{"id":15675088,"url":"https://github.com/cicirello/javapermutationtools","last_synced_at":"2025-04-15T21:17:33.632Z","repository":{"id":37905919,"uuid":"139182095","full_name":"cicirello/JavaPermutationTools","owner":"cicirello","description":"A Java library for computation on permutations and sequences","archived":false,"fork":false,"pushed_at":"2025-04-15T11:49:18.000Z","size":6923,"stargazers_count":17,"open_issues_count":1,"forks_count":11,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-15T21:17:25.366Z","etag":null,"topics":["edit-distance","permutation-distance","permutation-distance-metrics","permutations","sequences","string-distance"],"latest_commit_sha":null,"homepage":"https://jpt.cicirello.org/","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cicirello.png","metadata":{"funding":{"github":"cicirello","patreon":null,"open_collective":null,"ko_fi":"cicirello","tidelift":null,"community_bridge":null,"liberapay":"cicirello","issuehunt":null,"otechie":null,"custom":null},"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":".zenodo.json"}},"created_at":"2018-06-29T18:20:12.000Z","updated_at":"2025-04-15T11:49:16.000Z","dependencies_parsed_at":"2024-01-15T21:00:26.501Z","dependency_job_id":"34936d1f-85a6-48ae-a0aa-dcbbbe408ebb","html_url":"https://github.com/cicirello/JavaPermutationTools","commit_stats":{"total_commits":1159,"total_committers":3,"mean_commits":386.3333333333333,"dds":0.1553062985332183,"last_synced_commit":"881ca24855f701ecf827629627296cffdebe78fd"},"previous_names":[],"tags_count":49,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cicirello%2FJavaPermutationTools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cicirello%2FJavaPermutationTools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cicirello%2FJavaPermutationTools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cicirello%2FJavaPermutationTools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cicirello","download_url":"https://codeload.github.com/cicirello/JavaPermutationTools/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249153953,"owners_count":21221330,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["edit-distance","permutation-distance","permutation-distance-metrics","permutations","sequences","string-distance"],"created_at":"2024-10-03T15:56:14.125Z","updated_at":"2025-04-15T21:17:33.614Z","avatar_url":"https://github.com/cicirello.png","language":"Java","readme":"# JavaPermutationTools (JPT): A Java library for computation on permutations and sequences \n\n[![JavaPermutationTools - A Java library for computation on permutations and sequences](https://jpt.cicirello.org/images/jpt640.png)](#javapermutationtools-jpt-a-java-library-for-computation-on-permutations-and-sequences)\n\nCopyright (C) 2018-2024 [Vincent A. Cicirello](https://www.cicirello.org/).\n\nWebsite: https://jpt.cicirello.org/\n\nAPI documentation: https://jpt.cicirello.org/api\n\n| __Publications About the Library__ | [![DOI](http://joss.theoj.org/papers/10.21105/joss.00950/status.svg)](https://doi.org/10.21105/joss.00950) |\n| :--- | :--- |\n| __Packages and Releases__ | [![Maven Central](https://img.shields.io/maven-central/v/org.cicirello/jpt.svg?label=Maven%20Central\u0026logo=apachemaven)](https://central.sonatype.com/artifact/org.cicirello/jpt/) [![GitHub release (latest by date)](https://img.shields.io/github/v/release/cicirello/JavaPermutationTools?logo=GitHub)](https://github.com/cicirello/JavaPermutationTools/releases) |\n| __Build Status__ | [![build](https://github.com/cicirello/JavaPermutationTools/actions/workflows/build.yml/badge.svg)](https://github.com/cicirello/JavaPermutationTools/actions/workflows/build.yml) [![docs](https://github.com/cicirello/JavaPermutationTools/actions/workflows/docs.yml/badge.svg)](https://jpt.cicirello.org/api/) [![CodeQL](https://github.com/cicirello/JavaPermutationTools/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/cicirello/JavaPermutationTools/actions/workflows/codeql-analysis.yml) |\n| __JaCoCo Test Coverage__ | [![coverage](https://raw.githubusercontent.com/cicirello/JavaPermutationTools/badges/jacoco.svg)](https://github.com/cicirello/JavaPermutationTools/actions/workflows/build.yml) [![branch coverage](https://raw.githubusercontent.com/cicirello/JavaPermutationTools/badges/branches.svg)](https://github.com/cicirello/JavaPermutationTools/actions/workflows/build.yml) |\n| __Security__ | [![Snyk security score](https://snyk-widget.herokuapp.com/badge/mvn/org.cicirello/jpt/badge.svg)](https://snyk.io/vuln/maven%3Aorg.cicirello%3Ajpt) [![Snyk Known Vulnerabilities](https://snyk.io/test/github/cicirello/JavaPermutationTools/badge.svg)](https://snyk.io/test/github/cicirello/JavaPermutationTools) |\n| __DOI__ | [![DOI](https://zenodo.org/badge/139182095.svg)](https://zenodo.org/badge/latestdoi/139182095) |\n| __Other Information__ | [![GitHub](https://img.shields.io/github/license/cicirello/JavaPermutationTools)](https://github.com/cicirello/JavaPermutationTools/blob/master/LICENSE) [![style](https://img.shields.io/badge/style-Google%20Java%20Style-informational)](https://google.github.io/styleguide/javaguide.html) | \n| __Support__ | [![GitHub Sponsors](https://img.shields.io/badge/sponsor-30363D?logo=GitHub-Sponsors\u0026logoColor=#EA4AAA)](https://github.com/sponsors/cicirello) [![Liberapay](https://img.shields.io/badge/Liberapay-F6C915?logo=liberapay\u0026logoColor=black)](https://liberapay.com/cicirello) [![Ko-Fi](https://img.shields.io/badge/Ko--fi-F16061?logo=ko-fi\u0026logoColor=white)](https://ko-fi.com/cicirello) | \n\n## How to Cite\n\nIf you use this library in your research, please cite the following paper:\n\n\u003e Cicirello, Vincent A (2018). JavaPermutationTools: A Java Library of Permutation Distance Metrics. *Journal of Open Source Software*, 3(31), 950.  https://doi.org/10.21105/joss.00950 .\n\n## Overview\n\nThe JavaPermutationTools (JPT) library provides Java classes and interfaces, etc that \nenable representing and generating permutations and sequences, as well as performing \ncomputation on permutations and sequences. It includes implementations of a variety \nof permutation distance metrics as well as distance metrics on sequences (i.e., Strings, \narrays, and other ordered data types). \n\n## Java 17+\n\nWe currently support Java 17+. See the following table for mapping between library version\nand minimum supported Java version.\n\n| version | Java requirements |\n| --- | --- |\n| 4.w.x to 6.y.z | Java 17+ |\n| 3.x.y | Java 11+ |\n| 1.w.x to 2.y.z | Java 8+ |\n\nThe jar files of the library are released via Maven Central, GitHub Packages, \nand GitHub Releases.\n\n## Versioning Scheme\n\nThe JPT uses [Semantic Versioning](https://semver.org/) with version \nnumbers of the form: MAJOR.MINOR.PATCH, where differences in MAJOR \ncorrespond to incompatible API changes, differences in MINOR correspond \nto introduction of backwards compatible new functionality, and PATCH \ncorresponds to backwards compatible bug fixes. \n\n## Building the Library (with Maven)\n\nThe JavaPermutationTools library is built using Maven. The root of the\nrepository contains a Maven `pom.xml`.  To build the library, \nexecute `mvn package` at the root of the repository, which\nwill compile all classes, run all tests, run javadoc, and generate \njar files of the library, the sources, and the javadocs. All build \noutputs will then be found in the directory `target`.\n\nTo include generation of a code coverage report during the build,\nexecute `mvn package -Pcoverage` at the root of the repository to \nenable a Maven profile that executes JaCoCo during the test \nphase. The JaCoCo report will also be found in the target directory.\n\nTo run all static analysis tools (i.e., SpotBugs, Find Security Bugs,\nrefactor-first), execute `mvn package -Panalysis` to enable a Maven \nprofile that executes the various static analysis tools that we are \nusing. The SpotBugs html report will be found in the `target` directory, \nor you can use the SpotBugs GUI with: `mvn spotbugs:gui -Panalysis`. The \nrefactor-first report will be found in the `target/site` directory.\n\nTo run all of the above: `mvn package -P \"analysis,coverage\"`.\n\n## Example Programs\n\nThere are several example programs available in a separate \nrepository: [cicirello/jpt-examples](https://github.com/cicirello/jpt-examples). The\nexamples repository contains example usage of several of the classes of the \nlibrary. Each of the examples contains detailed comments within the source \ncode explaining the example. Running the examples without reading the source \ncomments is not advised. Some of the example in the examples repository are\nbased on the experiments from published papers that have either used the library\ndirectly, or which led to some of the code in the library.\n\n## Java Modules\n\nThis library provides a Java module, `org.cicirello.jpt`. To use in your project,\nadd the following to your `module-info.java`:\n\n```Java\nmodule your.module.name.here {\n\trequires org.cicirello.jpt;\n}\n```\n\nThis module includes the `org.cicirello.permutations` and `org.cicirello.sequences`\npackages as well as their subpackages. See the [API documentation](https://jpt.cicirello.org/api) \nfor details of all packages included in this module.\n\nBeginning with version 3.0.0, randomization and other math utilities, and some\ngeneric utilities, have been\nmoved to a pair of new libraries [\u0026rho;\u0026mu;](https://github.com/cicirello/rho-mu)\nand [org.cicirello.core](https://github.com/cicirello/core), which are\nnow dependencies of JavaPermutationTools. Your dependency manager (see next section)\nwill handle downloading these for you. \n\nIf you are directly utilizing the functionality of the dependencies, then you may instead \nneed the following:\n\n```Java\nmodule your.module.name.here {\n\trequires org.cicirello.jpt;\n\trequires org.cicirello.rho_mu;\n\trequires org.cicirello.core;\n}\n```\n\n## Importing the Library from Maven Central\n\nAdd this to the dependencies section of your pom.xml, replacing the version number \nwith the version you want to use.\n\n```XML\n\u003cdependency\u003e\n  \u003cgroupId\u003eorg.cicirello\u003c/groupId\u003e\n  \u003cartifactId\u003ejpt\u003c/artifactId\u003e\n  \u003cversion\u003e5.0.0\u003c/version\u003e\n\u003c/dependency\u003e\n```\n\n## Importing the Library from Github Packages\n\nIf you'd prefer to import from Github Packages, rather than Maven Central, \nthen: (1) add the dependency as indicated in previous section above, \nand (2) add the following to the repositories section of your pom.xml:\n\n```XML\n\u003crepository\u003e\n  \u003cid\u003egithub\u003c/id\u003e\n  \u003cname\u003eGitHub cicirello Apache Maven Packages\u003c/name\u003e\n  \u003curl\u003ehttps://maven.pkg.github.com/cicirello/JavaPermutationTools\u003c/url\u003e\n  \u003creleases\u003e\u003cenabled\u003etrue\u003c/enabled\u003e\u003c/releases\u003e\n  \u003csnapshots\u003e\u003cenabled\u003etrue\u003c/enabled\u003e\u003c/snapshots\u003e\n\u003c/repository\u003e\n```\n\n## Downloading Jar Files\n\nIf you don't use a dependency manager that supports importing from Maven Central,\nor if you simply prefer to download manually, prebuilt jars are also attached to \neach [GitHub Release](https://github.com/cicirello/JavaPermutationTools). If you\nmanually download jar files, make sure you also get the relevant versions of the\ndependencies. The simplest way to do this is to import from Maven Central, which\nwill obtain the relevant dependencies automatically.\n\n## License\n\nThe JPT library is licensed under the [GNU General Public License 3.0](https://www.gnu.org/licenses/gpl-3.0.en.html).\n\n## Contribute\n\nIf you would like to contribute in any way, such \nas reporting bugs, suggesting new functionality, or code contributions \nsuch as bug fixes or implementations of new functionality, then start \nby reading the [contribution guidelines](https://github.com/cicirello/.github/blob/main/CONTRIBUTING.md).\nThis project has adopted \nthe [Contributor Covenant Code of Conduct](https://github.com/cicirello/.github/blob/main/CODE_OF_CONDUCT.md).\n","funding_links":["https://github.com/sponsors/cicirello","https://ko-fi.com/cicirello","https://liberapay.com/cicirello"],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcicirello%2Fjavapermutationtools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcicirello%2Fjavapermutationtools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcicirello%2Fjavapermutationtools/lists"}