Add page for highlighted references

_quarto.yml

@@ -45,10 +45,12 @@ book:
     - chapters/rewriting-history.qmd
     - misc/exercises.qmd
     - misc/cheatsheet.qmd
+    - misc/resources.qmd
     - misc/courses.qmd
     - misc/references.qmd
     - misc/acknowledgements.qmd
     - misc/contributing.qmd
+    # - misc/style-guide.qmd
   page-navigation: true
   back-to-top-navigation: true
   # side navigation (https://quarto.org/docs/websites/website-navigation.html#side-navigation):

misc/resources.qmd

@@ -0,0 +1,116 @@
+# Resources {.unnumbered}
+
+## Git for beginners
+
+### The Turing Way: Version Control
+
+The [Turing Way](https://www.turing.ac.uk/research/research-projects/turing-way) is a community-driven, open-source project developed by [The Alan Turing Institute](https://www.turing.ac.uk). 
+Its primary goal is to provide guidance on conducting reproducible, ethical, and collaborative data science. T
+The project aims to make data science accessible and inclusive by offering a set of resources, guidelines, and best practices.
+The Turing way handbook is organized into multiple chapters, each focusing on different aspects of data science and research methodology. 
+The chapter on Version Control in The Turing Way Handbook is dedicated to teaching users the fundamentals and benefits of using version control systems, with a particular focus on Git. 
+It not only teaches the technical aspects of version control but also embeds these practices within the broader context of reproducibility and collaboration in research.
+
+```{r}
+#| eval: true
+#| echo: false
+#| message: false
+#| warning: false
+#| output: asis
+bibtexkeys = c("community2022")
+knitr::kable(ref_table(bibtexkeys), format = "markdown")
+```
+
+### Software Carprentry: Version Control with Git
+
+[The Carpentries](https://carpentries.org) is a non-profit organization that teaches foundational coding, data science, and computational skills to researchers, scientists, educators, and data professionals. 
+The Carpentries organizes and runs workshops around the world, focusing on teaching foundational skills in programming, version control, data analysis, and more.
+[Software Carpentry](https://software-carpentry.org/lessons/index.html) is one of the key programs under the broader Carpentries umbrella, focused on teaching researchers and professionals foundational software skills that are essential for effective and reproducible computational research.
+The "Software Carpentry: Version Control" with Git session is a good, comprehensive and beginner-friendly introduction to Git.
+However, topics like branching strategies, rebasing, stashing, and cherry-picking, which are crucial for more complex workflows, are not covered. 
+
+```{r}
+#| eval: true
+#| echo: false
+#| message: false
+#| warning: false
+#| output: asis
+bibtexkeys = c("koziar2023")
+knitr::kable(ref_table(bibtexkeys), format = "markdown")
+```
+
+### Pro Git
+
+The Pro Git book is a standard resource for learning Git, offering a comprehensive and in-depth guide to version control with Git. 
+Written by Scott Chacon and Ben Straub, the book covers everything from the basics of Git to advanced topics like branching strategies, workflows, and Git internals. 
+The book is available for free online, making it an excellent resource for anyone looking to deepen their understanding of Git.
+However, the Pro Git book can be dense, and some sections may feel overwhelming for newcomers. Additionally, while it’s very thorough, users looking for quick, specific answers might find the book's extensive coverage a bit too detailed. 
+Despite these drawbacks, the Pro Git book is one of the best resources available for mastering Git.
+
+```{r}
+#| eval: true
+#| echo: false
+#| message: false
+#| warning: false
+#| output: asis
+bibtexkeys = c("chacon2014")
+knitr::kable(ref_table(bibtexkeys), format = "markdown")
+```
+
+## GitHub 
+
+### Official GitHub documentation
+
+The official GitHub resources are essential for anyone working with Git and GitHub. 
+They offer clear, detailed guidance on using GitHub for version control, collaboration, and project management, covering everything from basic Git commands to advanced features like Actions, Pull Requests, and Issues. 
+The documentation is well-organized and comprehensive.
+A downside is that the documentation can sometimes be overwhelming due to its depth and the wide range of topics it covers.
+
+```{r}
+#| eval: true
+#| echo: false
+#| message: false
+#| warning: false
+#| output: asis
+bibtexkeys = c("GitHub2023")
+knitr::kable(ref_table(bibtexkeys), format = "markdown")
+```
+
+## Git with R
+
+### Happy Git with R
+
+[Jennifer Bryan](https://jennybryan.org) is a prominent figure in the data science and statistics community, particularly known for her work in the R programming language. She is a statistician, data scientist, educator, and open-source advocate with a record in the fields of data analysis, data visualization, and reproducible research.
+"Happy Git with R" is a user-friendly guide authored by her that focuses on helping R users integrate Git and GitHub into their data science workflows. 
+The guide is particularly useful for those working in data science and using R, providing clear, step-by-step instructions on how to use version control and collaboration tools.
+
+
+```{r}
+#| eval: true
+#| echo: false
+#| message: false
+#| warning: false
+#| output: asis
+bibtexkeys = c("bryan2023")
+knitr::kable(ref_table(bibtexkeys), format = "markdown")
+```
+
+## DataLad
+
+[DataLad](https://www.datalad.org) is an open-source tool designed for the management, sharing, and reproducibility of large-scale data and code, particularly in research environments. 
+It builds on top of Git and [Git-annex](https://git-annex.branchable.com) to provide a version control system for data, making it easier for researchers to handle datasets that are too large to be efficiently managed by Git alone.
+
+### Official DataLad documentation
+
+The DataLad documentation is a comprehensive resource that provides users with guidance on how to use DataLad for managing, sharing, and reproducibly analyzing data.
+It is available online as the DataLad Handbook and is designed to be a practical, user-friendly guide for both beginners and advanced users of DataLad.
+
+```{r}
+#| eval: true
+#| echo: false
+#| message: false
+#| warning: false
+#| output: asis
+bibtexkeys = c("wagner2021")
+knitr::kable(ref_table(bibtexkeys), format = "markdown")
+```

references.bib

@@ -7,7 +7,7 @@ @book{community2022
 	publisher = {Zenodo},
 	doi = {10.5281/zenodo.3233853},
 	url = {https://zenodo.org/record/3233853},
-	note = {License: \href{https://creativecommons.org/licenses/by/4.0/}{CC BY 4.0}. Source: \url{https://github.com/the-turing-way/the-turing-way}. Website: \url{https://the-turing-way.netlify.app/}}
+	note = {License: \href{https://creativecommons.org/licenses/by/4.0/}{CC BY 4.0}. Source: \url{https://github.com/the-turing-way/the-turing-way}. Website: \url{https://book.the-turing-way.org/reproducible-research/vcs}}
 }
 
 @book{chacon2014,
@@ -68,7 +68,6 @@ @misc{mcbain2019
   note = {License: \href{http://creativecommons.org/licenses/by-sa/4.0/}{CC BY-SA 4.0}. Source: \url{https://github.com/MilesMcBain/git_4_sci/}. Website: \url{https://milesmcbain.github.io/git_4_sci/}}
 }
 
-
 @book{capes2023,
 	title = {swcarpentry/shell-novice: Software Carpentry: the UNIX shell},
 	author = {Capes, Gerard and {Bkmgit} and Deppen, Jacob and Devenyi, G. A. and Ball, Alexander James and Fowler-Wright, Piper and Visconti, Alessia and Dusenberry, Jeff and Vera, Jessica and Harrison, Randal Sean and Bilke, Andreas and Welch, Jessica Nicole and Thorp, Kelly and Hernandez, Alfredo and {Ashkan Mirzaee} and Winjum, Benjamin and Daley, Chris and Wright, Clay and {Colinmorris} and George, Dave and {Ephantus2017} and Myklebust, Erik and {Löffler}, Frank and {HariEpuri} and Wolff, Holger and {Kairsten Fay} and Reyes, Luna Luisa Sanchez and Politze, Marius and Belkin, Maxim and Porter, Nathaniel and {, Nkicg6} and Ziegner, Norman and Stevens, Sarah LR and McCartney, Sean and Njambi, Serah and {Ramisetti} and Borrego, Stacey and Brown, Andrew Christopher and Cryan, Ashley and {Mehrdadbn9} and {Md Intekhabul Hafiz} and {Niketagrawal} and Benson, Noah and McDivitt, Aaron and Budd, Aidan and Stahlke, Amanda and {Andra{\v{s}} T{\v{s}}it{\v{s}}kan} and Stewart, Andrew and Smith, Becky and Martlin, Catherine and {Knüpfer}, Christian and McKain, David and Wilby, David and Salmanidou, Dimitra and Turner, Dave and Scriven, Edan and Wallace, Edward and McAulay, Elizabeth and Roesch, Etienne and Solinsky, Frank and Lipari, Giordano and Starling, Hamish and Barrass, Iain and {Isil Poyraz Bilgin} and {JSheffield159} and Acris, James and Bradley, Jonathan and Juvonen, Matti and Napier, Kathryn and Ross, Kenton and Ernst, Kevin and Trombach, Lukas and Chorley, Martin and {, Melissa} and Lake, Mike and Renfro, Mike and Renfro, Mike and {NJ} and {, Natali} and McKinlay, Nathan and Soranzo, Nicola and {Rodríguez-Sánchez}, Pablo and Wiringa, Peter and Viktorin, Petr and Rigby, Richard and {, Rkm} and Elliott, Ryan S. and {Lelièvre}, Samuel and Lacalle, Santiago and Kumar, Sujai and Liang, Tong and Gatua, Winfred and Sun, Yi and {Cgmerrick} and {Daking4} and Patel, Deep and {Erich333} and {Karl-Holten} and {Kathymd} and {Laporpe} and {Naveendangeti} and {Nbehrnd} and {, Sophie} and {Tbert} and Couch, Tom and Shrestha, Ram Krishna and {Zzhang60} and {{"}Eli}},
@@ -82,7 +81,7 @@ @book{capes2023
 }
 
 @book{koziar2023,
-	title = {swcarpentry/git-novice: Software Carpentry: Version Control with Git 2023-05},
+	title = {Software Carpentry: Version Control with Git},
 	author = {Koziar, Katherine E. and {Madicken Munk} and Greene, Andrew and Rasel, Annajiat Alim and Bennett, Ed and Stevens, Sarah LR and Turnator, Ece and {Gorroño}, Jon Haitz Legarreta and Leinweber, Katrin and Nederbragt, Lex and {Lelièvre}, Samuel and {Vyas Ramasubramani} and Gitter, Anthony and Cassol, Daniela and Zhu, Judy and Soranzo, Nicola and Hejazi, Nima S and Deconinck, Wouter and {Laurentheirendt} and Clarke, Alison and Bressan, Camilla and Guan, Charles and Urizar, Cristina and Horsfall, Dave and {, David} and {, Deborah} and Lowther, Ed and {Fwoerister} and Bissey, {François} and {HaoZeke} and Kent, James and Holmes, Jessica and Huddleston, John and Lehtonen, Juho and Word, Karen and Lieret, Kilian and Modenese, Luca and Foscato, Marco and {Bjørnstad}, Marius and Matney, Mark and Juvonen, Matti and Belkin, Maxim and {Mingrui Yang} and Silantyeva, Olga and McCann, Patrick and Lanfear, Riley and Bartholomew, Sadie L. and Cox, Sam and Gruber, Scott and Jamieson, Stewart Christopher and Arabas, Sylwester and Russell, Tom and Koskela, Tuomas and {, Will} and Wolff, Benjamin and {, Catherinef37} and {Huijun ZHU} and {Kerimoff}},
 	year = {2023},
 	month = {05},
@@ -168,7 +167,7 @@ @book{GitHub2023
   year = {2023},
   publisher = {GitHub},
   url = {https://docs.github.com/en},
-  note = {License: \href{https://creativecommons.org/licenses/by-nc/4.0/}{CC BY-NC 4.0}. Source: \href{https://docs.github.com/en}{https://docs.github.com/en}}
+  note = {License: \href{https://creativecommons.org/licenses/by-nc/4.0/}{CC BY-NC 4.0}. Source: \url{https://docs.github.com/en}. Website: \url{https://docs.github.com/en}}
 }
 
 @article{blischak2016,
@@ -213,3 +212,13 @@ @online{amin2023
   url = {https://medium.com/@abhay.pixolo/naming-conventions-for-git-branches-a-cheatsheet-8549feca2534},
   note = {License: \href{NA}{NA}. Source: \url{NA}. Website: \url{https://medium.com/@abhay.pixolo/naming-conventions-for-git-branches-a-cheatsheet-8549feca2534}}
 }
+
+@book{wagner2021,
+  title        = {The DataLad Handbook},
+  author       = {DataLad Community},
+  year         = {2021},
+  publisher    = {DataLad},
+  url          = {https://handbook.datalad.org/},
+  doi          = {https://doi.org/10.5281/zenodo.3608611},
+  note = {License: \href{https://creativecommons.org/licenses/by-sa/4.0/}{CC BY-SA 4.0}. Source: \url{https://github.com/datalad-handbook/book?tab=License-1-ov-file}}
+}