Update README.md

README.md

@@ -1,8 +1,6 @@
 # Best Practices for Writing Reproducible Code
 
-_If you are looking at a GitHub README, please note that the slides are best viewed [via GitHub pages](https://utrechtuniversity.github.io/workshop-computational-reproducibility/)._
-
-_You can view the workshop book here: [check it out](https://utrechtuniversity.github.io/workshop-computational-reproducibility/docs/index.html)!_
+_If you are looking at a GitHub README, please note that the course book and the slides are available via the [course website](https://utrechtuniversity.github.io/workshop-computational-reproducibility/)._
 
 Ensuring your research is reproducible can be a difficult task.
 Scripting your analysis is a start, but this in and of itself is no guarantee that you, or someone else, can faithfully repeat your work at a later stage.
@@ -14,7 +12,7 @@ Reproducibility requires extra effort, but we will focus on teaching you skills
 ## Preparation
 
 If you are attending this workshop, you can prepare a few things so we can hit the ground running!
-We have [more details on this page](preparations).
+We have [more details on this page](https://utrechtuniversity.github.io/workshop-computational-reproducibility/chapters/preparation.html).
 
 
 ## Schedule
@@ -23,11 +21,11 @@ We have [more details on this page](preparations).
 
 | Time  | Activity |
 |-------:|----------|
-| 9:00 | Welcome & introduction ([slides](slides/slides_introduction.html))| 
-| 9:30 | [Project setup & version control with git](exercises/project-setup.md) |
+| 9:00 | [Welcome & introduction](https://utrechtuniversity.github.io/workshop-computational-reproducibility/chapters/introduction.html))| 
+| 9:30 | [Project setup & version control with git](https://utrechtuniversity.github.io/workshop-computational-reproducibility/chapters/project-management.html) |
 | 10:45 | Questions & discussion |
 | _11:00_ | _Break_ |
-| 11:15 | [Code quality](exercises/code-quality.md)  |
+| 11:15 | [Code quality](https://utrechtuniversity.github.io/workshop-computational-reproducibility/chapters/code-quality.html)  |
 | 12:45 | Questions & discussion |
 | _13:00_ | _End_ |
 
@@ -37,11 +35,11 @@ We have [more details on this page](preparations).
 | Time  | Activity |
 |-------:|----------|
 | 9:00 | Code quality discussion | 
-| 9:15 | [Documentation](exercises/documentation.md)  |
+| 9:15 | [Documentation](https://utrechtuniversity.github.io/workshop-computational-reproducibility/chapters/documentation.html)  |
 | 10:45 | Questions & discussion |
 | _11:00_ | _Break_ |
-| 11:15 | [Accessibility & reproducibility](exercises/reproducibility.md)  |
-| 12:15 | [Reproduction of projects](slides/slides_reproducibility.html#18) |
+| 11:15 | [Accessibility & reproducibility](https://utrechtuniversity.github.io/workshop-computational-reproducibility/chapters/accessibility-and-reproducibility.html)  |
+| 12:15 | [Reproduction of projects](https://utrechtuniversity.github.io/workshop-computational-reproducibility/chapters/reproducibility-check.html) |
 | _13:00_ | _End_ |
 
 
@@ -53,45 +51,34 @@ We have [more details on this page](preparations).
 - [Pro GIT](https://www.git-scm.com/book/en/v2)
 - [Good Enough Practices in Scientific Computing](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510)
 
-## Course materials (for reference, these are also linked in the schedule above!)
-
-### Slides
-1. [Introduction](slides/slides_introduction.html)
-1. [Project setup and version control](slides/slides_project-setup.html)
-1. [Code quality](slides/slides_code-quality.html)
-1. [Project documentation](slides/slides_documentation.html)
-2. [Accessibility & Reproducibility: Dependency Management](slides/slides_environment.html)
-3. [Accessibility & Reproducibility: Archiving](slides/slides_reproducibility.html)
-
-
-### Exercises
-1. [Project setup & version control with git](exercises/project-setup.md)
-1. [Code quality](exercises/code-quality.md) 
-1. [Project documentation](exercises/documentation.md) 
-1. [Accessibility & reproducibility](exercises/reproducibility.md) 
-
-
 ## License
 
-All workshop material is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/). [View the license here](https://github.com/UtrechtUniversity/workshop-computational-reproducibility/blob/master/LICENSE.md).
+All workshop material is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/). [View the license here](https://github.com/UtrechtUniversity/workshop-computational-reproducibility/blob/main/LICENSE.md).
 
 
 ## History and acknowledgements
 
 This course was developed at Utrecht University, supported by the [Open Science Community Utrecht (OSCU)](https://openscience-utrecht.com) and [Research Data Management (RDM) support](https://www.uu.nl/en/research/research-data-management).
 
 Workshop development is being coordinated by [Neha Moopen](https://github.com/nehamoopen), and the course received contributions from (in alphabetical order):
-[Armel Lefebvre](https://github.com/armell)
-| [Barbara Vreede](https://github.com/bvreede)
-| [Bianca Kramer](https://github.com/bmkramer)
-| [Cedric Thieulot](https://github.com/cedrict)
-| [Erik van Sebille](https://github.com/erikvansebille)
-| [Jeroen Bosman](https://github.com/JeroenBosman)
-| [Jeroen Ooms](https://github.com/jeroen)
-| [Jonathan de Bruin](https://github.com/J535D165)
-| [Lukas van de Wiel](https://github.com/hooiberg)
-| [Mateusz Kuzak](https://twitter.com/matkuzak)
-| [Menno Fraters](https://github.com/MFraters)
-| [Philippe Delandmeter](https://github.com/delandmeterp)
-| [Renato Alves](https://github.com/unode)
+
+-   [Armel Lefebvre](https://github.com/armell)
+-   [Barbara Vreede](https://github.com/bvreede)
+-   [Bianca Kramer](https://github.com/bmkramer)
+-   [Cedric Thieulot](https://github.com/cedrict)
+-   [Christine Staiger](https://github.com/chStaiger)
+-   [Erik van Sebille](https://github.com/erikvansebille)
+-   [Jacques Flores](https://github.com/Mish-JPFD)
+-   [Jelle Treep](https://github.com/jelletreep)
+-   [Jeroen Bosman](https://github.com/JeroenBosman)
+-   [Jeroen Ooms](https://github.com/jeroen)
+-   [Jonathan de Bruin](https://github.com/J535D165)
+-   [Lukas van de Wiel](https://github.com/hooiberg)
+-   [Mateusz Kuzak](https://twitter.com/matkuzak)
+-   [Menno Fraters](https://github.com/MFraters)
+-   [Neha Moopen](https://github.com/nehamoopen)
+-   [Parisa Zahedi](https://github.com/parisa-zahedi)
+-   [Philippe Delandmeter](https://github.com/delandmeterp)
+-   [Raoul Schram](https://github.com/qubixes)
+-   [Renato Alves](https://github.com/unode)