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Merge pull request #38 from cicirello/development
Documentation and workflow updates
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‎.github/workflows/maven-publish.yml

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# This workflow will build a package using Maven and then publish it to GitHub packages when a release is created
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# For more information see: https://github.com/actions/setup-java#apache-maven-with-a-settings-path
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name: Maven Package
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on:
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release:
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types: [created]
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jobs:
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build:
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publish:
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runs-on: ubuntu-latest
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run: mvn versions:set -DnewVersion=${{ steps.get_version.outputs.VERSION }}
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- name: Publish to Apache Maven Central
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run: mvn deploy
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run: mvn deploy -PossrhDeploy
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env:
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MAVEN_USERNAME: ${{ secrets.MAVEN_CENTRAL_USERNAME }}
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MAVEN_CENTRAL_TOKEN: ${{ secrets.MAVEN_CENTRAL_TOKEN }}
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java-version: 1.8
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server-id: github
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- name: Temporary multi-pom hack
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run: mv -f pomgh.xml pom.xml
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- name: Build with Maven
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run: mvn -B package --file pom.xml
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- name: Update package version
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run: mvn versions:set -DnewVersion=${{ steps.get_version.outputs.VERSION }}
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- name: Publish to GitHub Packages Apache Maven
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run: mvn deploy
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run: mvn deploy -PgithubDeploy
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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‎CHANGELOG.md

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@@ -16,6 +16,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Fixed
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## [2.1.3] - 2020-09-16
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### Changed
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* Revised workflow for publishing packages to publish to both Maven Central and Github Packages using one pom.xml.
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* Documentation updates
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## [2.1.2] - 2020-09-15
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### Other
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* Working on getting workflow for publishing to maven central working properly. No functional difference from previous release.
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## [2.1.1] - 2020-09-15
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### Other
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* Working on getting workflow for publishing to maven central working properly. No functional difference from previous release.
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## [2.1.0] - 2020-09-15
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### Added
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* Automated generation of sitemap.xml via GitHub actions for the documentation website.

‎README.md

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[![DOI](http://joss.theoj.org/papers/10.21105/joss.00950/status.svg)](https://doi.org/10.21105/joss.00950)
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[![DOI](https://zenodo.org/badge/139182095.svg)](https://zenodo.org/badge/latestdoi/139182095)
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[![Maven Central](https://img.shields.io/maven-central/v/org.cicirello/jpt.svg?label=Maven%20Central)](https://search.maven.org/artifact/org.cicirello/jpt)
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[![GitHub release (latest by date)](https://img.shields.io/github/v/release/cicirello/JavaPermutationTools?logo=GitHub)](https://github.com/cicirello/JavaPermutationTools/releases)
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[![build](https://github.com/cicirello/JavaPermutationTools/workflows/build/badge.svg)](https://github.com/cicirello/JavaPermutationTools/actions?query=workflow%3Abuild)
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[![GitHub](https://img.shields.io/github/license/cicirello/JavaPermutationTools)](https://github.com/cicirello/JavaPermutationTools/blob/master/LICENSE)
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[![GitHub release (latest by date)](https://img.shields.io/github/v/release/cicirello/JavaPermutationTools?logo=GitHub)](https://github.com/cicirello/JavaPermutationTools/releases)
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## How to Cite
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## Overview
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The JavaPermutationTools (JPT) API provides Java classes that enable representing and generating
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permutations and sequences, as well as performing computation on permutations and sequences.
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It includes implementations of a variety of permutation distance metrics as well as distance
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metrics on sequences (i.e., Strings, arrays, and other ordered data types).
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The JavaPermutationTools (JPT) library provides Java classes and interfaces, etc that
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enable representing and generating permutations and sequences, as well as performing
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computation on permutations and sequences. It includes implementations of a variety
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of permutation distance metrics as well as distance metrics on sequences (i.e., Strings,
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arrays, and other ordered data types).
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JPT is organized into the following packages:
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* __org.cicirello.permutations__: Permutation class and a class for iterating over permutations.
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* __org.cicirello.permutations.distance__: Collection of permutation distance metric implementations.
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* __org.cicirello.sequences__: Classes that perform a variety of operations on sequences (such as arrays, etc).
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* __org.cicirello.sequences.distance__: Collection of distance metrics on Strings and other sequences.
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* __org.cicirello.math.la__ : Linear algebra related classes.
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* __org.cicirello.math.rand__ : Classes related to efficient, or specialized, random number generation.
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* __org.cicirello.math.stats__: Statistics related classes.
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## Repository Organization
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Javadoc documentation is in the /docs folder as well as at https://jpt.cicirello.org/
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The GitHub repository is organized as follows:
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* The [/build](build) directory contains an ant build file, and other resources related to building the library.
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* The [/dist](dist) directory contains the compiled jar files of the library.
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* The [/docs](docs) directory contains the javadoc documentation in a sub-directory [/docs/api](docs/api). The /docs directory is also the location of the website for the project hosted via GitHub pages at https://jpt.cicirello.org/.
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* The [/examples](examples) directory contains several example programs that use the library, and which demonstrate usage of various features.
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* The [/replication](replication) directory includes source code that recreates results found in publications associated with the library.
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* The [/src](src) directory contains all of the source code.
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* The [/tests](tests) directory contains JUnit test cases for all functionality of the library.
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Source code is found in the /src folder. JUnit test classes are found in the /tests folder, which
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mirrors the package structure of /src.
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## Java 8
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Compiled jar files of the library are in the /dist folder.
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The library supports Java 8 or higher, including both Oracle JDK 8 and OpenJDK 8.
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The /examples folder includes source code to illustrate how to use the library. The /replication
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folder includes source code that recreates results found in publications associated with the library.
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## Versioning Scheme
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The JPT uses [Semantic Versioning](https://semver.org/) with version
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numbers of the form: MAJOR.MINOR.PATCH, where differences in MAJOR
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correspond to incompatible API changes, differences in MINOR correspond
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to introduction of backwards compatible new functionality, and PATCH
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corresponds to backwards compatible bug fixes.
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## Building the Library (with ant)
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experiments from published papers that have used the library. Those directories contain
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READMEs that provide more detail on the examples, including on running the examples.
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## Importing the Library from Maven Central
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Add this to the dependencies section of your pom.xml, replacing the version number
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with the version you want to use (note that the library has been available in Maven
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Central since version 2.1.2).
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```XML
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<dependency>
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<groupId>org.cicirello</groupId>
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<artifactId>jpt</artifactId>
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<version>2.1.2</version>
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</dependency>
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```
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## Importing the Library from Github Packages
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If you'd prefer to import from Github Packages, rather than Maven Central,
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then: (1) add the dependency as indicated in previous section above,
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and (2) add the following to the repositories section of your pom.xml:
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```XML
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<repository>
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<id>github</id>
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<name>GitHub cicirello Apache Maven Packages</name>
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<url>https://maven.pkg.github.com/cicirello/JavaPermutationTools</url>
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<releases><enabled>true</enabled></releases>
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<snapshots><enabled>true</enabled></snapshots>
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</repository>
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```
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## License
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The JPT library is licensed under the [GNU General Public License 3.0](https://www.gnu.org/licenses/gpl-3.0.en.html).
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## Contribute
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Report bugs, suggestions, feature requests, etc via the [issues tracker](https://github.com/cicirello/JavaPermutationTools/issues). If you would

‎dist/jpt-2.0.1.jar

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‎pom.xml

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<version>2.1.0</version>
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<packaging>jar</packaging>
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<name>JavaPermutationTools</name>
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<description>JavaPermutationTools (JPT) is a library for
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computation on permutations and sequences.</description>
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<url>https://jpt.cicirello.org/</url>
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<name>JavaPermutationTools</name>
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<description>JavaPermutationTools (JPT) is a library for
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computation on permutations and sequences.
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JPT provides Java classes that enable representing and
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generating permutations and sequences, as well as
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performing computation on permutations and sequences.
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It includes implementations of a variety of permutation
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distance metrics as well as distance metrics on sequences
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(i.e., Strings, arrays, and other ordered data types).</description>
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<url>https://jpt.cicirello.org/</url>
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<licenses>
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<license>
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<name>GPL-3.0-or-later</name>
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<url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
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<distribution>repo</distribution>
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<comments>
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JavaPermutationTools (JPT): A library for computation on permutations and sequences.
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Copyright (C) 2005-2020 Vincent A. Cicirello.
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JavaPermutationTools is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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<licenses>
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<license>
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<name>GPL-3.0-or-later</name>
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<url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
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<distribution>repo</distribution>
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<comments>
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JavaPermutationTools (JPT): A library for computation on permutations and sequences.
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Copyright (C) 2005-2020 Vincent A. Cicirello.
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JavaPermutationTools is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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JavaPermutationTools is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see https://www.gnu.org/licenses/.
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</comments>
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</license>
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</licenses>
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<developers>
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<developer>
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<name>Vincent A Cicirello</name>
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<email>[email protected]</email>
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<url>https://www.cicirello.org/</url>
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<organization>Cicirello.Org</organization>
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<organizationUrl>https://www.cicirello.org/</organizationUrl>
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</developer>
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</developers>
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JavaPermutationTools is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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<organization>
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<name>Cicirello.Org</name>
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You should have received a copy of the GNU General Public License
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along with this program. If not, see https://www.gnu.org/licenses/.
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</comments>
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</license>
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</licenses>
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<developers>
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<developer>
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<name>Vincent A Cicirello</name>
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<email>[email protected]</email>
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<url>https://www.cicirello.org/</url>
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</organization>
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<organization>Cicirello.Org</organization>
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<organizationUrl>https://www.cicirello.org/</organizationUrl>
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</developer>
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</developers>
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<organization>
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<name>Cicirello.Org</name>
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<url>https://www.cicirello.org/</url>
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</organization>
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<profiles>
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<profile>
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<id>ossrhDeploy</id>
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<distributionManagement>
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<repository>
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<url>https://oss.sonatype.org/content/repositories/snapshots</url>
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</snapshotRepository>
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</distributionManagement>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-gpg-plugin</artifactId>
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<version>1.6</version>
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<executions>
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<execution>
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<id>sign-artifacts</id>
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<phase>verify</phase>
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<goals>
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<goal>sign</goal>
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</goals>
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<configuration>
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<gpgArguments>
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<arg>--pinentry-mode</arg>
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<arg>loopback</arg>
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</gpgArguments>
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</configuration>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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</profile>
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<profile>
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<id>githubDeploy</id>
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<distributionManagement>
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<repository>
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<id>github</id>
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<name>GitHub cicirello Apache Maven Packages</name>
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<url>https://maven.pkg.github.com/cicirello/JavaPermutationTools</url>
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</repository>
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</distributionManagement>
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</profile>
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</profiles>
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<issueManagement>
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<system>github</system>
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<url>https://github.com/cicirello/JavaPermutationTools/issues</url>
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<issueManagement>
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<system>github</system>
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<url>https://github.com/cicirello/JavaPermutationTools/issues</url>
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<scm>
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<scm>
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<connection>scm:git:git://github.com/cicirello/JavaPermutationTools.git</connection>
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<developerConnection>scm:git:ssh://github.com:cicirello/JavaPermutationTools.git</developerConnection>
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<version>1.6</version>
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<executions>
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<execution>
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<id>sign-artifacts</id>
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<goals>
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<goal>sign</goal>
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</gpgArguments>
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</configuration>
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</execution>
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</executions>
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</plugin>
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