fix references and update plot

[ci skip] This build is based on c1a99f1. This commit was created by the following CI build and job: https://github.com/yt-project/yt-4.0-paper/commit/c1a99f15e46ef0307c7e4596b4446fb48ecd5dc1/checks https://github.com/yt-project/yt-4.0-paper/actions/runs/5831099538
yt-project · Aug 11, 2023 · aa56472 · aa56472
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diff --git a/manuscript.html b/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="2023-08-11T00:06:17+00:00" />
-  <meta property="article:modified_time" content="2023-08-11T00:06:17+00:00" />
+  <meta name="dc.modified" content="2023-08-11T09:39:10+00:00" />
+  <meta property="article:modified_time" content="2023-08-11T09:39:10+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" />
   <link rel="alternate" type="application/pdf" href="https://yt-project.github.io/yt-4.0-paper/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://yt-project.github.io/yt-4.0-paper/v/4643cc98eec97781251d222b087a847d3825fb6c/" />
-  <meta name="manubot_html_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/4643cc98eec97781251d222b087a847d3825fb6c/" />
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+  <link rel="alternate" type="text/html" href="https://yt-project.github.io/yt-4.0-paper/v/c1a99f15e46ef0307c7e4596b4446fb48ecd5dc1/" />
+  <meta name="manubot_html_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/c1a99f15e46ef0307c7e4596b4446fb48ecd5dc1/" />
+  <meta name="manubot_pdf_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/c1a99f15e46ef0307c7e4596b4446fb48ecd5dc1/manuscript.pdf" />
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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/4643cc98eec97781251d222b087a847d3825fb6c/">permalink</a>)
+(<a href="https://yt-project.github.io/yt-4.0-paper/v/c1a99f15e46ef0307c7e4596b4446fb48ecd5dc1/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/yt-project/yt-4.0-paper/tree/4643cc98eec97781251d222b087a847d3825fb6c">yt-project/yt-4.0-paper@4643cc9</a>
+from <a href="https://github.com/yt-project/yt-4.0-paper/tree/c1a99f15e46ef0307c7e4596b4446fb48ecd5dc1">yt-project/yt-4.0-paper@c1a99f1</a>
 on August 11, 2023.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -1306,7 +1306,7 @@ <h2 id="sec:development">Development Procedure</h2>
 One result of this is in figures such as the top row of Figure <a href="#fig:commit-graph">1</a>, some contributors appear to have made a smaller quantity of contributions than an informed observer would recognize.
 Specifically, this applies to Clément Robert, who has contributed a considerable amount of change to the code base but has done so in a way that does not maximize the “statistics” presented below.
 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 ??.
+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">
 
@@ -1334,7 +1334,7 @@ <h2 id="sec:development">Development Procedure</h2>
 </figure>
 </div>
 <script>
-vegaEmbed('#figure-pr-closing-time', "images/pr_stats.vl");
+vegaEmbed('#figure-pr-closing-time', "images/pr_times.vl');
 </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.

diff --git a/manuscript.md b/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="2023-08-11T00:06:17+00:00" />
-  <meta property="article:modified_time" content="2023-08-11T00:06:17+00:00" />
+  <meta name="dc.modified" content="2023-08-11T09:39:10+00:00" />
+  <meta property="article:modified_time" content="2023-08-11T09:39:10+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: |
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   <meta name="citation_pdf_url" content="https://yt-project.github.io/yt-4.0-paper/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="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/4643cc98eec97781251d222b087a847d3825fb6c/" />
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+  <link rel="alternate" type="text/html" href="https://yt-project.github.io/yt-4.0-paper/v/c1a99f15e46ef0307c7e4596b4446fb48ecd5dc1/" />
+  <meta name="manubot_html_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/c1a99f15e46ef0307c7e4596b4446fb48ecd5dc1/" />
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   <meta property="og:type" content="article" />
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   <link rel="icon" type="image/png" sizes="192x192" href="https://manubot.org/favicon-192x192.png" />
@@ -323,9 +323,9 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://yt-project.github.io/yt-4.0-paper/v/4643cc98eec97781251d222b087a847d3825fb6c/))
+([permalink](https://yt-project.github.io/yt-4.0-paper/v/c1a99f15e46ef0307c7e4596b4446fb48ecd5dc1/))
 was automatically generated
-from [yt-project/yt-4.0-paper@4643cc9](https://github.com/yt-project/yt-4.0-paper/tree/4643cc98eec97781251d222b087a847d3825fb6c)
+from [yt-project/yt-4.0-paper@c1a99f1](https://github.com/yt-project/yt-4.0-paper/tree/c1a99f15e46ef0307c7e4596b4446fb48ecd5dc1)
 on August 11, 2023.
 </em></small>
 
@@ -1243,7 +1243,7 @@ Recent practice, however, is more inclined toward commit "squashing," where mult
 One result of this is in figures such as the top row of Figure @fig:commit-graph, some contributors appear to have made a smaller quantity of contributions than an informed observer would recognize.
 Specifically, this applies to Clément Robert, who has contributed a considerable amount of change to the code base but has done so in a way that does not maximize the "statistics" presented below.
 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 @fig:figure-commit-graph.
+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>
@@ -1268,7 +1268,7 @@ The distribution of pull requests as a function of how long it took to close the
 ](images/blank.svg){#fig:pr-closing-time width="1px"}
 
 <script>
-vegaEmbed('#figure-pr-closing-time', "images/pr_stats.vl");
+vegaEmbed('#figure-pr-closing-time', "images/pr_times.vl');
 </script>
 
 

diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/references.json b/references.json
@@ -1185,7 +1185,7 @@
         [
           "2023",
           8,
-          10
+          11
         ]
       ]
     },
@@ -6530,7 +6530,7 @@
         [
           "2023",
           8,
-          10
+          11
         ]
       ]
     },

diff --git a/spelling-errors.txt b/spelling-errors.txt
@@ -4,25 +4,25 @@ ahf
 AIP
 Aitoff
 Alamos
-alankar
+Alankar
 Alpes
 Altay
 AMR
 AMReX
 AMRKDTree
-amrvac
+AMRVAC
 Aperio
 APIs
-Arepo
+AREPO
 Arraki
 arraylike
-artio
+ARTIO
 arwetzel
 AST
-astro
+Astro
 astrojaz
 astrophysically
-astropy
+AstroPy
 astrosmith
 AthenaPK
 atmyers
@@ -37,11 +37,11 @@ binarily
 Biondo
 Birla
 Bitbucket
-Bitwise
+bitwise
 bookkeepping
-bool
+Bool
 Borro
-boxlib
+BoxLib
 Britton
 brittonsmith
 Bugfix
@@ -72,9 +72,9 @@ colorbar
 colorbars
 colormap
 colormapping
-colormaps
+Colormaps
 colorspace
-comoving
+Comoving
 conda
 connectedness
 coord
@@ -156,7 +156,7 @@ Gurvich
 Halbert
 Havlin
 HDF
-hexahedral
+Hexahedral
 HippoDraw
 histogramming
 Hix
@@ -211,7 +211,7 @@ LLC
 logarithmically
 LSST
 Madicken
-Matplotlib
+matplotlib
 Matplotlib’s
 MatthewTurk
 megaparsec
@@ -246,11 +246,11 @@ NMSU
 nosetests
 NSSC
 NumFOCUS
-NumPy
+numpy
 OAC
 octants
 octree
-Octrees
+octrees
 octs
 odowska
 olebole
@@ -275,7 +275,7 @@ pixelization
 pixelize
 pixelized
 pixelizer
-pixelizers
+Pixelizers
 pixelizes
 Pixelizing
 Planétologie
@@ -291,7 +291,7 @@ protoplanetary
 pydata
 pytest
 PyThreeJS
-pyXSIM
+pyxsim
 qobilidop
 quadtree
 radiative
@@ -394,7 +394,7 @@ ytree
 yt’s
 Yu
 Yurlungur
-Zingale
+zingale
 zorder
 Zuckerberg
 ZuHone