Merge branch 'main' of https://github.com/cct-datascience/repro-data-sci

colloquium.qmd

@@ -0,0 +1,39 @@
+---
+title: "Reproducibility Colloquium"
+---
+
+The [final session](index.qmd#schedule) of this workshop series is our ✨**Reproducibility Colloquium**✨, where you all get a chance to share what you've learned with each other and anyone you'd like to invite to attend.
+You are invited to give a short (about 5min) talk with slides (about 5).
+To make this as low stakes as possible, here is an outline you may follow when putting together your presentation.
+
+::: callout-important
+For each slide, you don't need to address **all** of the bullet points—focus on what is relevant for the specific aspects of your project you focused on!
+:::
+
+::: callout-note
+Feel free to adapt this outline—add or remove slides as fits your project.
+:::
+
+-   Slide 1: Super short description of your project for a ***general audience.***[^1]
+-   Slide 2: Describe the data and code components of your project.
+    -   What data types/sources do you work with?
+        -   Hand-collected field data? A data compilation? Instrument data?
+        -   Data type (e.g., numeric, survey responses, DNA sequences, geospatial)?
+        -   File types and sizes?
+    -   What computational tools are you using, and what are you using them for?
+        -   e.g. Excel for data entry; R for data cleaning and analysis; Illustrator for polishing figures
+-   Slide 3: Which aspects of the project did you focus on improving? What was the state of the project before the "makeover"?
+    -   e.g. "I focused on transitioning to using git for version control; previously, I was saving my scripts with a new name each time I worked on them."
+    -   Screen shots of the "before" are encouraged as visuals
+-   Slide 4: What changes did you make as part of the "makeover"?
+    -   Why did you focus on these?
+    -   How did you implement the changes?
+    -   Screen shots of the "after" are encouraged as visuals
+-   Slide 5: Reflections
+    -   What are you most proud of about this?
+    -   Did you run into any challenges?
+    -   What do you see as the next steps?
+
+[^1]: This is a good opportunity to practice an elevator pitch!
+    Try to keep it to just a couple sentences—just enough background to give some context to your data and code.
+    The goal of the presentation is to focus on your project organization and reproducibility, *not* the details of your research topic.

index.qmd

@@ -12,8 +12,7 @@ Welcome to the syllabus for the CCT Data Science fall workshop series: **Reprodu
 
 We'll meet on Tuesdays and Thursdays from 11am to 1pm via Zoom (link pinned in Slack channel)
 
-
-<!-- Edit by editing schedule.csv. To add links, use markdown [text](url) separated by commas. This code turns that into a bulleted list.-->
+<!-- Edit by editing schedule.csv. To add links, use markdown [text](url) separated by commas. This code turns that into a bulleted list. -->
 
 ```{r}
 #| echo: false

lessons/1-project-management/notes.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Project Management and Documentation"
-format: html
+format: 
+  html: default
+  typst: default
 ---
 
 ## Objective

lessons/10-get-credit/notes.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Getting Credit For Your Hard Work"
-format: html
+format: 
+  html: default
+  typst: default
 bibliography: references.bib
 ---
 

lessons/11-getting-help/notes.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Getting help"
-format: html
+format: 
+  html: default
+  typst: default
 ---
 
 [Slides](slides.qmd)

lessons/12-drop-in/notes.qmd

@@ -1,5 +1,8 @@
 ---
 title: "Drop-in / Q&A"
+format: 
+  html: default
+  typst: default
 ---
 
 We asked learners to vote on the following topics for a mini-lesson for the last session before the show-and-tell session:

lessons/2-markdown-quarto/notes.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Documentation and Literate Programming"
-format: html
+format: 
+  html: default
+  typst: default
 ---
 
 ## Objective

lessons/3-shell/notes.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Using the Shell"
-format: html
+format: 
+  html: default
+  typst: default
 ---
 
 ## Objectives

lessons/4-git/notes.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Version control with git"
-format: html
+format: 
+  html: default
+  typst: default
 ---
 
 ## Objective
@@ -24,10 +26,10 @@ format: html
     -   SW Carpentry Git lesson 2 https://swcarpentry.github.io/git-novice/02-setup
     -   Setting up git using git config
         -   Make sure participants use their GH email/intended GH email
-        - `git` `verb` `options`
-        - `git config --global core.editor "vim"`
-        - `git` `verb` `--help`
--   Live coding: git init 
+        -   `git` `verb` `options`
+        -   `git config --global core.editor "vim"`
+        -   `git` `verb` `--help`
+-   Live coding: git init
     -   SW Carpentry Git lesson 3 https://swcarpentry.github.io/git-novice/03-create.html
     -   Introduce the concept of a repository
     -   Go over 3 ways to init a git repo and when to use each
@@ -49,8 +51,8 @@ format: html
 -   Live coding: `.gitignore`
     -   SW Carpentry Git lesson 6https://swcarpentry.github.io/git-novice/06-ignore
     -   .gitignore:
-        - `DS_Store`
-        - Create a file and then ignore it.
+        -   `DS_Store`
+        -   Create a file and then ignore it.
 -   (Time permitting): SW Carpentry Git lesson 5
     -   https://swcarpentry.github.io/git-novice/05-history
     -   Navigating git history
@@ -67,6 +69,7 @@ format: html
 5.  [Software Carpentry Version Control with Git episode #6](https://swcarpentry.github.io/git-novice/06-ignore)
 6.  (optional) [Software Carpentry Version Control with Git episode #5](https://swcarpentry.github.io/git-novice/05-history)
 
+```{=html}
 <!---
  
 ## Notes from before
@@ -97,4 +100,5 @@ Warm up with the review question in slide deck.
 Create a GitHub account if you don't already have one.
 For an extra challenge, identify an existing folder and turn into a repository.
  
---->
+--->
+```

lessons/5-github-basics/notes.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Developing Code on Github"
-format: html
+format: 
+  html: default
+  typst: default
 ---
 
 ## Objective

lessons/5-github-basics/slides.qmd

@@ -36,6 +36,10 @@ bibliography: references.bib
 
 The most common git commands can be used with the RStudio GUI.
 
+::: notes
+Demo save, add, commit cycle with Git pane AND git menu in RStudio
+:::
+
 ## Sharing with GitHub
 
 ![](github-diagram-bryan.png){fig-align="center" width="671"}
@@ -57,11 +61,25 @@ Figure 2 from [@bryan2018]
 -   Connect your local git repo to a remote GitHub repo with `use_github()`
 -   Explore the GitHub interface
 
+::: notes
+Demo "starting from scratch" by running `gitcreds::gitcreds_delete()`.
+Remember to delete the PAT you create and show on camera.\
+
+\
+Remind learners that repos can be private.
+`use_github(private = TRUE)`
+:::
+
 ## Work With RStudio and GitHub (Live Coding)
 
 -   Push local changes to GitHub
 -   Pull GitHub changes to local
 
+::: notes
+Demo save, add, commit, push and check GitHub for changes.
+Then, edit README on github and pull changes.
+:::
+
 ## Ignoring files {.smaller}
 
 ::: incremental
@@ -91,6 +109,10 @@ Can use .gitkeep to get git to track an empty folder.
 -   Put your research compendium on GitHub (e.g. with `use_github()`) and share the link in our Slack channel (if it can be made public)
 -   Explore other research compendia shared in Slack
 
+::: notes
+If there is extra time, encourage learners to use it to practice these new skills with a *real* project repo while you're all still there to help troubleshoot.
+:::
+
 ## References
 
 ::: refs

lessons/6-github-collab/notes.qmd

@@ -1,6 +1,9 @@
 ---
 title: "Collaborating with GitHub"
-format: html
+format:
+  typst: 
+    output-file: "lesson-6-notes.pdf"
+  html: default
 ---
 
 ## Objective

lessons/6-github-collab/slides.qmd

@@ -52,7 +52,7 @@ Ask for a volunteer and give them permission to push to a repo
 
 ## Example repo
 
--   Everyone practice cloning this example repo as a new RStudio project: <https://github.com/cct-datascience/repro-workshop-demo> [^1]
+-   Everyone practice cloning this example repo as a new RStudio project: <https://github.com/cct-datascience/demo-repo-2024> [^1]
 
 -   Need **one** volunteer to edit the README.md and practice commit + push
 
@@ -92,19 +92,19 @@ git config --global pull.rebase false
 
 ![](merge_conflict.png)
 
--   Resolve the conflict however you want (i.e. keep one of the two sections)
+1.  Resolve the conflict however you want (i.e. keep one of the two sections)
 
--   Delete all lines with `<<<<<<<`, `>>>>>>>`, or `=======`
+2.  Delete all lines with `<<<<<<<`, `>>>>>>>`, or `=======`
 
--   Save and commit
+3.  Save and commit
 
 ::: notes
 Let's have a round of applause for our volunteer!
 :::
 
 ## Avoid merge conflicts by working on branches
 
-Each person works on a "branch"---an independent series of commits that can be merged back into the "main" branch.
+Each person works on a "branch"—an independent series of commits that can be merged back into the "main" branch.
 
 ```{mermaid}
 gitGraph
@@ -129,10 +129,25 @@ gitGraph
 
 -   Make a new branch using RStudio's Git pane (for this demo, use your name)
 
--   Commit changes and push to your branch
+-   Make some edits (e.g. to README.md), save, add, commit.
+
+-   You can go back to the "main" version of your project at any time.
+
+::: notes
+Demonstrate how switching branches changes the files on their computer.
+Hammer home that this is why it is a bad idea to use git for projects on shared drives.
+:::
+
+## Working on a Branch
+
+-   Push your branch to GitHub
 
 -   View changes on GitHub
 
+::: notes
+Show how to look at different branches on GitHub
+:::
+
 ## Pull Requests
 
 A request to merge changes into the main branch
@@ -187,7 +202,7 @@ Learn more, including handy `usethis` shortcuts: <https://happygitwithr.com/fork
 ::: callout-tip
 ## Exercise
 
-In pairs, practice **forking** and **cloning** a demo repo you do *not* have permission to push to.
+In pairs, practice **forking** and **cloning** a demo repo you do *not* have permission to push to: <https://github.com/cct-datascience/demo-repo-fork-2024>.\
 Make a new branch, make commits, and make a pull request to the upstream repo.
 :::
 

lessons/7-data-manipulation/lesson_script.R

@@ -25,7 +25,7 @@ penguins_data <- penguins
 
 write.csv(
   penguins_data,
-  "lessons/7-data-manipulation/data_raw/penguins_data_raw.csv",
+  "penguins_data_raw.csv",
   row.names = F
 )
 
@@ -142,7 +142,7 @@ ggplot(penguins_coords, aes(longitude, body_mass_g, color = species)) +
 
 #### Modify - add - commit ####
 
-# adds penguins + penguins_long to repo
+# adds penguins_data_raw repo
 # commit and push
 
 #### Palmer penguins citation ####

lessons/7-data-manipulation/notes.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Data manipulation"
-format: html
+format: 
+  html: default
+  typst: default
 ---
 
 ## Objective

lessons/8-intermediate-r-1/notes.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Intermediate R programming I"
-format: html
+format: 
+  html: default
+  typst: default
 ---
 
 ## Objective

lessons/9-intermediate-r-2/notes.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Intermediate R programming II"
-format: html
+format: 
+  html: default
+  typst: default
 ---
 
 ## Objective

schedule.csv

@@ -10,4 +10,4 @@ Lesson,Date,Theme,Topic,Links,Notes
 9,2024-10-01,Repeat & Reproduce,Intermediate R programming II,,iteration (and anonymous functions)
 10,2024-10-03,Document & Publish,Getting credit for your hard work,,"renv, LICENSE, CITATION.cff, Zenodo, GitHub releases"
 11,2024-10-08,Review,Drop-in co-working,,
-12,2024-10-10,Reproducibility Colloquium,An opportunity for you to show off what you've learned,,
+12,2024-10-10,Reproducibility Colloquium,An opportunity for you to show off what you've learned,[guidelines](colloquium.html),