docs(sessions): add execution location context to code blocks

preamble/pre-course.qmd

@@ -117,6 +117,7 @@ haven't used it, please do these tasks:
     type in the RStudio Console:
 
     ``` r
+    #| filename: Console
     # A pop-up to type in your name (first and last), 
     # as well as your email
     r3::setup_git_config()
@@ -138,6 +139,7 @@ Regardless of whether you've done the steps above or not, *everyone*
 needs to run:
 
 ``` r
+#| filename: Console
 r3::check_setup()
 ```
 
@@ -204,6 +206,7 @@ by either:
     `prodigenr::setup_project("~/Desktop/LearnR3")` in the R Console.
 
 ```{r admin-create-project}
+#| filename: Console
 #| include: false
 prodigenr::setup_project(project_path)
 ```
@@ -212,6 +215,7 @@ When the RStudio Project opens up again, run these three commands in the
 R Console:
 
 ``` r
+#| filename: Console
 prodigenr::setup_with_git()
 usethis::use_blank_slate()
 usethis::use_r("functions", open = FALSE)
@@ -253,6 +257,7 @@ analysis. Please do these two tasks:
     `learning.qmd` in the `doc/` folder.
 
     ``` r
+    #| filename: Console
     r3::create_qmd_doc()
     ```
 
@@ -300,6 +305,7 @@ the dataset to prepare it for later processing. While in your `LearnR3`
 R Project, go to the Console pane in RStudio and type out:
 
 ``` r
+#| filename: Console
 usethis::use_data_raw("mmash")
 ```
 
@@ -324,6 +330,7 @@ added there by default. Then we'll create a new line at the top and type
 out:
 
 ```{r data-raw-script-add-here}
+#| filename: "data-raw/mmash.R"
 library(here)
 ```
 
@@ -365,6 +372,7 @@ function from the `{fs}` package, which means "filesystem", by running
 the following code in the R Console:
 
 ``` r
+#| filename: "Console"
 # To print the file list.
 fs::dir_tree("~/Desktop/LearnR3", recurse = 1)
 ```
@@ -384,6 +392,7 @@ Alright, the next step is to download the dataset. Paste this code into
 the `data-raw/mmash.R` script:
 
 ``` r
+#| filename: "data-raw/mmash.R"
 mmash_link <- "https://physionet.org/static/published-projects/mmash/multilevel-monitoring-of-activity-and-sleep-in-healthy-people-1.0.0.zip"
 ```
 
@@ -398,6 +407,7 @@ be written in the `data-raw/mmash.R` file. Run these lines of code to
 download the dataset.
 
 ``` r
+#| filename: "data-raw/mmash.R"
 download.file(mmash_link, destfile = here("data-raw/mmash-data.zip"))
 ```
 
@@ -415,6 +425,7 @@ in the `data-raw/` folder), comment out this line, so that inside the
 `data-raw/mmash.R` script it looks like:
 
 ``` r
+#| filename: "data-raw/mmash.R"
 # download.file(mmash_link, destfile = here("data-raw/mmash-data.zip"))
 ```
 
@@ -427,6 +438,7 @@ list by typing out and run this code in the Console. You only need to do
 this once.
 
 ``` r
+#| filename: "Console"
 usethis::use_git_ignore("data-raw/mmash-data.zip")
 ```
 
@@ -480,6 +492,7 @@ extract everything to the `data-raw/` folder (no idea why it's called
 `data-raw/mmash.R` script.
 
 ```{r unzip-main-file}
+#| filename: "data-raw/mmash.R"
 unzip(here("data-raw/mmash-data.zip"),
   exdir = here("data-raw"),
   junkpaths = TRUE
@@ -498,6 +511,7 @@ script. We'll also add a `Sys.sleep(1)` to pause the script for a second
 because sometimes the unzipping can be too fast and cause problems.
 
 ```{r unzip-data-file}
+#| filename: "data-raw/mmash.R"
 Sys.sleep(1)
 unzip(here("data-raw/MMASH.zip"),
   exdir = here("data-raw")
@@ -513,6 +527,7 @@ usethis::with_project(
       exdir = "data-raw",
       junkpaths = TRUE
     )
+    Sys.sleep(1)
     unzip("data-raw/MMASH.zip",
       exdir = "data-raw"
     )
@@ -527,6 +542,7 @@ look into the `data-raw/` folder and confirm that the below listed files
 and folders are there.
 
 ``` r
+#| filename: "Console"
 # NOTE: You don't need to run this code,
 # its here to show how we got the file list.
 fs::dir_tree("data-raw", recurse = 1)
@@ -554,6 +570,7 @@ new folder `data-raw/DataPaper/` to something more explicit like
 script and run them:
 
 ```{r delete-rename-files}
+#| filename: "data-raw/mmash.R"
 library(fs)
 file_delete(here(c(
   "data-raw/MMASH.zip",
@@ -603,6 +620,7 @@ us, we don't need to have Git track it. So, in the Console, type out and
 run this command:
 
 ``` r
+#| filename: "Console"
 usethis::use_git_ignore("data-raw/mmash/")
 ```
 
@@ -619,6 +637,7 @@ usethis::with_project(
 The `data-raw/mmash.R` script should look like this at this point:
 
 ```{r pre-course-state-of-script}
+#| filename: "data-raw/mmash.R"
 #| file: R/pre-course-script.R
 #| eval: false
 ```
@@ -636,6 +655,7 @@ You now have the data ready for the course! At this point, please run
 this function in the Console:
 
 ``` r
+#| filename: "Console"
 r3::check_project_setup()
 ```
 

sessions/introduction.qmd

@@ -228,7 +228,7 @@ the next steps. But first, we need to do a few things. Since we did all
 that work in the pre-course tasks downloading the data and unzipping it,
 we need to save these changes to the Git history. Open the Git interface
 with either the Git icon at the top near the menu bar, or with
-{{< var keybind.git >}}. When the Git inferface opens up we'll click the
+{{< var keybind.git >}}. When the Git interface opens up we'll click the
 checkbox beside the `.gitignore` and `data-raw/mmash.R` files. Then we
 write a commit message in the text box on the right, something like
 `Code to download data zip file`. Click the "Commit" button and close
@@ -238,7 +238,7 @@ Next, delete these two files we don't need by using the `{fs}` package.
 
 In the **Console**, type out:
 
-``` r
+``` {.r filename="Console"}
 fs::file_delete("TODO.md")
 fs::file_delete("doc/report.Rmd")
 ```
@@ -247,7 +247,7 @@ Then, open up the `README.md` and fix some of the TODO items. After
 cleaning everything up, now we need to use Git to add and commit all the
 current files into the history. Open up the Git interface in RStudio
 with {{< var keybind.git >}} or through the Git button. Write a message
-in the commit textbox saying `Added initial files`.
+in the commit text box saying `Added initial files`.
 
 ## Styling your files