Update from scikit-bio/scikit-bio@86118f4

mataton · mataton · commit 7daaf47af31c · 2025-10-28T17:27:26.000Z
diff --git a/_sources/contribute.rst.txt b/_sources/contribute.rst.txt
@@ -173,7 +173,9 @@ When done, activate the environment::
 
 This will install scikit-bio to the current conda environment. After this, you can use scikit-bio like a normal user (e.g., you can do ``import skbio`` in Python code). When you edit the code in the this directory, the changes will be immediately reflected as you use the software.
 
-.. note:: If you run into OpenMP compile issues (or have other reasons to avoid OpenMP), you can avoid it by setting ``DISABLE_OPENMP=Y`` in the build environment.
+.. note::
+    
+   If you run into OpenMP compile issues (or have other reasons to avoid OpenMP), you can avoid it by setting ``DISABLE_OPENMP=1`` in the build environment.
 
 5. Test the installation::
 
diff --git a/_sources/install.rst.txt b/_sources/install.rst.txt
@@ -89,6 +89,20 @@ For a more robust verification of the installation you may run the scikit-bio's
     python -m skbio.test
 
 
+Parallelization
+---------------
+
+Many scikit-bio functions automatically take advantage of parallel processing to improve performance. By default, they utilize all available CPU cores when possible. There is currently no per-function parameter to control the number of threads used. You can set the environment variable ``OMP_NUM_THREADS`` to control the global parallelization behavior, or use `threadpoolctl <https://github.com/joblib/threadpoolctl>`_ to achieve more granular control within Python code.
+
+Multiple compute-intensive algorithms in scikit-bio are implemented in Cython and use OpenMP for parallel execution. If your system does not support OpenMP, or if you prefer to disable it, you can build from the scikit-bio source code with OpenMP disabled:
+
+    DISABLE_OPENMP=1 pip install scikit-bio --no-binary scikit-bio
+
+Or, if you have downloaded the repository:
+
+    DISABLE_OPENMP=1 pip install .
+
+
 Acceleration
 ------------
 
diff --git a/about.html b/about.html
@@ -102,9 +102,6 @@
   <div class="pst-async-banner-revealer d-none">
   <aside id="bd-header-version-warning" class="d-none d-print-none" aria-label="Version warning"></aside>
 </div>
-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
-</aside>
 
   
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diff --git a/contribute.html b/contribute.html
@@ -102,9 +102,6 @@
   <div class="pst-async-banner-revealer d-none">
   <aside id="bd-header-version-warning" class="d-none d-print-none" aria-label="Version warning"></aside>
 </div>
-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
-</aside>
 
   
     <header class="bd-header navbar navbar-expand-lg bd-navbar d-print-none">
@@ -588,7 +585,7 @@ <h2>Set up a workspace<a class="headerlink" href="#set-up-a-workspace" title="Li
 <p>This will install scikit-bio to the current conda environment. After this, you can use scikit-bio like a normal user (e.g., you can do <code class="docutils literal notranslate"><span class="pre">import</span> <span class="pre">skbio</span></code> in Python code). When you edit the code in the this directory, the changes will be immediately reflected as you use the software.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>If you run into OpenMP compile issues (or have other reasons to avoid OpenMP), you can avoid it by setting <code class="docutils literal notranslate"><span class="pre">DISABLE_OPENMP=Y</span></code> in the build environment.</p>
+<p>If you run into OpenMP compile issues (or have other reasons to avoid OpenMP), you can avoid it by setting <code class="docutils literal notranslate"><span class="pre">DISABLE_OPENMP=1</span></code> in the build environment.</p>
 </div>
 <ol class="arabic" start="5">
 <li><p>Test the installation:</p>
diff --git a/devdoc/code_guide.html b/devdoc/code_guide.html
@@ -102,9 +102,6 @@
   <div class="pst-async-banner-revealer d-none">
   <aside id="bd-header-version-warning" class="d-none d-print-none" aria-label="Version warning"></aside>
 </div>
-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
-</aside>
 
   
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diff --git a/devdoc/doc_guide.html b/devdoc/doc_guide.html
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   <aside id="bd-header-version-warning" class="d-none d-print-none" aria-label="Version warning"></aside>
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-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
-</aside>
 
   
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diff --git a/devdoc/new_module.html b/devdoc/new_module.html
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-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
-</aside>
 
   
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diff --git a/devdoc/release.html b/devdoc/release.html
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-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
-</aside>
 
   
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diff --git a/devdoc/review.html b/devdoc/review.html
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-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
-</aside>
 
   
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diff --git a/genindex.html b/genindex.html
@@ -99,9 +99,6 @@
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   <aside id="bd-header-version-warning" class="d-none d-print-none" aria-label="Version warning"></aside>
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-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
-</aside>
 
   
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diff --git a/index.html b/index.html
@@ -101,9 +101,6 @@
   <div class="pst-async-banner-revealer d-none">
   <aside id="bd-header-version-warning" class="d-none d-print-none" aria-label="Version warning"></aside>
 </div>
-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
-</aside>
 
   
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diff --git a/install.html b/install.html
@@ -102,9 +102,6 @@
   <div class="pst-async-banner-revealer d-none">
   <aside id="bd-header-version-warning" class="d-none d-print-none" aria-label="Version warning"></aside>
 </div>
-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
-</aside>
 
   
     <header class="bd-header navbar navbar-expand-lg bd-navbar d-print-none">
@@ -519,6 +516,18 @@ <h2>Verifying the installation<a class="headerlink" href="#verifying-the-install
 </pre></div>
 </div>
 </section>
+<section id="parallelization">
+<h2>Parallelization<a class="headerlink" href="#parallelization" title="Link to this heading">#</a></h2>
+<p>Many scikit-bio functions automatically take advantage of parallel processing to improve performance. By default, they utilize all available CPU cores when possible. There is currently no per-function parameter to control the number of threads used. You can set the environment variable <code class="docutils literal notranslate"><span class="pre">OMP_NUM_THREADS</span></code> to control the global parallelization behavior, or use <a class="reference external" href="https://github.com/joblib/threadpoolctl">threadpoolctl</a> to achieve more granular control within Python code.</p>
+<p>Multiple compute-intensive algorithms in scikit-bio are implemented in Cython and use OpenMP for parallel execution. If your system does not support OpenMP, or if you prefer to disable it, you can build from the scikit-bio source code with OpenMP disabled:</p>
+<blockquote>
+<div><p>DISABLE_OPENMP=1 pip install scikit-bio –no-binary scikit-bio</p>
+</div></blockquote>
+<p>Or, if you have downloaded the repository:</p>
+<blockquote>
+<div><p>DISABLE_OPENMP=1 pip install .</p>
+</div></blockquote>
+</section>
 <section id="acceleration">
 <h2>Acceleration<a class="headerlink" href="#acceleration" title="Link to this heading">#</a></h2>
 <p>The new <a class="reference external" href="https://github.com/scikit-bio/scikit-bio-binaries">scikit-bio-binaries</a> package is a separate package from scikit-bio, written in C++, which when installed in the same environment as scikit-bio will dramatically increase performance of select functions. Installation of scikit-bio-binaries is currently available with conda:</p>
@@ -569,6 +578,7 @@ <h2>Python version support<a class="headerlink" href="#python-version-support" t
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pre-compiled-wheels">Pre-compiled wheels</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#development-version">Development version</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#verifying-the-installation">Verifying the installation</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#parallelization">Parallelization</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#acceleration">Acceleration</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#python-version-support">Python version support</a></li>
 </ul>
diff --git a/learn.html b/learn.html
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-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
-</aside>
 
   
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diff --git a/objects.inv b/objects.inv
diff --git a/roadmap.html b/roadmap.html
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-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
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-<aside class="bd-header-announcement" aria-label="Announcement">
-  <div class="bd-header-announcement__content">scikit-bio 0.7.0 has been released! <a href='https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.0'>Check it out</a>.</div>
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diff --git a/searchindex.js b/searchindex.js
