Merge pull request #62 from leoisl/v0.5.0_release

Preparing v0.5.0 release

CHANGELOG.md

@@ -6,7 +6,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [0.4.0] - 2022-22-11
+## [0.5.0] - 2023-07-18
+
+### Fixed
+
+- Properly handling Ns in the MSA, and in the denovo sequences (see [PR #60](https://github.com/iqbal-lab-org/make_prg/pull/60)
+and [PR #61](https://github.com/iqbal-lab-org/make_prg/pull/61) for more details);
+
+### Changed
+- `scikit-learn`, `numpy` and `pytest` dependencies updated;
+- The KMeans algorithm used is now `elkan`;
+
+## [0.4.0] - 2022-11-22
 
 ### Added
 - `make_prg update` command, that updates PRGs without requiring to rebuild MSAs and the PRG itself from scratch;
@@ -103,8 +114,9 @@ operations.
   source project CHANGELOG.
 
 
-[Unreleased]: https://github.com/iqbal-lab-org/make_prg/compare/0.4.0...HEAD
+[Unreleased]: https://github.com/iqbal-lab-org/make_prg/compare/0.5.0...HEAD
 
+[0.5.0]: https://github.com/iqbal-lab-org/make_prg/compare/0.4.0...0.5.0
 [0.4.0]: https://github.com/iqbal-lab-org/make_prg/compare/0.2.0...0.4.0
 [0.2.0]: https://github.com/iqbal-lab-org/make_prg/compare/0.1.1...0.2.0
 [0.1.1]: https://github.com/iqbal-lab-org/make_prg/compare/0.1.0...0.1.1

Dockerfile

@@ -1,4 +1,4 @@
-# To build: docker build . -t make_prg:0.4.0
+# To build: docker build . -t make_prg:0.5.0
 # Tagged as such, it can be used in scripts/build_precompiled_binary/build_precompiled_binary.sh to build the precompiled binary
 FROM python:3.10-slim
 

README.md

@@ -37,13 +37,13 @@ In this binary, all libraries are linked statically. Compilation is done using [
 
 #### Download
 ```
-wget https://github.com/iqbal-lab-org/make_prg/releases/download/0.4.0/make_prg_0.4.0
+wget https://github.com/iqbal-lab-org/make_prg/releases/download/0.5.0/make_prg_0.5.0
 ```
 
 #### Run
 ```
-chmod +x make_prg_0.4.0
-./make_prg_0.4.0 -h
+chmod +x make_prg_0.5.0
+./make_prg_0.5.0 -h
 ```
 
 ### pip
@@ -77,7 +77,7 @@ The above will use the latest version. If you want to specify a version then use
 [tag][quay.io] (or commit) like so.
 
 ```sh
-VERSION="0.4.0"
+VERSION="0.5.0"
 URI="docker://quay.io/iqballab/make_prg:${VERSION}"
 ```
 

make_prg/from_msa/cluster_sequences.py

@@ -259,7 +259,9 @@ def kmeans_cluster_seqs(
             break
         if num_clusters == num_sequences:
             break
-        kmeans = KMeans(n_clusters=num_clusters, random_state=2).fit(count_matrix)
+        kmeans = KMeans(n_clusters=num_clusters, random_state=2, algorithm="elkan").fit(
+            count_matrix
+        )
         prev_cluster_assignment = cluster_assignment
         cluster_assignment = list(kmeans.predict(count_matrix))
         num_fitted_clusters = len(set(cluster_assignment))