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dependency update stuff

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eugenefischer
2025-04-10 10:54:05 -05:00
parent b5c0568e22
commit 81d8a12765
8 changed files with 59 additions and 41 deletions
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29
.idea/artifacts/BiGpairSEQ_Sim_jar.xml generated
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@@ -1,16 +1,27 @@
<component name="ArtifactManager"> <component name="ArtifactManager">
<artifact type="jar" build-on-make="true" name="BiGpairSEQ_Sim:jar"> <artifact type="jar" name="BiGpairSEQ_Sim:jar">
<output-path>$PROJECT_DIR$/out/artifacts/BiGpairSEQ_Sim_jar</output-path> <output-path>$PROJECT_DIR$/out/artifacts/BiGpairSEQ_Sim_jar</output-path>
<root id="archive" name="BiGpairSEQ_Sim.jar"> <root id="archive" name="TCellSim.jar">
<element id="directory" name="META-INF"> <element id="directory" name="META-INF">
<element id="file-copy" path="$PROJECT_DIR$/src/main/java/META-INF/MANIFEST.MF" /> <element id="file-copy" path="$PROJECT_DIR$/META-INF/MANIFEST.MF" />
</element> </element>
<element id="module-output" name="BigPairSEQ" /> <element id="module-output" name="TCellSim" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.1/jgrapht-core-1.5.1.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-client-api/1.6/commons-rng-client-api-1.6.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.13/jheaps-0.13.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-csv/1.14.0/commons-csv-1.14.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.5.0/commons-cli-1.5.0.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-io/commons-io/2.18.0/commons-io-2.18.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-csv/1.9.0/commons-csv-1.9.0.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.18.0/commons-codec-1.18.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jetbrains/annotations/23.0.0/annotations-23.0.0.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-sampling/1.6/commons-rng-sampling-1.6.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-io/1.5.2/jgrapht-io-1.5.2.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.2/jgrapht-core-1.5.2.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.14/jheaps-0.14.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apfloat/apfloat/1.10.1/apfloat-1.10.1.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/antlr/antlr4-runtime/4.12.0/antlr4-runtime-4.12.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-text/1.10.0/commons-text-1.10.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-lang3/3.12.0/commons-lang3-3.12.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jetbrains/annotations/26.0.2/annotations-26.0.2.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-simple/1.6/commons-rng-simple-1.6.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.9.0/commons-cli-1.9.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-core/1.6/commons-rng-core-1.6.jar" path-in-jar="/" />
</root> </root>
</artifact> </artifact>
</component> </component>

1
.idea/compiler.xml generated
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@@ -6,6 +6,7 @@
<sourceOutputDir name="target/generated-sources/annotations" /> <sourceOutputDir name="target/generated-sources/annotations" />
<sourceTestOutputDir name="target/generated-test-sources/test-annotations" /> <sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
<outputRelativeToContentRoot value="true" /> <outputRelativeToContentRoot value="true" />
<module name="TCellSim" />
<module name="BigPairSEQ" /> <module name="BigPairSEQ" />
</profile> </profile>
</annotationProcessing> </annotationProcessing>

25
.idea/jarRepositories.xml generated
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@@ -1,20 +1,35 @@
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<project version="4"> <project version="4">
<component name="RemoteRepositoriesConfiguration"> <component name="RemoteRepositoriesConfiguration">
<remote-repository>
<option name="id" value="my-internal-site" />
<option name="name" value="my-internal-site" />
<option name="url" value="https://myserver/repo" />
</remote-repository>
<remote-repository>
<option name="id" value="central" />
<option name="name" value="Central Repository" />
<option name="url" value="https://repo1.maven.org/maven2" />
</remote-repository>
<remote-repository>
<option name="id" value="central repo" />
<option name="name" value="central repo" />
<option name="url" value="https://repo1.maven.org/maven2/" />
</remote-repository>
<remote-repository> <remote-repository>
<option name="id" value="central" /> <option name="id" value="central" />
<option name="name" value="Central Repository" /> <option name="name" value="Central Repository" />
<option name="url" value="https://repo.maven.apache.org/maven2" /> <option name="url" value="https://repo.maven.apache.org/maven2" />
</remote-repository> </remote-repository>
<remote-repository>
<option name="id" value="central" />
<option name="name" value="Maven Central repository" />
<option name="url" value="https://repo1.maven.org/maven2" />
</remote-repository>
<remote-repository> <remote-repository>
<option name="id" value="jboss.community" /> <option name="id" value="jboss.community" />
<option name="name" value="JBoss Community repository" /> <option name="name" value="JBoss Community repository" />
<option name="url" value="https://repository.jboss.org/nexus/content/repositories/public/" /> <option name="url" value="https://repository.jboss.org/nexus/content/repositories/public/" />
</remote-repository> </remote-repository>
<remote-repository>
<option name="id" value="34d16bdc-85f0-48ee-8e8b-144091765be1" />
<option name="name" value="34d16bdc-85f0-48ee-8e8b-144091765be1" />
<option name="url" value="https://repository.mulesoft.org/nexus/content/repositories/public/" />
</remote-repository>
</component> </component>
</project> </project>

6
.idea/libraries/apache_commons_csv.xml generated
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@@ -1,8 +1,10 @@
<component name="libraryTable"> <component name="libraryTable">
<library name="apache.commons.csv" type="repository"> <library name="apache.commons.csv" type="repository">
<properties maven-id="org.apache.commons:commons-csv:1.9.0" /> <properties maven-id="org.apache.commons:commons-csv:1.14.0" />
<CLASSES> <CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-csv/1.9.0/commons-csv-1.9.0.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-csv/1.14.0/commons-csv-1.14.0.jar!/" />
<root url="jar://$MAVEN_REPOSITORY$/commons-io/commons-io/2.18.0/commons-io-2.18.0.jar!/" />
<root url="jar://$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.18.0/commons-codec-1.18.0.jar!/" />
</CLASSES> </CLASSES>
<JAVADOC /> <JAVADOC />
<SOURCES /> <SOURCES />

4
.idea/libraries/commons_cli.xml generated
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@@ -1,8 +1,8 @@
<component name="libraryTable"> <component name="libraryTable">
<library name="commons.cli" type="repository"> <library name="commons.cli" type="repository">
<properties maven-id="commons-cli:commons-cli:1.5.0" /> <properties maven-id="commons-cli:commons-cli:1.9.0" />
<CLASSES> <CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.5.0/commons-cli-1.5.0.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.9.0/commons-cli-1.9.0.jar!/" />
</CLASSES> </CLASSES>
<JAVADOC /> <JAVADOC />
<SOURCES /> <SOURCES />

13
.idea/libraries/commons_rng_1.xml generated
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@@ -1,13 +0,0 @@
<component name="libraryTable">
<library name="commons-rng-1">
<CLASSES>
<root url="file://$USER_HOME$/Downloads/commons-rng-1.6" />
</CLASSES>
<JAVADOC />
<SOURCES>
<root url="file://$USER_HOME$/Downloads/commons-rng-1.6" />
</SOURCES>
<jarDirectory url="file://$USER_HOME$/Downloads/commons-rng-1.6" recursive="false" />
<jarDirectory url="file://$USER_HOME$/Downloads/commons-rng-1.6" recursive="false" type="SOURCES" />
</library>
</component>

7
.idea/libraries/jgrapht_core.xml generated
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@@ -1,9 +1,10 @@
<component name="libraryTable"> <component name="libraryTable">
<library name="jgrapht.core" type="repository"> <library name="jgrapht.core" type="repository">
<properties maven-id="org.jgrapht:jgrapht-core:1.5.1" /> <properties maven-id="org.jgrapht:jgrapht-core:1.5.2" />
<CLASSES> <CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.1/jgrapht-core-1.5.1.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.2/jgrapht-core-1.5.2.jar!/" />
<root url="jar://$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.13/jheaps-0.13.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.14/jheaps-0.14.jar!/" />
<root url="jar://$MAVEN_REPOSITORY$/org/apfloat/apfloat/1.10.1/apfloat-1.10.1.jar!/" />
</CLASSES> </CLASSES>
<JAVADOC /> <JAVADOC />
<SOURCES /> <SOURCES />

15
.idea/libraries/jgrapht_io.xml generated
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@@ -1,13 +1,14 @@
<component name="libraryTable"> <component name="libraryTable">
<library name="jgrapht.io" type="repository"> <library name="jgrapht.io" type="repository">
<properties maven-id="org.jgrapht:jgrapht-io:1.5.1" /> <properties maven-id="org.jgrapht:jgrapht-io:1.5.2" />
<CLASSES> <CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-io/1.5.1/jgrapht-io-1.5.1.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-io/1.5.2/jgrapht-io-1.5.2.jar!/" />
<root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.1/jgrapht-core-1.5.1.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.2/jgrapht-core-1.5.2.jar!/" />
<root url="jar://$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.13/jheaps-0.13.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.14/jheaps-0.14.jar!/" />
<root url="jar://$MAVEN_REPOSITORY$/org/antlr/antlr4-runtime/4.8-1/antlr4-runtime-4.8-1.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/org/apfloat/apfloat/1.10.1/apfloat-1.10.1.jar!/" />
<root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-text/1.8/commons-text-1.8.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/org/antlr/antlr4-runtime/4.12.0/antlr4-runtime-4.12.0.jar!/" />
<root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-lang3/3.9/commons-lang3-3.9.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-text/1.10.0/commons-text-1.10.0.jar!/" />
<root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-lang3/3.12.0/commons-lang3-3.12.0.jar!/" />
</CLASSES> </CLASSES>
<JAVADOC /> <JAVADOC />
<SOURCES /> <SOURCES />