deploy: 269ce3f

Author: hovey

book/appendix_d.html

@@ -187,7 +187,7 @@ <h2 id="appendix-d-synthetic-example-problem-using-state-space-metrics"><a class
                                 <i class="fa fa-angle-left"></i>
                             </a>
 
-                            <a rel="next prefetch" href="bibliography.html" class="mobile-nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
+                            <a rel="next prefetch" href="contributors.html" class="mobile-nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
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@@ -201,7 +201,7 @@ <h2 id="appendix-d-synthetic-example-problem-using-state-space-metrics"><a class
                         <i class="fa fa-angle-left"></i>
                     </a>
 
-                    <a rel="next prefetch" href="bibliography.html" class="nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
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book/bibliography.bib

@@ -0,0 +1,6 @@
+@book{knuth1986computer,
+  title={The Computer Science of TeX and Metafont: An Inaugural Lecture},
+  author={Knuth, Donald E},
+  year={1986},
+  publisher={American Mathematical Society}
+}

book/chapter_03.html

@@ -316,6 +316,9 @@ <h3 id="run-test"><a class="header" href="#run-test">Run Test</a></h3>
 <p>Figure 3-10 shows an example <code>Run Test</code> tab with test profile events.</p>
 <p><img src="figures/run_test_tab.png" alt="run_test_tab" /></p>
 <p><strong>Figure 3-10. Run Test Tab.</strong></p>
+<h3 id="rattlesnake-output-files"><a class="header" href="#rattlesnake-output-files">Rattlesnake Output Files</a></h3>
+<p>After data is acquired, the user may wish to analyze or plot the data acquired for a given test report.  Rattlesnake stores data in a self-documenting netCDF file {{#cite unidata2019_netcdf}}, which can be read by multiple platforms.  The output file is described as self-documenting because it contains all parameters necessary to reconstruct a given test using the Rattlesnake controller.  Any parameter that is set by the user in the GUI is stored to the netCDF file.</p>
+<p>A full description of the netCDF file format is out of this document's scope, but the important points are briefly described here.  NetCDF files have a number of data structures.  Variables are multi-dimensional arrays of data.  Dimensions describe the axes of the variable arrays.  Attributes are used to store small data such as scalars or 1D arrays.  NetCDF files can be separated into different groups, and each group can have its own variables, dimensions, and attributes.</p>
 
                     </main>
 

book/contributors.html

@@ -210,13 +210,64 @@ <h4 id="documentation"><a class="header" href="#documentation">Documentation</a>
 
 # visualize the mdbook in a local web browser
 mdbook serve --open
+</code></pre>
+<h5 id="bibliography"><a class="header" href="#bibliography">Bibliography</a></h5>
+<p>To create the bibliography, use <a href="https://crates.io/crates/mdbook-bib"><code>mdbook-bib</code></a>, a popular and well-documented third-party plugin.</p>
+<p><a href="https://rust-lang.org/tools/install/">Cargo</a>,
+the Rust programming language's package manager, is a prerequisite to get the plugin.</p>
+<ol>
+<li>Install the plugin via Cargo:</li>
+</ol>
+<pre><code class="language-sh">cargo install mdbook-bib
+</code></pre>
+<ol start="2">
+<li>Prepare your bibliography file:</li>
+</ol>
+<p>The <code>mdbook-bib</code> plugin uses the standard BibLaTeX (<code>.bib</code>) format for references.
+Create a <code>.bib</code> file (e.g., <code>bibliography.bib</code>) in the root of the <code>documentation/mdbook/src/</code> directory.  Populate the file with references, e.g.,</p>
+<pre><code class="language-sh">@book{knuth1986computer,
+  title={The Computer Science of TeX and Metafont: An Inaugural Lecture},
+  author={Knuth, Donald E},
+  year={1986},
+  publisher={American Mathematical Society}
+}
+</code></pre>
+<ol start="3">
+<li>Configure <code>book.toml</code></li>
+</ol>
+<p>Tell mdBook to use the <code>mdbook-bib</code> preprocessor and specify the path to the
+bibliography file in the <code>book.toml</code> configuration file.  Add the following section
+to the <code>book.toml</code>:</p>
+<pre><code class="language-sh">[preprocessor.bib]
+# The name of your .bib file, relative to the src directory
+bibliography = "bibliography.bib"
+
+# Optional: Set the title for the automatically generated bibliography chapter
+title = "Bibliography"
+
+# Optional: Render the entire bibliography ("all") or only cited entries ("cited")
+render-bib = "cited"
+</code></pre>
+<ol start="4">
+<li>Add in-text citations</li>
+</ol>
+<p>In a markdown file, use <code>{{</code> and <code>}}</code> to surround the
+citation key, <code># cite key</code>, for example:</p>
+<p><code>{{</code> <code>#cite knuth1986computer</code> <code>}}</code></p>
+<ol start="5">
+<li>Build the book</li>
+</ol>
+<p>Run the <code>mdbook build</code> command.  The preprocessor will automatically run, finding the
+citations, generating the citation numbering, and creating a new chapter containing the
+formatted bibliography based on the entries in the <code>.bib</code> file.</p>
+<pre><code class="language-sh">mdbook build
 </code></pre>
 
                     </main>
 
                     <nav class="nav-wrapper" aria-label="Page navigation">
                         <!-- Mobile navigation buttons -->
-                            <a rel="prev" href="bibliography.html" class="mobile-nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
+                            <a rel="prev" href="appendix_d.html" class="mobile-nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
                                 <i class="fa fa-angle-left"></i>
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@@ -227,7 +278,7 @@ <h4 id="documentation"><a class="header" href="#documentation">Documentation</a>
             </div>
 
             <nav class="nav-wide-wrapper" aria-label="Page navigation">
-                    <a rel="prev" href="bibliography.html" class="nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
+                    <a rel="prev" href="appendix_d.html" class="nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
                         <i class="fa fa-angle-left"></i>
                     </a>
 

book/print.html

@@ -436,6 +436,9 @@ <h3 id="run-test"><a class="header" href="#run-test">Run Test</a></h3>
 <p>Figure 3-10 shows an example <code>Run Test</code> tab with test profile events.</p>
 <p><img src="figures/run_test_tab.png" alt="run_test_tab" /></p>
 <p><strong>Figure 3-10. Run Test Tab.</strong></p>
+<h3 id="rattlesnake-output-files"><a class="header" href="#rattlesnake-output-files">Rattlesnake Output Files</a></h3>
+<p>After data is acquired, the user may wish to analyze or plot the data acquired for a given test report.  Rattlesnake stores data in a self-documenting netCDF file {{#cite unidata2019_netcdf}}, which can be read by multiple platforms.  The output file is described as self-documenting because it contains all parameters necessary to reconstruct a given test using the Rattlesnake controller.  Any parameter that is set by the user in the GUI is stored to the netCDF file.</p>
+<p>A full description of the netCDF file format is out of this document's scope, but the important points are briefly described here.  NetCDF files have a number of data structures.  Variables are multi-dimensional arrays of data.  Dimensions describe the axes of the variable arrays.  Attributes are used to store small data such as scalars or 1D arrays.  NetCDF files can be separated into different groups, and each group can have its own variables, dimensions, and attributes.</p>
 <div style="break-before: page; page-break-before: always;"></div><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/katex.min.css">
 <h1 id="part-ii-rattlesnake-hardware-devices"><a class="header" href="#part-ii-rattlesnake-hardware-devices">Part II. Rattlesnake Hardware Devices</a></h1>
 <p>Designed for flexibility, Rattlesnake can be used with multiple hardware devices and even perform virtual control using a synthetic data acquisition system.  This Part will cover the hardware-specific implementation details that must be considered when running Rattlesnake with each hardware device.</p>
@@ -500,8 +503,6 @@ <h2 id="appendix-c-synthetic-example-problem-with-a-sdynpy-system"><a class="hea
 <h2 id="appendix-d-synthetic-example-problem-using-state-space-metrics"><a class="header" href="#appendix-d-synthetic-example-problem-using-state-space-metrics">Appendix D. Synthetic Example Problem using State Space Metrics</a></h2>
 <p>One final example will</p>
 <div style="break-before: page; page-break-before: always;"></div><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/katex.min.css">
-<h2 id="bibliography"><a class="header" href="#bibliography">Bibliography</a></h2>
-<div style="break-before: page; page-break-before: always;"></div><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/katex.min.css">
 <h2 id="contributors"><a class="header" href="#contributors">Contributors</a></h2>
 <ul>
 <li>Daniel P. Rohe</li>
@@ -536,6 +537,57 @@ <h4 id="documentation"><a class="header" href="#documentation">Documentation</a>
 
 # visualize the mdbook in a local web browser
 mdbook serve --open
+</code></pre>
+<h5 id="bibliography"><a class="header" href="#bibliography">Bibliography</a></h5>
+<p>To create the bibliography, use <a href="https://crates.io/crates/mdbook-bib"><code>mdbook-bib</code></a>, a popular and well-documented third-party plugin.</p>
+<p><a href="https://rust-lang.org/tools/install/">Cargo</a>,
+the Rust programming language's package manager, is a prerequisite to get the plugin.</p>
+<ol>
+<li>Install the plugin via Cargo:</li>
+</ol>
+<pre><code class="language-sh">cargo install mdbook-bib
+</code></pre>
+<ol start="2">
+<li>Prepare your bibliography file:</li>
+</ol>
+<p>The <code>mdbook-bib</code> plugin uses the standard BibLaTeX (<code>.bib</code>) format for references.
+Create a <code>.bib</code> file (e.g., <code>bibliography.bib</code>) in the root of the <code>documentation/mdbook/src/</code> directory.  Populate the file with references, e.g.,</p>
+<pre><code class="language-sh">@book{knuth1986computer,
+  title={The Computer Science of TeX and Metafont: An Inaugural Lecture},
+  author={Knuth, Donald E},
+  year={1986},
+  publisher={American Mathematical Society}
+}
+</code></pre>
+<ol start="3">
+<li>Configure <code>book.toml</code></li>
+</ol>
+<p>Tell mdBook to use the <code>mdbook-bib</code> preprocessor and specify the path to the
+bibliography file in the <code>book.toml</code> configuration file.  Add the following section
+to the <code>book.toml</code>:</p>
+<pre><code class="language-sh">[preprocessor.bib]
+# The name of your .bib file, relative to the src directory
+bibliography = "bibliography.bib"
+
+# Optional: Set the title for the automatically generated bibliography chapter
+title = "Bibliography"
+
+# Optional: Render the entire bibliography ("all") or only cited entries ("cited")
+render-bib = "cited"
+</code></pre>
+<ol start="4">
+<li>Add in-text citations</li>
+</ol>
+<p>In a markdown file, use <code>{{</code> and <code>}}</code> to surround the
+citation key, <code># cite key</code>, for example:</p>
+<p><code>{{</code> <code>#cite knuth1986computer</code> <code>}}</code></p>
+<ol start="5">
+<li>Build the book</li>
+</ol>
+<p>Run the <code>mdbook build</code> command.  The preprocessor will automatically run, finding the
+citations, generating the citation numbering, and creating a new chapter containing the
+formatted bibliography based on the entries in the <code>.bib</code> file.</p>
+<pre><code class="language-sh">mdbook build
 </code></pre>
 
                     </main>