workflows + beginning of publishing

1-reproducible-research.qmd

@@ -23,8 +23,7 @@ Afterwards go through the following assignments:
 - What are hurdles for you in producing FAIR data? What can you do for the data you work with?
 - Which of the points in the 8 steps for Planning a Community does your research team already check off? Which should be discussed? If possible, bring open points to your team meeting. 
 
-Discuss your progress with your accountability buddy. Bring any questions and
-problems that you cannot solve with your buddy to the weekly meeting.
+Bring any questions and problems that come up to the weekly meeting.
 :::
 
 

2-project-organization.qmd

@@ -17,10 +17,8 @@
 Read this chapter and watch this week's videos. 
 Afterwards go through the following assignments:
 
-- What questions came up for you while watching the videos and going through the booklet?
-- What are your personal hurdles for reproducible research? What can you do to address them?
-- What are hurdles for you in producing FAIR data? What can you do for the data you work with?
-- Which of the points in the 8 steps for Planning a Community does your research team already check off? Which should be discussed? If possible, bring open points to your team meeting. 
+- Create a folder structure template that would work for most of your projects. If possible, discuss it with your team.
+- For your current project, implement the organization and documentation practices that you learned about. Write down questions that come up in the process.
 
 Discuss your progress with your accountability buddy. Bring any questions and
 problems that you cannot solve with your buddy to the weekly meeting.

3-1-version-control.qmd

@@ -0,0 +1,50 @@
+## Version control
+
+Version control is a big topic for me. It completely changed the way I work. I am happy that we get to talk about version control as part of this 6 step process towards reproducibility.
+
+### What is version control? 
+
+Let's say you are writing a paper. You will edit your paper and might want to keep different versions of it. A common way to handle that is by using different file names for different versions.
+
+
+
+::: captioned-image-container
+![http://www.phdcomics.com/comics/archive/phd101212s.gif](http://www.phdcomics.com/comics/archive/phd101212s.gif){fig-alt="http://www.phdcomics.com/comics/archive/phd101212s.gif"}
+:::
+
+This way of "version control" is outdated and error-prone (hence the pixelated image 😜). The most common proper version control system today is [Git](https://git-scm.com/), which I'd like to introduce to you now.
+
+### Git for version control
+
+Git is free and open source 😃🙌.
+
+With Git you can track different versions of your paper. For each version you can add a description ("commit message") and you even automatically track who made which change if you are working in a group. You can always go back to old versions.
+
+The way you work with Git is that you have the version database both on our computers and on a server. To get the changes from and to the server you use commands (`pull` = download stuff from server, `push` = upload stuff to server).
+
+::: captioned-image-container
+![](images/vc-server.jpg){fig-alt="Reproducibility scale: a scale showing **not reproducible** on one end and **reproducible** on the other end."}
+:::
+
+Most researchers use GitLab or GitHub as platforms for working with Git and they also serve as a neat front end for the server. GitLab and GitHub give us some extra neat features for collaboration (e.g. issues, Wiki, ...).
+
+Learning Git can be daunting 🙀. I recommend learning it with a group or in a class. I am always happy to teach version control. You can also check if there is a free [Software Carpentry](https://software-carpentry.org/) class in your area.
+
+### Other version control systems
+
+There are many other ways of doing version control out there.
+
+**Subversion:** Simpler systems like Subversion are used less these days as Git offers more flexibility.
+
+**Google docs and friends:** Many online text editors (Google Docs, OneDrive, ...) offer versioning now. It is not as advanced and versatile, but a nice way to work in a [WYSIWYG](https://en.wikipedia.org/wiki/WYSIWYG) (What You See Is What You Get) editor. Git really only works with real text files, so people usually use LaTeX or Markdown (not WYSIWYG) to write texts when using Git.
+
+**Versioning data:** Version control of data is a difficult task. Let's leave that for another day. See [here](https://the-turing-way.netlify.app/reproducible-research/vcs/vcs-data.html) for more info for now.
+
+
+## Further reading
+-   [Version Control](https://the-turing-way.netlify.app/reproducible-research/vcs.html), The Turing Way
+-   [Version Control with Git](https://swcarpentry.github.io/git-novice/), Software Carpentry
+-   [Version Control with Git](https://annakrystalli.me/rrresearchACCE20/version-control-with-git.html) (for R users), Anna Krystalli
+-   [Set up Git with RStudio & GitLab](https://gitlab.com/HeidiSeibold/setup-git-rstudio-gitlab), Heidi Seibold
+
+

3-2-stabilize.qmd

@@ -0,0 +1,100 @@
+## Stabilize your computing environment and software
+
+This topic may sound technical and boring at first, but please bare
+with me 🙏. **It will be useful!**
+
+
+Have you ever had the problem that you ran an old code and it just did
+not work anymore? After hours of digging into the issue you find that it's because the
+software package you use has changed in the meantime 🧐
+
+Or have you tried to reproduce someone else's code, which seems to run on
+their machine but not on yours and you just don't know why.
+
+This chapter is all about avoiding such problems in the future
+by **stabilizing your computing environment and software**. ✅
+
+
+### What is a computing environment?
+
+Your computing environment is defined by your computer, the operating
+system and the software installed. If you update your operating system
+or your software, your computing environment changes. In R, for example,
+you can learn a lot about your computing environment by typing
+`sessionInfo()`.
+
+```{r}
+sessionInfo()
+```
+
+It tells the R version, operating system, loaded R packages as well as
+their versions.
+
+### Options for stabilizing your computing environment
+
+#### 1) Record your computing environment {.unnumbered}
+
+Document the software versions you used. For example if you use R, you
+could copy the output of `sessionInfo()` into your README or somewhere
+else where future you (and others) can find this information. This is
+not exactly "stabilizing" but it gives the possibility to install the
+same software versions again.
+
+#### 2) Use one virtual machine per research project {.unnumbered}
+
+You don't need to know what a virtual machine is or how to set it up to
+be able to do this. I used to ask the wonderful IT person at my
+institute to set up a virtual machine for me and if your IT supporters
+know their job, they'll be able to help you here.
+
+A virtual machine is essentially a virtual computer on another computer
+or server (To those nerds out there, I know I am probably explaining it
+incorrectly but for the purpose of what we want to achieve here, it's
+good enough). If you have one virtual machine for each project, you can
+keep the computing environment stable by not installing or updating
+software after you've finished the research project.
+
+The downside of this strategy is that this is only for future you and
+your collaborators, but not for other researchers who want to work with
+the same computing environment.
+
+#### 3) Use one container per research project {.unnumbered}
+
+Containers are similar to virtual machines (think little computer inside
+your computer). The big difference is that you can make them available
+for others. So you can send your container image (or the file describing
+it) to others.
+
+::: captioned-image-container
+![](images/docker-computers.jpg)
+:::
+
+Popular container tools are **Docker and Apptainer** (formerly
+Singularity). Learning to work with containers is not super easy, but it
+is worth the time and actually can be applied in so many other
+situations. So, a great skill to have even if you decide to quit
+research.
+
+#### 4) Other {.unnumbered}
+
+There are many other options out there. I wrote down the three that are
+least dependent on the actual software you use. For R users, check out
+packages `logrx`, `rang`, `packrat`, `versions`, and `renv`.
+
+
+### Further reading
+
+-   [Reproducible
+    Environments](https://the-turing-way.netlify.app/reproducible-research/renv.html),
+    The Turing Way
+-   Video: [How can software containers help your
+    research?](https://youtu.be/HelrQnm3v4g), Paula Andrea Martinez +
+    Australian Research Data Commons
+-   [R Docker tutorial](https://jsta.github.io/r-docker-tutorial/),
+    maintained by Jemma Stachelek
+
+That's all for this chapter. I hope it was helpful and not too technical. Happy
+researching! 🙌
+
+
+

3-3-automate.qmd

@@ -0,0 +1,3 @@
+## Automate your code
+
+TODO

3-computational-workflows.qmd

@@ -1,4 +1,5 @@
 # Computational workflows
+
 ::: {.callout-note}
 ## Learning targets
 
@@ -9,3 +10,23 @@
 - You will have a roadmap on how to automate your code. 
 :::
 
+::: {.callout-important}
+This week's assignments are a bit more difficult and will take longer to implement
+that the previous. Please plan for this.
+:::
+
+::: {.callout-caution}
+## Tasks
+
+Read this chapter and watch this week's videos. 
+Afterwards go through the following assignments:
+
+- Install git: For R users, I recommend following [these](https://gitlab.com/HeidiSeibold/setup-git-rstudio-gitlab) instructions. Otherwise the Carpentries have good [instructions](https://swcarpentry.github.io/git-novice/index.html) for all systems (follow along until end of `2. Setting up Git`)
+- Create a project on GitLab (or GitHub). Then `clone` it, edit a file, `add`, 
+`commit`, and `push` your changes.
+- View the open issues for our course booklet and choose one where you can make a contribution. Create a merge request with your contribution and mark it in the respective issue.
+- Optional: try using Make to automate something in your current research project.
+
+Discuss your progress with your accountability buddy. Bring any questions and
+problems that you cannot solve with your buddy to the weekly meeting.
+:::

4-1-licensing.qmd

@@ -0,0 +1 @@
+## Licensing

4-2-where-to-publish.qmd

@@ -0,0 +1 @@
+## Where to publish

4-3-fair-revisited.qmd

@@ -0,0 +1 @@
+## FAIR revisited

4-publishing-research.qmd

@@ -10,8 +10,17 @@
 - You will know how to implement the FAIR principles in practice.
 :::
 
-## Licensing
 
-## Where to publish
 
-## FAIR revisited
+
+::: {.callout-caution}
+## Tasks
+
+Read this chapter and watch this week's videos. 
+Afterwards go through the following assignments:
+
+- Upload something (e.g. data or a slide deck) to a repository of your choice. How FAIR can you make it?
+
+Discuss your progress with your accountability buddy. Bring any questions and
+problems that you cannot solve with your buddy to the weekly meeting.
+:::

_quarto.yml

@@ -20,6 +20,10 @@ book:
     - 2-2-organisation.qmd
     - 2-3-documentation.qmd
   - part: 3-computational-workflows.qmd
+    chapters:
+    - 3-1-version-control.qmd
+    - 3-2-stabilize.qmd
+    - 3-3-automate.qmd
   - part: 4-publishing-research.qmd
   - part: summary.qmd
     chapters: