene finding in *meta* mode ([#24](https://github.com/althonos/pyrodigal/issues/24)).
+- `metagenomic_bin` attribute to `Genes` referencing the metagenomic model with which the genes were predicted, if in *meta* mode.
+- Additional `TrainingInfo` properties (`missing_motif_weight`, `coding_statistics`).
+- Setters for all remaining `TrainingInfo` properties.
+- Proper `TrainingInfo` constructor with configuration option for all attributes.
+- `TrainingInfo.to_dict` method to extract all parameters from a `TrainingInfo`.
+- `Genes.write_genbank` method to write a GenBank record with all predicted genes from a sequence.
+- `include_stop` flag to `Gene.translate` and `Genes.write_translations` to allow excluding the stop codon from the translated sequence.
+- `include_translation_table` flag to `Genes.write_gff` to include the translation table to the GFF attributes of each gene.
+- `gbk` output format to the Pyrodigal CLI.
 - `Sequence.unknown` property exposing the number of unknown nucleotides in the sequence.
 - `Sequence.start_probability` and `Sequence.stop_probability` to estimate the probability of encountering a start and a stop codon based on the GC%.
 
+### Fixed
+- `Genes.write_gff` not properly reporting the number of bytes written.
+- Merge several `nogil` sections in `Sequence` constructor.
+- Several Cython functions missing a `noexcept` qualifier.
+
 ### Changed
+- **BREAKING**: Rename `OrfFinder` to `GeneFinder` for consistency.
+- **BREAKING**: Use `memoryview` to expose all `TrainingInfo` attributes instead manually building lists or tuples.
+- Reorganize memory management of the built-in metagenomic models.
+- Make the internal Cython model public (`pyrodigal.lib`) to allow importing the underlying classes in other Cython projects.
+- Use `typing.Literal` for allowed translation table values in `pyrodigal.lib` annotations
 - Cache intermediate log-odds in `Nodes._raw_coding_score` to reduce calls to `pow` and `log` functions.
 - Inline connection scoring functions to reduce function call overhead.
 - Reorganize `struct _node` fields to reduce size in memory.
 - Make `GeneFinder.find_genes` and `GeneFinder.train` reserve memory for the `Nodes` based on the GC% of the input sequence.
 - Avoid storing temporary results in the generic implementation of `ConnectionScorer.compute_skippable`.
+- Use Cython `freelist` for allocating `Node`, `Gene`, `MetagenomicBin` and `Mask`.
+- Increase minimum allocation for `Genes` and `Nodes` to reduce early reallocations.
+
+### Removed
+- **BREAKING**: `metagenomic_bin` attribute of `TrainingInfo`.
 
 
 ## [v3.0.0-alpha3] - 2023-09-11
 [v3.0.0-alpha3]: https://github.com/althonos/pyrodigal/compare/v3.0.0-alpha2...v3.0.0-alpha3
 
-### Fixed
-- Merge several `nogil` sections in `Sequence` constructor.
-- Several Cython functions missing a `noexcept` qualifier.
+
 
 ### Changed
-- Use Cython `freelist` for allocating `Node`, `Gene`, `MetagenomicBin` and `Mask`.
-- Increase minimum allocation for `Genes` and `Nodes` to reduce early reallocations.
+
 
 
 ## [v3.0.0-alpha2] - 2023-09-11
 [v3.0.0-alpha2]: https://github.com/althonos/pyrodigal/compare/v3.0.0-alpha1...v3.0.0-alpha2
 
-### Added
-- `Genes.write_genbank` method to write a GenBank record with all predicted genes from a sequence.
-- `include_stop` flag to `Gene.translate` and `Genes.write_translations` to allow excluding the stop codon from the translated sequence.
-- `include_translation_table` flag to `Genes.write_gff` to include the translation table to the GFF attributes of each gene.
-- `gbk` output format to the Pyrodigal CLI.
-
 ### Fixed
-- `Genes.write_gff` not properly reporting the number of bytes written.
 
 ### Changed
-- Use `typing.Literal` for allowed translation table values in `pyrodigal.lib` annotations
+
 
 
 ## [v3.0.0-alpha1] - 2023-09-07
 [v3.0.0-alpha1]: https://github.com/althonos/pyrodigal/compare/v2.3.0...v3.0.0-alpha1
 
-### Added
-- `MetagenomicBins` collection to store a dense array of `MetagenomicBin` objects.
-- `metagenomic_bins` keyword argument to `GeneFinder` allowing to control which models are used when running gene finding in *meta* mode ([#24](https://github.com/althonos/pyrodigal/issues/24)).
-- `metagenomic_bin` attribute to `Genes` referencing the metagenomic model with which the genes were predicted, if in *meta* mode.
-- Additional `TrainingInfo` properties (`missing_motif_weight`, `coding_statistics`).
-- Setters for all remaining `TrainingInfo` properties.
-- Proper `TrainingInfo` constructor with configuration option for all attributes.
-- `TrainingInfo.to_dict` method to extract all parameters from a `TrainingInfo`.
 
 ### Changed
-- **BREAKING**: Rename `OrfFinder` to `GeneFinder` for consistency.
-- Reorganize memory management of the built-in metagenomic models.
-- Make the internal Cython model public (`pyrodigal.lib`) to allow importing the underlying classes in other Cython projects.
-- **BREAKING**: Use `memoryview` to expose all `TrainingInfo` attributes instead manually building lists or tuples.
 
-### Removed
-- **BREAKING**: `metagenomic_bin` attribute of `TrainingInfo`.
+
+
 
 
 ## [v2.3.0] - 2023-07-20

pyrodigal/_version.py

@@ -1 +1 @@
-__version__ = "3.0.0-alpha4"
+__version__ = "3.0.0"