Use new bootstrap 4 style and update images

Author: jeroenjanssens

Makefile

@@ -26,7 +26,7 @@ publish-production: hugo
 	netlify deploy --prod --dir www/public
 
 book/2e/%.utf8.md: book/2e/%.Rmd
-	cd book/2e && Rscript --vanilla -e 'bookdown::render_book("$*.Rmd", encoding = "UTF-8", preview = TRUE, clean = FALSE)'
+	cd book/2e && Rscript --vanilla -e 'bookdown::render_book("$*.Rmd", encoding = "UTF-8", preview = TRUE, clean = FALSE, new_session = TRUE)'
 
 foreword: book/2e/foreword.utf8.md
 preface: book/2e/preface.utf8.md

README.md

@@ -1,8 +1,10 @@
-Data Science at the Command Line
-================================
+# Data Science at the Command Line
 
 [![License: CC BY-ND 4.0](https://img.shields.io/badge/License-CC%20BY--ND%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-nd/4.0/)
 
-<img src="https://www.datascienceatthecommandline.com/img/cover-readme.png" width="302px" />
+<a href="https://datascienceatthecommandline.com/">
+<img src="https://datascienceatthecommandline.com/2e/images/cover-small.png" width="224px" /></a>
 
-This repository contains the full text, data, scripts, and custom command-line tools used in the book [Data Science at the Command Line](http://datascienceatthecommandline.com). The book is licensed under the Creative Commons Attribution-NoDerivatives 4.0 International License.
+This repository contains the full text, data, and scripts used in the second edition of the book *Data Science at the Command Line*. The book is licensed under the Creative Commons Attribution-NoDerivatives 4.0 International License.
+
+You can read the book for free at https://datascienceatthecommandline.com.

book/2e/01.Rmd

@@ -48,8 +48,8 @@ Although the five steps are discussed in a linear and incremental fashion, in pr
 \@ref(fig:diagram-osemn) illustrates that doing data science is an iterative and non-linear process.
 For example, once you have modeled your data, and you look at the results, you may decide to go back to the scrubbing step to the adjust the features of the dataset.
 
-```{r diagram-osemn, echo=FALSE, fig.cap="Doing data science is an iterative and non-linear process", fig.align="center"}
-knitr::include_graphics("images/diagram_osemn.png")
+```{r diagram-osemn, echo=FALSE, fig.cap="Doing data science is an iterative and non-linear process", fig.align="center", out.width="90%"}
+knitr::include_graphics("images/dscl_0101.png")
 ```
 
 Below I explain what each step entails.

book/2e/02.Rmd

@@ -237,7 +237,7 @@ Under the hood, each command-line tool is one of the following five types:
 - An alias
 
 ```{r umbrella, echo=FALSE, fig.cap="I use the term command-line tool as an umbrella term", fig.align="center"}
-knitr::include_graphics("images/diagram_umbrella.png")
+knitr::include_graphics("images/dscl_0201.png")
 ```
 
 It’s good to know the difference between the types.
@@ -338,7 +338,7 @@ Try typing a sentence and press **`Enter`**.
 You can stop sending input by pressing **`Ctrl-D`** after which `rev` will stop.
 
 ```{r diagram-essential-streams, echo=FALSE, fig.cap="Every tool has three standard streams: standard input (*`stdin`*), standard output (*`stdout`*), and standard error (*`stderr`*)", fig.align="center"}
-knitr::include_graphics("images/diagram_essential_streams.png")
+knitr::include_graphics("images/dscl_0202.png")
 ```
 
 In practice, you'll not use the keyboard as a source of input, but the output generated by other tools and the contents of files.
@@ -347,7 +347,7 @@ For example, with `curl` we can download the book *Alice’s Adventures in Wonde
 This is done using the pipe operator (`|`).
 
 ```{r diagram-essential-pipe, echo=FALSE, fig.cap="The output from a tool can be piped to another tool", fig.align="center"}
-knitr::include_graphics("images/diagram_essential_pipe.png")
+knitr::include_graphics("images/dscl_0203.png")
 ```
 
 We can *pipe* the output of `curl` to `grep` to filter lines on a pattern.
@@ -389,7 +389,7 @@ If this file already exists, its contents are overwritten.
 Note that the standard error is still redirected to the terminal.
 
 ```{r diagram-essential-redirect-stdout, echo=FALSE, fig.cap="The output from a tool can be redirected to a file", fig.align="center"}
-knitr::include_graphics("images/diagram_essential_redirect_stdout.png")
+knitr::include_graphics("images/dscl_0204.png")
 ```
 
 You can also append the output to a file with `>>`, meaning the output is added after the original contents:
@@ -422,7 +422,7 @@ This way, you are directly passing the file to the standard input of `wc` withou
 Again, the final output is the same.
 
 ```{r diagram-essential-stdin-cat, echo=FALSE, fig.cap="Two ways to use the contents of a file as input", fig.align="center"}
-knitr::include_graphics("images/diagram_essential_stdin_cat.png")
+knitr::include_graphics("images/dscl_0205.png")
 ```
 
 Like many command-line tools, `wc` allows one or more filenames to be specified as arguments.
@@ -450,19 +450,18 @@ cat movies.txt 404.txt 2> /dev/null
 ```
 <1> The *`2`* refers to standard error.
 
-```{r diagram-essential-redirect-devnull, echo=FALSE, fig.cap="Redirecting *`stderr`* to */dev/null*", fig.align="center"}
-knitr::include_graphics("images/diagram_essential_redirect_devnull.png")
+```{r diagram-essential-redirect-devnull, echo=FALSE, fig.cap="Redirecting *`stderr`* to */dev/null*", fig.align="center", out.width="50%"}
+knitr::include_graphics("images/dscl_0206.png")
 ```
 
-
 Be careful not to read from and write to the same file.
 If you do, you'll end up with an empty file.
 That's because the tool of which the output is redirected, immediately opens that file for writing, and thereby emptying it.
 There are two workarounds for this: (1) write to a different file and rename it afterwards with `mv` or (2) use `sponge` [@sponge], which soaks up all its input before writing to a file.
 \@ref(fig:diagram-essential-sponge) illustrates how this works.
 
 ```{r diagram-essential-sponge, echo=FALSE, fig.cap="Unless you use `sponge`, you cannot read from and write to the same file in one pipeline", fig.align="center"}
-knitr::include_graphics("images/diagram_essential_sponge.png")
+knitr::include_graphics("images/dscl_0207.png")
 ```
 
 For example, imagine you have used `dseq`[@dseq] to generate a file *dates.txt* and now you'd like to add line numbers using `nl`[@nl].
@@ -619,7 +618,7 @@ seq 0 2 100 | tee even.txt | trim 5
 ```
 
 ```{r diagram-essential-tee, echo=FALSE, fig.cap="With `tee`, you can write intermediate output to a file", fig.align="center"}
-knitr::include_graphics("images/diagram_essential_tee.png")
+knitr::include_graphics("images/dscl_0208.png")
 ```
 
 Lastly, to insert images that have been generated by command-line tools (so every image except screenshots and diagrams) I use `display`.

book/2e/03.Rmd

@@ -12,6 +12,12 @@ console_start()
  rm -f $HISTFILE
 ```
 
+```{console install_pup_arm64, include=FALSE}
+curl -sL https://github.com/ericchiang/pup/releases/download/v0.4.0/pup_v0.4.0_linux_arm64.zip -o pup.zip
+unzip pup.zip
+sudo mv pup /usr/bin/
+rm pup.zip
+```
 
 # Obtaining Data {#chapter-3-obtaining-data}
 

book/2e/05.Rmd

@@ -12,6 +12,13 @@ console_start()
  rm -f $HISTFILE
 ```
 
+```{console install_pup_arm64, include=FALSE}
+curl -sL https://github.com/ericchiang/pup/releases/download/v0.4.0/pup_v0.4.0_linux_arm64.zip -o pup.zip
+unzip pup.zip
+sudo mv pup /usr/bin/
+rm pup.zip
+```
+
 # Scrubbing Data {#chapter-5-scrubbing-data}
 
 Two chapters ago, in the first step of the OSEMN model for data science, we looked at *obtaining* data from a variety of sources.

book/2e/06.Rmd

@@ -274,7 +274,7 @@ There are five targets: *`all`*, *`data`*, *`data/starwars.csv`*, *`top10`*, and
 \@ref(fig:starwars-image) provides an overview of these targets and the dependencies between them.
 
 ```{r dependencies, echo=FALSE, fig.cap="Dependencies between targets", fig.align="center"}
-knitr::include_graphics("images/diagram_dependencies.png")
+knitr::include_graphics("images/dscl_0602.png")
 ```
 
 Let's discuss each target in turn:

book/2e/07.Rmd

@@ -462,7 +462,7 @@ Once you've plotted something, you can visit *localhost:8000* in your browser an
 The default port is 8000, but you can change this by specifying it as an argument to `servewd`:
 
 ```{console}
-servewd 9999 > display#!enter=FALSE
+servewd 9999#!enter=FALSE
 C-C#!literal=FALSE
 ```
 

book/2e/08.Rmd

@@ -200,8 +200,8 @@ API calls may be limited to a certain number, or some commands can only have one
 
 \@ref(fig:diagram-parallel-processing) illustrates, on a conceptual level, the difference between serial processing, naive parallel processing, and parallel processing with GNU Parallel in terms of the number of concurrent processes and the total amount of time it takes to run everything.
 
-```{r diagram-parallel-processing, echo=FALSE, fig.cap="Serial processing, naive parallel processing, and parallel processing with GNU Parallel", fig.align="center"}
-knitr::include_graphics("images/diagram_parallel_processing.png")
+```{r diagram-parallel-processing, echo=FALSE, fig.cap="Serial processing, naive parallel processing, and parallel processing with GNU Parallel", fig.align="center", out.width="60%"}
+knitr::include_graphics("images/dscl_0801.png")
 ```
 
 There are two problems with this naive approach.
@@ -234,7 +234,7 @@ This is `parallel` in its simplest form: the items to loop over are passed via s
 See \@ref(fig:diagram-parallel-output) for an illustration of how `parallel` concurrently distributes input among processes and collects their outputs.
 
 ```{r diagram-parallel-output, echo=FALSE, fig.cap="GNU Parallel concurrently distributes input among processes and collects their outputs", fig.align="center"}
-knitr::include_graphics("images/diagram_parallel_output.png")
+knitr::include_graphics("images/dscl_0802.png")
 ```
 
 As you can see it basically acts as a for loop.
@@ -373,7 +373,7 @@ tree outdir | trim
 See \@ref(fig:diagram-parallel-results) for a pictorial overview of how the `--results` option works.
 
 ```{r diagram-parallel-results, echo=FALSE, fig.cap="GNU Parallel stores output in separate files with the `--results` option", fig.align="center"}
-knitr::include_graphics("images/diagram_parallel_results.png")
+knitr::include_graphics("images/dscl_0803.png")
 ```
 
 When you're running multiple jobs in parallel, the order in which the jobs are run may not correspond to the order of the input.

book/2e/12-references.Rmd

@@ -0,0 +1 @@
+`r if (knitr:::is_html_output()) '# References {-}'`