Release v0.9.0

althonos · Sep 2, 2024 · 84d3669 · 84d3669
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diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
@@ -142,6 +142,6 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v3
     - name: Release a Changelog
-      uses: rasmus-saks/release-a-changelog-action@v1.0.1
+      uses: rasmus-saks/release-a-changelog-action@v1.2.0
       with:
         github-token: '${{ secrets.GITHUB_TOKEN }}'
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,7 +6,42 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/lightmotif/compare/v0.8.0...HEAD
+[Unreleased]: https://github.com/althonos/lightmotif/compare/v0.9.0...HEAD
+
+
+## [v0.9.0] - 2024-09-02
+[v0.9.0]: https://github.com/althonos/lightmotif/compare/v0.8.0...v0.9.0
+
+### Added
+
+#### `lightmotif`
+- `DenseMatrix::ravel` to get the array of a `DenseMatrix` as a single continuous slice.
+
+#### `lightmotif-py`
+- Support for protein alphabets ([#5](https://github.com/althonos/lightmotif/issues/5)).
+- `protein` property to `CountMatrix`, `WeightMatrix`, `ScoringMatrix`, `EncodedSequence` and `StripedSequence`.
+- `Scanner` class to use the new DNA scanning algorithm.
+- Buffer protocol implmementation for `ScoringMatrix` objects.
+- `lightmotif.load` function to load one or more `Motif` from a file-like object ([#6](https://github.com/althonos/lightmotif/issues/6)).
+- `Motif.name` property to store the optional name of a `Motif`.
+- Several `Motif` subclasses to store motif and metadata loaded from a file.
+- Type annotations for the `lightmotif.lib` package.
+
+### Fixed
+
+#### `lightmotif-io`
+- Parsing of floating-point numbers in JASPAR parser.
+- Panic on error unwrapping in `lightmotif-io`.
+
+### Changed
+
+#### `lightmotif`
+- Rewrite `DenseMatrix` with constant platform-specific alignment to reduce amount of `unsafe` code.
+
+### Removed
+
+#### `lightmotif-py`
+- `alphabet` parameter of `ScoringMatrix` and `EncodedSequence`.
 
 
 ## [v0.8.0] - 2024-06-28

diff --git a/lightmotif-bench/Cargo.toml b/lightmotif-bench/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "lightmotif-bench"
-version = "0.8.0"
+version = "0.9.0"
 edition = "2021"
 publish = false
 

diff --git a/lightmotif-io/Cargo.toml b/lightmotif-io/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "lightmotif-io"
-version = "0.8.0"
+version = "0.9.0"
 authors = ["Martin Larralde <martin.larralde@embl.de>"]
 edition = "2021"
 license = "MIT"
@@ -20,4 +20,4 @@ generic-array = "1.0"
 
 [dependencies.lightmotif]
 path = "../lightmotif"
-version = "0.8.0"
+version = "0.9.0"
diff --git a/lightmotif-py/Cargo.toml b/lightmotif-py/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "lightmotif-py"
-version = "0.8.0"
+version = "0.9.0"
 authors = ["Martin Larralde <martin.larralde@embl.de>"]
 edition = "2021"
 license = "MIT OR GPL-3.0-or-later"
@@ -18,14 +18,14 @@ doctest = false
 
 [dependencies.lightmotif]
 path = "../lightmotif"
-version = "0.8.0"
+version = "0.9.0"
 [dependencies.lightmotif-io]
 path = "../lightmotif-io"
-version = "0.8.0"
+version = "0.9.0"
 [dependencies.lightmotif-tfmpvalue]
 optional = true
 path = "../lightmotif-tfmpvalue"
-version = "0.8.0"
+version = "0.9.0"
 [dependencies]
 pyo3 = "0.22.0"
 generic-array = "1.0.0"

diff --git a/lightmotif-py/docs/_static/json/switcher.json b/lightmotif-py/docs/_static/json/switcher.json
@@ -1,6 +1,11 @@
 [
     {
-        "name": "v0.8 (latest)",
+        "name": "v0.9 (latest)",
+        "version": "0.9.0",
+        "url": "https://lightmotif.readthedocs.io/en/v0.9.0/"
+    },
+    {
+        "name": "v0.8",
         "version": "0.8.0",
         "url": "https://lightmotif.readthedocs.io/en/v0.8.0/"
     },

diff --git a/lightmotif-py/lightmotif/__init__.py b/lightmotif-py/lightmotif/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.8.0"
+__version__ = "0.9.0"
 
 from . import lib
 from .lib import (

diff --git a/lightmotif-tfmpvalue/Cargo.toml b/lightmotif-tfmpvalue/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "lightmotif-tfmpvalue"
-version = "0.8.0"
+version = "0.9.0"
 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 = "0.8.0"
+version = "0.9.0"
 
diff --git a/lightmotif/Cargo.toml b/lightmotif/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "lightmotif"
-version = "0.8.0"
+version = "0.9.0"
 authors = ["Martin Larralde <martin.larralde@embl.de>"]
 edition = "2021"
 license = "MIT"