From f6b6dfa16fdc78e4fd6d6ac1bd204f1d63b3b956 Mon Sep 17 00:00:00 2001 From: Martin Larralde Date: Sun, 20 Jun 2021 01:36:03 +0200 Subject: [PATCH] Release v0.2.0 --- CHANGELOG.md | 15 ++++++++++++++- README.md | 4 ++-- pyfastani/__init__.py | 2 +- setup.cfg | 4 ++-- 4 files changed, 19 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3905739..d0a64d6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,20 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unreleased] -[Unreleased]: https://github.com/althonos/pyrodigal/compare/v0.1.2...HEAD +[Unreleased]: https://github.com/althonos/pyrodigal/compare/v0.2.0...HEAD + + +## [v0.2.0] - 2021-06-20 +[Unreleased]: https://github.com/althonos/pyrodigal/compare/v0.1.2...v0.2.0 + +### Added +- `Sketch.clear` method to remove all sequences currently in a `Sketch` and reset the list of minimizers. +- SIMD code to read and reverse-complement the input sequences efficiently on supported platforms (x86-64 with SSE2 or SSSE3, and ARM with NEON). +### Changed +- Split the `Sketch` type in two depending on whether the object is at the sketching stage (`Sketch`) or at the querying stage (`Mapper`). +- `Sketch.add_genome`, `Sketch.add_draft`, `Mapper.query_genome` and `Mapper.query_draft` can now be passed a Unicode string for the sequence. +### Fixed +- Integer underflow causing minimizers out of the block window to be added to the final minimizers list. ## [v0.1.2] - 2021-06-15 diff --git a/README.md b/README.md index adacdc6..495a769 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ [![GitHub issues](https://img.shields.io/github/issues/althonos/pyfastani.svg?style=flat-square&maxAge=600)](https://github.com/althonos/pyfastani/issues) [![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/pyfastani/blob/master/CHANGELOG.md) [![Downloads](https://img.shields.io/badge/dynamic/json?style=flat-square&color=303f9f&maxAge=86400&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Fpyfastani)](https://pepy.tech/project/pyfastani) -[![DOI](https://img.shields.io/badge/doi-10.5281%2Fzenodo.4940238-purple?style=flat-square&maxAge=86400)](https://doi.org/10.5281/zenodo.4940238) +[![DOI](https://img.shields.io/badge/doi-10.5281%2Fzenodo.4940237-purple?style=flat-square&maxAge=86400)](https://doi.org/10.5281/zenodo.4940237) ## 🗺️ Overview @@ -42,7 +42,7 @@ FastANI internals, which has the following advantages over CLI wrappers: without needing to write them to a temporary file. *This library is still a work-in-progress, and in an experimental stage, -but it should already pack enough features to run one-to-one computations.* +but it should already pack enough features to be used in a standard pipeline.* ## 🔧 Installing diff --git a/pyfastani/__init__.py b/pyfastani/__init__.py index abb782f..ec5ed82 100644 --- a/pyfastani/__init__.py +++ b/pyfastani/__init__.py @@ -3,7 +3,7 @@ __author__ = "Martin Larralde " __license__ = "MIT" -__version__ = "0.1.2" +__version__ = "0.2.0" __all__ = ["Sketch", "Mapper", "Hit", "MAX_KMER_SIZE"] __doc__ = _fastani.__doc__ diff --git a/setup.cfg b/setup.cfg index 2b434d4..0eb15bb 100644 --- a/setup.cfg +++ b/setup.cfg @@ -37,13 +37,13 @@ project_urls = Coverage = https://codecov.io/gh/althonos/pyfastani/ Builds = https://github.com/althonos/pyfastani/actions/ PyPI = https://pypi.org/project/pyfastani - Zenodo = https://doi.org/10.5281/zenodo.4940238 + Zenodo = https://doi.org/10.5281/zenodo.4940237 [options] zip_safe = false packages = pyfastani, pyfastani.tests python_requires = >=3.6 -test_suite = tests +test_suite = pyfastani.tests include_package_data = true setup_requires = setuptools >=46.4