Merge pull request #157 from yt-project/script_update

[ci skip]

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43c6762.

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manuscript.html

@@ -177,8 +177,8 @@
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   <meta name="citation_publication_date" content="2023-08-11" />
   <meta property="article:published_time" content="2023-08-11" />
-  <meta name="dc.modified" content="2023-08-11T10:09:03+00:00" />
-  <meta property="article:modified_time" content="2023-08-11T10:09:03+00:00" />
+  <meta name="dc.modified" content="2023-08-11T14:45:39+00:00" />
+  <meta property="article:modified_time" content="2023-08-11T14:45:39+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
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@@ -388,9 +388,9 @@
   <meta name="citation_fulltext_html_url" content="https://yt-project.github.io/yt-4.0-paper/" />
   <meta name="citation_pdf_url" content="https://yt-project.github.io/yt-4.0-paper/manuscript.pdf" />
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-  <meta name="manubot_html_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/554114725ff615de380fbeb11684e2949e1c79c7/" />
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+  <link rel="alternate" type="text/html" href="https://yt-project.github.io/yt-4.0-paper/v/43c6762bdf877a759c7f73e9b993e4684ce563c9/" />
+  <meta name="manubot_html_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/43c6762bdf877a759c7f73e9b993e4684ce563c9/" />
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@@ -508,9 +508,9 @@ <h1 class="title">Introducing yt 4.0: Analysis and Visualization of Volumetric D
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://yt-project.github.io/yt-4.0-paper/v/554114725ff615de380fbeb11684e2949e1c79c7/">permalink</a>)
+(<a href="https://yt-project.github.io/yt-4.0-paper/v/43c6762bdf877a759c7f73e9b993e4684ce563c9/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/yt-project/yt-4.0-paper/tree/554114725ff615de380fbeb11684e2949e1c79c7">yt-project/yt-4.0-paper@5541147</a>
+from <a href="https://github.com/yt-project/yt-4.0-paper/tree/43c6762bdf877a759c7f73e9b993e4684ce563c9">yt-project/yt-4.0-paper@43c6762</a>
 on August 11, 2023.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -1308,7 +1308,7 @@ <h2 id="sec:development">Development Procedure</h2>
 This particular bias, toward contributions measured in count, is one that affects other members of the community as well, especially those whose participation is through community engagement, documentation, tutorials, and mentoring, rather than through direct modifications of the code base.
 To mitigate this shortcoming, we present the number of pull requests merged into the code base, as a function of time, as well as the time between their creation and their merge, in the lower row of Figure <a href="#fig:commit-graph">1</a>.
 This demonstrates that in many cases, the number of discrete contributions to the codebase varies greatly depending on the developer, and we believe gives a more informed perception of the activity in the code base.</p>
-<div id="figure-commit-graph">
+<div id="figure-commit-graph" class="center">
 
 </div>
 <div id="fig:commit-graph" class="fignos">
@@ -1318,13 +1318,13 @@ <h2 id="sec:development">Development Procedure</h2>
 </figure>
 </div>
 <script>
-vegaEmbed('#figure-commit-graph', "images/yt_repo.vl");
+vegaEmbed('#figure-commit-graph', "images/yt_repo.vl", {"actions": false});
 </script>
 <p>In Figure <a href="#fig:pr-closing-time">2</a> we have plotted distribution of pull requests based on the time between their creation and their merge.
 The longest time between opening a pull request and merging it was nearly four years; this was the addition of the <code>cf_radial</code> frontend, which occurred in fits and starts over a very long period of time.
 The next longest pull request durations are for splitting the code used for bitmap indexing (see <a href="#sec:point_indexing">1.9</a>) and a per-field configuration system.
 This includes only those pull requests that occurred on GitHub.</p>
-<div id="figure-pr-closing-time">
+<div id="figure-pr-closing-time" class="center">
 
 </div>
 <div id="fig:pr-closing-time" class="fignos">
@@ -1334,7 +1334,7 @@ <h2 id="sec:development">Development Procedure</h2>
 </figure>
 </div>
 <script>
-vegaEmbed('#figure-pr-closing-time', "images/pr_times.vl");
+vegaEmbed('#figure-pr-closing-time', "images/pr_times.vl", {"actions": false});
 </script>
 <h3 id="sec:unit_testing">Unit Testing</h3>
 <p>The <code>yt</code> codebase includes a number of unit tests; although extensive, their existence post-dates the initial development of the code, and they largely work around the extant APIs at the time of their creation.

manuscript.md

@@ -87,8 +87,8 @@ header-includes: |
   <meta name="dc.date" content="2023-08-11" />
   <meta name="citation_publication_date" content="2023-08-11" />
   <meta property="article:published_time" content="2023-08-11" />
-  <meta name="dc.modified" content="2023-08-11T10:09:03+00:00" />
-  <meta property="article:modified_time" content="2023-08-11T10:09:03+00:00" />
+  <meta name="dc.modified" content="2023-08-11T14:45:39+00:00" />
+  <meta property="article:modified_time" content="2023-08-11T14:45:39+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -298,9 +298,9 @@ header-includes: |
   <meta name="citation_fulltext_html_url" content="https://yt-project.github.io/yt-4.0-paper/" />
   <meta name="citation_pdf_url" content="https://yt-project.github.io/yt-4.0-paper/manuscript.pdf" />
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-  <meta name="manubot_html_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/554114725ff615de380fbeb11684e2949e1c79c7/" />
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+  <link rel="alternate" type="text/html" href="https://yt-project.github.io/yt-4.0-paper/v/43c6762bdf877a759c7f73e9b993e4684ce563c9/" />
+  <meta name="manubot_html_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/43c6762bdf877a759c7f73e9b993e4684ce563c9/" />
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@@ -323,9 +323,9 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://yt-project.github.io/yt-4.0-paper/v/554114725ff615de380fbeb11684e2949e1c79c7/))
+([permalink](https://yt-project.github.io/yt-4.0-paper/v/43c6762bdf877a759c7f73e9b993e4684ce563c9/))
 was automatically generated
-from [yt-project/yt-4.0-paper@5541147](https://github.com/yt-project/yt-4.0-paper/tree/554114725ff615de380fbeb11684e2949e1c79c7)
+from [yt-project/yt-4.0-paper@43c6762](https://github.com/yt-project/yt-4.0-paper/tree/43c6762bdf877a759c7f73e9b993e4684ce563c9)
 on August 11, 2023.
 </em></small>
 
@@ -1246,29 +1246,29 @@ This particular bias, toward contributions measured in count, is one that affect
 To mitigate this shortcoming, we present the number of pull requests merged into the code base, as a function of time, as well as the time between their creation and their merge, in the lower row of Figure @fig:commit-graph.
 This demonstrates that in many cases, the number of discrete contributions to the codebase varies greatly depending on the developer, and we believe gives a more informed perception of the activity in the code base.
 
-<div id="figure-commit-graph"></div>
+<div id="figure-commit-graph" class="center"></div>
 
 ![
 Commits and pull requests to the source code as a function of time.
 ](images/blank.svg){#fig:commit-graph width="1px"}
 
 <script>
-vegaEmbed('#figure-commit-graph', "images/yt_repo.vl");
+vegaEmbed('#figure-commit-graph', "images/yt_repo.vl", {"actions": false});
 </script>
 
 In Figure @fig:pr-closing-time we have plotted distribution of pull requests based on the time between their creation and their merge.
 The longest time between opening a pull request and merging it was nearly four years; this was the addition of the `cf_radial` frontend, which occurred in fits and starts over a very long period of time.
 The next longest pull request durations are for splitting the code used for bitmap indexing (see @sec:point_indexing) and a per-field configuration system.
 This includes only those pull requests that occurred on GitHub.
 
-<div id="figure-pr-closing-time"></div>
+<div id="figure-pr-closing-time" class="center"></div>
 
 ![
 The distribution of pull requests as a function of how long it took to close them.
 ](images/blank.svg){#fig:pr-closing-time width="1px"}
 
 <script>
-vegaEmbed('#figure-pr-closing-time', "images/pr_times.vl");
+vegaEmbed('#figure-pr-closing-time', "images/pr_times.vl", {"actions": false});
 </script>
 
 

spelling-errors.txt

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 AMReX
 AMRKDTree
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+amrvac
 Aperio
 APIs
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 Arraki
 arraylike
 ARTIO
 arwetzel
 AST
-Astro
+astro
 astrojaz
 astrophysically
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+astropy
 astrosmith
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 atmyers
@@ -37,7 +37,7 @@ binarily
 Biondo
 Birla
 Bitbucket
-Bitwise
+bitwise
 bookkeepping
 bool
 Borro
@@ -51,7 +51,7 @@ bwoshea
 Cadair
 Cadiou
 Cartopy
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+CGS
 Champaign
 changeset
 changesets
@@ -72,12 +72,12 @@ colorbar
 colorbars
 colormap
 colormapping
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+colormaps
 colorspace
-comoving
+Comoving
 conda
 connectedness
-coord
+Coord
 Coords
 Corentin
 cosmosquark
@@ -118,7 +118,7 @@ Dutta
 easies
 elliottbiondo
 entrypoints
-enzo
+Enzo
 Enzo’s
 ethlau
 EWAH
@@ -226,7 +226,7 @@ moab
 Mollweide
 Monaghan
 mornkr
-mpi
+MPI
 mtryan
 Munk
 munkm
@@ -275,14 +275,14 @@ pixelization
 pixelize
 pixelized
 pixelizer
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+Pixelizers
 pixelizes
 Pixelizing
 Planétologie
 PlotCollection
 pmd
 potentia
-powderday
+Powderday
 pre
 programmatically
 programme
@@ -291,7 +291,7 @@ protoplanetary
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 pytest
 PyThreeJS
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+pyXSIM
 qobilidop
 quadtree
 radiative
@@ -385,7 +385,7 @@ yipihey
 yournamehere
 YTArray
 ytdata
-ytep
+YTEP
 YTEPs
 ytini
 YTQuadTreeProj