From 725f3babf1c610ad5eab40d2c8642f0e609a18a3 Mon Sep 17 00:00:00 2001 From: Martin Larralde <martin.larralde@embl.de> Date: Mon, 17 Jun 2024 20:21:40 +0200 Subject: [PATCH] Release v0.7.3 --- CHANGELOG.md | 26 +++++++++++++++++++++++++- lightmotif-bench/Cargo.toml | 2 +- lightmotif-io/Cargo.toml | 4 ++-- lightmotif-py/Cargo.toml | 6 +++--- lightmotif-py/lightmotif/__init__.py | 2 +- lightmotif-tfmpvalue/Cargo.toml | 4 ++-- lightmotif/Cargo.toml | 2 +- 7 files changed, 35 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e0dc8ae..4929086 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,31 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unreleased] -[Unreleased]: https://github.com/althonos/lightmotif/compare/v0.7.2...HEAD +[Unreleased]: https://github.com/althonos/lightmotif/compare/v0.7.3...HEAD + + +## [v0.7.3] - 2024-06-17 +[v0.7.3]: https://github.com/althonos/lightmotif/compare/v0.7.2...v0.7.3 + +### Added + +#### `lightmotif-io` +- `lightmotif_io::jaspar` to read matrices in raw JASPAR format. +- Implementation of `Clone` and `Error` for the `lightmotif_io::error::Error` type. + +### Changed + +#### `lightmotif` +- Use logarithmic subtraction in `FrequencyMatrix::to_scoring`. +- Use `_mm256_permutevara8x32_ps` instead of `_mm256_permutevar_ps` in AVX2 implementation to avoid special handling of unknown matric character `N`. + +### Fixed + +#### `lightmotif` +- Striping of empty sequences panicking on AVX2 implementation. +- Scoring of empty range of rows panicking. +- Invalid alignment of data in AVX2 code. +- `Clone` implementation of `DenseMatrix` not preserving memory alignment. ## [v0.7.2] - 2024-06-14 diff --git a/lightmotif-bench/Cargo.toml b/lightmotif-bench/Cargo.toml index 38275ad..80316f1 100644 --- a/lightmotif-bench/Cargo.toml +++ b/lightmotif-bench/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "lightmotif-bench" -version = "0.7.2" +version = "0.7.3" edition = "2021" publish = false diff --git a/lightmotif-io/Cargo.toml b/lightmotif-io/Cargo.toml index 4d6da17..3c33ca4 100644 --- a/lightmotif-io/Cargo.toml +++ b/lightmotif-io/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "lightmotif-io" -version = "0.7.2" +version = "0.7.3" authors = ["Martin Larralde <martin.larralde@embl.de>"] edition = "2021" license = "MIT" @@ -20,4 +20,4 @@ generic-array = "1.0" [dependencies.lightmotif] path = "../lightmotif" -version = "0.7.2" +version = "0.7.3" diff --git a/lightmotif-py/Cargo.toml b/lightmotif-py/Cargo.toml index f8fe79a..3f15da0 100644 --- a/lightmotif-py/Cargo.toml +++ b/lightmotif-py/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "lightmotif-py" -version = "0.7.2" +version = "0.7.3" authors = ["Martin Larralde <martin.larralde@embl.de>"] edition = "2021" license = "MIT OR GPL-3.0-or-later" @@ -17,11 +17,11 @@ path = "lightmotif/lib.rs" [dependencies.lightmotif] path = "../lightmotif" -version = "0.7.2" +version = "0.7.3" [dependencies.lightmotif-tfmpvalue] optional = true path = "../lightmotif-tfmpvalue" -version = "0.7.2" +version = "0.7.3" [dependencies] pyo3 = "0.18.3" generic-array = "1.0.0" diff --git a/lightmotif-py/lightmotif/__init__.py b/lightmotif-py/lightmotif/__init__.py index 4c49dac..59cb1ab 100644 --- a/lightmotif-py/lightmotif/__init__.py +++ b/lightmotif-py/lightmotif/__init__.py @@ -1,4 +1,4 @@ -__version__ = "0.7.2" +__version__ = "0.7.3" from . import lib from .lib import ( diff --git a/lightmotif-tfmpvalue/Cargo.toml b/lightmotif-tfmpvalue/Cargo.toml index 40df343..952f4f0 100644 --- a/lightmotif-tfmpvalue/Cargo.toml +++ b/lightmotif-tfmpvalue/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "lightmotif-tfmpvalue" -version = "0.7.2" +version = "0.7.3" authors = ["Martin Larralde <martin.larralde@embl.de>"] edition = "2021" license = "GPL-3.0-or-later" @@ -13,5 +13,5 @@ keywords = ["bioinformatics", "motif", "pssm", "pvalue"] [dependencies.lightmotif] path = "../lightmotif" -version = "0.7.2" +version = "0.7.3" diff --git a/lightmotif/Cargo.toml b/lightmotif/Cargo.toml index 30e11a0..7995814 100644 --- a/lightmotif/Cargo.toml +++ b/lightmotif/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "lightmotif" -version = "0.7.2" +version = "0.7.3" authors = ["Martin Larralde <martin.larralde@embl.de>"] edition = "2021" license = "MIT" -- GitLab