Sharing documents with bibtex bibliography from org to non-org users

Sharing documents with bibtex bibliography from org to non-org users

[Martin Leduc]

Hi orgers,

People using org-mode or LaTeX to write scientific papers inevitably 
face problems when time comes to share a manuscript with co-authors for 
reviewing. Unless one decides to restrict the choice of his co-authors 
based exclusively on their knowledge of LaTeX, collaborators generally 
use Microsoft Word to write their documents.

One way to share LaTeX documents with non-LaTeX users is to simply 
copy-paste the LaTeX file into a Word document. You can then share this 
file with other people along with a pdf-compiled version of the 
manuscript allowing them to see all references, bibliography, equations 
and figures. This is the most convenient approach for the first author, 
who can simply copy-paste back the text into a tex file after the rounds 
of review and then compile the LaTeX manuscript again following some 
minor debugging.

However, the latter approach may not be suitable in situations where the 
document is intended to stay into a word format for whatever reason. It 
could be for instance because you want to be kind with some co-authors 
that wouldn't pay much interest into a scary document filled with 
complicated codes.

So I would like to know what are the best known strategies to circumvent 
the latter issue. To simplify, I accept that I will need to rewrite the 
equations (and eq. numbers) in the Word document. What I really want, 
however, is all the citations and the list of references being managed 
automatically at the step of exporting from org to ODT or to Plain Text.

The only solution I see now is to export the org document to a plain pdf 
(e.g. with no page numbers) and then to copy-paste the pdf into a Word 
document. This strategy is cumbersome because a lot of work is generally 
needed to format the word document (page wrapping, no line breaks 
between paragraphs, words hyphenation, etc).

Is there any cleaner solutions to this issue ? Or more general ideas on 
how we could facilitate the sharing of documents containing a bibtex 
bibliography between org and non-org users ?

Thanks

Martin

Re: Sharing documents with bibtex bibliography from org to non-org users

[Julian M. Burgos]

Hi Martin,

The best solution I found so far is to export to latex, and then use
pandoc to convert the tex document into word.  You can point pandoc to
your .bib file, so the bibliography gets into the word document, doing
something like this:

pandoc --bibliography /home/julian/Documents/org_files/myrefs.bib -o mypaper.docx mypaper.tex

This works ok.  Figures sometimes do not get inserted into the Word document,
and there are other relatively minor issues.  I have not bother looking
very deeply to figure out if they can be solved, I just pass the word
document to my collaborators for editing (so they can use the track
changes options and so for), and I also send the pdf file (from latex)
so they can see exactly how the document would look, in terms of figures
and tables.

When you get your reviews back, you need to manually insert them into
your org document, which is a pain in the back.

An alternative way is to pass the org document to your coworker, so they
can edit them in word directly.  They should ignore all the markup
language, do not use the track changes option, and save the resulting
document as a text file.  Then you can incorporate the changes directly
into your org file using ediff.  But as you said, the markup language
may turn off people that are not very friendly to some code and strange
commands.

A third way would be to export to odt.  I think you can set the exporter
so it uses libre office to convert the resulting file into .doc or
.docx.  I have not tried this very well, so I am not sure how this works
with references, figures and tables.

Hopefully somebody on the list may have a better option,

All the best,

Julian

Martin Leduc writes:

> Hi orgers,
>
> People using org-mode or LaTeX to write scientific papers inevitably 
> face problems when time comes to share a manuscript with co-authors for 
> reviewing. Unless one decides to restrict the choice of his co-authors 
> based exclusively on their knowledge of LaTeX, collaborators generally 
> use Microsoft Word to write their documents.
>
> One way to share LaTeX documents with non-LaTeX users is to simply 
> copy-paste the LaTeX file into a Word document. You can then share this 
> file with other people along with a pdf-compiled version of the 
> manuscript allowing them to see all references, bibliography, equations 
> and figures. This is the most convenient approach for the first author, 
> who can simply copy-paste back the text into a tex file after the rounds 
> of review and then compile the LaTeX manuscript again following some 
> minor debugging.
>
> However, the latter approach may not be suitable in situations where the 
> document is intended to stay into a word format for whatever reason. It 
> could be for instance because you want to be kind with some co-authors 
> that wouldn't pay much interest into a scary document filled with 
> complicated codes.
>
> So I would like to know what are the best known strategies to circumvent 
> the latter issue. To simplify, I accept that I will need to rewrite the 
> equations (and eq. numbers) in the Word document. What I really want, 
> however, is all the citations and the list of references being managed 
> automatically at the step of exporting from org to ODT or to Plain Text.
>
> The only solution I see now is to export the org document to a plain pdf 
> (e.g. with no page numbers) and then to copy-paste the pdf into a Word 
> document. This strategy is cumbersome because a lot of work is generally 
> needed to format the word document (page wrapping, no line breaks 
> between paragraphs, words hyphenation, etc).
>
> Is there any cleaner solutions to this issue ? Or more general ideas on 
> how we could facilitate the sharing of documents containing a bibtex 
> bibliography between org and non-org users ?
>
> Thanks
>
> Martin


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.burgos@hafogvatn.is

Re: Sharing documents with bibtex bibliography from org to non-org users

[Martin Leduc]

On 08/15/2016 11:36 PM, Martin Leduc wrote:
> Hi orgers,
>
> People using org-mode or LaTeX to write scientific papers inevitably
> face problems when time comes to share a manuscript with co-authors for
> reviewing. Unless one decides to restrict the choice of his co-authors
> based exclusively on their knowledge of LaTeX, collaborators generally
> use Microsoft Word to write their documents.
>
> One way to share LaTeX documents with non-LaTeX users is to simply
> copy-paste the LaTeX file into a Word document. You can then share this
> file with other people along with a pdf-compiled version of the
> manuscript allowing them to see all references, bibliography, equations
> and figures. This is the most convenient approach for the first author,
> who can simply copy-paste back the text into a tex file after the rounds
> of review and then compile the LaTeX manuscript again following some
> minor debugging.
>
> However, the latter approach may not be suitable in situations where the
> document is intended to stay into a word format for whatever reason. It
> could be for instance because you want to be kind with some co-authors
> that wouldn't pay much interest into a scary document filled with
> complicated codes.
>
> So I would like to know what are the best known strategies to circumvent
> the latter issue. To simplify, I accept that I will need to rewrite the
> equations (and eq. numbers) in the Word document. What I really want,
> however, is all the citations and the list of references being managed
> automatically at the step of exporting from org to ODT or to Plain Text.
>
> The only solution I see now is to export the org document to a plain pdf
> (e.g. with no page numbers) and then to copy-paste the pdf into a Word
> document. This strategy is cumbersome because a lot of work is generally
> needed to format the word document (page wrapping, no line breaks
> between paragraphs, words hyphenation, etc).
>
> Is there any cleaner solutions to this issue ? Or more general ideas on
> how we could facilitate the sharing of documents containing a bibtex
> bibliography between org and non-org users ?
>
> Thanks
>
> Martin
>
>
>
>
Sorry for double posting... please take this one.
M.

Re: Sharing documents with bibtex bibliography from org to non-org users

[Ken Mankoff]

Hi Martin,

The workflow I've been using for the past few months is this:

1) Export to ODT and then use LibreOffice to convert ODT to DOC with,

(use-package ox-odt
  :ensure nil
  :config (progn
	    (setq org-odt-preferred-output-format "doc")
	    (setq org-odt-convert-processes
		  '(("LibreOffice" "/Applications/LibreOffice.app/Contents/MacOS/soffice --headless --convert-to %f%x %i")))))

Note that LibreOffice *cannot* be open/running while exporting, or the conversion fails.

2) Clean up the DOC file using the following LibreOffice macro (you can give its own toolbar button for easy access). This removes some LaTeX-specific formatting (examples: \( and \), \begin{equation}, \ref, etc.) and replaces some (examples: ^{-2} to -2).

Sub ReplaceTeXStrings
  Dim mTeXStringsNO(99) As String
  Dim mTeXStringsCNVfrom(99) As String
  Dim mTexStringsCNVto(99) As String
  Dim n As Long
  Dim oDocument As Object
  Dim oReplace As Object

  mTeXStringsNO() = Array("\(", "\)", "\ref", "\mathrm", _
  		"\begin{equation}", "\end{equation}", "\left", "\right", _
  		"\singlespacing", "\doublespacing", "\,")
  		
   mTeXStringsCNV() = Array("\sigma","σ", "\rho","ρ", "\sum", "∑", _
   "\phi","ɸ", "\partial","∂", "\Theta","Θ", "^{th}","th", "^{{th}}","th", _
   "^{-1}","-1", "^{-2}","-2", "^{2}","^2", "^{3}", "^3",  "^{-3}", "^-3")
 
   		
  oDocument = ThisComponent
  oReplace = oDocument.createReplaceDescriptor
  For n = lbound(mTeXStringsNO()) To ubound(mTeXStringsNO())
    oReplace.SearchString = mTexStringsNO(n)
    oReplace.ReplaceString = ""
    oDocument.replaceAll(oReplace)
  Next n
  For n = lbound(mTeXStringsCNV()) To ubound(mTeXStringsCNV()) Step 2
    oReplace.SearchString = mTexStringsCNV(n)
    oReplace.ReplaceString = mTexStringsCNV(n+1)
    oDocument.replaceAll(oReplace)
  Next n
  End Sub


At this point, the DOC file is in decent shape, but equations are in raw LaTeX. The text does say things like see Figure {fig:foo} and Equation {eq:bar}. Figures are all numbered SEC.N, where SEC is the section number, and N restarts at 1 each section. References appear correctly as (Someone, 1942), or inline as Someone (1942), but there is no bibliography. It is easily readable, decently formatted, and much better than asking a co-author to read the raw LaTeX. 

3) Export to PDF and compile the final product

4) Send both PDF and DOC to co-authors. Let them know they can read and mark up the DOC via Track Changes, but the PDF is the canonical version and should be used when looking at Equations, Figures, Bibliography, or anything else that appears suspect in the DOC file.

5) I manually integrate changes back into the Org file.

Alternative workflows I've used in the past include Org -> LaTeX and then using Pandoc LaTeX -> DOCX. This version includes a bibliography, but overall I found the DOC more poorly formatted than the above workflow. If you prefer a cut-and-paste method, I'd consider Org -> HTML and then cut-and-paste that, rather than cut-and-paste PDF contents.

I hope this helps,

  -k.


On 2016-08-16 at 03:36, Martin Leduc <ldcmrtn@gmail.com> wrote:
> Hi orgers,
>
> People using org-mode or LaTeX to write scientific papers inevitably 
> face problems when time comes to share a manuscript with co-authors for 
> reviewing. Unless one decides to restrict the choice of his co-authors 
> based exclusively on their knowledge of LaTeX, collaborators generally 
> use Microsoft Word to write their documents.
>
> One way to share LaTeX documents with non-LaTeX users is to simply 
> copy-paste the LaTeX file into a Word document. You can then share this 
> file with other people along with a pdf-compiled version of the 
> manuscript allowing them to see all references, bibliography, equations 
> and figures. This is the most convenient approach for the first author, 
> who can simply copy-paste back the text into a tex file after the rounds 
> of review and then compile the LaTeX manuscript again following some 
> minor debugging.
>
> However, the latter approach may not be suitable in situations where the 
> document is intended to stay into a word format for whatever reason. It 
> could be for instance because you want to be kind with some co-authors 
> that wouldn't pay much interest into a scary document filled with 
> complicated codes.
>
> So I would like to know what are the best known strategies to circumvent 
> the latter issue. To simplify, I accept that I will need to rewrite the 
> equations (and eq. numbers) in the Word document. What I really want, 
> however, is all the citations and the list of references being managed 
> automatically at the step of exporting from org to ODT or to Plain Text.
>
> The only solution I see now is to export the org document to a plain pdf 
> (e.g. with no page numbers) and then to copy-paste the pdf into a Word 
> document. This strategy is cumbersome because a lot of work is generally 
> needed to format the word document (page wrapping, no line breaks 
> between paragraphs, words hyphenation, etc).
>
> Is there any cleaner solutions to this issue ? Or more general ideas on 
> how we could facilitate the sharing of documents containing a bibtex 
> bibliography between org and non-org users ?
>
> Thanks
>
> Martin

Re: Sharing documents with bibtex bibliography from org to non-org users

[Eric Abrahamsen]

Ken Mankoff <mankoff@gmail.com> writes:

> Hi Martin,
>
> The workflow I've been using for the past few months is this:
>
> 1) Export to ODT and then use LibreOffice to convert ODT to DOC with,
>
> (use-package ox-odt
>   :ensure nil
>   :config (progn
> 	    (setq org-odt-preferred-output-format "doc")
> 	    (setq org-odt-convert-processes
> 		  '(("LibreOffice" "/Applications/LibreOffice.app/Contents/MacOS/soffice --headless --convert-to %f%x %i")))))
>
> Note that LibreOffice *cannot* be open/running while exporting, or the conversion fails.

So *that's* what's going on! I could never figure out why it failed
sometimes -- there was no pattern that I could see. Is it possible for
the export process to know that this is why it failed, and provide a
more specific error message?

Re: Sharing documents with bibtex bibliography from org to non-org users

[Ken Mankoff]

On 2016-08-16 at 11:48, Eric Abrahamsen <eric@ericabrahamsen.net> wrote:
> Ken Mankoff <mankoff@gmail.com> writes:
>> Note that LibreOffice *cannot* be open/running while exporting, or
>> the conversion fails.
>
> So *that's* what's going on! I could never figure out why it failed
> sometimes -- there was no pattern that I could see. Is it possible for
> the export process to know that this is why it failed, and provide a
> more specific error message?

I don't see a way to get the reason for the failure, but you could preempt the failure with a check. Advise the org ODT export function, and have it check for an active LibreOffice process, and then warn.

  -k.
  

Re: Sharing documents with bibtex bibliography from org to non-org users

[Maria Shinoto]

Hi,

in the recent year and a half I have been writing in Pandoc Markdown, 
exchanging documents and research papers with others as .docx documents 
that I converted directly in Pandoc, or, if a biblatex bibliography was 
involved, via Latex document.

The route back to Pandoc was copy and paste, which was not as time 
consuming as one might suppose. I had to go over the changes anyway.

I am an archaeologist, so there are no problems with equations ;)

A lot of idea exchange is via email, and composing ideas in Pandoc 
Markdown before sending the mail was a well organised way of developing 
research.

Now I hope to get org-mode running the same way, either using direct 
export to word or Pandoc.


Best,
Maria







Am 16.08.16 um 20:41 schrieb Ken Mankoff:
> Hi Martin,
>
> The workflow I've been using for the past few months is this:
>
> 1) Export to ODT and then use LibreOffice to convert ODT to DOC with,
>
> (use-package ox-odt
>   :ensure nil
>   :config (progn
> 	    (setq org-odt-preferred-output-format "doc")
> 	    (setq org-odt-convert-processes
> 		  '(("LibreOffice" "/Applications/LibreOffice.app/Contents/MacOS/soffice --headless --convert-to %f%x %i")))))
>
> Note that LibreOffice *cannot* be open/running while exporting, or the conversion fails.
>
> 2) Clean up the DOC file using the following LibreOffice macro (you can give its own toolbar button for easy access). This removes some LaTeX-specific formatting (examples: \( and \), \begin{equation}, \ref, etc.) and replaces some (examples: ^{-2} to -2).
>
> Sub ReplaceTeXStrings
>   Dim mTeXStringsNO(99) As String
>   Dim mTeXStringsCNVfrom(99) As String
>   Dim mTexStringsCNVto(99) As String
>   Dim n As Long
>   Dim oDocument As Object
>   Dim oReplace As Object
>
>   mTeXStringsNO() = Array("\(", "\)", "\ref", "\mathrm", _
>   		"\begin{equation}", "\end{equation}", "\left", "\right", _
>   		"\singlespacing", "\doublespacing", "\,")
>   		
>    mTeXStringsCNV() = Array("\sigma","σ", "\rho","ρ", "\sum", "∑", _
>    "\phi","ɸ", "\partial","∂", "\Theta","Θ", "^{th}","th", "^{{th}}","th", _
>    "^{-1}","-1", "^{-2}","-2", "^{2}","^2", "^{3}", "^3",  "^{-3}", "^-3")
>
>    		
>   oDocument = ThisComponent
>   oReplace = oDocument.createReplaceDescriptor
>   For n = lbound(mTeXStringsNO()) To ubound(mTeXStringsNO())
>     oReplace.SearchString = mTexStringsNO(n)
>     oReplace.ReplaceString = ""
>     oDocument.replaceAll(oReplace)
>   Next n
>   For n = lbound(mTeXStringsCNV()) To ubound(mTeXStringsCNV()) Step 2
>     oReplace.SearchString = mTexStringsCNV(n)
>     oReplace.ReplaceString = mTexStringsCNV(n+1)
>     oDocument.replaceAll(oReplace)
>   Next n
>   End Sub
>
>
> At this point, the DOC file is in decent shape, but equations are in raw LaTeX. The text does say things like see Figure {fig:foo} and Equation {eq:bar}. Figures are all numbered SEC.N, where SEC is the section number, and N restarts at 1 each section. References appear correctly as (Someone, 1942), or inline as Someone (1942), but there is no bibliography. It is easily readable, decently formatted, and much better than asking a co-author to read the raw LaTeX.
>
> 3) Export to PDF and compile the final product
>
> 4) Send both PDF and DOC to co-authors. Let them know they can read and mark up the DOC via Track Changes, but the PDF is the canonical version and should be used when looking at Equations, Figures, Bibliography, or anything else that appears suspect in the DOC file.
>
> 5) I manually integrate changes back into the Org file.
>
> Alternative workflows I've used in the past include Org -> LaTeX and then using Pandoc LaTeX -> DOCX. This version includes a bibliography, but overall I found the DOC more poorly formatted than the above workflow. If you prefer a cut-and-paste method, I'd consider Org -> HTML and then cut-and-paste that, rather than cut-and-paste PDF contents.
>
> I hope this helps,
>
>   -k.
>
>
> On 2016-08-16 at 03:36, Martin Leduc <ldcmrtn@gmail.com> wrote:
>> Hi orgers,
>>
>> People using org-mode or LaTeX to write scientific papers inevitably
>> face problems when time comes to share a manuscript with co-authors for
>> reviewing. Unless one decides to restrict the choice of his co-authors
>> based exclusively on their knowledge of LaTeX, collaborators generally
>> use Microsoft Word to write their documents.
>>
>> One way to share LaTeX documents with non-LaTeX users is to simply
>> copy-paste the LaTeX file into a Word document. You can then share this
>> file with other people along with a pdf-compiled version of the
>> manuscript allowing them to see all references, bibliography, equations
>> and figures. This is the most convenient approach for the first author,
>> who can simply copy-paste back the text into a tex file after the rounds
>> of review and then compile the LaTeX manuscript again following some
>> minor debugging.
>>
>> However, the latter approach may not be suitable in situations where the
>> document is intended to stay into a word format for whatever reason. It
>> could be for instance because you want to be kind with some co-authors
>> that wouldn't pay much interest into a scary document filled with
>> complicated codes.
>>
>> So I would like to know what are the best known strategies to circumvent
>> the latter issue. To simplify, I accept that I will need to rewrite the
>> equations (and eq. numbers) in the Word document. What I really want,
>> however, is all the citations and the list of references being managed
>> automatically at the step of exporting from org to ODT or to Plain Text.
>>
>> The only solution I see now is to export the org document to a plain pdf
>> (e.g. with no page numbers) and then to copy-paste the pdf into a Word
>> document. This strategy is cumbersome because a lot of work is generally
>> needed to format the word document (page wrapping, no line breaks
>> between paragraphs, words hyphenation, etc).
>>
>> Is there any cleaner solutions to this issue ? Or more general ideas on
>> how we could facilitate the sharing of documents containing a bibtex
>> bibliography between org and non-org users ?
>>
>> Thanks
>>
>> Martin
>
>

Re: Sharing documents with bibtex bibliography from org to non-org users

[Martin Leduc]

Hi Ken, I tried the Pandoc solution first and the result appears quite 
satisfying to me. In the docx document, I can see citations, 
bibliography, figures and even equations. I will keep note of your first 
suggestion if I face issues with pandoc.

Thanks,
Martin


On 08/16/2016 07:41 AM, Ken Mankoff wrote:
> Hi Martin,
>
> The workflow I've been using for the past few months is this:
>
> 1) Export to ODT and then use LibreOffice to convert ODT to DOC with,
>
> (use-package ox-odt
>   :ensure nil
>   :config (progn
> 	    (setq org-odt-preferred-output-format "doc")
> 	    (setq org-odt-convert-processes
> 		  '(("LibreOffice" "/Applications/LibreOffice.app/Contents/MacOS/soffice --headless --convert-to %f%x %i")))))
>
> Note that LibreOffice *cannot* be open/running while exporting, or the conversion fails.
>
> 2) Clean up the DOC file using the following LibreOffice macro (you can give its own toolbar button for easy access). This removes some LaTeX-specific formatting (examples: \( and \), \begin{equation}, \ref, etc.) and replaces some (examples: ^{-2} to -2).
>
> Sub ReplaceTeXStrings
>   Dim mTeXStringsNO(99) As String
>   Dim mTeXStringsCNVfrom(99) As String
>   Dim mTexStringsCNVto(99) As String
>   Dim n As Long
>   Dim oDocument As Object
>   Dim oReplace As Object
>
>   mTeXStringsNO() = Array("\(", "\)", "\ref", "\mathrm", _
>   		"\begin{equation}", "\end{equation}", "\left", "\right", _
>   		"\singlespacing", "\doublespacing", "\,")
>   		
>    mTeXStringsCNV() = Array("\sigma","σ", "\rho","ρ", "\sum", "∑", _
>    "\phi","ɸ", "\partial","∂", "\Theta","Θ", "^{th}","th", "^{{th}}","th", _
>    "^{-1}","-1", "^{-2}","-2", "^{2}","^2", "^{3}", "^3",  "^{-3}", "^-3")
>
>    		
>   oDocument = ThisComponent
>   oReplace = oDocument.createReplaceDescriptor
>   For n = lbound(mTeXStringsNO()) To ubound(mTeXStringsNO())
>     oReplace.SearchString = mTexStringsNO(n)
>     oReplace.ReplaceString = ""
>     oDocument.replaceAll(oReplace)
>   Next n
>   For n = lbound(mTeXStringsCNV()) To ubound(mTeXStringsCNV()) Step 2
>     oReplace.SearchString = mTexStringsCNV(n)
>     oReplace.ReplaceString = mTexStringsCNV(n+1)
>     oDocument.replaceAll(oReplace)
>   Next n
>   End Sub
>
>
> At this point, the DOC file is in decent shape, but equations are in raw LaTeX. The text does say things like see Figure {fig:foo} and Equation {eq:bar}. Figures are all numbered SEC.N, where SEC is the section number, and N restarts at 1 each section. References appear correctly as (Someone, 1942), or inline as Someone (1942), but there is no bibliography. It is easily readable, decently formatted, and much better than asking a co-author to read the raw LaTeX.
>
> 3) Export to PDF and compile the final product
>
> 4) Send both PDF and DOC to co-authors. Let them know they can read and mark up the DOC via Track Changes, but the PDF is the canonical version and should be used when looking at Equations, Figures, Bibliography, or anything else that appears suspect in the DOC file.
>
> 5) I manually integrate changes back into the Org file.
>
> Alternative workflows I've used in the past include Org -> LaTeX and then using Pandoc LaTeX -> DOCX. This version includes a bibliography, but overall I found the DOC more poorly formatted than the above workflow. If you prefer a cut-and-paste method, I'd consider Org -> HTML and then cut-and-paste that, rather than cut-and-paste PDF contents.
>
> I hope this helps,
>
>   -k.
>
>
> On 2016-08-16 at 03:36, Martin Leduc <ldcmrtn@gmail.com> wrote:
>> Hi orgers,
>>
>> People using org-mode or LaTeX to write scientific papers inevitably
>> face problems when time comes to share a manuscript with co-authors for
>> reviewing. Unless one decides to restrict the choice of his co-authors
>> based exclusively on their knowledge of LaTeX, collaborators generally
>> use Microsoft Word to write their documents.
>>
>> One way to share LaTeX documents with non-LaTeX users is to simply
>> copy-paste the LaTeX file into a Word document. You can then share this
>> file with other people along with a pdf-compiled version of the
>> manuscript allowing them to see all references, bibliography, equations
>> and figures. This is the most convenient approach for the first author,
>> who can simply copy-paste back the text into a tex file after the rounds
>> of review and then compile the LaTeX manuscript again following some
>> minor debugging.
>>
>> However, the latter approach may not be suitable in situations where the
>> document is intended to stay into a word format for whatever reason. It
>> could be for instance because you want to be kind with some co-authors
>> that wouldn't pay much interest into a scary document filled with
>> complicated codes.
>>
>> So I would like to know what are the best known strategies to circumvent
>> the latter issue. To simplify, I accept that I will need to rewrite the
>> equations (and eq. numbers) in the Word document. What I really want,
>> however, is all the citations and the list of references being managed
>> automatically at the step of exporting from org to ODT or to Plain Text.
>>
>> The only solution I see now is to export the org document to a plain pdf
>> (e.g. with no page numbers) and then to copy-paste the pdf into a Word
>> document. This strategy is cumbersome because a lot of work is generally
>> needed to format the word document (page wrapping, no line breaks
>> between paragraphs, words hyphenation, etc).
>>
>> Is there any cleaner solutions to this issue ? Or more general ideas on
>> how we could facilitate the sharing of documents containing a bibtex
>> bibliography between org and non-org users ?
>>
>> Thanks
>>
>> Martin
>
>
>

Re: Sharing documents with bibtex bibliography from org to non-org users

[Ken Mankoff]

On 2016-08-17 at 01:30, Martin Leduc <ldcmrtn@gmail.com> wrote:
> Hi Ken, I tried the Pandoc solution first and the result appears quite
> satisfying to me. In the docx document, I can see citations,
> bibliography, figures and even equations. I will keep note of your
> first suggestion if I face issues with pandoc.


Pandoc does work well, but I notice you didn't say tables. Does it do that for you well? For me, they are unreadable, with each column a full page width, and the table therefore far too wide.

I think I run into a another common problem though where my Org text has words like "\(x\) = 42 kg m\(^{-3}\)". I think this is correct LaTeX syntax?

Anyway, in pandoc "x" is properly exported as a math symbol, but it doesn't look very good and has a box around it. The m^-3 is not exported properly. I see a "m", and then an empty math box, and then the superscript "-3".

If I do Org -> ODT, the "x" is not technically correct, but looks better. It is just italicized. The exponent is properly written next to them without an empty math box between the two.

If someone has a different suggestion for how to write this in Org for pandoc->DOCX, I'd be grateful, because references and figures are handled better by pandoc than Org -> ODT.

  -k.

Re: Sharing documents with bibtex bibliography from org to non-org users

[Maria Shinoto]

Hi,


Am 17.08.16 um 11:00 schrieb Ken Mankoff:

> Pandoc does work well, but I notice you didn't say tables. Does it
> do
 > that for you well? For me, they are unreadable, with each column a
 > full
 > page width, and the table therefore far too wide.

You could write the tables in Latex, Pandoc accepts that. But I think in 
this case you cannot work with .docx -- I am not sure. But you can also 
work on the default template and change the settings for tables. I have 
several templates (Latex, beamer) for several purposes, really a nice 
feature.

> Anyway, in pandoc "x" is properly exported as a math symbol, but it
 > doesn't look very good and has a box around it. The m^-3 is not exported
 > properly. I see a "m", and then an empty math box, and then the
 > superscript "-3".
>
> If I do Org -> ODT, the "x" is not technically correct, but looks
 > better. It is just italicized. The exponent is properly written next to
 > them without an empty math box between the two.

Both problems can be solved in the template either. You can have a look 
at the Latex Pandoc produces, then change to what you need and enter 
this into the template.

Best,
Maria



>
> If someone has a different suggestion for how to write this in Org
> for
pandoc->DOCX, I'd be grateful, because references and figures are
handled better by pandoc than Org -> ODT.
>
> -k.
>

Re: Sharing documents with bibtex bibliography from org to non-org users

[Julian M. Burgos]

Hi Martin,

The best solution I found so far is to export to latex, and then use
pandoc to convert the tex document into word.  You can point pandoc to
your .bib file, so the bibliography gets into the word document, doing
something like this:

pandoc --bibliography /home/julian/Documents/org_files/myrefs.bib -o mypaper.docx mypaper.tex

This works ok.  Figures sometimes do not get inserted into the Word document,
and there are other relatively minor issues.  I have not bother looking
very deeply to figure out if they can be solved, I just pass the word
document to my collaborators for editing (so they can use the track
changes options and so for), and I also send the pdf file (from latex)
so they can see exactly how the document would look, in terms of figures
and tables.

When you get your reviews back, you need to manually insert them into
your org document, which is a pain in the back.

An alternative way is to pass the org document to your coworker, so they
can edit them in word directly.  They should ignore all the markup
language, do not use the track changes option, and save the resulting
document as a text file.  Then you can incorporate the changes directly
into your org file using ediff.  But as you said, the markup language
may turn off people that are not very friendly to some code and strange
commands.

A third way would be to export to odt.  I think you can set the exporter
so it uses libre office to convert the resulting file into .doc or
.docx.  I have not tried this very well, so I am not sure how this works
with references, figures and tables.

Hopefully somebody on the list may have a better option,

All the best,

Julian

Martin Leduc writes:

> Hi orgers,
>
> People using org-mode or LaTeX to write scientific papers inevitably 
> face problems when time comes to share a manuscript with co-authors for 
> reviewing. Unless one decides to restrict the choice of his co-authors 
> based exclusively on their knowledge of LaTeX, collaborators generally 
> use Microsoft Word to write their documents.
>
> One way to share LaTeX documents with non-LaTeX users is to simply 
> copy-paste the LaTeX file into a Word document. You can then share this 
> file with other people along with a pdf-compiled version of the 
> manuscript allowing them to see all references, bibliography, equations 
> and figures. This is the most convenient approach for the first author, 
> who can simply copy-paste back the text into a tex file after the rounds 
> of review and then compile the LaTeX manuscript again following some 
> minor debugging.
>
> However, the latter approach may not be suitable in situations where the 
> document is intended to stay into a word format for whatever reason. It 
> could be for instance because you want to be kind with some co-authors 
> that wouldn't pay much interest into a scary document filled with 
> complicated codes.
>
> So I would like to know what are the best known strategies to circumvent 
> the latter issue. To simplify, I accept that I will need to rewrite the 
> equations (and eq. numbers) in the Word document. What I really want, 
> however, is all the citations and the list of references being managed 
> automatically at the step of exporting from org to ODT or to Plain Text.
>
> The only solution I see now is to export the org document to a plain pdf 
> (e.g. with no page numbers) and then to copy-paste the pdf into a Word 
> document. This strategy is cumbersome because a lot of work is generally 
> needed to format the word document (page wrapping, no line breaks 
> between paragraphs, words hyphenation, etc).
>
> Is there any cleaner solutions to this issue ? Or more general ideas on 
> how we could facilitate the sharing of documents containing a bibtex 
> bibliography between org and non-org users ?
>
> Thanks
>
> Martin


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.burgos@hafogvatn.is

Re: Sharing documents with bibtex bibliography from org to non-org users

[Martin Leduc]

Hi Julian, thank you for the suggestion. I didn't know pandoc, and 
didn't expect to find something so near from what I was searching !

Converting the tex file to docx using pandoc, I can see the correct 
citations and bibliography, and even equations (in openoffice, haven't 
tested it with Microsoft word) and figures. I see minor issues such as 
the equation numbers that are not compiled (references stay as labels), 
but overall it is quite satisfying.

On the other hand, exporting from org to odt is more or less like 
copy-pasting latex source code (no references, no bibliography, but... 
figures !)

All the best,

Martin




On 08/16/2016 11:16 AM, Julian M. Burgos wrote:
> Hi Martin,
>
> The best solution I found so far is to export to latex, and then use
> pandoc to convert the tex document into word.  You can point pandoc to
> your .bib file, so the bibliography gets into the word document, doing
> something like this:
>
> pandoc --bibliography /home/julian/Documents/org_files/myrefs.bib -o mypaper.docx mypaper.tex
>
> This works ok.  Figures sometimes do not get inserted into the Word document,
> and there are other relatively minor issues.  I have not bother looking
> very deeply to figure out if they can be solved, I just pass the word
> document to my collaborators for editing (so they can use the track
> changes options and so for), and I also send the pdf file (from latex)
> so they can see exactly how the document would look, in terms of figures
> and tables.
>
> When you get your reviews back, you need to manually insert them into
> your org document, which is a pain in the back.
>
> An alternative way is to pass the org document to your coworker, so they
> can edit them in word directly.  They should ignore all the markup
> language, do not use the track changes option, and save the resulting
> document as a text file.  Then you can incorporate the changes directly
> into your org file using ediff.  But as you said, the markup language
> may turn off people that are not very friendly to some code and strange
> commands.
>
> A third way would be to export to odt.  I think you can set the exporter
> so it uses libre office to convert the resulting file into .doc or
> .docx.  I have not tried this very well, so I am not sure how this works
> with references, figures and tables.
>
> Hopefully somebody on the list may have a better option,
>
> All the best,
>
> Julian
>
> Martin Leduc writes:
>
>> Hi orgers,
>>
>> People using org-mode or LaTeX to write scientific papers inevitably
>> face problems when time comes to share a manuscript with co-authors for
>> reviewing. Unless one decides to restrict the choice of his co-authors
>> based exclusively on their knowledge of LaTeX, collaborators generally
>> use Microsoft Word to write their documents.
>>
>> One way to share LaTeX documents with non-LaTeX users is to simply
>> copy-paste the LaTeX file into a Word document. You can then share this
>> file with other people along with a pdf-compiled version of the
>> manuscript allowing them to see all references, bibliography, equations
>> and figures. This is the most convenient approach for the first author,
>> who can simply copy-paste back the text into a tex file after the rounds
>> of review and then compile the LaTeX manuscript again following some
>> minor debugging.
>>
>> However, the latter approach may not be suitable in situations where the
>> document is intended to stay into a word format for whatever reason. It
>> could be for instance because you want to be kind with some co-authors
>> that wouldn't pay much interest into a scary document filled with
>> complicated codes.
>>
>> So I would like to know what are the best known strategies to circumvent
>> the latter issue. To simplify, I accept that I will need to rewrite the
>> equations (and eq. numbers) in the Word document. What I really want,
>> however, is all the citations and the list of references being managed
>> automatically at the step of exporting from org to ODT or to Plain Text.
>>
>> The only solution I see now is to export the org document to a plain pdf
>> (e.g. with no page numbers) and then to copy-paste the pdf into a Word
>> document. This strategy is cumbersome because a lot of work is generally
>> needed to format the word document (page wrapping, no line breaks
>> between paragraphs, words hyphenation, etc).
>>
>> Is there any cleaner solutions to this issue ? Or more general ideas on
>> how we could facilitate the sharing of documents containing a bibtex
>> bibliography between org and non-org users ?
>>
>> Thanks
>>
>> Martin
>

Re: Sharing documents with bibtex bibliography from org to non-org users

[Uwe Brauer]

>>> "Martin" == Martin Leduc <ldcmrtn@gmail.com> writes:

   > Hi orgers,
   > People using org-mode or LaTeX to write scientific papers inevitably
   > face problems when time comes to share a manuscript with co-authors
   > for reviewing. Unless one decides to restrict the choice of his
   > co-authors based exclusively on their knowledge of LaTeX,
   > collaborators generally use Microsoft Word to write their documents.


In my experience 
    - Pandoc is one possibility but does not allow ordering of the
      references.

So the following works best:

    -  Use an org file (and the org-ref pkg). See the file org-ref.org
       for details. I have some addons, John, the author of org-ref.org
       provided for my needs, if you want I can send them to you.
       *Important* export the odt file to html, not to ascii text, nor
       to odt. Open the html file with openoffice/libreoffice and save
       it then to odt or doc or docx.

The other way from docx seems somehow to work with pandoc.

Uwe Brauer 

Sharing documents with bibtex bibliography from org to non-org users

[Martin Leduc]

Hi orgers,

People using org-mode or LaTeX to write scientific papers inevitably 
face problems when the time comes to share a manuscript with co-authors 
for reviewing. Unless one decides to restrict the choice of his 
co-authors based exclusively on their knowledge of LaTeX, collaborators 
generally use Microsoft Word to write their documents.

One way to share LaTeX documents with non-LaTeX users is to simply 
copy-paste the LaTeX file into a Word document. You can then share this 
file with other people along with the pdf-compiled version to allow them 
to see all references, bibliography, equations and figures. This is the 
most convenient approach for the first author, who can simply copy-paste 
back the text into a tex file after the rounds of review and then 
compile the LaTeX manuscript again following some minor debugging.

However, the latter approach may not be suitable in several situations. 
For instance, it could be because the document is intended to stay into 
a word format for whatever reason, or simply because you want to be kind 
with some co-authors that wouldn't pay much interest into a scary 
document filled with complicated codes.

So I would like to know what are the best known strategies to circumvent 
the latter issue. To simplify, I accept that I will need to rewrite the 
equations (and eq. numbers) in the Word document. What I really want, 
however, is all the citations and the list of references being managed 
automatically at the step of exporting from org to ODT or to Plain Text.

The only solution I see from now is to export the org document to a 
plain pdf (e.g. with no page numbers) and then to copy paste from the 
pdf to a Word documents. This strategy is rather cumbersome as a lot of 
work is needed in terms of formatting the word document (page wrapping, 
no line breaks between paragraphs, words hyphenation, etc).

Is there any cleaner solutions to this issue ? Or more general ideas on 
how we could facilitate the sharing documents containing a bibtex 
bibliography between org and non-org users ?

Thanks

Martin