Merge branch 'trunk' into complete

glotzerlab · Dec 5, 2024 · 6b2d16e · 6b2d16e
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -3,7 +3,7 @@ build:
   os: "ubuntu-22.04"
   commands:
     - mkdir -p bin
-    - curl -sSL "https://github.com/rust-lang/mdBook/releases/download/v0.4.40/mdbook-v0.4.40-x86_64-unknown-linux-gnu.tar.gz" | tar -xvz --directory "bin"
+    - curl -sSL "https://github.com/rust-lang/mdBook/releases/download/v0.4.43/mdbook-v0.4.43-x86_64-unknown-linux-gnu.tar.gz" | tar -xvz --directory "bin"
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - echo "site-url = \"/$READTHEDOCS_LANGUAGE/$READTHEDOCS_VERSION/\"" >> doc/book.toml
     - bin/mdbook build doc --dest-dir=$READTHEDOCS_OUTPUT/html
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/THIRDPARTY.yaml b/THIRDPARTY.yaml
@@ -4010,7 +4010,7 @@ third_party_libraries:
   - license: Apache-2.0
     text: "                              Apache License\n                        Version 2.0, January 2004\n                     https://www.apache.org/licenses/\n\nTERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n\n1. Definitions.\n\n   \"License\" shall mean the terms and conditions for use, reproduction,\n   and distribution as defined by Sections 1 through 9 of this document.\n\n   \"Licensor\" shall mean the copyright owner or entity authorized by\n   the copyright owner that is granting the License.\n\n   \"Legal Entity\" shall mean the union of the acting entity and all\n   other entities that control, are controlled by, or are under common\n   control with that entity. For the purposes of this definition,\n   \"control\" means (i) the power, direct or indirect, to cause the\n   direction or management of such entity, whether by contract or\n   otherwise, or (ii) ownership of fifty percent (50%) or more of the\n   outstanding shares, or (iii) beneficial ownership of such entity.\n\n   \"You\" (or \"Your\") shall mean an individual or Legal Entity\n   exercising permissions granted by this License.\n\n   \"Source\" form shall mean the preferred form for making modifications,\n   including but not limited to software source code, documentation\n   source, and configuration files.\n\n   \"Object\" form shall mean any form resulting from mechanical\n   transformation or translation of a Source form, including but\n   not limited to compiled object code, generated documentation,\n   and conversions to other media types.\n\n   \"Work\" shall mean the work of authorship, whether in Source or\n   Object form, made available under the License, as indicated by a\n   copyright notice that is included in or attached to the work\n   (an example is provided in the Appendix below).\n\n   \"Derivative Works\" shall mean any work, whether in Source or Object\n   form, that is based on (or derived from) the Work and for which the\n   editorial revisions, annotations, elaborations, or other modifications\n   represent, as a whole, an original work of authorship. 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The text should be enclosed in the appropriate\n   comment syntax for the file format. We also recommend that a\n   file or class name and description of purpose be included on the\n   same \"printed page\" as the copyright notice for easier\n   identification within third-party archives.\n\nCopyright [yyyy] [name of copyright owner]\n\nLicensed under the Apache License, Version 2.0 (the \"License\");\nyou may not use this file except in compliance with the License.\nYou may obtain a copy of the License at\n\n\thttps://www.apache.org/licenses/LICENSE-2.0\n\nUnless required by applicable law or agreed to in writing, software\ndistributed under the License is distributed on an \"AS IS\" BASIS,\nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\nSee the License for the specific language governing permissions and\nlimitations under the License.\n"
 - package_name: hashbrown
-  package_version: 0.15.0
+  package_version: 0.15.2
   repository: https://github.com/rust-lang/hashbrown
   license: MIT OR Apache-2.0
   licenses:

diff --git a/doc/src/contributors.md b/doc/src/contributors.md
@@ -7,3 +7,4 @@ The following people have contributed to the development of **row**:
 * Joseph Burkhart, University of Michigan
 * Kate Jensen, University of Michigan
 * Tim Moore, University of Michigan
+* Corwin Kerr, University of Michigan
diff --git a/doc/src/guide/concepts/hoomd-example.py b/doc/src/guide/concepts/hoomd-example.py
@@ -17,7 +17,7 @@ def action_implementation(job, communicator):
 
 def action(*jobs):
     """Execute actions on directories in parallel using HOOMD-blue."""
-    processes_per_directory = os.environ['ACTION_PROCESSES_PER_DIRECTORY']
+    processes_per_directory = int(os.environ['ACTION_PROCESSES_PER_DIRECTORY'])
     communicator = hoomd.communicator.Communicator(ranks_per_partition=processes_per_directory)
     action_implementation(jobs[communicator.partition], communicator)
     # ANCHOR_END: action

diff --git a/doc/src/guide/concepts/multiprocessing-example.py b/doc/src/guide/concepts/multiprocessing-example.py
@@ -15,7 +15,7 @@ def action_implementation(job):
 
 def action(*jobs):
     """Process any number of jobs in parallel with the multiprocessing package."""
-    processes = os.environ.get('ACTION_THREADS_PER_PROCESS', multiprocessing.cpu_count())
+    processes = int(os.environ.get('ACTION_THREADS_PER_PROCESS', multiprocessing.cpu_count()))
     if hasattr(os, 'sched_getaffinity'):
         processes = len(os.sched_getaffinity(0))
 

diff --git a/doc/src/release-notes.md b/doc/src/release-notes.md
@@ -31,6 +31,8 @@ command in your shell's profile:
 * All user-provided content (directories, action names, cluster names, and values) are
   properly escaped in the bash script output.
 * Typographical errors in the documentation.
+* The documentation now builds correctly with mdbook 0.4.43.
+* Example code converts environment variables to ints where needed.
 
 ## 0.3.1 (2024-10-04)
 

diff --git a/doc/theme/index.hbs b/doc/theme/index.hbs
@@ -1,5 +1,5 @@
 <!DOCTYPE HTML>
-<html lang="{{ language }}" class="{{ default_theme }}" dir="{{ text_direction }}">
+<html lang="{{ language }}" class="{{ default_theme }} sidebar-visible" dir="{{ text_direction }}">
     <head>
         <!-- Book generated using mdBook -->
         <meta charset="UTF-8">
@@ -52,15 +52,17 @@
         <!-- MathJax -->
         <script async src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
         {{/if}}
-    </head>
-    <body class="sidebar-visible no-js">
-    <div id="body-container">
+
         <!-- Provide site root to javascript -->
         <script>
             var path_to_root = "{{ path_to_root }}";
             var default_theme = window.matchMedia("(prefers-color-scheme: dark)").matches ? "{{ preferred_dark_theme }}" : "{{ default_theme }}";
         </script>
-
+        <!-- Start loading toc.js asap -->
+        <script src="{{ path_to_root }}toc.js"></script>
+    </head>
+    <body>
+    <div id="body-container">
         <!-- Work around some values being stored in localStorage wrapped in quotes -->
         <script>
             try {
@@ -82,19 +84,16 @@
             var theme;
             try { theme = localStorage.getItem('mdbook-theme'); } catch(e) { }
             if (theme === null || theme === undefined) { theme = default_theme; }
-            var html = document.querySelector('html');
+            const html = document.documentElement;
             html.classList.remove('{{ default_theme }}')
             html.classList.add(theme);
-            var body = document.querySelector('body');
-            body.classList.remove('no-js')
-            body.classList.add('js');
+            html.classList.add("js");
         </script>
 
         <input type="checkbox" id="sidebar-toggle-anchor" class="hidden">
 
         <!-- Hide / unhide sidebar before it is displayed -->
         <script>
-            var body = document.querySelector('body');
             var sidebar = null;
             var sidebar_toggle = document.getElementById("sidebar-toggle-anchor");
             if (document.body.clientWidth >= 1080) {
@@ -104,49 +103,21 @@
                 sidebar = 'hidden';
             }
             sidebar_toggle.checked = sidebar === 'visible';
-            body.classList.remove('sidebar-visible');
-            body.classList.add("sidebar-" + sidebar);
+            html.classList.remove('sidebar-visible');
+            html.classList.add("sidebar-" + sidebar);
         </script>
 
         <nav id="sidebar" class="sidebar" aria-label="Table of contents">
-            <div class="sidebar-scrollbox">
-                {{#toc}}{{/toc}}
-                <div
-                  id="mdbook-ad-placement"
-                  class="flat"
-                  data-ea-publisher="readthedocs"
-                  data-ea-type="readthedocs-sidebar"
-                  data-ea-manual="true"
-                  style="width: 70%; margin: 0 auto;"
-                ></div>
-            </div>
+            <!-- populated by js -->
+            <mdbook-sidebar-scrollbox class="sidebar-scrollbox"></mdbook-sidebar-scrollbox>
+            <noscript>
+                <iframe class="sidebar-iframe-outer" src="{{ path_to_root }}toc.html"></iframe>
+            </noscript>
             <div id="sidebar-resize-handle" class="sidebar-resize-handle">
                 <div class="sidebar-resize-indicator"></div>
             </div>
         </nav>
 
-        <!-- Track and set sidebar scroll position -->
-        <script>
-            var sidebarScrollbox = document.querySelector('#sidebar .sidebar-scrollbox');
-            sidebarScrollbox.addEventListener('click', function(e) {
-                if (e.target.tagName === 'A') {
-                    sessionStorage.setItem('sidebar-scroll', sidebarScrollbox.scrollTop);
-                }
-            }, { passive: true });
-            var sidebarScrollTop = sessionStorage.getItem('sidebar-scroll');
-            sessionStorage.removeItem('sidebar-scroll');
-            if (sidebarScrollTop) {
-                // preserve sidebar scroll position when navigating via links within sidebar
-                sidebarScrollbox.scrollTop = sidebarScrollTop;
-            } else {
-                // scroll sidebar to current active section when navigating via "next/previous chapter" buttons
-                var activeSection = document.querySelector('#sidebar .active');
-                if (activeSection) {
-                    activeSection.scrollIntoView({ block: 'center' });
-                }
-            }
-        </script>
-
         <div id="page-wrapper" class="page-wrapper">
 
             <div class="page">
@@ -222,19 +193,19 @@
                     <main>
                         {{{ content }}}
 
-						<!-- Page footer -->
-						<hr>
-						<div class="left" style="width: 75%">
-					    <p>Development of <b>row</b> is led by the <a href="https://glotzerlab.engin.umich.edu">Glotzer Group</a> at the <a href="https://umich.edu">University of Michigan</a>.
-						<p>Copyright &#169; 2024 The Regents of the University of Michigan.
-						</div>
-						<div class="right">
-						<a href="https://umich.edu">
-						<img class="right" src="{{ path_to_root }}images/umich-block-M.svg" alt="University of Michigan logo" style="width: 84px" />
-						</a>
-						</div>
-						<div style="clear:both" />
-					</main>
+                        <!-- Page footer -->
+                        <hr>
+                        <div class="left" style="width: 75%">
+                        <p>Development of <b>row</b> is led by the <a href="https://glotzerlab.engin.umich.edu">Glotzer Group</a> at the <a href="https://umich.edu">University of Michigan</a>.
+                        <p>Copyright &#169; 2024 The Regents of the University of Michigan.
+                        </div>
+                        <div class="right">
+                        <a href="https://umich.edu">
+                        <img class="right" src="{{ path_to_root }}images/umich-block-M.svg" alt="University of Michigan logo" style="width: 84px" />
+                        </a>
+                        </div>
+                        <div style="clear:both" />
+                    </main>
 
                     <nav class="nav-wrapper" aria-label="Page navigation">
                         <!-- Mobile navigation buttons -->