HTML anchor in noweb style literate programming by org-mode - org-mode

This is my simple C source code in org-mode.
#+name: hello_one.c
#+begin_src C :noweb tangle :tangle hello_one.c
#include <stdio.h>
int main()
{
printf("Hello, world!\n");
reurn 0;
}
#+end_src
Maybe I can break this whole thing into many blocks.
#+name:hello.c
#+begin_src C :noweb tangle :tangle hello.c
<<include>>
<<main>>
#+end_src
#+name: include
#+begin_src C
#include <stdio.h>
#+end_src
#+name: main
#+begin_src C
int main()
{
printf("Hello, world!\n");
reurn 0;
}
#+end_src
I can successfully tangle it into a source code 'hello.c' and I can successfully weave it into a html document. But I'd like to have a HTML anchor as you many see in LiteratePrograms wiki. One example is the article on Fibonacci Numbers.
As you can see in this page, you can click each chunk name (for example, 'includes', 'fib', 'fastfib' and 'main.) and that brings you to that chunk description.
And each chunk description has its name displayed at the beginning. For example, if you hit the anchor 'fib' in LiteratePrograms article on Fibonacci numbers, it brings you the chunk description and that chunk begins with the chunk name 'fib'.
Is there any way I can implement these two features?

Related

Literate programming, org mode, function declaration

I want to write a Literate Program with org-mode. Let's say I have the following function:
fn do_stuff()
{
// 200 lines of code go here.
}
I would write something like that in org-mode:
#+BEGIN_SRC rust :tangle /some/path
fn do_stuff()
{
#+END_SRC
// Many more blocks of `BEGIN_SRC` go here to exlpain 200 lines of code mentioned above.
// They will have formatting, and prose between them, and headings with different nesting levels.
// The whole shebang in short.
#+BEGIN_SRC rust :tangle /some/path
}
#+END_SRC
Now, here is the question. I hope I will explain it well, it's kinda hard to put in words.
What do I do with the first and last #+BEGIN_SRC blocks shown above?
How do I style the function declaration with org-mode and/or Literate Programming?
It seems kind of out of place with all the “formatting, prose, headings” of the 200 lines of code mentioned above.
I need ideas please :-)
Thanks in advance.
I would use noweb to tangle the full code without necessarily presenting it all in order. That is, I would do something like this:
The core code is
#+name: code1
#+begin_src rust :noweb yes :tangle no
...
#+end_src
More code etc. and then, at the end:
#+BEGIN_SRC rust :tangle /some/path
fn do_stuff()
{
<<code1>>
}
#+END_SRC
You may need :noweb yes on the full code block as well.

What can cause org-auto-tangle to result nil for all noweb code block evaluations

I'm using literate programming for some configuration files and would like to have some parts from elisp code block evaluations. I tried evaluating named code blocks with :noweb tangle but they always results nil and I do not see any errors in the *Messages*. Here's a simplified hello world example and the results I got.
Org file
#+title: Hello
#+PROPERTY: header-args :tangle hello.txt :cache no :exports none
#+auto_tangle: t
#+name: hello-world-output
#+begin_src emacs-lisp :tangle no :eval no-export :results output
(print "Hello world")
#+end_src
#+name: hello-world-value
#+begin_src emacs-lisp :tangle no :eval no-export :results value
"Hello world"
#+end_src
#+begin_src text :noweb tangle
<<hello-world-output>> -> <<hello-world-output()>>
<<hello-world-value>> -> <<hello-world-value()>>
#+end_src
Tangled results
(print "Hello world") -> nil
"Hello world" -> nil
I also checked that org-link-elisp-confirm-function and org-confirm-babel-evaluate both have nil value, so they should not be preventing evaluation.
EDIT: I forgot to mention that I used org-auto-tangle. Issue doesn't occur when calling org-bable-tangle directly.
I had the same issue and below solved it for me.
According to the code of org-auto-tangle the code will not be evaluated by default. In order to have the code auto evaluated you need to add your org file to the org-auto-tangle-babel-safelist. I've posted the definition of the variable and a link to the README with an example of how to set the variable.
(defvar org-auto-tangle-babel-safelist '()
"List of full path of files for which code blocks need to be evaluated.
By default, code blocks are not evaluated during the auto-tangle to avoid
possible code execution from unstrusted source. To enable code blocks evaluation
for a specific file, add its full path to this list.")
https://github.com/yilkalargaw/org-auto-tangle#babel-auto-tangle-safelist

Can org-mode tangle during export

I can use the org-babel-tangle to tangle the current file. I was wondering if you could have org export tangle all the code blocks in the org file.
thanks
EA
This runs org-babel-tangle when exporting:
#+NAME: tangle-it
#+BEGIN_SRC emacs-lisp :exports none
(org-babel-tangle)
#+END_SRC
#+BEGIN_SRC text :results silent :noweb yes :exports results
<<tangle-it()>>
#+END_SRC
#+BEGIN_SRC css :tangle test.css
body {
font-size: 12px;
}
#+END_SRC
It doesn't work when using it with #+CALL: tangle-it().
It is also possible to do this with a macro:
#+MACRO: tangle-it (eval (progn (org-babel-tangle) ""))
{{{tangle-it()}}}
#+BEGIN_SRC css :tangle test.css
body {
font-size: 12px;
}
#+END_SRC
I do this to export my elisp source blocks to specific files
#+BEGIN_SRC emacs-lisp :tangle lisp-file.el
(message "Hello lisp-file")
#+END_SRC
I think you can also set this as a property, so you could set properties at the node/tree level.
I would do it like this:
* build :noexport:
#+BEGIN_SRC emacs-lisp
(org-babel-tangle)
(org-latex-export-as-latex)
#+END_SRC
Then just type C-c C-c in the code block to tangle, then export. You can change the export command to whatever you want for other export types.

org-babel: want all noweb block references to appear verbatim on export

Consider the following MVE in org-mode -- it contains my full question in detail. But, in summary, with some code blocks, some noweb references to other code blocks are substituted inline when I export the document, and, with other code blocks, the noweb references, in double broket quotes, are copied verbatim into the exported PDF. I do not know what causes this difference in behavior and I don't know how to control it, but I'd like to. I'd like to be able to specify that some blocks have behavior 1 (references substituted) and other blocks have behavior 2 (references verbatim).
The PDF that results from org-export is at this link
#+BEGIN_COMMENT
The emacs lisp block must export results, even though the results are none,
otherwise the block will not be eval'ed on export, and we will get
unacceptable confirmation requests for all the subsequent python blocks.
#+END_COMMENT
#+BEGIN_SRC emacs-lisp :exports results :results none
(setq org-confirm-babel-evaluate nil)
#+END_SRC
** PyTests
Define the test and cases. This code must be tangled out to an external file
so =py.test= can see it.
When I /export/ this to PDF, the noweb references, namely =<<imports>>= and
=<<definitions>>=, are substituted inline, so the typeset version of this
block in the PDF shows ALL the code. This is not what I want.
#+NAME: test-block
#+BEGIN_SRC python :noweb yes :tangle test_foo.py
<<imports>>
<<definitions>>
def test_smoke ():
np.testing.assert_approx_equal (foo_func (), foo_constant)
#+END_SRC
#+RESULTS: test-block
: None
The following blocks import prerequisites and do a quick smoke test:
** Do Some Imports
#+NAME: imports
#+BEGIN_SRC python
import numpy as np
#+END_SRC
#+RESULTS: imports
: None
** Define Some Variables
However, in the typeset PDF, the noweb reference =<<foo-func>>= in the block
below is /not/ substituted in-line, but rather appears verbatim. I want /all/
noweb references to appear verbatim in the exported, typeset, PDF document,
just like this one.
#+NAME: definitions
#+BEGIN_SRC python
foo_constant = 42.0
<<foo-func>>
#+END_SRC
#+RESULTS: definitions
** Define Some Functions
*** Foo Function is Really Interesting
#+NAME: foo-func
#+BEGIN_SRC python
def foo_func () :
return 42.000
#+END_SRC
#+RESULTS: foo-func
: None
We want results from pytest whether it succeeds or fails, hence the /OR/ with
=true= in the shell
#+BEGIN_SRC sh :results output replace :exports both
py.test || true
#+END_SRC
#+RESULTS:
: ============================= test session starts ==============================
: platform darwin -- Python 2.7.10, pytest-2.8.0, py-1.4.30, pluggy-0.3.1
: rootdir: /Users/bbeckman/foo, inifile:
: collected 1 items
:
: test_foo.py .
:
: =========================== 1 passed in 0.06 seconds ===========================
Found the appropriate references here
Here is a corrected PDF exported from the following .org file.
And here is the corrected MVE (it, itself, explains the correction):
#+BEGIN_COMMENT
The emacs lisp block must export results, even though the exports are none,
otherwise the block will not be eval'ed on export, and we will get unacceptable
confirmation requests for all the subsequent python blocks.
#+END_COMMENT
#+BEGIN_SRC emacs-lisp :exports results :results none
(setq org-confirm-babel-evaluate nil)
#+END_SRC
** PyTests
Define the test and cases. This code must be tangled out to an external file
so =py.test= can see it.
When I /export/ this to PDF, the noweb references, namely =<<imports>>= and
=<<definitions>>=, are *NOT* substituted inline, but typeset verbatim. This
is what I want. You get this behavior by saying =:noweb no-export= in the
header.
#+NAME: test-block
#+BEGIN_SRC python :tangle test_foo.py :noweb no-export :exports code :results none
dummy_for_org_mode = True
<<imports>>
<<definitions>>
def test_smoke ():
np.testing.assert_approx_equal (foo_func (), foo_constant)
#+END_SRC
The following blocks import prerequisites and do a quick smoke test:
** Do Some Imports
#+NAME: imports
#+BEGIN_SRC python :exports code :results none
import numpy as np
#+END_SRC
** Define Some Variables and Functions
In this block, I want the noweb reference =<<foo-func>>= in the block to be
substituted in-line and not to appear verbatim. Do that by saying
=:noweb yes= in the header.
#+NAME: definitions
#+BEGIN_SRC python :noweb yes :exports code :results none
foo_constant = 42.0
<<foo-func>>
#+END_SRC
** Define Some Functions
*** Foo Function is Really Interesting
Here, I want to talk about the implementation of foo function in detail, but I
don't want its code to be exported again, just to appear in the original
=.org= file as I reminder or note to me.
#+NAME: foo-func
#+BEGIN_SRC python :exports none :results none
def foo_func () :
return 42.000
#+END_SRC
** Run the Tests
We want results from pytest whether it succeeds or fails, hence the /OR/ with
=true= in the shell
#+BEGIN_SRC sh :results output replace :exports both
py.test || true
#+END_SRC
#+RESULTS:
: ============================= test session starts ==============================
: platform darwin -- Python 2.7.10, pytest-2.8.0, py-1.4.30, pluggy-0.3.1
: rootdir: /Users/bbeckman/foo, inifile:
: collected 1 items
:
: test_foo.py .
:
: =========================== 1 passed in 0.08 seconds ===========================

Any way to make org-babel properly indent noweb tangled code?

Tangling this:
#+BEGIN_SRC C :tangle no :noweb-ref begin
int main() {
printf("Line 1\n");
#+END_SRC
#+BEGIN_SRC C :tangle no :noweb-ref middle
printf("Second\n");
#+END_SRC
#+BEGIN_SRC C :tangle no :noweb-ref end
}
#+END_SRC
#+BEGIN_SRC C :tangle ~/test.c :noweb no-export
<<begin>>
<<middle>>
<<end>>
#+END_SRC
Yields this:
int main() {
printf("Line 1\n");
printf("Second\n");
}
I have org-src-preserve-indentation turned on, but it can't preserve what isn't there. The code editing windows can't set it correctly if it doesn't see the parts from the previous source code blocks. Finally, I don't want to have to go through all the previous snippets to figure out what the indentation should start at every time I start a new source code block.
Current hack is to tangle the source code, open the tangled file in a new buffer, select all and run c-indent-line-or-region, but I'm hoping there's something better than that.
Org-mode version: 8.2.5h
As mentioned, hooking into the org-babel-post-tangle-hook is the way to go. I use the following:
(defun tnez/src-cleanup ()
(indent-region (point-min) (point-max)))
(add-hook 'org-babel-post-tangle-hook 'tnez/src-cleanup)