Proposal: references from code to text.

Proposal: references from code to text.

[ZHUO QL (KDr2)]

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Hi all, I just post a proposal for orgmode on my website(generated by orgmode):
http://kdr2.com/tech/emacs/1805-proposal-org-ref-code-to-text.html .
Here is the source of the proposal:
# -*- mode: org; mode: auto-fill; -*-
#+TITLE: Proposal for Orgmode: references from code to text.
#+AUTHOR: KDr2

#+OPTIONS: toc:nil
#+OPTIONS: num:nil

#+BEGIN: inc-file :file "common.inc.org"
#+END:
#+CALL: dynamic-header() :results raw
#+CALL: meta-keywords(kws='("orgmode" "literate programming")) :results raw

# - DATE
<2018-05-12 Sat>


Literate programming is writing out the program logic in a human
language with included (separated by a primitive markup) code snippets
and macros. A preprocessor is used to substitute arbitrary
hierarchies, or rather "interconnected 'webs' of macros", to produce
the compilable source code with one command ("tangle"), and
documentation with another ("weave").

So in a literate programming source file, any chunk is either a block
of code or a block of document in a human language, I'll call them
*code* and *text* below.

In my opinion, code and text should be able to reference each other:

- *Text refers to text* \\
  In the exported/woven documentation, these references act as links,
  make interconnections between relevant topics.
- *Text refers to code* \\
  The links in the exported/woven documentation can also link to a
  line of code if the code blocks are also included in the
  exported/woven documentation.
- *Code refers to code* \\
  That's the most important part of the literate programming. This
  kind of references act as placeholders or something like macro in
  the C-programming language. With it, literate programming provides
  an ability to change the order of the source code from a
  machine-imposed sequence to one convenient to the human mind. [[https://en.wikipedia.org/wiki/Literate_programming#Example][Here
  is a simple Example depicts this concept]].
- *Code refers to text* \\
  So far as I know, no literate programming tool has this kind of
  references. However, this kind of references could be very benifical
  too. Many programming languages have a mechanism to support
  embedding documentation(usually as comments) in the source code, AKA
  [[https://en.wikipedia.org/wiki/Docstring][Docstring]]. These embedded documentations are widely and conveniently
  used in editor, REPL and IDE. For instance, the docs of any elisp
  function that we can read in Emacs are from the elisp source.

  But in literate programming we seldom embed comments into the code
  blocks, as an impliaction the extracted/tangled code has no docs
  embeded. If we can refer to chunks of text in the code blocks, we
  will have the chance to include these chunks of text as embeded docs
  in the code in the tangling process, which results in
  well-documented source code. This is useful especially while the
  programmer are authoring reusable source code, like libraries or
  frameworks.

Here is the implementation status of these kinds of references of
noweb and Org mode (~->~ means 'has the ability to make reference
to'):

  | tool     | text -> text | code -> code     | text -> code   | code -> text |
  |----------+--------------+------------------+----------------+--------------|
  | noweb    | No           | Yes              | No             | No           |
  | Org mode | Yes, links   | Yes, noweb style | Yes, ~(ref:*)~ | No           |


As we saw, both noweb and Org mode do not implement the reference from
code to text. Could we provide this feature in Org mode -- the best
and widely used literate programming tool?

As a proposal, in Org mode, we can mimic the labels in
code blocks(i.e. text -> code reference), use something like
~(ref:text:<REF-NAME>)~ as the reference from code to text:

#+BEGIN_SRC org
  ,#+NAME: DOC-OF-ADD
  We use the function add to calculate the sum of two numbers.

  ,#+BEGIN_SRC elisp
  (defun add (x y)
    "(ref:text:DOC-OF-ADD)"
    (+ x y))
  ,#+END_SRC
#+END_SRC

The Org file above will produce the code below:

#+BEGIN_SRC elisp
  (defun add (x y)
    "We use the function add to calculate the sum of two numbers."
    (+ x y))
#+END_SRC

- Beside the ~NAME~, we could also support reference via the
  ~CUSTOM_ID~ property or anything else that can locate a text chunk.
- In the tangling process, we should do some kind of transformation of
  the target text, for example, escape the quote mark. A hook may be
  needed to let the user customize the transformation too.

What do you think?

* References
  - https://en.wikipedia.org/wiki/Literate_programming
  - https://en.wikipedia.org/wiki/Noweb
  - https://en.wikipedia.org/wiki/Docstring
  - http://orgmode.org/manual/Extracting-source-code.html#Extracting-source-code
  - http://orgmode.org/manual/Noweb-reference-syntax.html#Noweb-reference-syntax
  - http://orgmode.org/manual/Literal-examples.html#Literal-examples
  - https://orgmode.org/worg/dev/org-syntax.html

* Discuss and Comment
  #+BEGIN: inc-file :file "comment.inc.org"
  #+END:

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Re: Proposal: references from code to text.

[Eric S Fraga]

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On Saturday, 12 May 2018 at 13:29, ZHUO QL (KDr2) wrote:
> Hi all, I just post a proposal for orgmode on my website(generated by orgmode):
> http://kdr2.com/tech/emacs/1805-proposal-org-ref-code-to-text.html .
> Here is the source of the proposal:
> # -*- mode: org; mode: auto-fill; -*-
>
> #+TITLE: Proposal for Orgmode: references from code to text.
> #+AUTHOR: KDr2

[...]

> - Beside the ~NAME~, we could also support reference via the
>   ~CUSTOM_ID~ property or anything else that can locate a text chunk.
> - In the tangling process, we should do some kind of transformation of
>   the target text, for example, escape the quote mark. A hook may be
>   needed to let the user customize the transformation too.
>
> What do you think?

I like the symmetry of having src reference text.  I guess, in what you
propose above, that the text that would be incorporated would be a
single element (in org parsing parlance) or else we would have to
specify an extent in the link information.

Are you able to implement something?  I would definitely help test it.

-- 
Eric S Fraga via Emacs 27.0.50, Org release_9.1.6-591-gee336b

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Re: Proposal: references from code to text.

[John Kitchin]

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It seems like this is nearly all possible already (see below). It is a
little wonky that you have to put text in a src txt block to achieve it,
but otherwise what is missing?

* Main document

See [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only
support two args]] (text to text) for notes about this function. The
addition is done in line [[(add)]] (text to code).

#+NAME: DOC-OF-ADD
#+BEGIN_SRC txt
"We use the function add to calculate the sum of two numbers."
#+END_SRC

#+NAME: ADD
#+BEGIN_SRC emacs-lisp -n -r :noweb yes :tangle test.el
(defun add (x y)
  <<DOC-OF-ADD>> ;; code to code
  ;; [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only
support two args]] code to text
  (+ x y) (ref:add)
  )
#+END_SRC

#+RESULTS: ADD
: add


** Notes

*** There is a reason we only support two args
    :PROPERTIES:
    :ID:       BAD97113-3561-4A4A-BA07-0CD5BF6BA35F
    :END:


John

-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Sun, May 13, 2018 at 10:48 PM, Eric S Fraga <esflists@gmail.com> wrote:

> On Saturday, 12 May 2018 at 13:29, ZHUO QL (KDr2) wrote:
> > Hi all, I just post a proposal for orgmode on my website(generated by
> orgmode):
> > http://kdr2.com/tech/emacs/1805-proposal-org-ref-code-to-text.html .
> > Here is the source of the proposal:
> > # -*- mode: org; mode: auto-fill; -*-
> >
> > #+TITLE: Proposal for Orgmode: references from code to text.
> > #+AUTHOR: KDr2
>
> [...]
>
> > - Beside the ~NAME~, we could also support reference via the
> >   ~CUSTOM_ID~ property or anything else that can locate a text chunk.
> > - In the tangling process, we should do some kind of transformation of
> >   the target text, for example, escape the quote mark. A hook may be
> >   needed to let the user customize the transformation too.
> >
> > What do you think?
>
> I like the symmetry of having src reference text.  I guess, in what you
> propose above, that the text that would be incorporated would be a
> single element (in org parsing parlance) or else we would have to
> specify an extent in the link information.
>
> Are you able to implement something?  I would definitely help test it.
>
> --
> Eric S Fraga via Emacs 27.0.50, Org release_9.1.6-591-gee336b
>

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Re: Proposal: references from code to text.

[Eric S Fraga]

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On Monday, 14 May 2018 at 08:05, John Kitchin wrote:
> It seems like this is nearly all possible already (see below). It is a
> little wonky that you have to put text in a src txt block to achieve it,
> but otherwise what is missing?

Ah, yes, quite nice.  Thanks!

-- 
Eric S Fraga via Emacs 27.0.50, Org release_9.1.6-591-gee336b

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Re: Proposal: references from code to text.

[Eric S Fraga]

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... continued ...

although I found a strange bug in the tangling and noweb syntax.  I
didn't want to have quotes in the text so I removed them and put them in
the lisp src block instead:

#+begin_src org
  ,#+NAME: ADD
  ,#+BEGIN_SRC emacs-lisp -n -r :noweb yes :tangle test.el

  (defun add (x y)
    "<<DOC-OF-ADD>>" ;; code to code
    (+ x y) (ref:add)
    )
  ,#+END_SRC
#+end_src

which when exported or tangled resulted in some strange quoting:

#+begin_src emacs-lisp
  (defun add (x y)
    "
    "We use the function add to calculate the sum of two numbers." ;; code to code
    (+ x y) 
    )
#+end_src

I'm probably not supposed to put a <<...>> link within quotes but the
output is surprising in any case.

-- 
Eric S Fraga via Emacs 27.0.50, Org release_9.1.6-591-gee336b

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Re: Proposal: references from code to text.

[ZHUO QL (KDr2)]

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Well, it's a nice approach.
But it has a few cons:
1. Putting text in a source block is not a very natural way. It may disturb the fluidity, both for writing the Org source and reading the exported document(e.g. html);2. The bug Eric just found while putting a <<...>> link within quotes, although, it may be easy to fix. 

 Greetings.

ZHUO QL (KDr2, http://kdr2.com)

 

   On Monday, May 14, 2018, 11:06:34 PM GMT+8, John Kitchin <jkitchin@andrew.cmu.edu> wrote: 
 
 It seems like this is nearly all possible already (see below). It is a little wonky that you have to put text in a src txt block to achieve it, but otherwise what is missing?
* Main document
See [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only support two args]] (text to text) for notes about this function. The addition is done in line [[(add)]] (text to code).
#+NAME: DOC-OF-ADD#+BEGIN_SRC txt"We use the function add to calculate the sum of two numbers."#+END_SRC
#+NAME: ADD#+BEGIN_SRC emacs-lisp -n -r :noweb yes :tangle test.el(defun add (x y)  <<DOC-OF-ADD>> ;; code to code  ;; [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only support two args]] code to text  (+ x y) (ref:add)  )#+END_SRC
#+RESULTS: ADD: add

** Notes
*** There is a reason we only support two args    :PROPERTIES:    :ID:       BAD97113-3561-4A4A-BA07-0CD5BF6BA35F    :END:

John

-----------------------------------
Professor John Kitchin 
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803@johnkitchin
http://kitchingroup.cheme.cmu.edu

  

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Re: Proposal: references from code to text.

[Eric S Fraga]

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On Tuesday, 15 May 2018 at 04:49, ZHUO QL (KDr2) wrote:
> 2. The bug Eric just found while putting a <> link within
> quotes, although, it may be easy to fix.  

I realised afterwards that it is not a bug but is a feature: org assumes
that anything before the << start of the link should be repeated on each
line of the incorporated src block.  This allows for easy incorporation
of code into a comment block, e.g. for C or sh etc.

-- 
Eric S Fraga via Emacs 27.0.50, Org release_9.1.6-591-gee336b

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Re: Proposal: references from code to text.

[ZHUO QL (KDr2)]

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Oh, that makes sense.
So in this way, we must put the text into quotes, and then into a txt code block. And also we don't have a chance to do any transformation of the text(e.g. org-mode list to javadoc format).  
I think the direct reference from code to text is better. I will try to implement it, but I'm not very familiar with the code base and don't have much time, so I can't give any commitment. But once I have anything to show, I'll be back here  :)
 Greetings.

ZHUO QL (KDr2, http://kdr2.com)

 

   On Tuesday, May 15, 2018, 6:05:31 PM GMT+8, Eric S Fraga <esflists@gmail.com> wrote: 
 
 On Tuesday, 15 May 2018 at 04:49, ZHUO QL (KDr2) wrote:
> 2. The bug Eric just found while putting a <> link within
> quotes, although, it may be easy to fix. 

I realised afterwards that it is not a bug but is a feature: org assumes
that anything before the << start of the link should be repeated on each
line of the incorporated src block.  This allows for easy incorporation
of code into a comment block, e.g. for C or sh etc.

-- 
Eric S Fraga via Emacs 27.0.50, Org release_9.1.6-591-gee336b  

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Re: Proposal: references from code to text.

[John Kitchin]

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* Main document

See [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only
support two args]] (text to text) for notes about this function. The
addition is done in line [[(add)]] (text to code).

Here we put names on different kinds of elements so we can put them into a
tangled file later.

#+NAME: DOC-OF-ADD
We use the function add to calculate the sum of two numbers.

#+NAME: add-options
- one
- two
- three
- and of course "optional things"


We use a block like this to get the contents of an org-element by name as a
string, and possibly transform it some how, e.g. in this case I escape
quotes. I guess you could also use an exporter to convert it to what ever
form you want. You might bury this block at the end in an appendix so it
isn't in the middle of your document like this.

#+name: get-string
#+BEGIN_SRC emacs-lisp :var name="add-options"
(let ((el (org-element-map (org-element-parse-buffer)
org-element-all-elements
    (lambda (el)
      (when (string= (org-element-property :name el) name)
el))
    nil t)))
  (let ((s (buffer-substring (org-element-property :contents-begin el)
     (org-element-property :contents-end el))))
    (replace-regexp-in-string "\\\"" "\\\\\"" s)))
#+END_SRC


Now, we can use those elements in a src-block like this.

#+NAME: ADD
#+BEGIN_SRC emacs-lisp -n -r :noweb yes :tangle test.el
(defun add (x y)
  "One line description of adding X and Y.
  <<get-string("DOC-OF-ADD")>> ;; code to code
  <<get-string("add-options")>>"
  ;; [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only
support two args]] code to text
  (+ x y) (ref:add)
  ;; it appears the coderef needs to be on it's own line, otherwise you get
a org-link-search: No match for coderef: add when you click on the link.
  )
#+END_SRC

#+RESULTS: ADD
: add

The above block tangles to this for me:

#+BEGIN_SRC emacs-lisp
(defun add (x y)
  "One line description of adding X and Y.
  We use the function add to calculate the sum of two numbers.
   ;; code to code
  - one
  - two
  - three
  - and of course \"optional things\"
  "
  ;; [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only
support two args]] code to text
  (+ x y)
  ;; it appears the coderef needs to be on it's own line, otherwise you get
a org-link-search: No match for coderef: add when you click on the link.
  )

#+END_SRC


** Notes

*** There is a reason we only support two args
    :PROPERTIES:
    :ID:       BAD97113-3561-4A4A-BA07-0CD5BF6BA35F
    :END:


John

-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Wed, May 16, 2018 at 12:04 AM, ZHUO QL (KDr2) <zhuoql@yahoo.com> wrote:

> Oh, that makes sense.
>
> So in this way, we must put the text into quotes, and then into a txt code
> block. And also we don't have a chance to do any transformation of the
> text(e.g. org-mode list to javadoc format).
>
> I think the direct reference from code to text is better. I will try to
> implement it, but I'm not very familiar with the code base and don't have
> much time, so I can't give any commitment. But once I have anything to
> show, I'll be back here  :)
>
> Greetings.
>
> ZHUO QL (KDr2, http://kdr2.com)
>
>
>
> On Tuesday, May 15, 2018, 6:05:31 PM GMT+8, Eric S Fraga <
> esflists@gmail.com> wrote:
>
>
> On Tuesday, 15 May 2018 at 04:49, ZHUO QL (KDr2) wrote:
>
> > 2. The bug Eric just found while putting a <> link within
> > quotes, although, it may be easy to fix.
>
>
> I realised afterwards that it is not a bug but is a feature: org assumes
> that anything before the << start of the link should be repeated on each
> line of the incorporated src block.  This allows for easy incorporation
> of code into a comment block, e.g. for C or sh etc.
>
> --
> Eric S Fraga via Emacs 27.0.50, Org release_9.1.6-591-gee336b
>

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Re: Proposal: references from code to text.

[Samuel Wales]

i'm not sure if i understand the goal.  is it babel-only?

this email might be off-topic.

what i want is links, using something like org-id,

  - from non-org [for example, a link in file.el in a comment]
  - to non-org [for example, a named or id'ed location in the same file]
  - or to org [e.g. an org-id'ed org entry, or a named or id'ed
location in a babel block]

that can be, if needed, effectively, bidirectional.  thus, you could
document a function in file.el using a subtree in main.org and bounce
between the function and the documentation because there is a link for
each.

non-org [e.g. file.el] can be an original file [i.e. no babel
anywhere] or the result of tangling from babel.

i find that org-link-minor-mode is /highly/ useful for the non-org
part of this, but it doesn't support all of the above functionality
automatically.

i'd want a general package that is like org-link-minor-mode, but takes
care of supporting the user by creating good ids and links as needed.

-- 
The Kafka Pandemic: <http://thekafkapandemic.blogspot.com>

The disease DOES progress. MANY people have died from it. And ANYBODY
can get it at any time.

Re: Proposal: references from code to text.

[John Kitchin]

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You might want to check out linkd: https://www.emacswiki.org/emacs/linkd.el

It does a lot of what you describe independently of org-mode.

John

-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Wed, May 16, 2018 at 12:37 PM, Samuel Wales <samologist@gmail.com> wrote:

> i'm not sure if i understand the goal.  is it babel-only?
>
> this email might be off-topic.
>
> what i want is links, using something like org-id,
>
>   - from non-org [for example, a link in file.el in a comment]
>   - to non-org [for example, a named or id'ed location in the same file]
>   - or to org [e.g. an org-id'ed org entry, or a named or id'ed
> location in a babel block]
>
> that can be, if needed, effectively, bidirectional.  thus, you could
> document a function in file.el using a subtree in main.org and bounce
> between the function and the documentation because there is a link for
> each.
>
> non-org [e.g. file.el] can be an original file [i.e. no babel
> anywhere] or the result of tangling from babel.
>
> i find that org-link-minor-mode is /highly/ useful for the non-org
> part of this, but it doesn't support all of the above functionality
> automatically.
>
> i'd want a general package that is like org-link-minor-mode, but takes
> care of supporting the user by creating good ids and links as needed.
>
> --
> The Kafka Pandemic: <http://thekafkapandemic.blogspot.com>
>
> The disease DOES progress. MANY people have died from it. And ANYBODY
> can get it at any time.
>

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Re: Proposal: references from code to text.

[Samuel Wales]

interesting package!  but i'm not sure it would work with org as well
as org-link-minor-mode does.

On 5/16/18, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
> You might want to check out linkd: https://www.emacswiki.org/emacs/linkd.el
>
> It does a lot of what you describe independently of org-mode.
>
> John
>
> -----------------------------------
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
>
>
> On Wed, May 16, 2018 at 12:37 PM, Samuel Wales <samologist@gmail.com>
> wrote:
>
>> i'm not sure if i understand the goal.  is it babel-only?
>>
>> this email might be off-topic.
>>
>> what i want is links, using something like org-id,
>>
>>   - from non-org [for example, a link in file.el in a comment]
>>   - to non-org [for example, a named or id'ed location in the same file]
>>   - or to org [e.g. an org-id'ed org entry, or a named or id'ed
>> location in a babel block]
>>
>> that can be, if needed, effectively, bidirectional.  thus, you could
>> document a function in file.el using a subtree in main.org and bounce
>> between the function and the documentation because there is a link for
>> each.
>>
>> non-org [e.g. file.el] can be an original file [i.e. no babel
>> anywhere] or the result of tangling from babel.
>>
>> i find that org-link-minor-mode is /highly/ useful for the non-org
>> part of this, but it doesn't support all of the above functionality
>> automatically.
>>
>> i'd want a general package that is like org-link-minor-mode, but takes
>> care of supporting the user by creating good ids and links as needed.
>>
>> --
>> The Kafka Pandemic: <http://thekafkapandemic.blogspot.com>
>>
>> The disease DOES progress. MANY people have died from it. And ANYBODY
>> can get it at any time.
>>
>


-- 
The Kafka Pandemic: <http://thekafkapandemic.blogspot.com>

The disease DOES progress. MANY people have died from it. And ANYBODY
can get it at any time.

"You’ve really gotta quit this and get moving, because this is murder
by neglect." ---
<http://www.meaction.net/2017/02/03/pwme-people-with-me-are-being-murdered-by-neglect>.

Re: Proposal: references from code to text.

[ZHUO QL (KDr2)]

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Hooray!
Do we have a way to make that piece of code a predefined and callable code block that can be seen and called in any Org file? 
 Greetings.

ZHUO QL (KDr2, http://kdr2.com)

 

    On Wednesday, May 16, 2018, 10:26:41 PM GMT+8, John Kitchin <jkitchin@andrew.cmu.edu> wrote:  
 
 * Main document
See [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only support two args]] (text to text) for notes about this function. The addition is done in line [[(add)]] (text to code).
Here we put names on different kinds of elements so we can put them into a tangled file later.
#+NAME: DOC-OF-ADDWe use the function add to calculate the sum of two numbers.
#+NAME: add-options- one- two- three- and of course "optional things"

We use a block like this to get the contents of an org-element by name as a string, and possibly transform it some how, e.g. in this case I escape quotes. I guess you could also use an exporter to convert it to what ever form you want. You might bury this block at the end in an appendix so it isn't in the middle of your document like this.
#+name: get-string#+BEGIN_SRC emacs-lisp :var name="add-options"(let ((el (org-element-map (org-element-parse-buffer) org-element-all-elements     (lambda (el)       (when (string= (org-element-property :name el) name) el))     nil t)))  (let ((s (buffer-substring (org-element-property :contents-begin el)      (org-element-property :contents-end el))))    (replace-regexp-in-string "\\\"" "\\\\\"" s)))#+END_SRC

Now, we can use those elements in a src-block like this.
#+NAME: ADD#+BEGIN_SRC emacs-lisp -n -r :noweb yes :tangle test.el(defun add (x y)  "One line description of adding X and Y.  <<get-string("DOC-OF-ADD")>> ;; code to code  <<get-string("add-options")>>"  ;; [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only support two args]] code to text  (+ x y) (ref:add)  ;; it appears the coderef needs to be on it's own line, otherwise you get a org-link-search: No match for coderef: add when you click on the link.  )#+END_SRC
#+RESULTS: ADD: add
The above block tangles to this for me:
#+BEGIN_SRC emacs-lisp(defun add (x y)  "One line description of adding X and Y.  We use the function add to calculate the sum of two numbers.   ;; code to code  - one  - two  - three  - and of course \"optional things\"  "  ;; [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only support two args]] code to text  (+ x y)   ;; it appears the coderef needs to be on it's own line, otherwise you get a org-link-search: No match for coderef: add when you click on the link.  )
#+END_SRC

** Notes
*** There is a reason we only support two args    :PROPERTIES:    :ID:       BAD97113-3561-4A4A-BA07-0CD5BF6BA35F    :END:

John

-----------------------------------
Professor John Kitchin 
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Wed, May 16, 2018 at 12:04 AM, ZHUO QL (KDr2) <zhuoql@yahoo.com> wrote:

Oh, that makes sense.
So in this way, we must put the text into quotes, and then into a txt code block. And also we don't have a chance to do any transformation of the text(e.g. org-mode list to javadoc format).  
I think the direct reference from code to text is better. I will try to implement it, but I'm not very familiar with the code base and don't have much time, so I can't give any commitment. But once I have anything to show, I'll be back here  :)
 Greetings.

ZHUO QL (KDr2, http://kdr2.com)

 

   On Tuesday, May 15, 2018, 6:05:31 PM GMT+8, Eric S Fraga <esflists@gmail.com> wrote: 
 
 On Tuesday, 15 May 2018 at 04:49, ZHUO QL (KDr2) wrote:
> 2. The bug Eric just found while putting a <> link within
> quotes, although, it may be easy to fix. 

I realised afterwards that it is not a bug but is a feature: org assumes
that anything before the << start of the link should be repeated on each
line of the incorporated src block.  This allows for easy incorporation
of code into a comment block, e.g. for C or sh etc.

-- 
Eric S Fraga via Emacs 27.0.50, Org release_9.1.6-591-gee336b  

  

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Re: Proposal: references from code to text.

[John Kitchin]

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I believe you can do that with the Library of Babel (
https://orgmode.org/worg/org-contrib/babel/library-of-babel.html)

John

-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Wed, May 16, 2018 at 7:58 PM, ZHUO QL (KDr2) <zhuoql@yahoo.com> wrote:

>
> Hooray!
>
> Do we have a way to make that piece of code a predefined and callable code
> block that can be seen and called in any Org file?
>
> Greetings.
>
> ZHUO QL (KDr2, http://kdr2.com)
>
>
>
> On Wednesday, May 16, 2018, 10:26:41 PM GMT+8, John Kitchin <
> jkitchin@andrew.cmu.edu> wrote:
>
>
> * Main document
>
> See [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only
> support two args]] (text to text) for notes about this function. The
> addition is done in line [[(add)]] (text to code).
>
> Here we put names on different kinds of elements so we can put them into a
> tangled file later.
>
> #+NAME: DOC-OF-ADD
> We use the function add to calculate the sum of two numbers.
>
> #+NAME: add-options
> - one
> - two
> - three
> - and of course "optional things"
>
>
> We use a block like this to get the contents of an org-element by name as
> a string, and possibly transform it some how, e.g. in this case I escape
> quotes. I guess you could also use an exporter to convert it to what ever
> form you want. You might bury this block at the end in an appendix so it
> isn't in the middle of your document like this.
>
> #+name: get-string
> #+BEGIN_SRC emacs-lisp :var name="add-options"
> (let ((el (org-element-map (org-element-parse-buffer)
> org-element-all-elements
>     (lambda (el)
>       (when (string= (org-element-property :name el) name)
> el))
>     nil t)))
>   (let ((s (buffer-substring (org-element-property :contents-begin el)
>      (org-element-property :contents-end el))))
>     (replace-regexp-in-string "\\\"" "\\\\\"" s)))
> #+END_SRC
>
>
> Now, we can use those elements in a src-block like this.
>
> #+NAME: ADD
> #+BEGIN_SRC emacs-lisp -n -r :noweb yes :tangle test.el
> (defun add (x y)
>   "One line description of adding X and Y.
>   <<get-string("DOC-OF-ADD")>> ;; code to code
>   <<get-string("add-options")>>"
>   ;; [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only
> support two args]] code to text
>   (+ x y) (ref:add)
>   ;; it appears the coderef needs to be on it's own line, otherwise you
> get a org-link-search: No match for coderef: add when you click on the link.
>   )
> #+END_SRC
>
> #+RESULTS: ADD
> : add
>
> The above block tangles to this for me:
>
> #+BEGIN_SRC emacs-lisp
> (defun add (x y)
>   "One line description of adding X and Y.
>   We use the function add to calculate the sum of two numbers.
>    ;; code to code
>   - one
>   - two
>   - three
>   - and of course \"optional things\"
>   "
>   ;; [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only
> support two args]] code to text
>   (+ x y)
>   ;; it appears the coderef needs to be on it's own line, otherwise you
> get a org-link-search: No match for coderef: add when you click on the link.
>   )
>
> #+END_SRC
>
>
> ** Notes
>
> *** There is a reason we only support two args
>     :PROPERTIES:
>     :ID:       BAD97113-3561-4A4A-BA07-0CD5BF6BA35F
>     :END:
>
>
> John
>
> -----------------------------------
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
>
>
> On Wed, May 16, 2018 at 12:04 AM, ZHUO QL (KDr2) <zhuoql@yahoo.com> wrote:
>
> Oh, that makes sense.
>
> So in this way, we must put the text into quotes, and then into a txt code
> block. And also we don't have a chance to do any transformation of the
> text(e.g. org-mode list to javadoc format).
>
> I think the direct reference from code to text is better. I will try to
> implement it, but I'm not very familiar with the code base and don't have
> much time, so I can't give any commitment. But once I have anything to
> show, I'll be back here  :)
>
> Greetings.
>
> ZHUO QL (KDr2, http://kdr2.com)
>
>
>
> On Tuesday, May 15, 2018, 6:05:31 PM GMT+8, Eric S Fraga <
> esflists@gmail.com> wrote:
>
>
> On Tuesday, 15 May 2018 at 04:49, ZHUO QL (KDr2) wrote:
>
> > 2. The bug Eric just found while putting a <> link within
> > quotes, although, it may be easy to fix.
>
>
> I realised afterwards that it is not a bug but is a feature: org assumes
> that anything before the << start of the link should be repeated on each
> line of the incorporated src block.  This allows for easy incorporation
> of code into a comment block, e.g. for C or sh etc.
>
> --
> Eric S Fraga via Emacs 27.0.50, Org release_9.1.6-591-gee336b
>
>
>

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Re: Proposal: references from code to text.

[ZHUO QL (KDr2)]

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Thanks, that works perfectly. I made a simple summary of this thread on my site: http://kdr2.com/tech/emacs/1805-approach-org-ref-code-to-text.html

 Greetings.

ZHUO QL (KDr2, http://kdr2.com)

 

   On Thursday, May 17, 2018, 11:11:39 AM GMT+8, John Kitchin <jkitchin@andrew.cmu.edu> wrote: 
 
 I believe you can do that with the Library of Babel (https://orgmode.org/worg/org-contrib/babel/library-of-babel.html)
John

-----------------------------------
Professor John Kitchin 
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803@johnkitchin
http://kitchingroup.cheme.cmu.edu

  

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Re: Proposal: references from code to text.

[John Kitchin]

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Cool! I was inspired by this to try it with Python doctests. Check out the
result here: http://kitchingroup.cheme.cmu.edu/blog/2018/05/17/
Literate-programming-with-python-doctests/

Note: I thought I had sent this email before, but it appeared as a draft
just now, so I am just sending it again.

John

-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Thu, May 17, 2018 at 2:33 AM, ZHUO QL (KDr2) <zhuoql@yahoo.com> wrote:

> Thanks, that works perfectly. I made a simple summary of this thread on my
> site: http://kdr2.com/tech/emacs/1805-approach-org-ref-code-to-text.html
>
>
> Greetings.
>
> ZHUO QL (KDr2, http://kdr2.com)
>
>
>
> On Thursday, May 17, 2018, 11:11:39 AM GMT+8, John Kitchin <
> jkitchin@andrew.cmu.edu> wrote:
>
>
> I believe you can do that with the Library of Babel (
> https://orgmode.org/worg/org-contrib/babel/library-of-babel.html)
>
> John
>
> -----------------------------------
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
>
>

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Re: Proposal: references from code to text.

[Grant Rettke]

On Wed, May 16, 2018 at 9:25 AM, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
> #+NAME: DOC-OF-ADD
> We use the function add to calculate the sum of two numbers.
>
> #+NAME: add-options
> - one
> - two
> - three
> - and of course "optional things"
>
>
> We use a block like this to get the contents of an org-element by name as a
> string, and possibly transform it some how, e.g. in this case I escape
> quotes. I guess you could also use an exporter to convert it to what ever
> form you want. You might bury this block at the end in an appendix so it
> isn't in the middle of your document like this.
>
> #+name: get-string
> #+BEGIN_SRC emacs-lisp :var name="add-options"
> (let ((el (org-element-map (org-element-parse-buffer)
> org-element-all-elements
>     (lambda (el)
>       (when (string= (org-element-property :name el) name)
> el))
>     nil t)))
>   (let ((s (buffer-substring (org-element-property :contents-begin el)
>      (org-element-property :contents-end el))))
>     (replace-regexp-in-string "\\\"" "\\\\\"" s)))
> #+END_SRC
>
>
> Now, we can use those elements in a src-block like this.
>
> #+NAME: ADD
> #+BEGIN_SRC emacs-lisp -n -r :noweb yes :tangle test.el
> (defun add (x y)
>   "One line description of adding X and Y.
>   <<get-string("DOC-OF-ADD")>> ;; code to code
>   <<get-string("add-options")>>"
>   ;; [[id:BAD97113-3561-4A4A-BA07-0CD5BF6BA35F][There is a reason we only
> support two args]] code to text
>   (+ x y) (ref:add)
>   ;; it appears the coderef needs to be on it's own line, otherwise you get
> a org-link-search: No match for coderef: add when you click on the link.
>   )
> #+END_SRC

This thread is great. Got me thinking about "true" one-time
documentation definitions in the file itself. The blog post laid it
all out very nicely.

It got me wondering if I (or anybody) would like something like this
style of use where you write your documentation in-line of the
document using a macro that might look like this:

Add a macro that you could use in the documentation like this both to
define the string and include it in the export

"The document adding function is pretty important to the doc function Add. .

#+MACRO: add-string (eval (add-string "$1" "$2")

Add a file buffer-local variable of key/value pairs for strings named 'strings'.

Add helper functions with the same names here "get-string, add-string"
to use it (pseudo code follows)

#+name: add-string
#+begin_src emacs-lisp :var key="default" :var value="default
;; if the key doesn't exist in the hashmap then add it and return the value
;; otherwise just return the value so it doesn't stomp on the existing value
#+end_src

Add would return the string, and that would get inserted in the export.

Get-string would just get they key's value from the hashmap

#+name: get-string
#+begin_src emacs-lisp :var key="default"
;; if the key exists then return its value
;; otherwise return "UNDEFINED"
#+end_src

To use that documentation in the source block it would work the same as above

It would be easy to add prettification to cut down on the "noise" of
the syntax to use the macro and do the literate call, too that people
might like.

This is all pseudo code but I think it is in the same spirit of this
thread. Do you?