Merge branch 'main' of https://github.com/fhdsl/GitHub_Automation_for…

…_Scientists into main

docs/03-why-automation.md

@@ -1,6 +1,9 @@
 
 # Why Automation
 
+<img src="03-why-automation_files/figure-html//1x0Cnk2Wcsg8HYkmXnXo_0PxmYCxAwzVrUQzb8DUDvTA_g104d8c58b62_46_4.png" width="100%" />
+
+## Automation as an aid for reproducibility 
 
 All of science is built on results being reliable and continually working toward identifying more true/less wrong explanations about the world.
 

docs/404.html

@@ -126,13 +126,16 @@
 </ul></li>
 <li class="chapter" data-level="3" data-path="why-automation.html"><a href="why-automation.html"><i class="fa fa-check"></i><b>3</b> Why Automation</a>
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-<li class="chapter" data-level="3.0.1" data-path="why-automation.html"><a href="why-automation.html#why-reproducibility-is-so-important."><i class="fa fa-check"></i><b>3.0.1</b> Why reproducibility is so important.</a></li>
-<li class="chapter" data-level="3.0.2" data-path="why-automation.html"><a href="why-automation.html#automation-as-a-reproducibility-tool"><i class="fa fa-check"></i><b>3.0.2</b> Automation as a reproducibility tool</a></li>
-<li class="chapter" data-level="3.1" data-path="why-automation.html"><a href="why-automation.html#continuous-integration-continous-deployment"><i class="fa fa-check"></i><b>3.1</b> Continuous integration / Continous deployment</a>
+<li class="chapter" data-level="3.1" data-path="why-automation.html"><a href="why-automation.html#automation-as-an-aid-for-reproducibility"><i class="fa fa-check"></i><b>3.1</b> Automation as an aid for reproducibility</a>
 <ul>
-<li class="chapter" data-level="3.1.1" data-path="why-automation.html"><a href="why-automation.html#continous-integration-continuous-deployment"><i class="fa fa-check"></i><b>3.1.1</b> Continous Integration / Continuous Deployment</a></li>
-<li class="chapter" data-level="3.1.2" data-path="why-automation.html"><a href="why-automation.html#a-real-world-example"><i class="fa fa-check"></i><b>3.1.2</b> A real world example</a></li>
-<li class="chapter" data-level="3.1.3" data-path="why-automation.html"><a href="why-automation.html#other-cicd-services"><i class="fa fa-check"></i><b>3.1.3</b> Other CI/CD services</a></li>
+<li class="chapter" data-level="3.1.1" data-path="why-automation.html"><a href="why-automation.html#why-reproducibility-is-so-important."><i class="fa fa-check"></i><b>3.1.1</b> Why reproducibility is so important.</a></li>
+<li class="chapter" data-level="3.1.2" data-path="why-automation.html"><a href="why-automation.html#automation-as-a-reproducibility-tool"><i class="fa fa-check"></i><b>3.1.2</b> Automation as a reproducibility tool</a></li>
+</ul></li>
+<li class="chapter" data-level="3.2" data-path="why-automation.html"><a href="why-automation.html#continuous-integration-continous-deployment"><i class="fa fa-check"></i><b>3.2</b> Continuous integration / Continous deployment</a>
+<ul>
+<li class="chapter" data-level="3.2.1" data-path="why-automation.html"><a href="why-automation.html#continous-integration-continuous-deployment"><i class="fa fa-check"></i><b>3.2.1</b> Continous Integration / Continuous Deployment</a></li>
+<li class="chapter" data-level="3.2.2" data-path="why-automation.html"><a href="why-automation.html#a-real-world-example"><i class="fa fa-check"></i><b>3.2.2</b> A real world example</a></li>
+<li class="chapter" data-level="3.2.3" data-path="why-automation.html"><a href="why-automation.html#other-cicd-services"><i class="fa fa-check"></i><b>3.2.3</b> Other CI/CD services</a></li>
 </ul></li>
 </ul></li>
 <li class="chapter" data-level="4" data-path="github-actions-fundamentals.html"><a href="github-actions-fundamentals.html"><i class="fa fa-check"></i><b>4</b> GitHub Actions Fundamentals</a>
@@ -241,10 +244,17 @@ <h1>Page not found</h1>
 the table of contents to find the page you are looking for.</p>
 </div>
 <hr>
-<center> 
+<center>
+<div class="container">
+  <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course=github_actions" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+  </div>
+</center>
+
+<hr>
+<center>
   <div class="footer">
       All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
-      <br>
       All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
   </div>
 </center>

docs/About.md

@@ -37,7 +37,7 @@ These credits are based on our [course contributors table guidelines](https://ww
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 ##  ctype    en_US.UTF-8                 
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-##  date     2023-11-30                  
+##  date     2024-02-29                  
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 ##  package     * version date       lib source                            

docs/about-the-authors.html

@@ -126,13 +126,16 @@
 </ul></li>
 <li class="chapter" data-level="3" data-path="why-automation.html"><a href="why-automation.html"><i class="fa fa-check"></i><b>3</b> Why Automation</a>
 <ul>
-<li class="chapter" data-level="3.0.1" data-path="why-automation.html"><a href="why-automation.html#why-reproducibility-is-so-important."><i class="fa fa-check"></i><b>3.0.1</b> Why reproducibility is so important.</a></li>
-<li class="chapter" data-level="3.0.2" data-path="why-automation.html"><a href="why-automation.html#automation-as-a-reproducibility-tool"><i class="fa fa-check"></i><b>3.0.2</b> Automation as a reproducibility tool</a></li>
-<li class="chapter" data-level="3.1" data-path="why-automation.html"><a href="why-automation.html#continuous-integration-continous-deployment"><i class="fa fa-check"></i><b>3.1</b> Continuous integration / Continous deployment</a>
+<li class="chapter" data-level="3.1" data-path="why-automation.html"><a href="why-automation.html#automation-as-an-aid-for-reproducibility"><i class="fa fa-check"></i><b>3.1</b> Automation as an aid for reproducibility</a>
 <ul>
-<li class="chapter" data-level="3.1.1" data-path="why-automation.html"><a href="why-automation.html#continous-integration-continuous-deployment"><i class="fa fa-check"></i><b>3.1.1</b> Continous Integration / Continuous Deployment</a></li>
-<li class="chapter" data-level="3.1.2" data-path="why-automation.html"><a href="why-automation.html#a-real-world-example"><i class="fa fa-check"></i><b>3.1.2</b> A real world example</a></li>
-<li class="chapter" data-level="3.1.3" data-path="why-automation.html"><a href="why-automation.html#other-cicd-services"><i class="fa fa-check"></i><b>3.1.3</b> Other CI/CD services</a></li>
+<li class="chapter" data-level="3.1.1" data-path="why-automation.html"><a href="why-automation.html#why-reproducibility-is-so-important."><i class="fa fa-check"></i><b>3.1.1</b> Why reproducibility is so important.</a></li>
+<li class="chapter" data-level="3.1.2" data-path="why-automation.html"><a href="why-automation.html#automation-as-a-reproducibility-tool"><i class="fa fa-check"></i><b>3.1.2</b> Automation as a reproducibility tool</a></li>
+</ul></li>
+<li class="chapter" data-level="3.2" data-path="why-automation.html"><a href="why-automation.html#continuous-integration-continous-deployment"><i class="fa fa-check"></i><b>3.2</b> Continuous integration / Continous deployment</a>
+<ul>
+<li class="chapter" data-level="3.2.1" data-path="why-automation.html"><a href="why-automation.html#continous-integration-continuous-deployment"><i class="fa fa-check"></i><b>3.2.1</b> Continous Integration / Continuous Deployment</a></li>
+<li class="chapter" data-level="3.2.2" data-path="why-automation.html"><a href="why-automation.html#a-real-world-example"><i class="fa fa-check"></i><b>3.2.2</b> A real world example</a></li>
+<li class="chapter" data-level="3.2.3" data-path="why-automation.html"><a href="why-automation.html#other-cicd-services"><i class="fa fa-check"></i><b>3.2.3</b> Other CI/CD services</a></li>
 </ul></li>
 </ul></li>
 <li class="chapter" data-level="4" data-path="github-actions-fundamentals.html"><a href="github-actions-fundamentals.html"><i class="fa fa-check"></i><b>4</b> GitHub Actions Fundamentals</a>
@@ -320,7 +323,7 @@ <h1>About the Authors</h1>
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 ##  ctype    en_US.UTF-8                 
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-##  date     2023-11-30                  
+##  date     2024-02-29                  
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 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            
@@ -380,10 +383,17 @@ <h1>About the Authors</h1>
 
 </div>
 <hr>
-<center> 
+<center>
+<div class="container">
+  <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course=github_actions" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+  </div>
+</center>
+
+<hr>
+<center>
   <div class="footer">
       All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
-      <br>
       All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
   </div>
 </center>

docs/applying-github-actions-examples.html

@@ -126,13 +126,16 @@
 </ul></li>
 <li class="chapter" data-level="3" data-path="why-automation.html"><a href="why-automation.html"><i class="fa fa-check"></i><b>3</b> Why Automation</a>
 <ul>
-<li class="chapter" data-level="3.0.1" data-path="why-automation.html"><a href="why-automation.html#why-reproducibility-is-so-important."><i class="fa fa-check"></i><b>3.0.1</b> Why reproducibility is so important.</a></li>
-<li class="chapter" data-level="3.0.2" data-path="why-automation.html"><a href="why-automation.html#automation-as-a-reproducibility-tool"><i class="fa fa-check"></i><b>3.0.2</b> Automation as a reproducibility tool</a></li>
-<li class="chapter" data-level="3.1" data-path="why-automation.html"><a href="why-automation.html#continuous-integration-continous-deployment"><i class="fa fa-check"></i><b>3.1</b> Continuous integration / Continous deployment</a>
+<li class="chapter" data-level="3.1" data-path="why-automation.html"><a href="why-automation.html#automation-as-an-aid-for-reproducibility"><i class="fa fa-check"></i><b>3.1</b> Automation as an aid for reproducibility</a>
 <ul>
-<li class="chapter" data-level="3.1.1" data-path="why-automation.html"><a href="why-automation.html#continous-integration-continuous-deployment"><i class="fa fa-check"></i><b>3.1.1</b> Continous Integration / Continuous Deployment</a></li>
-<li class="chapter" data-level="3.1.2" data-path="why-automation.html"><a href="why-automation.html#a-real-world-example"><i class="fa fa-check"></i><b>3.1.2</b> A real world example</a></li>
-<li class="chapter" data-level="3.1.3" data-path="why-automation.html"><a href="why-automation.html#other-cicd-services"><i class="fa fa-check"></i><b>3.1.3</b> Other CI/CD services</a></li>
+<li class="chapter" data-level="3.1.1" data-path="why-automation.html"><a href="why-automation.html#why-reproducibility-is-so-important."><i class="fa fa-check"></i><b>3.1.1</b> Why reproducibility is so important.</a></li>
+<li class="chapter" data-level="3.1.2" data-path="why-automation.html"><a href="why-automation.html#automation-as-a-reproducibility-tool"><i class="fa fa-check"></i><b>3.1.2</b> Automation as a reproducibility tool</a></li>
+</ul></li>
+<li class="chapter" data-level="3.2" data-path="why-automation.html"><a href="why-automation.html#continuous-integration-continous-deployment"><i class="fa fa-check"></i><b>3.2</b> Continuous integration / Continous deployment</a>
+<ul>
+<li class="chapter" data-level="3.2.1" data-path="why-automation.html"><a href="why-automation.html#continous-integration-continuous-deployment"><i class="fa fa-check"></i><b>3.2.1</b> Continous Integration / Continuous Deployment</a></li>
+<li class="chapter" data-level="3.2.2" data-path="why-automation.html"><a href="why-automation.html#a-real-world-example"><i class="fa fa-check"></i><b>3.2.2</b> A real world example</a></li>
+<li class="chapter" data-level="3.2.3" data-path="why-automation.html"><a href="why-automation.html#other-cicd-services"><i class="fa fa-check"></i><b>3.2.3</b> Other CI/CD services</a></li>
 </ul></li>
 </ul></li>
 <li class="chapter" data-level="4" data-path="github-actions-fundamentals.html"><a href="github-actions-fundamentals.html"><i class="fa fa-check"></i><b>4</b> GitHub Actions Fundamentals</a>
@@ -369,10 +372,17 @@ <h3><span class="header-section-number">8.1.2</span> Tips for adapting these to
 </div>
 </div>
 <hr>
-<center> 
+<center>
+<div class="container">
+  <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course=github_actions" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+  </div>
+</center>
+
+<hr>
+<center>
   <div class="footer">
       All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
-      <br>
       All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
   </div>
 </center>

docs/automating-re-running-analyses.html

@@ -126,13 +126,16 @@
 </ul></li>
 <li class="chapter" data-level="3" data-path="why-automation.html"><a href="why-automation.html"><i class="fa fa-check"></i><b>3</b> Why Automation</a>
 <ul>
-<li class="chapter" data-level="3.0.1" data-path="why-automation.html"><a href="why-automation.html#why-reproducibility-is-so-important."><i class="fa fa-check"></i><b>3.0.1</b> Why reproducibility is so important.</a></li>
-<li class="chapter" data-level="3.0.2" data-path="why-automation.html"><a href="why-automation.html#automation-as-a-reproducibility-tool"><i class="fa fa-check"></i><b>3.0.2</b> Automation as a reproducibility tool</a></li>
-<li class="chapter" data-level="3.1" data-path="why-automation.html"><a href="why-automation.html#continuous-integration-continous-deployment"><i class="fa fa-check"></i><b>3.1</b> Continuous integration / Continous deployment</a>
+<li class="chapter" data-level="3.1" data-path="why-automation.html"><a href="why-automation.html#automation-as-an-aid-for-reproducibility"><i class="fa fa-check"></i><b>3.1</b> Automation as an aid for reproducibility</a>
 <ul>
-<li class="chapter" data-level="3.1.1" data-path="why-automation.html"><a href="why-automation.html#continous-integration-continuous-deployment"><i class="fa fa-check"></i><b>3.1.1</b> Continous Integration / Continuous Deployment</a></li>
-<li class="chapter" data-level="3.1.2" data-path="why-automation.html"><a href="why-automation.html#a-real-world-example"><i class="fa fa-check"></i><b>3.1.2</b> A real world example</a></li>
-<li class="chapter" data-level="3.1.3" data-path="why-automation.html"><a href="why-automation.html#other-cicd-services"><i class="fa fa-check"></i><b>3.1.3</b> Other CI/CD services</a></li>
+<li class="chapter" data-level="3.1.1" data-path="why-automation.html"><a href="why-automation.html#why-reproducibility-is-so-important."><i class="fa fa-check"></i><b>3.1.1</b> Why reproducibility is so important.</a></li>
+<li class="chapter" data-level="3.1.2" data-path="why-automation.html"><a href="why-automation.html#automation-as-a-reproducibility-tool"><i class="fa fa-check"></i><b>3.1.2</b> Automation as a reproducibility tool</a></li>
+</ul></li>
+<li class="chapter" data-level="3.2" data-path="why-automation.html"><a href="why-automation.html#continuous-integration-continous-deployment"><i class="fa fa-check"></i><b>3.2</b> Continuous integration / Continous deployment</a>
+<ul>
+<li class="chapter" data-level="3.2.1" data-path="why-automation.html"><a href="why-automation.html#continous-integration-continuous-deployment"><i class="fa fa-check"></i><b>3.2.1</b> Continous Integration / Continuous Deployment</a></li>
+<li class="chapter" data-level="3.2.2" data-path="why-automation.html"><a href="why-automation.html#a-real-world-example"><i class="fa fa-check"></i><b>3.2.2</b> A real world example</a></li>
+<li class="chapter" data-level="3.2.3" data-path="why-automation.html"><a href="why-automation.html#other-cicd-services"><i class="fa fa-check"></i><b>3.2.3</b> Other CI/CD services</a></li>
 </ul></li>
 </ul></li>
 <li class="chapter" data-level="4" data-path="github-actions-fundamentals.html"><a href="github-actions-fundamentals.html"><i class="fa fa-check"></i><b>4</b> GitHub Actions Fundamentals</a>
@@ -362,10 +365,17 @@ <h3><span class="header-section-number">5.2.3</span> Summary</h3>
 </div>
 </div>
 <hr>
-<center> 
+<center>
+<div class="container">
+  <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course=github_actions" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+  </div>
+</center>
+
+<hr>
+<center>
   <div class="footer">
       All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
-      <br>
       All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
   </div>
 </center>