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diff --git a/manuscript/1-Introduction.md b/manuscript/1-Introduction.md
diff --git a/manuscript/2-Scientific-software-development-best-practices.md b/manuscript/2-Scientific-software-development-best-practices.md
diff --git a/manuscript/3-Why-Automation.md b/manuscript/3-Why-Automation.md
diff --git a/manuscript/4-GitHub-Actions-Fundamentals.md b/manuscript/4-GitHub-Actions-Fundamentals.md
diff --git a/manuscript/5-Automating-Re-running-Analyses.md b/manuscript/5-Automating-Re-running-Analyses.md
diff --git a/manuscript/6-GitHub-Action-Variables.md b/manuscript/6-GitHub-Action-Variables.md
diff --git a/manuscript/7-Troubleshooting-GitHub-Actions.md b/manuscript/7-Troubleshooting-GitHub-Actions.md
diff --git a/manuscript/8-Applying-GitHub-Actions-Examples.md b/manuscript/8-Applying-GitHub-Actions-Examples.md
diff --git a/manuscript/9-References.md b/manuscript/9-References.md
diff --git a/manuscript/About-the-Authors.md b/manuscript/About-the-Authors.md
diff --git a/manuscript/About-this-Course.md b/manuscript/About-this-Course.md
diff --git a/manuscript/Book.txt b/manuscript/Book.txt
diff --git a/manuscript/resources/chapt_screen_images/about-the-authors.png b/manuscript/resources/chapt_screen_images/about-the-authors.png
diff --git a/manuscript/resources/chapt_screen_images/applying-github-actions-examples.png b/manuscript/resources/chapt_screen_images/applying-github-actions-examples.png
diff --git a/manuscript/resources/chapt_screen_images/automating-re-running-analyses.png b/manuscript/resources/chapt_screen_images/automating-re-running-analyses.png
diff --git a/manuscript/resources/chapt_screen_images/github-action-variables.png b/manuscript/resources/chapt_screen_images/github-action-variables.png
diff --git a/manuscript/resources/chapt_screen_images/github-actions-fundamentals.png b/manuscript/resources/chapt_screen_images/github-actions-fundamentals.png
diff --git a/manuscript/resources/chapt_screen_images/index.png b/manuscript/resources/chapt_screen_images/index.png
diff --git a/manuscript/resources/chapt_screen_images/introduction.png b/manuscript/resources/chapt_screen_images/introduction.png
diff --git a/manuscript/resources/chapt_screen_images/references.png b/manuscript/resources/chapt_screen_images/references.png
diff --git a/...esources/chapt_screen_images/scientific-software-development-best-practices.png b/...esources/chapt_screen_images/scientific-software-development-best-practices.png
diff --git a/manuscript/resources/chapt_screen_images/troubleshooting-github-actions.png b/manuscript/resources/chapt_screen_images/troubleshooting-github-actions.png
diff --git a/manuscript/resources/chapt_screen_images/why-automation.png b/manuscript/resources/chapt_screen_images/why-automation.png
diff --git a/resources/chapt_screen_images/about-the-authors.png b/resources/chapt_screen_images/about-the-authors.png
diff --git a/resources/chapt_screen_images/applying-github-actions-examples.png b/resources/chapt_screen_images/applying-github-actions-examples.png
diff --git a/resources/chapt_screen_images/automating-re-running-analyses.png b/resources/chapt_screen_images/automating-re-running-analyses.png
diff --git a/resources/chapt_screen_images/chapter_urls.tsv b/resources/chapt_screen_images/chapter_urls.tsv
@@ -1,12 +1,12 @@
 url	chapt_title	img_path
-http://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/index.html	About this Course	resources/chapt_screen_images/index.png
-http://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/introduction.html	1 Introduction	resources/chapt_screen_images/introduction.png
-http://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/scientific-software-development-best-practices.html	2 Scientific software development best practices	resources/chapt_screen_images/scientific-software-development-best-practices.png
-http://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/why-automation.html	3 Why Automation	resources/chapt_screen_images/why-automation.png
-http://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/github-actions-fundamentals.html	4 GitHub Actions Fundamentals	resources/chapt_screen_images/github-actions-fundamentals.png
-http://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/automating-re-running-analyses.html	5 Automating Re-running Analyses	resources/chapt_screen_images/automating-re-running-analyses.png
-http://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/github-action-variables.html	6 GitHub Action Variables	resources/chapt_screen_images/github-action-variables.png
-http://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/troubleshooting-github-actions.html	7 Troubleshooting GitHub Actions	resources/chapt_screen_images/troubleshooting-github-actions.png
-http://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/applying-github-actions-examples.html	8 Applying GitHub Actions Examples	resources/chapt_screen_images/applying-github-actions-examples.png
-http://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/about-the-authors.html	About the Authors	resources/chapt_screen_images/about-the-authors.png
-http://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/references.html	9 References	resources/chapt_screen_images/references.png
+https://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/index.html	About this Course	resources/chapt_screen_images/index.png
+https://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/introduction.html	1 Introduction	resources/chapt_screen_images/introduction.png
+https://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/scientific-software-development-best-practices.html	2 Scientific software development best practices	resources/chapt_screen_images/scientific-software-development-best-practices.png
+https://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/why-automation.html	3 Why Automation	resources/chapt_screen_images/why-automation.png
+https://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/github-actions-fundamentals.html	4 GitHub Actions Fundamentals	resources/chapt_screen_images/github-actions-fundamentals.png
+https://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/automating-re-running-analyses.html	5 Automating Re-running Analyses	resources/chapt_screen_images/automating-re-running-analyses.png
+https://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/github-action-variables.html	6 GitHub Action Variables	resources/chapt_screen_images/github-action-variables.png
+https://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/troubleshooting-github-actions.html	7 Troubleshooting GitHub Actions	resources/chapt_screen_images/troubleshooting-github-actions.png
+https://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/applying-github-actions-examples.html	8 Applying GitHub Actions Examples	resources/chapt_screen_images/applying-github-actions-examples.png
+https://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/about-the-authors.html	About the Authors	resources/chapt_screen_images/about-the-authors.png
+https://hutchdatascience.org/GitHub_Automation_for_Scientists/no_toc/references.html	9 References	resources/chapt_screen_images/references.png
diff --git a/resources/chapt_screen_images/github-action-variables.png b/resources/chapt_screen_images/github-action-variables.png
diff --git a/resources/chapt_screen_images/github-actions-fundamentals.png b/resources/chapt_screen_images/github-actions-fundamentals.png
diff --git a/resources/chapt_screen_images/index.png b/resources/chapt_screen_images/index.png
diff --git a/resources/chapt_screen_images/introduction.png b/resources/chapt_screen_images/introduction.png
diff --git a/resources/chapt_screen_images/references.png b/resources/chapt_screen_images/references.png
diff --git a/resources/chapt_screen_images/scientific-software-development-best-practices.png b/resources/chapt_screen_images/scientific-software-development-best-practices.png
diff --git a/resources/chapt_screen_images/troubleshooting-github-actions.png b/resources/chapt_screen_images/troubleshooting-github-actions.png
diff --git a/resources/chapt_screen_images/why-automation.png b/resources/chapt_screen_images/why-automation.png