Figures to jpg instead of png

[ci skip]

This build is based on
87d12dc.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/87d12dc4dbcdb1c873f6fea7b67cc88fde153936/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/10529240958

README.md

@@ -1,7 +1,7 @@
 # Output directory containing the formatted manuscript
 
 The [`gh-pages`](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/gh-pages) branch hosts the contents of this directory at <https://plantbreeding.github.io/BrAPI-Manuscript2/>.
-The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/8998e037698e8a4f49623488e852190a4658f851/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/87d12dc4dbcdb1c873f6fea7b67cc88fde153936/>.
 To redirect to the permalink for the latest manuscript version at anytime, use the link <https://plantbreeding.github.io/BrAPI-Manuscript2/v/freeze/>.
 
 ## Files
@@ -35,4 +35,4 @@ Verifying timestamps with the `ots verify` command requires running a local bitc
 ## Source
 
 The manuscripts in this directory were built from
-[`8998e037698e8a4f49623488e852190a4658f851`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/8998e037698e8a4f49623488e852190a4658f851).
+[`87d12dc4dbcdb1c873f6fea7b67cc88fde153936`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/87d12dc4dbcdb1c873f6fea7b67cc88fde153936).

index.html

@@ -129,8 +129,8 @@
   <meta name="dc.date" content="2024-08-23" />
   <meta name="citation_publication_date" content="2024-08-23" />
   <meta property="article:published_time" content="2024-08-23" />
-  <meta name="dc.modified" content="2024-08-23T15:28:45+00:00" />
-  <meta property="article:modified_time" content="2024-08-23T15:28:45+00:00" />
+  <meta name="dc.modified" content="2024-08-23T16:41:36+00:00" />
+  <meta property="article:modified_time" content="2024-08-23T16:41:36+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -368,9 +368,9 @@
   <meta name="citation_fulltext_html_url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/" />
   <meta name="citation_pdf_url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/8998e037698e8a4f49623488e852190a4658f851/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/8998e037698e8a4f49623488e852190a4658f851/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/8998e037698e8a4f49623488e852190a4658f851/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/87d12dc4dbcdb1c873f6fea7b67cc88fde153936/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/87d12dc4dbcdb1c873f6fea7b67cc88fde153936/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/87d12dc4dbcdb1c873f6fea7b67cc88fde153936/manuscript.pdf" />
   <meta property="og:type" content="article" />
   <meta property="twitter:card" content="summary_large_image" />
   <link rel="icon" type="image/png" sizes="192x192" href="https://manubot.org/favicon-192x192.png" />
@@ -387,9 +387,9 @@ <h1 class="title">BrAPI v2 - A unified framework for data integration and collab
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/8998e037698e8a4f49623488e852190a4658f851/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/87d12dc4dbcdb1c873f6fea7b67cc88fde153936/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/8998e037698e8a4f49623488e852190a4658f851">plantbreeding/BrAPI-Manuscript2@8998e03</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/87d12dc4dbcdb1c873f6fea7b67cc88fde153936">plantbreeding/BrAPI-Manuscript2@87d12dc</a>
 on August 23, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -1106,7 +1106,7 @@ <h3 id="project-updates">Project Updates</h3>
 <p>Over its lifetime, the BrAPI project has grown and changed substantially. The total size of the specification has almost quadrupled since the release of version v1.0 in 2017, increasing from 51 endpoints in v1.0 to 201 endpoints in v2.1. Because of this growth, the specification documents were reorganized into four modules: BrAPI-Core, BrAPI-Phenotyping, BrAPI-Genotyping, and BrAPI-Germplasm. Figure <a href="#fig:domains">1</a> is a simplified domain map of the whole BrAPI data model, showing what kinds of data are defined in each module. While early versions of the specification focused on read-only phenotype data, the specification now has representation from most of the major concepts related to breeding. The newest specification has also been updated to be internally consistent, easier to navigate, and allow for read, write, and update capabilities.</p>
 <div id="fig:domains" class="fignos">
 <figure>
-<img src="images/BrAPI_Domains_v2-1_vertical.png" style="width:100.0%" alt="Figure 1: A simplified domain map of the whole BrAPI data model, divided into organizational modules. A more detailed Entity Relationship Diagram (ERD) is available on brapi.org." />
+<img src="images/FIGURE_1_BrAPI_Domains_v2.jpg" style="width:100.0%" alt="Figure 1: A simplified domain map of the whole BrAPI data model, divided into organizational modules. A more detailed Entity Relationship Diagram (ERD) is available on brapi.org." />
 <figcaption aria-hidden="true"><span>Figure 1:</span> A simplified domain map of the whole BrAPI data model, divided into organizational modules. A more detailed Entity Relationship Diagram (ERD) is available on brapi.org.</figcaption>
 </figure>
 </div>
@@ -1119,7 +1119,7 @@ <h2 id="results">Results</h2>
 <p>Below are a number of short success stories from the BrAPI community. These tools, applications, and infrastructure projects serve as another indicator of community growth and success over the past 5 years. These stories clearly illustrate all the different ways the BrAPI standard can be used productively and in practice. Figure <a href="#fig:apps">2</a> contains a summary of many of the currently available BrAPI-compliant tools, and each will be further described below.</p>
 <div id="fig:apps" class="fignos">
 <figure>
-<img src="images/BrAPI_Paper_Applications_Chart.png" style="width:100.0%" alt="Figure 2: A summary of all the tools described below and the general areas each tool is designed to handle. The “Generation/Collection” column indicates that an application is used to input or create new data. The “Storage” column indicates the tool stores that type of data. The “Visualization” column indicates that application has a way of presenting data to a human user. The “Analysis” column indicates the tool does some calculation to provide new insight." />
+<img src="images/FIGURE_2_Applications_Chart.jpg" style="width:100.0%" alt="Figure 2: A summary of all the tools described below and the general areas each tool is designed to handle. The “Generation/Collection” column indicates that an application is used to input or create new data. The “Storage” column indicates the tool stores that type of data. The “Visualization” column indicates that application has a way of presenting data to a human user. The “Analysis” column indicates the tool does some calculation to provide new insight." />
 <figcaption aria-hidden="true"><span>Figure 2:</span> A summary of all the tools described below and the general areas each tool is designed to handle. The “Generation/Collection” column indicates that an application is used to input or create new data. The “Storage” column indicates the tool stores that type of data. The “Visualization” column indicates that application has a way of presenting data to a human user. The “Analysis” column indicates the tool does some calculation to provide new insight.</figcaption>
 </figure>
 </div>