numpy2.0

gagolews · Jun 17, 2024 · 5bbae1c · 5bbae1c
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diff --git a/.devel/sphinx/alphamarek.py b/.devel/sphinx/alphamarek.py
@@ -1,4 +1,4 @@
-# Copyleft (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com/>
+# Copyleft (C) 2020-2024, Marek Gagolewski <https://www.gagolewski.com/>
 
 # based on https://bitbucket.org/pybtex-devs/pybtex/src/HEAD/pybtex/style/formatting/unsrt.py
 

diff --git a/.devel/sphinx/conf.py b/.devel/sphinx/conf.py
@@ -1,4 +1,4 @@
-# Copyleft (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>
+# Copyleft (C) 2020-2024, Marek Gagolewski <https://www.gagolewski.com>
 # Configuration file for the Sphinx documentation builder.
 
 import sys, os
@@ -12,7 +12,7 @@
 pkg_name = "genieclust"
 pkg_title = "genieclust"
 pkg_version = genieclust.__version__
-copyright_year = "2018–2023"
+copyright_year = "2018–2024"
 html_baseurl = "https://genieclust.gagolewski.com/"
 html_logo = "https://www.gagolewski.com/_static/img/genieclust.png"
 html_favicon = "https://www.gagolewski.com/_static/img/genieclust.png"

diff --git a/.devel/sphinx/fix-html.sh b/.devel/sphinx/fix-html.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com/>
+# Copyright (C) 2020-2024, Marek Gagolewski <https://www.gagolewski.com/>
 
 set -e
 

diff --git a/.devel/sphinx/news.md b/.devel/sphinx/news.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## 1.1.5.9001 (under development)
+
+* [PYTHON] The packages now works with *numpy* 2.0.
+
+
 ## 1.1.5 (2023-10-18)
 
 * [BACKWARD INCOMPATIBILITY] [Python and R] Inequality measures

diff --git a/.devel/sphinx/weave/Makefile b/.devel/sphinx/weave/Makefile
@@ -1,4 +1,4 @@
-# Copyright (c) 2013-2023, Marek Gagolewski <https://www.gagolewski.com>
+# Copyright (c) 2013-2024, Marek Gagolewski <https://www.gagolewski.com>
 
 FILES_RMD = \
 	basics.Rmd              \

diff --git a/.devel/sphinx/weave/Rmd2md-patch.R b/.devel/sphinx/weave/Rmd2md-patch.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com/>
+# Copyright (C) 2020-2024, Marek Gagolewski <https://www.gagolewski.com/>
 
 # I only want ```{r...``` and ```{python...``` to be recognised as
 # chunks to-be processed by knitr so that they can be placed within

diff --git a/.devel/sphinx/weave/Rmd2md.sh b/.devel/sphinx/weave/Rmd2md.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com/>
+# Copyright (C) 2020-2024, Marek Gagolewski <https://www.gagolewski.com/>
 
 set -e
 

diff --git a/.devel/sphinx/weave/extract-code-comments.R b/.devel/sphinx/weave/extract-code-comments.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>
+# Copyright (C) 2020-2024, Marek Gagolewski <https://www.gagolewski.com>
 
 # Moves #> comments inside Markdown *highlighted* code blocks outside
 

diff --git a/.devel/sphinx/weave/options.R b/.devel/sphinx/weave/options.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>
+# Copyright (C) 2020-2024, Marek Gagolewski <https://www.gagolewski.com>
 
 options(encoding="UTF-8")
 set.seed(666)

diff --git a/.devel/sphinx/weave/pweave_custom.py b/.devel/sphinx/weave/pweave_custom.py
@@ -2,7 +2,7 @@
 
 # ########################################################################## #
 #  Marek's output hooks hacks                                                #
-#  Copyleft (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>     #
+#  Copyleft (C) 2020-2024, Marek Gagolewski <https://www.gagolewski.com>     #
 # ########################################################################## #
 
 

diff --git a/LICENSE b/LICENSE
@@ -1,5 +1,5 @@
 genieclust package for R and Python
-Copyleft (C) 2018-2023, Marek Gagolewski <https://www.gagolewski.com/>
+Copyleft (C) 2018-2024, 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) 2020-2023, Marek Gagolewski <https://www.gagolewski.com/>
+# Copyleft (C) 2020-2024, Marek Gagolewski <https://www.gagolewski.com/>
 
 .PHONY: python py-test py-check r r-check r r-build html docs clean
 

diff --git a/NEWS b/NEWS
@@ -1,5 +1,10 @@
 # Changelog
 
+## 1.1.5.9001 (under development)
+
+* [PYTHON] The packages now works with *numpy* 2.0.
+
+
 ## 1.1.5 (2023-10-18)
 
 * [BACKWARD INCOMPATIBILITY] [Python and R] Inequality measures

diff --git a/R/gclust.R b/R/gclust.R
@@ -2,7 +2,7 @@
 
 # ############################################################################ #
 #                                                                              #
-#   Copyleft (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>      #
+#   Copyleft (C) 2020-2024, 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) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>      #
+#   Copyleft (C) 2020-2024, 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) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>      #
+#   Copyleft (C) 2020-2024, 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
@@ -9,7 +9,7 @@
 
 
 > **Genie finds meaningful clusters quickly – even on large data sets.**
-> 
+>
 > A comprehensive tutorial, benchmarks, and a reference manual is available
 at <https://genieclust.gagolewski.com/>.
 
@@ -165,7 +165,7 @@ Any contributions are welcome (e.g., Julia, Matlab, ...).
 
 ## License
 
-Copyright (C) 2018–2023 Marek Gagolewski <https://www.gagolewski.com/>
+Copyright (C) 2018–2024 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

diff --git a/docs/_downloads/01c61da91a57cfdb372b0edb5845828a/genieclust_plots-4.pdf b/docs/_downloads/01c61da91a57cfdb372b0edb5845828a/genieclust_plots-4.pdf
diff --git a/docs/_downloads/36c4dad867b3fffadb9a35cb5700de0e/genieclust_plots-3.pdf b/docs/_downloads/36c4dad867b3fffadb9a35cb5700de0e/genieclust_plots-3.pdf
diff --git a/docs/_downloads/3db969050b6fe55b9afe4d23ba8ca159/genieclust_plots-1.pdf b/docs/_downloads/3db969050b6fe55b9afe4d23ba8ca159/genieclust_plots-1.pdf
diff --git a/docs/_downloads/45852431f09dd0f067debdafd9183f89/genieclust_plots-4.hires.png b/docs/_downloads/45852431f09dd0f067debdafd9183f89/genieclust_plots-4.hires.png
diff --git a/docs/_downloads/80b6e797cf4bfc1e75b448d4dd5ab97a/genieclust_plots-2.png b/docs/_downloads/80b6e797cf4bfc1e75b448d4dd5ab97a/genieclust_plots-2.png
diff --git a/docs/_downloads/87a64c806a70c3933ae7971e4274766d/genieclust_plots-3.png b/docs/_downloads/87a64c806a70c3933ae7971e4274766d/genieclust_plots-3.png
diff --git a/docs/_downloads/a93a0e04519e0a9f69f41a9fc3df0844/genieclust_plots-2.hires.png b/docs/_downloads/a93a0e04519e0a9f69f41a9fc3df0844/genieclust_plots-2.hires.png
diff --git a/docs/_downloads/aad27638b83bb016d016d86411e5bb69/genieclust_plots-4.png b/docs/_downloads/aad27638b83bb016d016d86411e5bb69/genieclust_plots-4.png
diff --git a/docs/_downloads/e8b0369125c8b9186ee63322221ea81a/genieclust_plots-3.hires.png b/docs/_downloads/e8b0369125c8b9186ee63322221ea81a/genieclust_plots-3.hires.png
diff --git a/docs/_downloads/ed494fd415c093d0a546f90cf51e4280/genieclust_plots-1.png b/docs/_downloads/ed494fd415c093d0a546f90cf51e4280/genieclust_plots-1.png
diff --git a/docs/_downloads/f10d82cc1a8914330c4324f07e968726/genieclust_plots-2.pdf b/docs/_downloads/f10d82cc1a8914330c4324f07e968726/genieclust_plots-2.pdf
diff --git a/docs/_downloads/feb2bbc6c795930ee090591ae6c4e6c1/genieclust_plots-1.hires.png b/docs/_downloads/feb2bbc6c795930ee090591ae6c4e6c1/genieclust_plots-1.hires.png
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/css/custom.css b/docs/_static/css/custom.css
@@ -1,17 +1,21 @@
 /* --------------------------------------------------------------------------
-   Copyleft (C) 2021-2023, Marek Gagolewski <https://www.gagolewski.com/>
+   Copyleft (C) 2021-2024, Marek Gagolewski <https://www.gagolewski.com/>
    -------------------------------------------------------------------------- */
 
 @import url("fonts/Alegreya-fontspec.css");
 @import url("fonts/ubuntu-fontspec.css");
 
+.katex {
+    font-size: inherit;
+}
+
 h1, h2, h3, h4, h5, h6 {
     font-weight: 700;
     font-family: Alegreya Sans,Roboto Slab,ff-tisa-web-pro,Georgia,Arial,sans-serif;
 }
 
 body {
-    font-family: Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;
+    font-family: Alegreya Sans,Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;
     font-weight: 400;
 }
 
@@ -128,7 +132,8 @@ p code.notranslate, p code.literal, p tt.literal {
 
 strong.command, strong.program, .rst-content code, .rst-content div[class^="highlight"] pre, .rst-content tt, .rst-content pre, pre, samp, kbd, code {
     font-family: Ubuntu Mono,SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,Courier,monospace;
-/*     font-size: 90%; */
+    letter-spacing: -0.15pt;
+    font-size: 95%;
 /*     font-style: normal; */
 }
 

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '1.1.5',
+    VERSION: '1.1.5.9001',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/genieclust.html b/docs/genieclust.html
@@ -13,7 +13,7 @@
     <link rel="stylesheet" type="text/css" href="_static/plot_directive.css" />
     <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=36a5483c" />
-    <link rel="stylesheet" type="text/css" href="_static/css/custom.css?v=dd03ec4f" />
+    <link rel="stylesheet" type="text/css" href="_static/css/custom.css?v=5282ffc2" />
 
 
 
@@ -168,7 +168,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5
+1.1.5.9001
 </div>
 <form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -401,11 +401,11 @@ <h1>Python Package <cite>genieclust</cite> Reference<a class="headerlink" href="
             <div class="copyright">
 
 
-              Copyright &#169; 2018–2023 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>.
+              Copyright &#169; 2018–2024 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/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-01-04T00:05:36+1100.
+              Last updated on 2024-06-17T16:06:11+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -420,7 +420,7 @@ <h1>Python Package <cite>genieclust</cite> Reference<a class="headerlink" href="
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=a48ae3df"></script>
+</div><script src="_static/documentation_options.js?v=bff10455"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/docs/genieclust_cluster_validity.html b/docs/genieclust_cluster_validity.html
@@ -13,7 +13,7 @@
     <link rel="stylesheet" type="text/css" href="_static/plot_directive.css" />
     <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=36a5483c" />
-    <link rel="stylesheet" type="text/css" href="_static/css/custom.css?v=dd03ec4f" />
+    <link rel="stylesheet" type="text/css" href="_static/css/custom.css?v=5282ffc2" />
 
 
 
@@ -168,7 +168,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5
+1.1.5.9001
 </div>
 <form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -967,11 +967,11 @@
             <div class="copyright">
 
 
-              Copyright &#169; 2018–2023 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>.
+              Copyright &#169; 2018–2024 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/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-01-04T00:05:36+1100.
+              Last updated on 2024-06-17T16:06:11+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -1013,7 +1013,7 @@
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=a48ae3df"></script>
+</div><script src="_static/documentation_options.js?v=bff10455"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/docs/genieclust_compare_partitions.html b/docs/genieclust_compare_partitions.html
@@ -13,7 +13,7 @@
     <link rel="stylesheet" type="text/css" href="_static/plot_directive.css" />
     <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=36a5483c" />
-    <link rel="stylesheet" type="text/css" href="_static/css/custom.css?v=dd03ec4f" />
+    <link rel="stylesheet" type="text/css" href="_static/css/custom.css?v=5282ffc2" />
 
 
 
@@ -168,7 +168,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5
+1.1.5.9001
 </div>
 <form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -1037,11 +1037,11 @@
             <div class="copyright">
 
 
-              Copyright &#169; 2018–2023 by <a href="https://www.gagolewski.com">Marek Gagolewski</a>.
+              Copyright &#169; 2018–2024 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/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-01-04T00:05:36+1100.
+              Last updated on 2024-06-17T16:06:11+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -1089,7 +1089,7 @@
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=a48ae3df"></script>
+</div><script src="_static/documentation_options.js?v=bff10455"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/docs/genieclust_genie.html b/docs/genieclust_genie.html
@@ -13,7 +13,7 @@
     <link rel="stylesheet" type="text/css" href="_static/plot_directive.css" />
     <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=36a5483c" />
-    <link rel="stylesheet" type="text/css" href="_static/css/custom.css?v=dd03ec4f" />
+    <link rel="stylesheet" type="text/css" href="_static/css/custom.css?v=5282ffc2" />
 
 
 
@@ -168,7 +168,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5
+1.1.5.9001
 </div>
 <form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -375,7 +375,7 @@ <h1>genieclust.Genie<a class="headerlink" href="#genieclust-genie" title="Link t
 at a cost of greater memory use. Otherwise, note that <cite>nmslib</cite>
 <em>requires</em> <code class="docutils literal notranslate"><span class="pre">float32</span></code> data anyway when using dense or sparse
 numeric matrix inputs.</p>
-<p>By setting <cite>cast_float32</cite> to <code class="docutils literal notranslate"><span class="pre">False</span></code> a user assures themself
+<p>By setting <cite>cast_float32</cite> to <code class="docutils literal notranslate"><span class="pre">False</span></code>, you must ensure
 that the inputs are of acceptable form.</p>
 </dd>
 <dt><strong>mlpack_enabled</strong><span class="classifier">“auto” or bool</span></dt><dd><p>Whether <cite>mlpack.emst</cite> should be used for computing the Euclidean
@@ -571,11 +571,11 @@ <h1>genieclust.Genie<a class="headerlink" href="#genieclust-genie" title="Link t
 <dt><strong>distances_</strong><span class="classifier">None or ndarray</span></dt><dd><p>If <cite>compute_full_tree</cite> is <code class="docutils literal notranslate"><span class="pre">True</span></code>, this is a vector that gives
 the distance between two clusters merged in each iteration,
 see the description of <code class="docutils literal notranslate"><span class="pre">Z[:,2]</span></code> in <cite>scipy.cluster.hierarchy.linkage</cite>.</p>
-<p>As the original Genie algorithm does not guarantee that that distances
-are ordered increasingly (there are other hierarchical
-clustering linkages that violate the ultrametricity property as well),
-these are corrected by applying
-<code class="docutils literal notranslate"><span class="pre">distances_</span> <span class="pre">=</span> <span class="pre">genieclust.tools.cummin(distances_[::-1])[::-1]</span></code>.</p>
+<p>As the original Genie algorithm does not guarantee that distances
+are ordered increasingly (there are other hierarchical clustering
+linkages that violate the ultrametricity property as well), Genie
+automatically applies the following correction:</p>
+<p><code class="docutils literal notranslate"><span class="pre">distances_</span> <span class="pre">=</span> <span class="pre">genieclust.tools.cummin(distances_[::-1])[::-1]</span></code>.</p>
 </dd>
 <dt><strong>counts_</strong><span class="classifier">None or ndarray</span></dt><dd><p>If <cite>compute_full_tree</cite> is <code class="docutils literal notranslate"><span class="pre">True</span></code>, this is a vector giving
 the number of elements in a cluster created in each iteration.
@@ -649,7 +649,7 @@ <h1>genieclust.Genie<a class="headerlink" href="#genieclust-genie" title="Link t
 This way the method becomes translation and scale invariant.
 What’s more, if data are recorded with small precision (say, up
 to few decimal digits), adding a tiny bit of Gaussian noise will
-assure the solution is unique (note that this generally applies
+ensure the solution is unique (note that this generally applies
 to other distance-based clustering algorithms as well).</p>
 </li>
 <li><p><cite>X</cite> when <cite>exact</cite> = <code class="docutils literal notranslate"><span class="pre">False</span></code>.</p>
@@ -709,11 +709,11 @@ <h1>genieclust.Genie<a class="headerlink" href="#genieclust-genie" title="Link t
             <div class="copyright">
 
 
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@@ -750,7 +750,7 @@ <h1>genieclust.Genie<a class="headerlink" href="#genieclust-genie" title="Link t
 
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