v1.1.3

gagolews · Jan 16, 2023 · 9f65c9f · 9f65c9f
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diff --git a/.devel/sphinx/conf.py b/.devel/sphinx/conf.py
@@ -1,4 +1,4 @@
-# Copyleft (C) 2020-2022, Marek Gagolewski <https://www.gagolewski.com>
+# Copyleft (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>
 # Configuration file for the Sphinx documentation builder.
 
 import sphinx_rtd_theme
@@ -7,7 +7,7 @@
 pkg_name = "genieclust"
 pkg_title = "genieclust"
 pkg_version = genieclust.__version__
-copyright_year = "2018–2022"
+copyright_year = "2018–2023"
 html_baseurl = "https://genieclust.gagolewski.com/"
 github_url = "https://github.com/gagolews/genieclust/"
 github_star_repo = "gagolews/genieclust"

diff --git a/.devel/sphinx/news.md b/.devel/sphinx/news.md
@@ -1,9 +1,9 @@
 # What Is New in *genieclust*
 
 
-## 1.1.2.9xxx (under development)
+## 1.1.3 (2023-01-17)
 
-*  [R] `mst.default` throws an error if any element in the input matrix
+*  [R] `mst.default` now throws an error if any element in the input matrix
    is missing/infinite.
 
 *  [Python] Fixed call to `mlpack.emst` that no longer worked

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: genieclust
 Type: Package
 Title: Fast and Robust Hierarchical Clustering with Noise Points Detection
-Version: 1.1.2.9001
-Date: 2022-11-15
+Version: 1.1.3
+Date: 2023-01-17
 Authors@R: c(
     person("Marek", "Gagolewski",
         role = c("aut", "cre", "cph"),

diff --git a/LICENSE b/LICENSE
@@ -1,5 +1,5 @@
 genieclust package for R and Python
-Copyleft (C) 2018-2022, Marek Gagolewski <https://www.gagolewski.com>
+Copyleft (C) 2018-2023, Marek Gagolewski <https://www.gagolewski.com>
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU Affero General Public License

diff --git a/Makefile b/Makefile
@@ -1,4 +1,4 @@
-# Copyleft (C) 2020-2022, Marek Gagolewski <https://www.gagolewski.com>
+# Copyleft (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>
 
 .PHONY: python py-test py-check r r-check r r-build sphinx docs clean
 
@@ -49,7 +49,7 @@ r: r-autoconf
 r-test: r
 	Rscript -e 'source(".devel/tinytest.R")'
 
-r-build:
+r-build: r-autoconf
 	cd .. && R CMD build ${PKGNAME}
 
 r-check: stop-on-utf8 r-build

diff --git a/NEWS b/NEWS
@@ -1,9 +1,9 @@
 # What Is New in *genieclust*
 
 
-## 1.1.2.9xxx (under development)
+## 1.1.3 (2023-01-17)
 
-*  [R] `mst.default` throws an error if any element in the input matrix
+*  [R] `mst.default` now throws an error if any element in the input matrix
    is missing/infinite.
 
 *  [Python] Fixed call to `mlpack.emst` that no longer worked

diff --git a/R/gclust.R b/R/gclust.R
@@ -2,7 +2,7 @@
 
 # ############################################################################ #
 #                                                                              #
-#   Copyleft (C) 2020-2022, Marek Gagolewski <https://www.gagolewski.com>      #
+#   Copyleft (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>      #
 #                                                                              #
 #                                                                              #
 #   This program is free software: you can redistribute it and/or modify       #

diff --git a/R/genieclust-package.R b/R/genieclust-package.R
@@ -2,7 +2,7 @@
 
 # ############################################################################ #
 #                                                                              #
-#   Copyleft (C) 2020-2022, Marek Gagolewski <https://www.gagolewski.com>      #
+#   Copyleft (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>      #
 #                                                                              #
 #                                                                              #
 #   This program is free software: you can redistribute it and/or modify       #

diff --git a/R/mst.R b/R/mst.R
@@ -2,7 +2,7 @@
 
 # ############################################################################ #
 #                                                                              #
-#   Copyleft (C) 2020-2022, Marek Gagolewski <https://www.gagolewski.com>      #
+#   Copyleft (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>      #
 #                                                                              #
 #                                                                              #
 #   This program is free software: you can redistribute it and/or modify       #

diff --git a/README.md b/README.md
@@ -157,7 +157,7 @@ Any contributions are welcome (e.g., Julia, Matlab, ...).
 
 ## License
 
-Copyright (C) 2018–2022 Marek Gagolewski <https://www.gagolewski.com>
+Copyright (C) 2018–2023 Marek Gagolewski <https://www.gagolewski.com>
 
 This program is free software: you can redistribute it and/or modify it
 under the terms of the GNU Affero General Public License Version 3, 19
@@ -188,6 +188,7 @@ Originally distributed under the GNU Affero General Public License Version 3.
 Gagolewski M., genieclust: Fast and robust hierarchical clustering,
 *SoftwareX* **15**, 2021, 100722.
 [DOI: 10.1016/j.softx.2021.100722](https://doi.org/10.1016/j.softx.2021.100722).
+<https://genieclust.gagolewski.com>.
 
 Gagolewski M., Bartoszuk M., Cena A., Genie: A new, fast, and
 outlier-resistant hierarchical clustering algorithm, *Information
@@ -202,10 +203,10 @@ Gagolewski M., *Adjusted asymmetric accuracy: A well-behaving external
 cluster validity measure*, under review (preprint),
 [DOI: 10.48550/arXiv.2209.02935](https://doi.org/10.48550/arXiv.2209.02935).
 
-Gagolewski M., *A Framework for Benchmarking Clustering Algorithms*,
-2022, <https://clustering-benchmarks.gagolewski.com>,
-[DOI: 10.48550/arXiv.2209.09493](https://doi.org/10.48550/arXiv.2209.09493),
-under review (preprint).
+Gagolewski M., A Framework for Benchmarking Clustering Algorithms,
+*SoftwareX* **20**, 2022, 101270.
+[DOI: 10.1016/j.softx.2022.101270](https://doi.org/10.1016/j.softx.2022.101270).
+<https://clustering-benchmarks.gagolewski.com>.
 
 Campello R.J.G.B., Moulavi D., Sander J.,
 Density-based clustering based on hierarchical density estimates,

diff --git a/docs/_images/genieclust_plots-1.png b/docs/_images/genieclust_plots-1.png
diff --git a/docs/_images/genieclust_plots-2.png b/docs/_images/genieclust_plots-2.png
diff --git a/docs/_images/genieclust_plots-3.png b/docs/_images/genieclust_plots-3.png
diff --git a/docs/_images/genieclust_plots-4.png b/docs/_images/genieclust_plots-4.png
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.1.2',
+    VERSION: '1.1.3',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/genieclust.html b/docs/genieclust.html
@@ -78,7 +78,7 @@
           </a>
 
           <div class="version">
-              Python and R Package<br />    v1.1.2
+              Python and R Package<br />    v1.1.3
           </div>
 
 <!--
@@ -150,6 +150,7 @@
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://clustering-benchmarks.gagolewski.com">Clustering Benchmarks</a></li>
 <li class="toctree-l1"><a class="reference external" href="https://datawranglingpy.gagolewski.com/">Data Wrangling in Python</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://deepr.gagolewski.com">Deep R Programming</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Appendix</span></p>
 <ul>
@@ -297,13 +298,13 @@ <h1>Python Package <cite>genieclust</cite> Reference<a class="headerlink" href="
 
   <div role="contentinfo">
     <p>
-        Copyright &#169; 2018–2022 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
+        Copyright &#169; 2018–2023 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
 
     Built with <a href="https://sphinx-doc.org/">Sphinx</a>
     and a customised <a href="https://github.com/rtfd/sphinx_rtd_theme">rtd</a>
     theme.
       <span class="lastupdated">
-        Last updated on 2022-09-22T18:55:42+1000.
+        Last updated on 2023-01-17T10:05:17+1100.
       </span>
 
 

diff --git a/docs/genieclust_cluster_validity.html b/docs/genieclust_cluster_validity.html
@@ -80,7 +80,7 @@
           </a>
 
           <div class="version">
-              Python and R Package<br />    v1.1.2
+              Python and R Package<br />    v1.1.3
           </div>
 
 <!--
@@ -152,6 +152,7 @@
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://clustering-benchmarks.gagolewski.com">Clustering Benchmarks</a></li>
 <li class="toctree-l1"><a class="reference external" href="https://datawranglingpy.gagolewski.com/">Data Wrangling in Python</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://deepr.gagolewski.com">Deep R Programming</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Appendix</span></p>
 <ul>
@@ -895,13 +896,13 @@
 
   <div role="contentinfo">
     <p>
-        Copyright &#169; 2018–2022 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
+        Copyright &#169; 2018–2023 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
 
     Built with <a href="https://sphinx-doc.org/">Sphinx</a>
     and a customised <a href="https://github.com/rtfd/sphinx_rtd_theme">rtd</a>
     theme.
       <span class="lastupdated">
-        Last updated on 2022-09-22T18:55:42+1000.
+        Last updated on 2023-01-17T10:05:17+1100.
       </span>
 
 

diff --git a/docs/genieclust_compare_partitions.html b/docs/genieclust_compare_partitions.html
@@ -80,7 +80,7 @@
           </a>
 
           <div class="version">
-              Python and R Package<br />    v1.1.2
+              Python and R Package<br />    v1.1.3
           </div>
 
 <!--
@@ -152,6 +152,7 @@
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://clustering-benchmarks.gagolewski.com">Clustering Benchmarks</a></li>
 <li class="toctree-l1"><a class="reference external" href="https://datawranglingpy.gagolewski.com/">Data Wrangling in Python</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://deepr.gagolewski.com">Deep R Programming</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Appendix</span></p>
 <ul>
@@ -1020,13 +1021,13 @@
 
   <div role="contentinfo">
     <p>
-        Copyright &#169; 2018–2022 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
+        Copyright &#169; 2018–2023 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
 
     Built with <a href="https://sphinx-doc.org/">Sphinx</a>
     and a customised <a href="https://github.com/rtfd/sphinx_rtd_theme">rtd</a>
     theme.
       <span class="lastupdated">
-        Last updated on 2022-09-22T18:55:42+1000.
+        Last updated on 2023-01-17T10:05:17+1100.
       </span>
 
 

diff --git a/docs/genieclust_genie.html b/docs/genieclust_genie.html
@@ -80,7 +80,7 @@
           </a>
 
           <div class="version">
-              Python and R Package<br />    v1.1.2
+              Python and R Package<br />    v1.1.3
           </div>
 
 <!--
@@ -152,6 +152,7 @@
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://clustering-benchmarks.gagolewski.com">Clustering Benchmarks</a></li>
 <li class="toctree-l1"><a class="reference external" href="https://datawranglingpy.gagolewski.com/">Data Wrangling in Python</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://deepr.gagolewski.com">Deep R Programming</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Appendix</span></p>
 <ul>
@@ -645,13 +646,13 @@ <h1>genieclust.Genie<a class="headerlink" href="#genieclust-genie" title="Permal
 
   <div role="contentinfo">
     <p>
-        Copyright &#169; 2018–2022 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
+        Copyright &#169; 2018–2023 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
 
     Built with <a href="https://sphinx-doc.org/">Sphinx</a>
     and a customised <a href="https://github.com/rtfd/sphinx_rtd_theme">rtd</a>
     theme.
       <span class="lastupdated">
-        Last updated on 2022-09-22T18:55:42+1000.
+        Last updated on 2023-01-17T10:05:17+1100.
       </span>
 
 

diff --git a/docs/genieclust_inequity.html b/docs/genieclust_inequity.html
@@ -80,7 +80,7 @@
           </a>
 
           <div class="version">
-              Python and R Package<br />    v1.1.2
+              Python and R Package<br />    v1.1.3
           </div>
 
 <!--
@@ -152,6 +152,7 @@
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://clustering-benchmarks.gagolewski.com">Clustering Benchmarks</a></li>
 <li class="toctree-l1"><a class="reference external" href="https://datawranglingpy.gagolewski.com/">Data Wrangling in Python</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://deepr.gagolewski.com">Deep R Programming</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Appendix</span></p>
 <ul>
@@ -480,13 +481,13 @@
 
   <div role="contentinfo">
     <p>
-        Copyright &#169; 2018–2022 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
+        Copyright &#169; 2018–2023 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
 
     Built with <a href="https://sphinx-doc.org/">Sphinx</a>
     and a customised <a href="https://github.com/rtfd/sphinx_rtd_theme">rtd</a>
     theme.
       <span class="lastupdated">
-        Last updated on 2022-09-22T18:55:42+1000.
+        Last updated on 2023-01-17T10:05:17+1100.
       </span>
 
 

diff --git a/docs/genieclust_internal.html b/docs/genieclust_internal.html
@@ -80,7 +80,7 @@
           </a>
 
           <div class="version">
-              Python and R Package<br />    v1.1.2
+              Python and R Package<br />    v1.1.3
           </div>
 
 <!--
@@ -152,6 +152,7 @@
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://clustering-benchmarks.gagolewski.com">Clustering Benchmarks</a></li>
 <li class="toctree-l1"><a class="reference external" href="https://datawranglingpy.gagolewski.com/">Data Wrangling in Python</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://deepr.gagolewski.com">Deep R Programming</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Appendix</span></p>
 <ul>
@@ -574,13 +575,13 @@
 
   <div role="contentinfo">
     <p>
-        Copyright &#169; 2018–2022 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
+        Copyright &#169; 2018–2023 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
 
     Built with <a href="https://sphinx-doc.org/">Sphinx</a>
     and a customised <a href="https://github.com/rtfd/sphinx_rtd_theme">rtd</a>
     theme.
       <span class="lastupdated">
-        Last updated on 2022-09-22T18:55:42+1000.
+        Last updated on 2023-01-17T10:05:17+1100.
       </span>
 
 

diff --git a/docs/genieclust_plots-1.hires.png b/docs/genieclust_plots-1.hires.png
diff --git a/docs/genieclust_plots-1.pdf b/docs/genieclust_plots-1.pdf
diff --git a/docs/genieclust_plots-1.png b/docs/genieclust_plots-1.png
diff --git a/docs/genieclust_plots-2.hires.png b/docs/genieclust_plots-2.hires.png
diff --git a/docs/genieclust_plots-2.pdf b/docs/genieclust_plots-2.pdf
diff --git a/docs/genieclust_plots-2.png b/docs/genieclust_plots-2.png
diff --git a/docs/genieclust_plots-3.hires.png b/docs/genieclust_plots-3.hires.png
diff --git a/docs/genieclust_plots-3.pdf b/docs/genieclust_plots-3.pdf
diff --git a/docs/genieclust_plots-3.png b/docs/genieclust_plots-3.png
diff --git a/docs/genieclust_plots-4.hires.png b/docs/genieclust_plots-4.hires.png
diff --git a/docs/genieclust_plots-4.pdf b/docs/genieclust_plots-4.pdf
diff --git a/docs/genieclust_plots-4.png b/docs/genieclust_plots-4.png
diff --git a/docs/genieclust_plots.html b/docs/genieclust_plots.html
@@ -78,7 +78,7 @@
           </a>
 
           <div class="version">
-              Python and R Package<br />    v1.1.2
+              Python and R Package<br />    v1.1.3
           </div>
 
 <!--
@@ -150,6 +150,7 @@
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://clustering-benchmarks.gagolewski.com">Clustering Benchmarks</a></li>
 <li class="toctree-l1"><a class="reference external" href="https://datawranglingpy.gagolewski.com/">Data Wrangling in Python</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://deepr.gagolewski.com">Deep R Programming</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Appendix</span></p>
 <ul>
@@ -391,13 +392,13 @@
 
   <div role="contentinfo">
     <p>
-        Copyright &#169; 2018–2022 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
+        Copyright &#169; 2018–2023 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>. Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
 
     Built with <a href="https://sphinx-doc.org/">Sphinx</a>
     and a customised <a href="https://github.com/rtfd/sphinx_rtd_theme">rtd</a>
     theme.
       <span class="lastupdated">
-        Last updated on 2022-09-22T18:55:42+1000.
+        Last updated on 2023-01-17T10:05:17+1100.
       </span>