Unify lesson pipeline with Reticulate

_episodes/01-design.md → _episodes_rmd/01-design.Rmd

@@ -10,6 +10,9 @@ objectives:
 keypoints:
 - "Lessons are design in four stages: conceptual, summative, formative, and connective."
 ---
+```{r, echo=FALSE}
+source("../bin/chunk-options.R")
+```
 
 This episode describes how we go about designing lessons and why.
 For more information on how we design lessons and why,

_episodes/02-tooling.md → _episodes_rmd/02-tooling.Rmd

@@ -15,6 +15,9 @@ keypoints:
 - "Each page's configuration is stored at the top of that page."
 - "Groups of files are stored in collection directories whose names begin with an underscore."
 ---
+```{r, echo=FALSE}
+source("../bin/chunk-options.R")
+```
 
 This episode describes the tools we use to build and manage lessons.
 These simplify many tasks, but make other things more complicated.

_episodes/03-organization.md → _episodes_rmd/03-organization.Rmd

@@ -13,6 +13,9 @@ keypoints:
 - "The home page, reference guide, setup instructions, discussion page, and instructors' guide must be updated for each lesson."
 - "The Makefile stores commonly-used commands."
 ---
+```{r, echo=FALSE}
+source("../bin/chunk-options.R")
+```
 
 Each lesson is made up of *episodes*, which are focused on a particular topic and
 include time for both teaching and exercises.

_episodes/04-formatting.md → _episodes_rmd/04-formatting.Rmd

@@ -17,6 +17,9 @@ keypoints:
 - "Special sections are formatted as blockquotes that open with a level-2 header and close with a class identifier."
 - "Special sections may be callouts or challenges; other styles are used by the template itself."
 ---
+```{r, echo=FALSE}
+source("../bin/chunk-options.R")
+```
 
 A lesson consists of one or more episodes,
 each of which has:

_episodes_rmd/05-bash-example.Rmd

@@ -0,0 +1,74 @@
+---
+source: Rmd
+title: "Using Bash with RMarkdown"
+teaching: 10
+exercises: 2
+questions:
+- "How to call `bash` from RMarkdown?"
+objectives:
+- "Demonstrate how to include pieces of Bash code, figures, and challenges."
+keypoints:
+- "`bash` code blocks"
+---
+```{r, echo=FALSE}
+source("../bin/chunk-options.R")
+```
+
+This episode demonstrates all the features that can be used
+when using Bash from [RMarkdown][r-markdown].
+
+You can include chunk for codes, just like you'd normally do.
+
+Normal output:
+
+```{bash}
+pwd
+```
+
+Output with error message:
+
+```{bash}
+foo
+```
+
+For the challenges and their solutions, you need to pay attention to where the
+`>` go and where to leave blank lines. You can include code chunks in both the
+instructions and solutions. For instance
+
+```
+> ## Challenge: Can you do it?
+>
+> What is the output of this command?
+>
+> ```{bash, eval=FALSE}`r ''`
+> ls data -a -F
+> ```
+>
+> > ## Solution
+> >
+> > ```{bash, echo=FALSE}`r ''`
+> > ls data -a -F
+> > ```
+> {: .solution}
+{: .challenge}
+```
+
+will generate
+
+> ## Challenge: Can you do it?
+>
+> What is the output of this command?
+>
+> ```{bash, eval=FALSE}
+> ls data -a -F
+> ```
+>
+> > ## Solution
+> >
+> > ```{bash, echo=FALSE}
+> > ls data -a -F
+> > ```
+> {: .solution}
+{: .challenge}
+
+{% include links.md %}

_episodes_rmd/06-python-example.Rmd

@@ -0,0 +1,83 @@
+---
+source: Rmd
+title: "Using Python with RMarkdown"
+teaching: 10
+exercises: 2
+questions:
+- "How to call `python` from RMarkdown?"
+objectives:
+- "Demonstrate how to include pieces of Python code, figures, and challenges."
+keypoints:
+- "`python` code blocks"
+---
+```{r, echo=FALSE}
+source("../bin/chunk-options.R")
+```
+
+This episode demonstrates all the features that can be used
+when using Python from [RMarkdown][r-markdown].
+
+You can include chunk for codes, just like you'd normally do.
+
+Normal output:
+
+```{python}
+1 + 1
+```
+
+Output with error message:
+
+```{python}
+x[10]
+```
+
+Output generating figures:
+
+```{python python-plot-example}
+import matplotlib.pyplot as plt
+
+plt.plot([1, 2, 3, 4])
+plt.show()
+```
+
+For the challenges and their solutions, you need to pay attention to where the
+`>` go and where to leave blank lines. You can include code chunks in both the
+instructions and solutions. For instance
+
+```
+> ## Challenge: Can you do it?
+>
+> What is the output of this command?
+>
+> ```{python, eval=FALSE}`r ''`
+> print("This new template looks good!")
+> ```
+>
+> > ## Solution
+> >
+> > ```{python, echo=FALSE}`r ''`
+> > print("This new template looks good!")
+> > ```
+> {: .solution}
+{: .challenge}
+```
+
+will generate
+
+> ## Challenge: Can you do it?
+>
+> What is the output of this command?
+>
+> ```{python, eval=FALSE}
+> print("This new template looks good!")
+> ```
+>
+> > ## Solution
+> >
+> > ```{python, echo=FALSE}
+> > print("This new template looks good!")
+> > ```
+> {: .solution}
+{: .challenge}
+
+{% include links.md %}

_episodes_rmd/05-rmarkdown-example.Rmd → _episodes_rmd/07-r-example.Rmd

@@ -1,6 +1,6 @@
 ---
 source: Rmd
-title: "Using RMarkdown"
+title: "Using R with RMarkdown"
 teaching: 10
 exercises: 2
 questions:
@@ -50,7 +50,7 @@ x[10]
 
 Output generating figures:
 
-```{r plot-example}
+```{r r-plot-example}
 library(ggplot2)
 ggplot(diamonds, aes(x = carat,  y = price, color = cut)) +
     geom_point()
@@ -65,13 +65,13 @@ instructions and solutions. For instance this:
 >
 > What is the output of this command?
 >
-> ```{r, eval=FALSE}
+> ```{r, eval=FALSE}`r ''`
 > paste("This", "new", "template", "looks", "good")
 > ```
 >
 > > ## Solution
 > >
-> > ```{r, echo=FALSE}
+> > ```{r, echo=FALSE}`r ''`
 > > paste("This", "new", "template", "looks", "good")
 > > ```
 > {: .solution}

_episodes/06-style-guide.md → _episodes_rmd/08-style-guide.Rmd

@@ -9,6 +9,9 @@ objectives:
 keypoints:
 - "Keyboard keys need to use `<kbd>` HTML tag."
 ---
+```{r, echo=FALSE}
+source("../bin/chunk-options.R")
+```
 
 ## Keyboard Key
 

_episodes/07-checking.md → _episodes_rmd/09-checking.Rmd

@@ -13,6 +13,9 @@ keypoints:
 - "The checker uses the same Markdown parser as Jekyll."
 - "Lessons can be previewed by running `make serve`."
 ---
+```{r, echo=FALSE}
+source("../bin/chunk-options.R")
+```
 
 The lesson template comes with several utilities to simplify lesson development and maintenance.
 

_episodes/08-coffee.md → _episodes_rmd/10-coffee.Rmd

@@ -3,6 +3,9 @@ layout: break
 title: "Coffee Break"
 break: 15
 ---
+```{r, echo=FALSE}
+source("../bin/chunk-options.R")
+```
 
 Use the `break` layout for placeholder episodes representing coffee breaks and lunches.
 These episodes do *not* have exercises, questions, objectives, or keypoints in their metadata,