Merge pull request #330 from sanger-pathogens/log4j_upgrade

Upgrade log4j and picard
sanger-pathogens · Mar 14, 2022 · 907092b · 907092b
2 parents 5256024 + 193b0ee
commit 907092b
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Showing 835 changed files with 74 additions and 366,203 deletions.
diff --git a/.classpath b/.classpath
@@ -29,7 +29,6 @@
 	<classpathentry kind="src" path="src/site"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
 		<attributes>
-			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
@@ -38,12 +37,5 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/evosuite">
-		<attributes>
-			<attribute name="test" value="true"/>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>
diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,4 @@ maven.properties
 maven-archiver
 .dribble.*
 .Dockerfile*
+*.jks
diff --git a/.scaffolding_list.tmp b/.scaffolding_list.tmp
diff --git a/.travis.yml b/.travis.yml
@@ -6,15 +6,9 @@ env:
 sudo: true
 matrix:
   include:
-    - jdk: oraclejdk12
-      env: 
-       - TEST_EXCLUDES="**/*_ESTest*"
-    - jdk: openjdk9
-      env: 
-       - TEST_EXCLUDES="**/*_ESTest*"
     - jdk: openjdk11
-      env: 
-       - TEST_EXCLUDES="**/*_ESTest*"
+    - jdk: oraclejdk12
+    - jdk: openjdk17
 cache:
   directories:
   - "${HOME}/dependencies"
@@ -32,5 +26,5 @@ script:
   - if [ "$RUN_TESTS" == "true" ]; then
       cd test;
       ln -s $(pwd)/../etc/log4j.properties .;
-      ./RunTravisTests.sh -e "$TEST_EXCLUDES" | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ];
+      ./RunTravisTests.sh | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ];
     fi
diff --git a/AUTHORS b/AUTHORS
@@ -1,4 +1,4 @@
 Tim Carver
 Sascha Steinbiss
 Kim Rutherford
-Kevin Pepper ([email protected])
+Kevin Pepper
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,8 @@
 # Change Log
 
+## [v18.2.0](https://github.com/sanger-pathogens/artemis/tree/v18.2.0) (2022-03-16)
+[Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v18.1.0...v18.2.0)
+
 ## [v18.1.0](https://github.com/sanger-pathogens/artemis/tree/v18.1.0) (2019-12-04)
 [Full Changelog](https://github.com/sanger-pathogens/artemis/compare/v18.0.3...v18.1.0)
 

diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-This software is Copyright (c) 2019 by Wellcome Trust Sanger Institute.
+This software is Copyright (c) 2022 by Wellcome Sanger Institute.
 
 This is free software, licensed under:
 

diff --git a/README.md b/README.md
@@ -3,8 +3,7 @@ The Artemis Software is a set of software tools for genome browsing and annotati
 
 [![Build Status](https://travis-ci.org/sanger-pathogens/Artemis.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Artemis)  
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/Artemis/blob/master/LICENSE)  
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/artemis/README.html)  
-![Docker Cloud Build Status](https://img.shields.io/docker/cloud/build/sangerpathogens/artemis)  
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/artemis/README.html)   
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2F16.10.944-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/16.10.944)  
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtr703-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btr703)   
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtn529-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btn529)   
@@ -14,7 +13,7 @@ The Artemis Software is a set of software tools for genome browsing and annotati
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtq010-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btq010)   
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtn578-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btn578)  
 
-![GitHub Releases (by Release)](https://img.shields.io/github/downloads/sanger-pathogens/artemis/v18.1.0/total)
+![GitHub Releases (by Release)](https://img.shields.io/github/downloads/sanger-pathogens/artemis/v18.2.0/total)
 
 ## Contents
   * [Introduction](#introduction)

diff --git a/SUT.log4j.properties b/SUT.log4j.properties
diff --git a/etc/log4j.properties b/etc/log4j.properties
@@ -2,6 +2,8 @@
 ! Configure categories (loggers)                                              !
 !-----------------------------------------------------------------------------!
 
+log4j1.compatibility=true
+
 #log4j.rootLogger=debug, R
 log4j.rootLogger=R
 #log4j.rootLogger=debug,stdout

diff --git a/etc/versions b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 18.1.0
-ACT Release 18.1.0
-DNAPlotter Release 18.1.0
-BamView 18.1.0
+Artemis Release 18.2.0
+ACT Release 18.2.0
+DNAPlotter Release 18.2.0
+BamView 18.2.0