Shorten the README chapter

CITATION.cff

@@ -17,6 +17,10 @@ authors:
     orcid: "https://orcid.org/0000-0002-8282-3910"
     affiliation: "LMU Munich"
     email: felix.schoenbrodt@psy.lmu.de
+  - given-names: Pat
+    family-names: Callahan
+    orcid: "https://orcid.org/0000-0003-1769-7580"
+    affiliation: "LMU Munich"
 
 title: "Code Publishing Tutorial"
 version: 0.1.0
@@ -36,12 +40,20 @@ preferred-citation:
     - given-names: Christoph
       family-names: Scheffel
       orcid: "https://orcid.org/0000-0001-5963-9229"
+    - given-names: Felix
+      family-names: Schönbrodt
+      orcid: "https://orcid.org/0000-0002-8282-3910"
+      affiliation: "LMU Munich"
+      email: felix.schoenbrodt@psy.lmu.de
+    - given-names: Pat
+      family-names: Callahan
+      orcid: "https://orcid.org/0000-0003-1769-7580"
+      affiliation: "LMU Munich"
   title: "Code Publishing Tutorial"
   year: 2025
   doi: "10.5281/zenodo.16631977"
   publisher:
     name: "LMU Open Science Center"
-    ror: "https://ror.org/029e6qe04"
   repository-code: "https://github.com/lmu-osc/code-publishing"
   url: "https://lmu-osc.github.io/code-publishing/"
   type: "book"

README.md

@@ -54,8 +54,8 @@ please read the [contributing notes](CONTRIBUTING.md) before.
 
 ## License
 
-Except where noted otherwise, the narrative text in this tutorial is licensed under [CC BY-SA 4.0][cc-by-sa];
-the code without any narrative text is also (at your option) available under [CC0 1.0][cc0].
+Except where noted otherwise, the narrative text in this tutorial is licensed under [CC\ BY-SA\ 4.0][cc-by-sa];
+the code without any narrative text is also (at your option) available under [CC0\ 1.0][cc0].
 
 [cc-by-sa]: LICENSE-CC-BY-SA.txt
 [cc0]: LICENSE-CC0.txt

_quarto.yml

@@ -1,19 +1,15 @@
 # Begin Project
 project:
   type: website
-  pre-render: wget -nc https://raw.githubusercontent.com/lmu-osc/branding-resources/refs/heads/main/lmu-osc-custom.scss
-  post-render: rm lmu-osc-custom.scss
 # End Project
 
-
-
 # Begin Website
 website:
   title: "Code Publishing Tutorial (Short version)"
   page-footer:
     center: |
       A recommended citation and license information for this tutorial
-      are provided on the [about page](about.qmd).
+      are provided on the [about page](/about.qmd).
     border: false
   search:
     location: sidebar
@@ -25,7 +21,6 @@ website:
   margin-header: |
     ![](/images/LMU-OSC_logo.jpg){width="175"}
 
-
   navbar:
     right:
       - about.qmd
@@ -36,9 +31,9 @@ website:
       - icon: github
         menu:
           - text: Source Code
-            url:  https://github.com/lmu-osc/code-publishing
+            url: https://github.com/lmu-osc/code-publishing
           - text: Report a Bug
-            url:  https://github.com/lmu-osc/code-publishing/issues
+            url: https://github.com/lmu-osc/code-publishing/issues
       - icon: house-heart
         url: https://www.osc.uni-muenchen.de/
 
@@ -53,22 +48,22 @@ website:
       - choose-license.qmd
       - make-readme.qmd
       - archive.qmd
-      - section: "💡 In-depth material"
+      - section: "Excursus: In-depth material 💡"
         contents:
           - href: in_depth_material/introduction_copyright.qmd
             text: "Introduction to Copyright and Licensing"
           - href: in_depth_material/data_dic_generation.qmd
             text: "Automatic Generation of Data Dictionaries"
+          - href: in_depth_material/other_dependencies.qmd
+            text: "Identify additional system dependencies for the README"
 # End Website
 
-
 # Begin Format
 format:
   html:
     theme:
       - cosmo
-      - lmu-osc-custom.scss
-    css: 
+    css:
       - https://raw.githubusercontent.com/lmu-osc/branding-resources/refs/heads/main/lmu-osc-styles.css
     toc: true
     fontsize: 13pt
@@ -80,7 +75,6 @@ format:
       - file: matomo_analytics.html
 # End Format
 
-
 csl: apa.csl
 bibliography: literature.bib
-lang: en-US
+lang: en-US

choose-license.qmd

@@ -562,9 +562,9 @@ while the bibliography is made available under CC0\ 1.0.
 [agpl]: https://www.gnu.org/licenses/agpl-3.0.html
 
 ```{.txt .code-overflow-wrap filename="LICENSE.txt"}
-The Quarto documents stored in "Manuscript.qmd", "Manuscript.tex", and "Manuscript.pdf" by Josephine Zerna, Christoph Scheffel, and <YOUR NAME> are available under AGPLv3 (or later) <https://www.gnu.org/licenses/agpl-3.0.html> or (at your option) under CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0/>.
+The Quarto documents stored in "Manuscript.qmd", "Manuscript.tex", and "Manuscript.pdf" by Josephine Zerna, Christoph Scheffel, and <YOUR NAME> are available under AGPLv3 (or later) <https://www.gnu.org/licenses/agpl-3.0.html> or (at your option) under CC\ BY-SA\ 4.0 <https://creativecommons.org/licenses/by-sa/4.0/>.
 
-The bibliography (stored in "Bibliography.bib") by Florian Kohrt and <YOUR NAME> is available under CC0 1.0 <https://creativecommons.org/publicdomain/zero/1.0/>.
+The bibliography (stored in "Bibliography.bib") by Florian Kohrt and <YOUR NAME> is available under CC0\ 1.0 <https://creativecommons.org/publicdomain/zero/1.0/>.
 ```
 
 As the AGPLv3 requires reusers adding the [full license text](https://www.gnu.org/licenses/agpl-3.0.txt),

code.qmd

@@ -275,7 +275,7 @@ We recommend adding a short paragraph to `LICENSE.txt` to describe its license.
 It is best to provide attribution even if the license does not require it.
 
 ```{.txt .code-overflow-wrap filename="LICENSE.txt"}
-"apaquarto" stored in "_extensions/wjschne/apaquarto" by W. Joel Schneider available from <https://github.com/wjschne/apaquarto> is licensed under CC0 1.0: <https://creativecommons.org/publicdomain/zero/1.0/>
+"apaquarto" stored in "_extensions/wjschne/apaquarto" by W. Joel Schneider available from <https://github.com/wjschne/apaquarto> is licensed under CC0\ 1.0: <https://creativecommons.org/publicdomain/zero/1.0/>
 ```
 
 Again, if the license required adding the full license text,

copyright.qmd

@@ -530,7 +530,7 @@ Also, their commercial use may require the consent of the depicted person.
 
 [commons-photographs]: https://commons.wikimedia.org/wiki/Commons:Photographs_of_identifiable_people
 
-## ✍️ Practical Exercise: Adding an Image
+## Practical Exercise: Adding an Image
 
 Let's practice what you learned by adding an image to the manuscript.
 We'll use [this picture of a penguin from Flickr](https://flic.kr/p/2pEKnUr).
@@ -566,20 +566,20 @@ we still recommend providing proper attribution.
 - Copyright notice: (not available)
 - Title of the work: `Chinstrap Penguin`
   - Link to the work: <https://www.flickr.com/photos/192320315@N02/53603388557/> or <https://flic.kr/p/2pEKnUr>
-- License name: `CC0 1.0`
+- License name: `CC0\ 1.0`
   - Link to the license: <https://creativecommons.org/publicdomain/zero/1.0/>
 - Link to warranty disclaimer: (not available)
 - Indicate modification: (no existing modification notices)
 
 ```{.md .code-overflow-wrap}
-!["[Chinstrap Penguin](https://flic.kr/p/2pEKnUr)" by "steve b" licensed under [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/)](penguin.jpg){width=50%}
+!["[Chinstrap Penguin](https://flic.kr/p/2pEKnUr)" by "steve b" licensed under [CC0\ 1.0](https://creativecommons.org/publicdomain/zero/1.0/)](penguin.jpg){width=50%}
 ```
 
 If it is likely that the article gets printed,
 you might want to ensure that the link to the work is retained in that case:
 
 ```{.md .code-overflow-wrap}
-!["[Chinstrap Penguin](https://flic.kr/p/2pEKnUr)" by "steve b" available under [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/) from [`flic.kr/p/2pEKnUr`](https://flic.kr/p/2pEKnUr)](penguin.jpg){width=50%}
+!["[Chinstrap Penguin](https://flic.kr/p/2pEKnUr)" by "steve b" available under [CC0\ 1.0](https://creativecommons.org/publicdomain/zero/1.0/) from [`flic.kr/p/2pEKnUr`](https://flic.kr/p/2pEKnUr)](penguin.jpg){width=50%}
 ```
 :::
 
@@ -597,7 +597,7 @@ then on _File_ > _Save_, and choose `LICENSE.txt` as filename.
 The license description can be worded as follows:
 
 ```{.txt .code-overflow-wrap filename="LICENSE.txt"}
-"Chinstrap Penguin" stored in "penguin.jpg" by "steve b" available from <https://flic.kr/p/2pEKnUr> is licensed under CC0 1.0: <https://creativecommons.org/publicdomain/zero/1.0/>
+"Chinstrap Penguin" stored in "penguin.jpg" by "steve b" available from <https://flic.kr/p/2pEKnUr> is licensed under CC0\ 1.0: <https://creativecommons.org/publicdomain/zero/1.0/>
 ```
 
 If the license required adding the full license text,

data.qmd

@@ -116,7 +116,7 @@ Here's an example from a different data set, with variables in rows, and the dic
 | life_satisfaction | Life Satisfaction         | integer | "How satisfied are you with your life?" | 1 = Very dissatisfied; 2 = Dissatisfied; 3 = Neutral; 4 = Satisfied; 5 = Very satisfied | scale (1–5) | -99 = Not answered |
 
 
-### ✍️ Practical Exercise: Add your own data dictionary
+### Practical Exercise: Add your own data dictionary
 
 Now go ahead and create a data dictionary for the penguins data set, 
 in a software (text or spreadsheet) of your choice.
@@ -139,7 +139,7 @@ Save the data dictionary in the same folder as the actual data set file.
 
 :::
 
-## ✍️ Practical Exercise: Add Data Citation and Attribution
+## Practical Exercise: Add Data Citation and Attribution
 
 All data relied upon should be cited in the manuscript
 to allow for precise identification and access.

in_depth_material/introduction_copyright.qmd

@@ -16,7 +16,7 @@ format:
           </style>
 ---
 
-**Note: This is an expanded version of the Chapter "[Sharing work of others: Copyright](/copyright.qmd)". Here you find more details on the choice of licenses.**
+*Note: This is an expanded version of the Chapter "[Sharing work of others: Copyright](/copyright.qmd)". Here you find more details on the choice of licenses.*
 
 By default, everything you put into the project folder will be shared publicly.
 In many instances, this will also include works by others than yourself or your co-authors,
@@ -178,15 +178,15 @@ for which the open editing phase began in 2006.
 They are largely viewed as compatible with one another.
 
 :::: {.column-margin}
-![](images/Definition_of_Free_Cultural_Works.svg){width=250px}
+![](/images/Definition_of_Free_Cultural_Works.svg){width=250px}
 ::::
 :::
 
 ### Can I Share That Work?
 
 To determine whether a particular work can be included in the project folder
 and shared publicly, the first step is to search for its license.
-For example, this tutorial has an [about page](../about.qmd) detailing its licensing,
+For example, this tutorial has an [about page](/about.qmd) detailing its licensing,
 whereas other websites sometimes state the license in the footer.
 Other places to look include a project's `README` file or a dedicated `LICENSE` or `COPYING` file.
 If a project has been stored in a research repository,

in_depth_material/other_dependencies.qmd

@@ -0,0 +1,96 @@
+---
+title: "Identify additional system dependencies for the README"
+engine: knitr
+---
+
+The specific version of R and the loaded packages is the most crucial information that should go into the README (or that is stored in the `renv` lockfile). Ideally, you list other system dependencies, such as the version of Quarto[^renv-quarto] that you used to render your paper.
+
+[^renv-quarto]: As of August 2024, a proposal for `renv` to record the version of Quarto
+has not been implemented, see [rstudio/renv#1143](https://github.com/rstudio/renv/issues/1143).
+
+An overview over the system dependencies of R packages can be created
+using the function `pak::pkg_sysreqs()`.
+In combination with `renv`, we can obtain the system dependencies
+of all R packages the current project directly depends on:
+
+```{.r filename="Console"}
+# Find all R package dependencies
+deps <- renv::dependencies()$Package |>
+  unique() |>
+  pak::pkg_deps(dependencies = NA) |>
+  getElement("package")
+
+# Identify their system dependencies
+pak::pkg_sysreqs(deps)
+```
+
+The output may look like the following:
+
+```txt
+── Install scripts ────────────────── Fedora 40 ── 
+dnf install -y make pandoc git
+
+── Packages and their system dependencies ────────
+fs        – make
+knitr     – pandoc
+remotes   – git
+rmarkdown – pandoc
+sass      – make
+```
+
+We can see that the programs `make`, `pandoc`,
+and `git` were identified as system dependencies.
+Often, one can obtain their version by running them with the `--version` argument:
+
+```{.bash filename="Terminal"}
+make --version
+pandoc --version
+git --version
+```
+
+However, this does not work for all system dependencies.
+Specifically, it does not work for libraries -- software that is not supposed to be run on its own.
+Identifying their version is beyond the scope of this tutorial.
+
+We also know that we need Quarto to create the PDF,
+so let's find out its version as well:
+
+```{.bash filename="Terminal"}
+quarto --version
+```
+
+If you installed `apaquarto` or any other Quarto extension,
+one can query their versions as follows:[^already-included]
+
+[^already-included]: Luckily, the extensions are included in the project folder,
+so technically their version is already recorded in the project's files.
+
+```{.bash filename="Terminal"}
+quarto list extensions
+```
+
+Finally, we know that we installed a $\TeX$ distribution to create the PDF,
+so let's find out its version by running:
+
+```{.bash filename="Terminal"}
+quarto check
+```
+
+The output is quite long and it might look slightly different for you,
+but the relevant sections are the following:
+
+```txt
+[✓] Checking tools....................OK
+      TinyTeX: v2024.09
+      Chromium: (not installed)
+
+[✓] Checking LaTeX....................OK
+      Using: TinyTex
+      Path: /home/r155953/.TinyTeX/bin/x86_64-linux
+      Version: 2024
+```
+
+Add these dependencies to the section **Computational Requirements / Dependencies** of your README file.
+
+Of course, all the system dependencies identified until now
+may have dependencies on their own. Use your own judgement to decide when not to dig deeper.