diff --git a/CHANGELOG.md b/CHANGELOG.md index c0d0d829f0d37c89ab63b9d6672601fbad7f56f2..2728b3f91aa4dd6ee809631044144857bd87be12 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 1009f8c4d350bc94fe824d7fcb8b043cf4dc6944..488588ff153b47d38396f3515d8eeb3a952c4cd6 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 2dd5a6bea2f844d6aa3fe690055d10b4de5a430e..6a5592bbcd9538ca3ef25d4e14ca613bfa325552 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 4f8a6d3f613cd03143c6dc58a66d8d2f5bd76368..0e564bcf2c1aea30f7653b8a25ba38fb8863a45f 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 cfd14e9f8851b9b12ca9ac06b8fda3aecc4c99a0..a1bb7414a336918efc8b36f6cd6cd4194544f724 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 4d065d3f7c945b6cf6aeca143ce5c48aab7547b5..1ea670e14078d27c7cea03555191743af706667a 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 f792c8863c6d1562bda2371fd1f793d1422695e4..9bc272594c3327e32ec3d757f08554039740d347 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 a8110d6d68400847f34f1de78daf5b44637c7064..c7550ee22122aab604e53ffa6a335d131c551822 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"