From be141692bde536bb968797aaad96d45a7c76def1 Mon Sep 17 00:00:00 2001 From: Martin Larralde Date: Wed, 20 Apr 2022 12:28:46 +0200 Subject: [PATCH] Release v1.0.0 --- CHANGELOG.md | 19 +- benches/connection_scoring/v1.0.0.json | 4604 ++++++++++++++++++++++++ benches/connection_scoring/v1.0.0.svg | 1050 ++++++ pyrodigal/_version.py | 2 +- setup.cfg | 2 +- 5 files changed, 5674 insertions(+), 3 deletions(-) create mode 100644 benches/connection_scoring/v1.0.0.json create mode 100644 benches/connection_scoring/v1.0.0.svg diff --git a/CHANGELOG.md b/CHANGELOG.md index 72280cf..4c5aa46 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,24 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unreleased] -[Unreleased]: https://github.com/althonos/pyrodigal/compare/v0.7.3...HEAD +[Unreleased]: https://github.com/althonos/pyrodigal/compare/v1.0.0...HEAD + + +## [v1.0.0] - 2022-04-20 +[v1.0.0]: https://github.com/althonos/pyrodigal/compare/v0.7.3...v1.0.0 + +Stable version, to be published in the [Journal of Open-Source Software](https://joss.theoj.org/). + +### 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] - 2022-04-06 diff --git a/benches/connection_scoring/v1.0.0.json b/benches/connection_scoring/v1.0.0.json new file mode 100644 index 0000000..dcfdc5d 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4910b9e..5becc17 100644 --- a/pyrodigal/_version.py +++ b/pyrodigal/_version.py @@ -1 +1 @@ -__version__ = "0.7.3" +__version__ = "1.0.0" diff --git a/setup.cfg b/setup.cfg index c02a02e..f3cbf92 100644 --- a/setup.cfg +++ b/setup.cfg @@ -11,7 +11,7 @@ license = GPLv3 platform = any keywords = bioinformatics, genome, orf, gene, prodigal classifier = - Development Status :: 4 - Beta + Development Status :: 5 - Production/Stable Intended Audience :: Developers Intended Audience :: Science/Research License :: OSI Approved :: GNU General Public License v3 (GPLv3)