|
|
@@ -121,7 +121,7 @@ way. [And in R it is possible to divert all graphical output to file] A
|
|
|
possible extension of the above might be to use a "magic variable" so
|
|
|
that a python variable is created e.g. __org_babel_output_file__ that
|
|
|
always holds a string corresponding to the file specified by :file. Eric
|
|
|
-may have further ideas / views here.
|
|
|
+may have further ideas / views here.
|
|
|
|
|
|
|
|
|
** DONE What function is bound to C-c '?
|
|
|
@@ -171,7 +171,7 @@ may have further ideas / views here.
|
|
|
Babel is to place your code in blocks in an Org-mode file, and to
|
|
|
use Babel's [[#literate-programming][Literate Programming]] support to extract pure code
|
|
|
from your Org files.
|
|
|
-
|
|
|
+
|
|
|
All of these use cases, as well as exhaustive documentation of the
|
|
|
features of Babel are covered in the [[https://orgmode.org/manual/Working-With-Source-Code.html#Working-With-Source-Code][Working with Source Code]]
|
|
|
section of the Org manual.
|
|
|
@@ -273,7 +273,7 @@ structure becomes:
|
|
|
Babel executes code blocks for *interpreted* languages such
|
|
|
as shell, python, R, etc. by passing code to the interpreter, which
|
|
|
must be installed on your system. You control what is done with the
|
|
|
-results of execution.
|
|
|
+results of execution.
|
|
|
|
|
|
Here are examples of code blocks in three different languages,
|
|
|
followed by their output. If you are viewing the Org-mode version of
|
|
|
@@ -309,7 +309,7 @@ HTML export of the resulting string:
|
|
|
#+resname:
|
|
|
: This file takes up 36K
|
|
|
|
|
|
-*** [[http://www.r-project.org/][R]]
|
|
|
+*** [[http://www.r-project.org/][R]]
|
|
|
What are the most common words in this file?
|
|
|
In the Org-mode file:
|
|
|
: #+begin_src R :colnames yes
|
|
|
@@ -378,7 +378,7 @@ HTML export of the resulting image:
|
|
|
returns tabular data (a vector, array or table of some sort) then
|
|
|
this will be held as an Org-mode table in the buffer. This
|
|
|
setting is the default.
|
|
|
-
|
|
|
+
|
|
|
For example, consider the following block of python code and its
|
|
|
output.
|
|
|
|
|
|
@@ -509,24 +509,24 @@ The table looks like this in the Org-mode buffer:
|
|
|
|
|
|
The [[http://www.gnu.org/software/emacs/manual/elisp.html][Emacs Lisp]] source code:
|
|
|
#+name: fibonacci-seq
|
|
|
-#+begin_src emacs-lisp :var fib-inputs=fibonacci-inputs
|
|
|
+#+begin_src emacs-lisp :var fib-inputs=fibonacci-inputs
|
|
|
(defun fibonacci (n)
|
|
|
(if (or (= n 0) (= n 1))
|
|
|
n
|
|
|
(+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
|
|
|
-
|
|
|
+
|
|
|
(mapcar (lambda (row)
|
|
|
(mapcar #'fibonacci row)) fib-inputs)
|
|
|
#+end_src
|
|
|
|
|
|
In the Org-mode buffer the function looks like this:
|
|
|
: #+name: fibonacci-seq
|
|
|
-: #+begin_src emacs-lisp :var fib-inputs=fibonacci-inputs
|
|
|
+: #+begin_src emacs-lisp :var fib-inputs=fibonacci-inputs
|
|
|
: (defun fibonacci (n)
|
|
|
: (if (or (= n 0) (= n 1))
|
|
|
: n
|
|
|
: (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
|
|
|
-:
|
|
|
+:
|
|
|
: (mapcar (lambda (row)
|
|
|
: (mapcar #'fibonacci row)) fib-inputs)
|
|
|
: #+end_src
|
|
|
@@ -540,7 +540,7 @@ The return value of =fibonacci-seq= is a table:
|
|
|
Code can be evaluated in-line using the following syntax:
|
|
|
|
|
|
: Without header args: src_lang{code} or with header args: src_lang[args]{code},
|
|
|
-: for example src_python[:session]{10*x}, where x is a variable existing in the
|
|
|
+: for example src_python[:session]{10*x}, where x is a variable existing in the
|
|
|
: python session.
|
|
|
|
|
|
** Code Block Body Expansion
|
|
|
@@ -556,10 +556,10 @@ The return value of =fibonacci-seq= is a table:
|
|
|
contents. This facility is useful for debugging.
|
|
|
|
|
|
- tangling :: The expanded body can be tangled. Tangling this way includes
|
|
|
- variable values that may be
|
|
|
- - the results of other code blocks,
|
|
|
- - variables stored in headline properties, or
|
|
|
- - tables.
|
|
|
+ variable values that may be
|
|
|
+ - the results of other code blocks,
|
|
|
+ - variables stored in headline properties, or
|
|
|
+ - tables.
|
|
|
|
|
|
One possible use for tangling expanded code block is for emacs
|
|
|
initialization. Values such as user names and passwords can be
|
|
|
@@ -580,7 +580,7 @@ The code block refers to the data table:
|
|
|
(setq my-special-username (first (first data)))
|
|
|
(setq my-special-password (first (second data)))
|
|
|
#+end_src
|
|
|
-
|
|
|
+
|
|
|
With point inside the code block, =C-c M-b p= expands the contents:
|
|
|
#+begin_src emacs-lisp
|
|
|
(let ((data (quote (("john-doe") ("abc123")))))
|
|
|
@@ -608,12 +608,12 @@ For example, let's take some system diagnostics in the shell and graph them with
|
|
|
directories in our home directory, together with their
|
|
|
sizes. Babel automatically converts the output into an Org-mode
|
|
|
table.
|
|
|
-
|
|
|
+
|
|
|
: #+name: directories
|
|
|
: #+begin_src sh :results replace
|
|
|
: cd ~ && du -sc * |grep -v total
|
|
|
: #+end_src
|
|
|
-
|
|
|
+
|
|
|
#+resname: directories
|
|
|
| 72 | "Desktop" |
|
|
|
| 12156104 | "Documents" |
|
|
|
@@ -636,7 +636,7 @@ For example, let's take some system diagnostics in the shell and graph them with
|
|
|
pie-chart. Note how this code block uses the =srcname=
|
|
|
of the previous code block to obtain the data.
|
|
|
|
|
|
-In the Org-mode file:
|
|
|
+In the Org-mode file:
|
|
|
: #+name: directory-pie-chart(dirs = directories)
|
|
|
: #+begin_src R :session R-pie-example :file ../../images/babel/dirs.png
|
|
|
: pie(dirs[,1], labels = dirs[,2])
|
|
|
@@ -672,7 +672,7 @@ following source block creates an Org-mode table filled with five random
|
|
|
numbers between 0 and 1.
|
|
|
|
|
|
: #+name: tbl-example-data
|
|
|
-: #+begin_src R
|
|
|
+: #+begin_src R
|
|
|
: runif(n=5, min=0, max=1)
|
|
|
: #+end_src
|
|
|
|
|
|
@@ -869,13 +869,13 @@ HTML export of code:
|
|
|
|
|
|
Babel comes pre-populated with the code blocks located in
|
|
|
the [[file:library-of-babel.org][Library of Babel]] file -- raw file at
|
|
|
-@@html: <a href="https://orgmode.org/w/org-mode.git/blob/HEAD:/doc/library-of-babel.org">library-of-babel.org</a>@@
|
|
|
+@@html: <a href="https://code.orgmode.org/bzg/worg/raw/master/library-of-babel.org">library-of-babel.org</a>@@
|
|
|
--. It is possible to add code blocks to the library from any
|
|
|
Org-mode file using the =org-babel-lob-ingest= (bound to =C-c C-v
|
|
|
l=).
|
|
|
|
|
|
#+name: add-file-to-lob
|
|
|
- #+begin_src emacs-lisp
|
|
|
+ #+begin_src emacs-lisp
|
|
|
(org-babel-lob-ingest "path/to/file.org")
|
|
|
#+end_src
|
|
|
|
|
|
@@ -991,7 +991,7 @@ Calling =org-babel-tangle= will result in the following shell source
|
|
|
code being written to the =hello.sh= file:
|
|
|
|
|
|
#+name: hello-world-output
|
|
|
-#+begin_src sh
|
|
|
+#+begin_src sh
|
|
|
#!/usr/bin/env sh
|
|
|
|
|
|
# [[file:~/org/temp/index.org::*Noweb%20test][hello-world]]
|
|
|
@@ -1048,7 +1048,7 @@ For a simple example of usage, follow these 5 steps:
|
|
|
|
|
|
1) create a directory named =.emacs.d= in the base of your home
|
|
|
directory;
|
|
|
- #+begin_src sh
|
|
|
+ #+begin_src sh
|
|
|
mkdir ~/.emacs.d
|
|
|
#+end_src
|
|
|
2) checkout the latest version of Org-mode into the src subdirectory
|
|
|
@@ -1062,15 +1062,15 @@ For a simple example of usage, follow these 5 steps:
|
|
|
3) place the following code block in a file called =init.el= in your Emacs
|
|
|
initialization directory (=~/.emacs.d=).
|
|
|
#+name: emacs-init
|
|
|
- #+begin_src emacs-lisp
|
|
|
+ #+begin_src emacs-lisp
|
|
|
;;; init.el --- Where all the magic begins
|
|
|
;;
|
|
|
;; This file loads Org-mode and then loads the rest of our Emacs initialization from Emacs lisp
|
|
|
;; embedded in literate Org-mode files.
|
|
|
-
|
|
|
+
|
|
|
;; Load up Org Mode and (now included) Org Babel for elisp embedded in Org Mode files
|
|
|
(setq dotfiles-dir (file-name-directory (or (buffer-file-name) load-file-name)))
|
|
|
-
|
|
|
+
|
|
|
(let* ((org-dir (expand-file-name
|
|
|
"lisp" (expand-file-name
|
|
|
"org" (expand-file-name
|
|
|
@@ -1084,10 +1084,10 @@ For a simple example of usage, follow these 5 steps:
|
|
|
;; load up Org-mode and Org-babel
|
|
|
(require 'org-install)
|
|
|
(require 'ob-tangle))
|
|
|
-
|
|
|
+
|
|
|
;; load up all literate org-mode files in this directory
|
|
|
(mapc #'org-babel-load-file (directory-files dotfiles-dir t "\\.org$"))
|
|
|
-
|
|
|
+
|
|
|
;;; init.el ends here
|
|
|
#+end_src
|
|
|
4) implement all of your Emacs customizations inside of Emacs Lisp
|
|
|
@@ -1099,7 +1099,7 @@ For a simple example of usage, follow these 5 steps:
|
|
|
:PROPERTIES:
|
|
|
:CUSTOM_ID: reproducable-research
|
|
|
:END:
|
|
|
-#+begin_quote
|
|
|
+#+begin_quote
|
|
|
An article about computational science in a scientific publication is
|
|
|
not the scholarship itself, it is merely advertising of the
|
|
|
scholarship. The actual scholarship is the complete software
|
|
|
@@ -1138,4 +1138,3 @@ advantages:
|
|
|
block's results in a separate buffer.
|
|
|
|
|
|
[fn:2] This mode will be familiar to Sweave users.
|
|
|
-
|
