diff --git a/CHANGELOG.md b/CHANGELOG.md index 9610b211df..aa0cc2b686 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,14 @@ BioJava Changelog ----------------- +BioJava 7.2.5 +============================== +### Fixed +* Fix NPE in Structure.toMMCIF() for some PDB entries (e.g. 2G10) +* Maven plugin duplication in main pom.xml +* Fixes for SonarQube S1155 +* Some library upgrades + BioJava 7.2.4 ============================== ### Fixed diff --git a/README.md b/README.md index eddeb65379..5c4b8f6ed2 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # Welcome to ![Build](https://github.com/biojava/biojava/actions/workflows/master.yml/badge.svg) -[![Version](http://img.shields.io/badge/version-7.2.4-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.2.4) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) +[![Version](http://img.shields.io/badge/version-7.2.5-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.2.5) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) BioJava is an open-source project dedicated to providing a Java framework for **processing biological data**. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. @@ -29,7 +29,7 @@ If you are using Maven you can add the BioJava repository by adding the followin org.biojava biojava-core - 7.2.4 + 7.2.5 diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index ca38a3aacc..1209448b5f 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT org.biojava biojava-structure - 7.2.5 + 7.2.6-SNAPSHOT diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index f73fa949c0..6f57e23426 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index cb7f3b5208..3ad7189c9e 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index aca993304f..698fa280c7 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT compile org.biojava biojava-alignment - 7.2.5 + 7.2.6-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index e3d4122962..349393cfa6 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.5 + 7.2.6-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index fbc0c89ad6..cec4445407 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.5 + 7.2.6-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index f99f80e60c..dff3450bc9 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index cf5b3181fc..3b43bc492d 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.5 + 7.2.6-SNAPSHOT org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT org.biojava biojava-structure - 7.2.5 + 7.2.6-SNAPSHOT org.biojava biojava-structure-gui - 7.2.5 + 7.2.6-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 5fe23d98ea..d0267a7519 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 36d676b671..314c32bf16 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.5 + 7.2.6-SNAPSHOT compile org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 6c70ab9c58..c80a8490bd 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.5 + 7.2.6-SNAPSHOT compile org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index e4ae967a4e..a8c8616fa1 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 920c77414d..eafd87dff8 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 94ef570778..9fae069ae0 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.5 + 7.2.6-SNAPSHOT biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the @@ -51,7 +51,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-7.2.5 + HEAD