make rerelease changes part 2

episodes/01-basics.md

@@ -60,19 +60,19 @@
 Google Docs' [version history](https://support.google.com/docs/answer/190843?hl=en), or
 LibreOffice's [Recording and Displaying Changes](https://help.libreoffice.org/Common/Recording_and_Displaying_Changes). Let's illustrate how Google Docs works.
 
 ![Tracking changes for the `git-test` file.](fig/gdocs-01.png)
 
 To use Google Docs version history click `File` > `Version history` > `See version history`. This highlights the new content added to the file in that version only.
 
 ![The most recent version of the `git-test` file is called "third version".](fig/gdocs-03.png)
 
 We can move to any previous version tagged with two metadata values: the modification date and the name of the author.
 
 ![We can view the "first version" of the file `git-test`. We can also restore it with the `Restore this version` button.](fig/gdocs-04.png)
 
 Google Docs’ version history tool is an automatic Version control system for single Word/Doc files that works online.
 
 ![The Turing Way project illustration by Scriberia. Used under a CC-BY 4.0 licence. DOI: <https://zenodo.org/doi/10.5281/zenodo.3332807>.](fig/ProjectHistory.jpg)
 
 ## Version control systems
 
@@ -165,24 +165,34 @@
 
 Plain text files can be text, code, and data. Example for each of these are Markdown files (`.md`), R files (`.R`), and `.csv` or `.tsv` files, respectively.
 
 ![Examples of non-plain and plain text files.](fig/plain-text-files.png)
 
 ::::::::::::::::: callout
 
-We can use `Git` to track changes of these plain text files. However, for [plain text data files](https://www.r4epi.com/importing-plain-text-files.html) (like `.csv` and `.tsv`) we prefer different version control systems.
+### data files
+
+We can use `Git` to track changes of **data files** (like `.csv` and `.tsv`). However, if we consider data files as **raw files**, which should not change in time, then we may not be needed to use Git with them. We'll take a look into this in the chapter on [Ignoring things](06-ignore.md).
+
+Also, if you consider your data file **large** with respect to your computer, you can opt to use: 
+
+- a file hosting service like Google Drive and the [`{googlesheets4}` R package](https://r4ds.hadley.nz/spreadsheets#google-sheets) to import data, 
+- a different version control system like [Git Large File Storage (LFS)](https://git-lfs.github.com/), or 
+- a different data format like the `parquet` format using [the `{arrow}` R package](https://r4ds.hadley.nz/arrow.html).
+
+<!-- [plain text data files](https://www.r4epi.com/importing-plain-text-files.html) -->
 
 :::::::::::::::::::::::::
 
 Plain text files like Markdown files (`.md`) and R files (`.R`) are integrated in Rmarkdown files (`.Rmd`) to generate manuscripts, websites, and R packages. These three products are outputs of **Open Science** projects, that leads to *Reproducible research* and *Sustainable software*.
 
 
 ![We can increase the reproducibility of our Open science projects with version control sytems like `Git`. Text and final results can be connected and executable by Data and code. From: "Ciencia reproducible: qué, por qué, cómo" <https://www.revistaecosistemas.net/index.php/ecosistemas/article/view/1178>](fig/gradient-reproducibility.png)
 
 ::::::::::::::::::: instructor
 
 ### Concept map
 
 ![Concept map for automatic version control.](fig/git-concept-03.drawio.png)
 
 ::::::::::::::::::::::::::::::
 

episodes/02-setup.md

@@ -45,7 +45,7 @@
 
 In this episode, we are going to use the [Rstudio Console](https://docs.posit.co/ide/user/ide/guide/code/console.html).
 
 ![Visual appearance of the Console.](fig/rstudio-tab-console.png)
 
 ::::::::::::::::::::::::::
 
@@ -100,7 +100,7 @@
 
 :::::::::::::::::::::::::::::::::::::::::  callout
 
-## Keeping your email private
+### Keeping your email private
 
 If you elect to use a private email address with GitHub, then use that same email address for the `user.email` value, e.g. `[email protected]` replacing `username` with your GitHub one.
 
@@ -197,12 +197,14 @@
 
  Click “Generate token”.
 
 ![Visual display with the recommended scopes selected. Optional scopes are "gist" and "delete_repo" to create a [gist](https://docs.github.com/en/get-started/writing-on-github/editing-and-sharing-content-with-gists/creating-gists) and delete repositories.](fig/git-token.png)
 
 Copy your token. Save it for the next step.
 
 ::::::::::::::::: callout
 
+### token options
+
 Briefly:
 
 - `"repo"` will give you control of your _private_ repositories online (YES! you can have private repos!).

episodes/04-changes.md

@@ -573,6 +573,86 @@ than you would like!
 
 :::::::::::::::::::::::::::
 
+## Group Challenges
+
+:::::::::::::::::::::::::::::::::::::::  challenge
+
+## Choosing a Commit Message
+
+Which of the following commit messages would be most appropriate for the
+last commit made to `sitrep.Rmd`?
+
+1. "Changes"
+2. "Added line 'Maps illustrate the spread and impact of outbreak' to sitrep.Rmd"
+3. "Discuss effects of Sitrep' climate on the Mummy"
+
+:::::::::::::::  solution
+
+## Solution
+
+Answer 1 is not descriptive enough, and the purpose of the commit is unclear;
+and answer 2 is redundant to using "git diff" to see what changed in this commit;
+but answer 3 is good: short, descriptive, and imperative.
+
+
+
+:::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+:::::::::::::::::::::::::::::::::::::::  challenge
+
+## Committing Changes to Git
+
+Which command(s) below would save the changes of `myfile.txt`
+to my local Git repository?
+
+1. ```bash
+  $ git commit -m "my recent changes"
+  ```
+2. ```bash
+  $ git init myfile.txt
+  $ git commit -m "my recent changes"
+  ```
+3. ```bash
+  $ git add myfile.txt
+  $ git commit -m "my recent changes"
+  ```
+4. ```bash
+  $ git commit -m myfile.txt "my recent changes"
+  ```
+
+:::::::::::::::  solution
+
+## Solution
+
+1. Would only create a commit if files have already been staged.
+2. Would try to create a new repository.
+3. Is correct: first add the file to the staging area, then commit.
+4. Would try to commit a file "my recent changes" with the message myfile.txt.
+
+
+
+:::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+::::::::::::::::::::::::::: testimonial
+
+### Your turn!
+
+Take 10 minutes to the following two sections:
+
+- Practice the workflow
+- Relevant callouts
+
+If you want to keep practicing, move to the last one:
+
+- Individual Challenges
+
+:::::::::::::::::::::::::::
+
 ## Practice the workflow
 
 Let's watch as our changes to a file move from our editor to the staging area and into long-term storage. First, __in the Console__, we'll add another line to the file:
@@ -831,69 +911,7 @@ repository (`git commit`):
 
 ![](fig/git-committing.svg){alt='The Git Commit Workflow'}
 
-## Challenges
-
-:::::::::::::::::::::::::::::::::::::::  challenge
-
-## Choosing a Commit Message
-
-Which of the following commit messages would be most appropriate for the
-last commit made to `sitrep.Rmd`?
-
-1. "Changes"
-2. "Added line 'Maps illustrate the spread and impact of outbreak' to sitrep.Rmd"
-3. "Discuss effects of Sitrep' climate on the Mummy"
-
-:::::::::::::::  solution
-
-## Solution
-
-Answer 1 is not descriptive enough, and the purpose of the commit is unclear;
-and answer 2 is redundant to using "git diff" to see what changed in this commit;
-but answer 3 is good: short, descriptive, and imperative.
-
-
-
-:::::::::::::::::::::::::
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-:::::::::::::::::::::::::::::::::::::::  challenge
-
-## Committing Changes to Git
-
-Which command(s) below would save the changes of `myfile.txt`
-to my local Git repository?
-
-1. ```bash
-  $ git commit -m "my recent changes"
-  ```
-2. ```bash
-  $ git init myfile.txt
-  $ git commit -m "my recent changes"
-  ```
-3. ```bash
-  $ git add myfile.txt
-  $ git commit -m "my recent changes"
-  ```
-4. ```bash
-  $ git commit -m myfile.txt "my recent changes"
-  ```
-
-:::::::::::::::  solution
-
-## Solution
-
-1. Would only create a commit if files have already been staged.
-2. Would try to create a new repository.
-3. Is correct: first add the file to the staging area, then commit.
-4. Would try to commit a file "my recent changes" with the message myfile.txt.
-
-
-
-:::::::::::::::::::::::::
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
+## Individual Challenges
 
 :::::::::::::::::::::::::::::::::::::::  challenge
 

episodes/06-ignore.md

@@ -133,6 +133,10 @@ a.csv
 Use -f if you really want to add them.
 ```
 
+::::::::::::::::::::::: spoiler
+
+### How to override our ignore settings?
+
 If we really want to override our ignore settings,
 we can use `git add -f` to force Git to add something. For example,
 `git add -f a.csv`.
@@ -155,6 +159,8 @@ Ignored files:
 nothing to commit, working tree clean
 ```
 
+:::::::::::::::::::::::
+
 ::::::::::::::::: checklist
 
 ### Good Practice
@@ -169,7 +175,22 @@ A good version control project:
 
 :::::::::::::::::::::::::::
 
-## Challenges
+::::::::::::::::::::::::::: testimonial
+
+### Your turn!
+
+Take 5 minutes to the following two challenges:
+
+- Ignoring Nested Files
+- Including Specific Files
+
+If you want to keep practicing, move to the last one:
+
+- Home challenges
+
+:::::::::::::::::::::::::::
+
+## Live challenges
 
 :::::::::::::::::::::::::::::::::::::::  challenge
 
@@ -229,7 +250,7 @@ How would you ignore all `.csv` files in your root directory except for
 
 ::::::::::::::: hint
 
-Find out what `!` (the exclamation point operator) does in the [Git Reference documentation](../learners/reference.md) for `gitignore`.
+Find out what `!` (the exclamation point operator) does for `gitignore` in the [Git Reference documentation](../learners/reference.md).
 
 :::::::::::::::
 
@@ -256,6 +277,8 @@ of `.csv` files added to the root directory will be ignored.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
+## Home challenges
+
 :::::::::::::::::::::::::::::::::::::::  challenge
 
 ## Ignoring Nested Files: Variation