What makes Org mode popular for reproducible research?
** Back
org-babel, the library that enables superpowers for Org mode source code blocks.
Among the list of features, org-babel makes the following things easier for creating lab notebooks.
- Execute the source code block and print results.
- Create files from source code blocks, making it possible to create an entire computational report with a single Org mode document.
- Metaprogramming with [[https://orgmode.org/manual/Noweb-Reference-Syntax.html][noweb-inspired system]] making dynamic content possible.
- Individual control over source code blocks with sessions, export options, and variables.
- Pass values between different source code blocks even in different programming languages.
* org-babel modes
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** Front
How to make org-babel pass values between different source code blocks?
** Back
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First, configure org-babel to work in functional mode (i.e., ~:results value~) in a source code block.
With functional mode, it will return values which will be handled by org-babel.
#+begin_src org
,#+name: num
,#+begin_src python :results value
return 53
,#+end_src
#+end_src
The value cannot be passed unless it has a name that others can reference yet so add a name property to the source code block (i.e., ~#+name: ${NAME}~).
Now here's a different source code block written in a different language.
To pass a value, you have to configure with ~:var ${VARNAME}=${NAME}~.
#+begin_src org
,#+begin_src ruby :var num=num :results output
print(num)
,#+end_src
#+end_src
* Creating files with Org mode
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** Front
How to create files with Org mode source code blocks?
** Back
The ~:tangle~ option enables extracting code blocks into files.
Accepted values include =yes=, =no=, or a relative path to the Org document where the file will be written.
* Dynamic content with Org mode
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** Front
Is creating dynamic content possible?
If so, how?
** Back
Yes!
With source code blocks and the [[https://orgmode.org/manual/Noweb-Reference-Syntax.html][noweb]] option enabled, you can make meta-programming in Org.
You can declare a function by assigning a name on the code block (i.e., ~#+name: ${FUNC_NAME}~).
Here's an example of a source code block with a default argument.
#+begin_src org
,#+name: greeting
,#+header: :var name="World"
,#+begin_src sh
echo "Hello ${name}"
,#+end_src
#+end_src
You can then call the function in different ways:
- For calling it inline, ~call_${FUNC_NAME}()~.
- For creating a block, ~#+call: ${FUNC_NAME}()~.
- For invoking inside a code block, ~<<${FUNC_NAME}()>>~, but you have to enable noweb (e.g., ~:noweb yes~).
You can then pass header arguments by appending in square brackets (=[]=) before invoking it — e.g., ~call_greeting[:results replaces]()~, ~#+call: greeting[:results replace]()~, ~<<greeting[:results replace]()>>~.
* Asciidoctor-styled callouts
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** Front
Are callouts possible?
If so, how?
** Back
Surprisingly, yes!
It is just hidden on the documentation.
Specifically, on the [[https://orgmode.org/manual/Literal-Examples.html][Literal examples]] section of the Org mode manual.
Here's an example to do it.
#+begin_src org
,#+begin_src python
print("Hello world") # (ref:hello)
print(2 + 5) # (ref:num)
,#+end_src
In [[(hello)][line 1]], we have printed the traditional "Hello world" program.
In [[(num)][the second line]], we've done a simple arithmetic and printed it into the console.
#+end_src
To create Asciidoctor-styled callouts, create a reference inside of the code block and refer to it (i.e., ~(${ref})~).
What function creates a buffer for certain elements in org-mode but it is especially useful for editing source code blocks where it will open with the correct major mode?
