From 80ed550b033c85e9f8f77ec078e75c8e346b5c57 Mon Sep 17 00:00:00 2001 From: Martin Larralde <martin.larralde@embl.de> Date: Wed, 13 Dec 2023 17:24:10 +0100 Subject: [PATCH] Release v0.6.0 --- CHANGELOG.md | 30 +++++++++++++++++++++++++++- lightmotif-bench/Cargo.toml | 2 +- lightmotif-io/Cargo.toml | 4 ++-- lightmotif-py/Cargo.toml | 4 ++-- lightmotif-py/lightmotif/__init__.py | 2 +- lightmotif-tfmpvalue/Cargo.toml | 4 ++-- lightmotif-transfac/Cargo.toml | 6 +++--- lightmotif/Cargo.toml | 2 +- 8 files changed, 41 insertions(+), 13 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c0d0d82..2728b3f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,35 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unreleased] -[Unreleased]: https://github.com/althonos/lightmotif/compare/v0.5.1...HEAD +[Unreleased]: https://github.com/althonos/lightmotif/compare/v0.6.0...HEAD + + +## [v0.6.0] - 2023-08-31 +[v0.6.0]: https://github.com/althonos/lightmotif/compare/v0.5.1...v0.6.0 + +### Added + +#### `lightmotif` +- Validating constructor `::pwm::FrequencyMatrix::new` testing for frequencies on each ranks. +- Getter to the raw data matrix of a `::pwm::FrequencyMatrix`. + +#### `lightmotif-io` +New crate with JASPAR, TRANSFAC and UNIPROBE format parsers. + +### Changed + +#### `lightmotif` +- Make `max_score` and `min_score` columns of `::pwm::ScoringMatrix` ignore the wildcard symbol column. + +#### `lightmotif-tfmpvalue` +- Invert decay in `TfmPvalue` to reduce rounding errors when computing granularity. +- Use a fast integer hashing algorithm for `i64` keys in maps used for recording *Q*-values. +- Compute the optimal column permutation to accelerate the computation of score distributions. + +### Removed + +#### `lightmotif-transfac` +Deprecate crate in favour of `lightmotif-io`. ## [v0.5.1] - 2023-08-31 diff --git a/lightmotif-bench/Cargo.toml b/lightmotif-bench/Cargo.toml index 1009f8c..488588f 100644 --- a/lightmotif-bench/Cargo.toml +++ b/lightmotif-bench/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "lightmotif-bench" -version = "0.5.1" +version = "0.6.0" edition = "2021" publish = false diff --git a/lightmotif-io/Cargo.toml b/lightmotif-io/Cargo.toml index 2dd5a6b..6a5592b 100644 --- a/lightmotif-io/Cargo.toml +++ b/lightmotif-io/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "lightmotif-io" -version = "0.5.1" +version = "0.6.0" authors = ["Martin Larralde <martin.larralde@embl.de>"] edition = "2021" license = "MIT" @@ -19,4 +19,4 @@ memchr = "2" [dependencies.lightmotif] path = "../lightmotif" -version = "0.5.1" +version = "0.6.0" diff --git a/lightmotif-py/Cargo.toml b/lightmotif-py/Cargo.toml index 4f8a6d3..0e564bc 100644 --- a/lightmotif-py/Cargo.toml +++ b/lightmotif-py/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "lightmotif-py" -version = "0.5.1" +version = "0.6.0" authors = ["Martin Larralde <martin.larralde@embl.de>"] edition = "2021" license = "MIT" @@ -17,7 +17,7 @@ path = "lightmotif/lib.rs" [dependencies.lightmotif] path = "../lightmotif" -version = "0.5.1" +version = "0.6.0" [dependencies] pyo3 = "0.18.3" generic-array = "0.14" diff --git a/lightmotif-py/lightmotif/__init__.py b/lightmotif-py/lightmotif/__init__.py index cfd14e9..a1bb741 100644 --- a/lightmotif-py/lightmotif/__init__.py +++ b/lightmotif-py/lightmotif/__init__.py @@ -1,4 +1,4 @@ -__version__ = "0.5.1" +__version__ = "0.6.0" from . import lib from .lib import ( diff --git a/lightmotif-tfmpvalue/Cargo.toml b/lightmotif-tfmpvalue/Cargo.toml index 4d065d3..1ea670e 100644 --- a/lightmotif-tfmpvalue/Cargo.toml +++ b/lightmotif-tfmpvalue/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "lightmotif-tfmpvalue" -version = "0.5.1" +version = "0.6.0" authors = ["Martin Larralde <martin.larralde@embl.de>"] edition = "2021" license = "GPL-3.0" @@ -13,5 +13,5 @@ keywords = ["bioinformatics", "motif", "pssm", "pvalue"] [dependencies.lightmotif] path = "../lightmotif" -version = "0.5.1" +version = "0.6.0" diff --git a/lightmotif-transfac/Cargo.toml b/lightmotif-transfac/Cargo.toml index f792c88..9bc2725 100644 --- a/lightmotif-transfac/Cargo.toml +++ b/lightmotif-transfac/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "lightmotif-transfac" -version = "0.5.1" +version = "0.6.0" authors = ["Martin Larralde <martin.larralde@embl.de>"] edition = "2021" license = "MIT" @@ -13,7 +13,7 @@ keywords = ["bioinformatics", "motif", "parser", "transfac"] [dependencies.lightmotif] path = "../lightmotif" -version = "0.5.1" +version = "0.6.0" [dependencies.lightmotif-io] path = "../lightmotif-io" -version = "0.5.1" +version = "0.6.0" diff --git a/lightmotif/Cargo.toml b/lightmotif/Cargo.toml index a8110d6..c7550ee 100644 --- a/lightmotif/Cargo.toml +++ b/lightmotif/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "lightmotif" -version = "0.5.1" +version = "0.6.0" authors = ["Martin Larralde <martin.larralde@embl.de>"] edition = "2021" license = "MIT" -- GitLab