Merge branch 'main' of https://github.com/jhudsl/Adv_Reproducibility_…

…in_Cancer_Informatics into main

docs/no_toc/03-version-control-with-github.md

@@ -193,9 +193,9 @@ One more note: if you do want to use the command line or if you want to know mor
 
 - [Happy Git and GitHub for the useR](https://happygitwithr.com/) by @Bryan2021.
 - [GitHub for data scientists](https://towardsdatascience.com/introduction-to-github-for-data-scientists-2cf8b9b25fba) by @Vickery2019.
-- [Intro to GitHub](https://lab.github.com/githubtraining/introduction-to-github) by @GitHub2021.
-- [First Day on GitHub](https://lab.github.com/githubtraining/first-day-on-github) by @GitHub2021c.
-- [First Week on GitHub](https://lab.github.com/githubtraining/first-week-on-github) by @GitHub2021d.
+- [Intro to GitHub](https://github.com/skills/introduction-to-github) by @GitHub2022.
+- [First Day on GitHub](https://skills.github.com/#first-day-on-github) by @GitHub2022c.
+- [First Week on GitHub](https://skills.github.com/#first-week-on-github) by @GitHub2022d.
 - [GitHub docs about creating a Pull Request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) by @GitHub2021b.
 - [Making a Pull Request](https://www.atlassian.com/git/tutorials/making-a-pull-request) by @Radigan2021.
 

docs/no_toc/04-data-handling.md

@@ -11,7 +11,7 @@ The first part of any analysis should be getting all the data needed to run it.
 
 ### Overview of data sharing
 
-- The data to be shared does not contain <a href="https://jhudatascience.org/Data_Management_for_Cancer_Research/data-privacy.html" target="_blank"> PII (personal identifiable information) or PHI (protected health information) information</a>.
+- The data to be shared does not contain [PII (personal identifiable information) or PHI (protected health information) information](https://jhudatascience.org/Ethical_Data_Handling_for_Cancer_Research/data-privacy.html).
 - The data are accessible by a download script that is automatically downloaded when re-running the analysis.
 - Every data file needed to run the analysis is available.
 - The data are downloaded to files in an organized manner. For more about project organization, see [this chapter from the Introduction to Reproducibility course](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/organizing-your-project.html).
@@ -42,4 +42,4 @@ You can download this [general template download file here](https://raw.githubus
 - [Data download script for multiple files of the same place](https://github.com/AlexsLemonade/training-modules/blob/master/machine-learning/setup/00-data-download.sh)
 - [Data download script - refine.bio example](https://github.com/jhudsl/reproducible-R-example/blob/main/00-download-data.py)
 
-For more about data sharing techniques, see the <a href="https://jhudatascience.org/Data_Management/data-sharing.html" target="_blank">Computing and Data Management course</a>.
+For more about data sharing techniques, see the [Ethical Data Handling for Cancer Research](https://jhudatascience.org/Ethical_Data_Handling_for_Cancer_Research/) course</a>.

docs/no_toc/05-code-review-author.md

@@ -103,8 +103,8 @@ Pull request templates are a way to give yourself and other contributors prompts
 
 1. Create a new branch as we described in the previous chapter.
 2. In your local repository, create a folder called `.github`
-3. Download this [pull request template file](https://raw.githubusercontent.com/jhudsl/Adv_Reproducibility_in_Cancer_Informatics/main/resources/PULL_REQUEST_TEMPLATE.md) to get you started.
-4. Feel free to edit this file to your own needs and add it to the `.github` folder.
+3. Copy and paste this [pull request template file](https://raw.githubusercontent.com/jhudsl/Adv_Reproducibility_in_Cancer_Informatics/main/.github/PULL_REQUEST_TEMPLATE.md) to a new text file and save it as a `.md` to get started.
+4. Feel free to edit this file to your own needs and add it to the `.github` folder of your repository.
 5. Use GitKraken to `add` and `commit` this new file.
 6. Push this commit.
 7. Open up a pull request.

docs/no_toc/09-automation.md

@@ -90,9 +90,9 @@ _Tips for developing a GitHub Action:_
 - Use `|` in your `run:` command to give a multi-line command.
 
 ### Resources for setting up your GitHub Actions
-- [Python example GitHub Actions to re-run notebook](https://github.com/jhudsl/reproducible-python-example/blob/main/.github/workflows/run-python-notebook.yml)
+- [Python example GitHub Actions to re-run notebook](https://github.com/jhudsl/reproducible-python-example/blob/49e1e33ad0c19d59f85d7c6a6ef8cb173cee0661/.github/workflows/run-py-notebook.yml)
 - [R example GitHub Actions to re-run notebook](https://github.com/jhudsl/reproducible-R-example/blob/main/.github/workflows/run-r-notebook.yml)
-- [Great course about GitHub actions](https://lab.github.com/githubtraining/github-actions:-hello-world)
+- [Great course about GitHub actions](https://skills.github.com/#automate-workflows-with-github-actions)
 - [Introduction to GitHub Actions for data scientists](https://towardsdatascience.com/introduction-to-github-actions-7fcb30d0f959).
 
 **If you have any feedback on this chapter, please [fill out this form](https://forms.gle/j3cJZX5CmNtQp6QKA), we'd love to hear your feedback!**

docs/no_toc/404.html

@@ -28,7 +28,7 @@
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
 
-  <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
+  <link rel="shortcut icon" href="assets/ITN_favicon.ico" type="image/x-icon" />
 
 
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>

docs/no_toc/About.md

@@ -46,7 +46,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2022-10-13                  
+##  date     2022-12-21                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version    date       lib source                            
@@ -108,7 +108,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 [Jimin Hwang]: https://www.linkedin.com/in/jimin-hwang-549835142/
 [Jeff Leek]: https://jtleek.com/
 [John Muschelli]: https://johnmuschelli.com/
-[Sarah Wheelan]: https://www.hopkinsmedicine.org/profiles/details/sarah-wheelan
+[Sarah Wheelan]: https://www.linkedin.com/in/sarah-wheelan-782688203/
 
 <!-- Links -->
 

docs/no_toc/about-the-authors.html

@@ -28,7 +28,7 @@
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
 
-  <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
+  <link rel="shortcut icon" href="assets/ITN_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="automation-as-a-reproducibility-tool.html"/>
 <link rel="next" href="references.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>
@@ -293,11 +293,11 @@ <h1>About the Authors</h1>
 </tr>
 <tr class="even">
 <td>Content Directors</td>
-<td><a href="https://jtleek.com/">Jeff Leek</a>, <a href="https://www.hopkinsmedicine.org/profiles/details/sarah-wheelan">Sarah Wheelan</a></td>
+<td><a href="https://jtleek.com/">Jeff Leek</a>, <a href="https://www.linkedin.com/in/sarah-wheelan-782688203/">Sarah Wheelan</a></td>
 </tr>
 <tr class="odd">
 <td>Content Reviewer</td>
-<td><a href="https://www.hopkinsmedicine.org/profiles/details/sarah-wheelan">Sarah Wheelan</a></td>
+<td><a href="https://www.linkedin.com/in/sarah-wheelan-782688203/">Sarah Wheelan</a></td>
 </tr>
 <tr class="even">
 <td>Content Editor</td>
@@ -388,7 +388,7 @@ <h1>About the Authors</h1>
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2022-10-13                  
+##  date     2022-12-21                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version    date       lib source                            

docs/no_toc/automation-as-a-reproducibility-tool.html

@@ -28,7 +28,7 @@
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
 
-  <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
+  <link rel="shortcut icon" href="assets/ITN_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="modifying-a-docker-image.html"/>
 <link rel="next" href="about-the-authors.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>
@@ -336,9 +336,9 @@ <h2><span class="header-section-number">9.3</span> Exercise: Set up a GitHub act
 <div id="resources-for-setting-up-your-github-actions" class="section level3" number="9.3.1">
 <h3><span class="header-section-number">9.3.1</span> Resources for setting up your GitHub Actions</h3>
 <ul>
-<li><a href="https://github.com/jhudsl/reproducible-python-example/blob/main/.github/workflows/run-python-notebook.yml">Python example GitHub Actions to re-run notebook</a></li>
+<li><a href="https://github.com/jhudsl/reproducible-python-example/blob/49e1e33ad0c19d59f85d7c6a6ef8cb173cee0661/.github/workflows/run-py-notebook.yml">Python example GitHub Actions to re-run notebook</a></li>
 <li><a href="https://github.com/jhudsl/reproducible-R-example/blob/main/.github/workflows/run-r-notebook.yml">R example GitHub Actions to re-run notebook</a></li>
-<li><a href="https://lab.github.com/githubtraining/github-actions:-hello-world">Great course about GitHub actions</a></li>
+<li><a href="https://skills.github.com/#automate-workflows-with-github-actions">Great course about GitHub actions</a></li>
 <li><a href="https://towardsdatascience.com/introduction-to-github-actions-7fcb30d0f959">Introduction to GitHub Actions for data scientists</a>.</li>
 </ul>
 <p><strong>If you have any feedback on this chapter, please <a href="https://forms.gle/j3cJZX5CmNtQp6QKA">fill out this form</a>, we’d love to hear your feedback!</strong></p>

docs/no_toc/defining-reproducibility.html

@@ -28,7 +28,7 @@
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
 
-  <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
+  <link rel="shortcut icon" href="assets/ITN_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="introduction.html"/>
 <link rel="next" href="using-version-control-with-github.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>

docs/no_toc/engaging-in-code-review---as-a-reviewer.html

@@ -28,7 +28,7 @@
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
 
-  <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
+  <link rel="shortcut icon" href="assets/ITN_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="engaging-in-code-review---as-an-author.html"/>
 <link rel="next" href="launching-a-docker-image.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>

docs/no_toc/engaging-in-code-review---as-an-author.html

@@ -28,7 +28,7 @@
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
 
-  <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
+  <link rel="shortcut icon" href="assets/ITN_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="providing-data.html"/>
 <link rel="next" href="engaging-in-code-review---as-a-reviewer.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>
@@ -353,8 +353,8 @@ <h4><span class="header-section-number">5.4.0.1</span> Set up a pull request tem
 <ol style="list-style-type: decimal">
 <li>Create a new branch as we described in the previous chapter.</li>
 <li>In your local repository, create a folder called <code>.github</code></li>
-<li>Download this <a href="https://raw.githubusercontent.com/jhudsl/Adv_Reproducibility_in_Cancer_Informatics/main/resources/PULL_REQUEST_TEMPLATE.md">pull request template file</a> to get you started.</li>
-<li>Feel free to edit this file to your own needs and add it to the <code>.github</code> folder.</li>
+<li>Copy and paste this <a href="https://raw.githubusercontent.com/jhudsl/Adv_Reproducibility_in_Cancer_Informatics/main/.github/PULL_REQUEST_TEMPLATE.md">pull request template file</a> to a new text file and save it as a <code>.md</code> to get started.</li>
+<li>Feel free to edit this file to your own needs and add it to the <code>.github</code> folder of your repository.</li>
 <li>Use GitKraken to <code>add</code> and <code>commit</code> this new file.</li>
 <li>Push this commit.</li>
 <li>Open up a pull request.</li>

docs/no_toc/index.html

@@ -28,7 +28,7 @@
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
 
-  <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
+  <link rel="shortcut icon" href="assets/ITN_favicon.ico" type="image/x-icon" />
 
 <link rel="next" href="introduction.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>
@@ -264,7 +264,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">Advanced Reproducibility in Cancer Informatics</h1>
-<p class="date"><em>October, 2022</em></p>
+<p class="date"><em>December, 2022</em></p>
 </div>
 <div id="about-this-course" class="section level1 unnumbered">
 <h1>About this Course</h1>

docs/no_toc/index.md

@@ -1,13 +1,13 @@
 ---
 title: "Advanced Reproducibility in Cancer Informatics"
-date: "October, 2022"
+date: "December, 2022"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib, packages.bib]
 biblio-style: apalike
 link-citations: yes
 description: "Description about Course/Book."
-favicon: assets/dasl_favicon.ico
+favicon: assets/ITN_favicon.ico
 output:
     bookdown::word_document2:
       toc: true

docs/no_toc/introduction.html

@@ -28,7 +28,7 @@
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
 
-  <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
+  <link rel="shortcut icon" href="assets/ITN_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="index.html"/>
 <link rel="next" href="defining-reproducibility.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>

docs/no_toc/launching-a-docker-image.html

@@ -28,7 +28,7 @@
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
 
-  <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
+  <link rel="shortcut icon" href="assets/ITN_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="engaging-in-code-review---as-a-reviewer.html"/>
 <link rel="next" href="modifying-a-docker-image.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>

docs/no_toc/modifying-a-docker-image.html

@@ -28,7 +28,7 @@
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
 
-  <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
+  <link rel="shortcut icon" href="assets/ITN_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="launching-a-docker-image.html"/>
 <link rel="next" href="automation-as-a-reproducibility-tool.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>

docs/no_toc/providing-data.html

@@ -28,7 +28,7 @@
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
 
-  <link rel="shortcut icon" href="assets/dasl_favicon.ico" type="image/x-icon" />
+  <link rel="shortcut icon" href="assets/ITN_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="using-version-control-with-github.html"/>
 <link rel="next" href="engaging-in-code-review---as-an-author.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>
@@ -271,7 +271,7 @@ <h2><span class="header-section-number">4.1</span> Learning Objectives</h2>
 <div id="overview-of-data-sharing" class="section level3" number="4.1.1">
 <h3><span class="header-section-number">4.1.1</span> Overview of data sharing</h3>
 <ul>
-<li>The data to be shared does not contain <a href="https://jhudatascience.org/Data_Management_for_Cancer_Research/data-privacy.html" target="_blank"> PII (personal identifiable information) or PHI (protected health information) information</a>.</li>
+<li>The data to be shared does not contain <a href="https://jhudatascience.org/Ethical_Data_Handling_for_Cancer_Research/data-privacy.html">PII (personal identifiable information) or PHI (protected health information) information</a>.</li>
 <li>The data are accessible by a download script that is automatically downloaded when re-running the analysis.</li>
 <li>Every data file needed to run the analysis is available.</li>
 <li>The data are downloaded to files in an organized manner. For more about project organization, see <a href="https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/organizing-your-project.html">this chapter from the Introduction to Reproducibility course</a>.</li>
@@ -301,7 +301,7 @@ <h3><span class="header-section-number">4.1.3</span> Examples of data download s
 <li><a href="https://github.com/AlexsLemonade/training-modules/blob/master/machine-learning/setup/00-data-download.sh">Data download script for multiple files of the same place</a></li>
 <li><a href="https://github.com/jhudsl/reproducible-R-example/blob/main/00-download-data.py">Data download script - refine.bio example</a></li>
 </ul>
-<p>For more about data sharing techniques, see the <a href="https://jhudatascience.org/Data_Management/data-sharing.html" target="_blank">Computing and Data Management course</a>.</p>
+<p>For more about data sharing techniques, see the <a href="https://jhudatascience.org/Ethical_Data_Handling_for_Cancer_Research/">Ethical Data Handling for Cancer Research</a> course</a>.</p>
 
 </div>
 </div>