Merge branch 'main' into javadoc

* main:
  Added more badges to readme
  Moved license header file to folder
  Another adjustment of license headers
  Corrected license header to GNU GPL v3 (formerly, it was an MIT license header);
  Added comments to JavaDoc publication yml file

.github/workflows/publish-javadoc.yml

@@ -1,6 +1,12 @@
 name: Deploy Javadoc
 
+#Note: The Javadoc-publisher action only commits to javadoc branch and triggers the GitHub pages update action if there
+# are changes in the JavaDoc, i.e. it ignores the Readme.md that is used as main landing page of the GitHub pages!
+# And these need to be merged into the javadoc branch.
+
 on:
+  #release: # to trigger this only at new releases, comment this in and the next three lines out
+    #types: [created, published, released]
   push:
     branches:
       - main
@@ -12,7 +18,7 @@ jobs:
       - name: Deploy JavaDoc 🚀
         uses: MathieuSoysal/Javadoc-publisher.yml@v2.4.0
         with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
           javadoc-branch: javadoc
           java-version: 17
           target-folder: javadoc

License-header/License-header.txt

@@ -0,0 +1,20 @@
+/*
+ * ART2a Clustering for Java
+ * Copyright (C) $today.year Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ *
+ * Source code is available at <https://github.com/JonasSchaub/ART2a-Clustering-for-Java>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+

README.md

@@ -1,4 +1,10 @@
-[![DOI](https://zenodo.org/badge/580826376.svg)](https://zenodo.org/badge/latestdoi/580826376) [![Javadoc](https://img.shields.io/badge/JavaDoc-Online-green)](https://jonasschaub.github.io/ART2a-Clustering-for-Java/javadoc/)
+[![DOI](https://zenodo.org/badge/580826376.svg)](https://zenodo.org/badge/latestdoi/580826376) 
+[![Javadoc](https://img.shields.io/badge/JavaDoc-Online-green)](https://jonasschaub.github.io/ART2a-Clustering-for-Java/javadoc/)
+[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0)
+[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-blue.svg)](https://GitHub.com/JonasSchaub/ART2a-Clustering-for-Java/graphs/commit-activity)
+[![GitHub issues](https://img.shields.io/github/issues/JonasSchaub/ART2a-Clustering-for-Java.svg)](https://GitHub.com/JonasSchaub/ART2a-Clustering-for-Java/issues/)
+[![GitHub contributors](https://img.shields.io/github/contributors/JonasSchaub/ART2a-Clustering-for-Java.svg)](https://GitHub.com/JonasSchaub/ART2a-Clustering-for-Java/graphs/contributors/)
+[![GitHub release](https://img.shields.io/github/release/JonasSchaub/ART2a-Clustering-for-Java.svg)](https://github.com/JonasSchaub/ART2a-Clustering-for-Java/releases/)
 # ART2a-Clustering-for-Java
 Implementation of the ART 2-A fingerprint clustering algorithm in Java.
 

build.gradle

@@ -62,7 +62,7 @@ spotless {
         indentWithSpaces(4) // doesn't really seem to work...
         trimTrailingWhitespace()
         endWithNewline()
-        licenseHeaderFile('License-header.txt')
+        licenseHeaderFile('License-header/License-header.txt')
         //eclipse() //not optimal, because indents with tabs..
         //googleJavaFormat() //not optimal, because indents with two spaces...
         //palantirJavaFormat() //not optimal, because unnecessary line breaks in head of for loop and corrupts editor folds

src/main/java/de/unijena/cheminf/clustering/art2a/Art2aClusteringTask.java

@@ -1,25 +1,21 @@
 /*
- * GNU General Public License v3.0
+ * ART2a Clustering for Java
+ * Copyright (C) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  *
- * Copyright (c) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Source code is available at <https://github.com/JonasSchaub/ART2a-Clustering-for-Java>
  *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
  *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
 package de.unijena.cheminf.clustering.art2a;

src/main/java/de/unijena/cheminf/clustering/art2a/abstractResult/Art2aAbstractResult.java

@@ -1,25 +1,21 @@
 /*
- * GNU General Public License v3.0
+ * ART2a Clustering for Java
+ * Copyright (C) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  *
- * Copyright (c) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Source code is available at <https://github.com/JonasSchaub/ART2a-Clustering-for-Java>
  *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
  *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
 package de.unijena.cheminf.clustering.art2a.abstractResult;

src/main/java/de/unijena/cheminf/clustering/art2a/clustering/Art2aDoubleClustering.java

@@ -1,25 +1,21 @@
 /*
- * GNU General Public License v3.0
+ * ART2a Clustering for Java
+ * Copyright (C) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  *
- * Copyright (c) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Source code is available at <https://github.com/JonasSchaub/ART2a-Clustering-for-Java>
  *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
  *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
 package de.unijena.cheminf.clustering.art2a.clustering;

src/main/java/de/unijena/cheminf/clustering/art2a/clustering/Art2aFloatClustering.java

@@ -1,25 +1,21 @@
 /*
- * GNU General Public License v3.0
+ * ART2a Clustering for Java
+ * Copyright (C) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  *
- * Copyright (c) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Source code is available at <https://github.com/JonasSchaub/ART2a-Clustering-for-Java>
  *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
  *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
 package de.unijena.cheminf.clustering.art2a.clustering;

src/main/java/de/unijena/cheminf/clustering/art2a/exceptions/ConvergenceFailedException.java

@@ -1,25 +1,21 @@
 /*
- * GNU General Public License v3.0
+ * ART2a Clustering for Java
+ * Copyright (C) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  *
- * Copyright (c) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Source code is available at <https://github.com/JonasSchaub/ART2a-Clustering-for-Java>
  *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
  *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
 package de.unijena.cheminf.clustering.art2a.exceptions;

src/main/java/de/unijena/cheminf/clustering/art2a/interfaces/IArt2aClustering.java

@@ -1,25 +1,21 @@
 /*
- * GNU General Public License v3.0
+ * ART2a Clustering for Java
+ * Copyright (C) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  *
- * Copyright (c) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Source code is available at <https://github.com/JonasSchaub/ART2a-Clustering-for-Java>
  *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
  *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
 package de.unijena.cheminf.clustering.art2a.interfaces;

src/main/java/de/unijena/cheminf/clustering/art2a/interfaces/IArt2aClusteringResult.java

@@ -1,25 +1,21 @@
 /*
- * GNU General Public License v3.0
+ * ART2a Clustering for Java
+ * Copyright (C) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
  *
- * Copyright (c) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
+ * Source code is available at <https://github.com/JonasSchaub/ART2a-Clustering-for-Java>
  *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
  *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
 package de.unijena.cheminf.clustering.art2a.interfaces;