Release v0.6.0

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

lightmotif-bench/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "lightmotif-bench"
-version = "0.5.1"
+version = "0.6.0"
 edition = "2021"
 publish = false
 

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"

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"

lightmotif-py/lightmotif/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.5.1"
+__version__ = "0.6.0"
 
 from . import lib
 from .lib import (

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"
 

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"

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"