Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Rainer M Krug
On 18/01/13 05:17, Jerry wrote:
 
 On Jan 17, 2013, at 2:30 AM, Alex Fernandez wrote:
 
 Hi Jerry,
 
 I am the primary author of eLyXer.
 
 On Thu, Jan 17, 2013 at 4:49 AM, Jerry lancebo...@qwest.net 
 mailto:lancebo...@qwest.net
 wrote:
 
 Thanks for that tip. I checked it out. It's just a Python thing so it works 
 fine on OS X,
 and LyX picked it up as advertised.
 
 
 Yes, I can confirm that OS X is fully supported.
 
 
 The output on my simple test case does look nice in a browser, but I get the 
 same error 
 opening with Word as I first described: The XML file bla bla bla cannot be 
 opened... etc.
 I thought maybe my copy of Word was broken but it reads other HTML files 
 fine--I'm guessing
 they don't have the XML stuff in them, however.
 
 
 Word does not like XHTML very much; you need to export to HTML 4, using the 
 --html option. 
 http://elyxer.nongnu.org/userguide.html#sub:HTML-Code If you are doing the 
 conversion inside
 LyX, instead of on the command line, you have to add the --html in the 
 conversion interface.
 
 
 I checked the HTML file that eLyXer made with the W3C page and got: The 
 uploaded document
 - was successfully checked as XHTML 1.0 Transitional.
 
 
 Yes, eLyXer outputs pure XHTML.
 
 
 Also--eLyXer does not appear to use MathML so I don't think there is any 
 hope of getting 
 editable math into Word using this method. (But I haven't read all of the 
 eLyXer docs.)
 
 
 eLyXer has several options for Math output: 
 http://elyxer.nongnu.org/userguide.html#sub:Math 
 Sadly, none of them is MathML, since at the time eLyXer was conceived it was 
 not very widely 
 supported, and I have not found the time to add it.
 
 Hope this helps,
 
 Alex Fernández.
 
 Hi, Alex,
 
 Thanks for the comments and for the great tool. It does what it claims to to, 
 convert LyX to
 HTML, with lots of math options. The default conversion looks great in a 
 browser.
 
 I tried your --html suggestion and indeed Word opens it, and displays it much 
 as a browser
 does. Unfortunately, the HTML limitations are apparent; this is probably as 
 good as a HTML-only
 conversion can get.
 
 In my slow-witted way, I'm starting to understand why Word will not open the 
 various XML
 formats that I'm throwing at it. (I also played with TeXht today (and the Mac 
 GUI over it,
 SimpleTeXht. This method also makes XML in some variations, and .odt.) So 
 Word isn't
 broken—it's just not made to recognize this particular kind of XML. (I want 
 to use the word
 schema but don't really know what I'm talking about.) So What is missing, 
 as has been stated
 in previous threads, is a converter from the XML that we're seeing to .docx, 
 it seems.

check pandoc - I am using pandoc to convert xhtml to docx and odt - works 
perfect for me. I just

\converter xhtml msdocx pandoc -o $$o $$i 
\converter xhtml odt lo pandoc -o $$o $$i added the following converter:

You have to play with the LyX xhtml or the eLyXer xhtml - I used LyXHTRML 
because it workded
better in my case.

I really think that pandoc should be detected automatically by LyX (when doing 
reconfigure) and
added as it provides very usable conversions.


Cheers,

Rainer

 
 Jerry



Re: Vancouver style options -changed to: almost soved

2013-01-18 Thread Wolfgang Engelmann
Am Dienstag, 15. Januar 2013, 14:39:07 schrieb Wolfgang Engelmann:
 Hi,
 
 still not done with Vancouver style
 
 I tried for quite some time but can't find the option for references, in
 which more than 2 authors are referenced as
 author1 et al
 
 Wolfgang

I found out how to solve it:

in vancouver.bst
(which is in my case in home/wolfgang/texlive/2012/texmf-dist/bibtex/bst/)

change
nameptr #6
to
nameptr #2

and 
numname #6
to
numname #2

I saved this changed vancouver.bst to vancouver2etal.bst
in order not to interfere with the original file 
and added this to documentsettings  bibliography styledefault style
WHICH DID NOT WORK
however, if I changed vancouver2etal.bst to vancouver.bst
(by saving the original vancouver.bst preliminary as vancouverOrig.bst)
IT WORKED
namely, only maximally 2 authors in the bibliography, if more: et al after 
the second one

My question:
why was vancouver2etal in bibliography styledefault style not recognized? 
I did a reconfigure before.

Wolfgang


Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Rainer M Krug
On 18/01/13 09:10, Rainer M Krug wrote:
 On 18/01/13 05:17, Jerry wrote:
 
 On Jan 17, 2013, at 2:30 AM, Alex Fernandez wrote:
 
 Hi Jerry,
 
 I am the primary author of eLyXer.
 
 On Thu, Jan 17, 2013 at 4:49 AM, Jerry lancebo...@qwest.net
 mailto:lancebo...@qwest.net wrote:
 
 Thanks for that tip. I checked it out. It's just a Python thing so it works 
 fine on OS X, 
 and LyX picked it up as advertised.
 
 
 Yes, I can confirm that OS X is fully supported.
 
 
 The output on my simple test case does look nice in a browser, but I get 
 the same error 
 opening with Word as I first described: The XML file bla bla bla cannot be 
 opened...
 etc. I thought maybe my copy of Word was broken but it reads other HTML 
 files fine--I'm
 guessing they don't have the XML stuff in them, however.
 
 
 Word does not like XHTML very much; you need to export to HTML 4, using the 
 --html option.
  http://elyxer.nongnu.org/userguide.html#sub:HTML-Code If you are doing the 
 conversion
 inside LyX, instead of on the command line, you have to add the --html in 
 the conversion
 interface.
 
 
 I checked the HTML file that eLyXer made with the W3C page and got: The 
 uploaded document 
 - was successfully checked as XHTML 1.0 Transitional.
 
 
 Yes, eLyXer outputs pure XHTML.
 
 
 Also--eLyXer does not appear to use MathML so I don't think there is any 
 hope of getting 
 editable math into Word using this method. (But I haven't read all of the 
 eLyXer docs.)
 
 
 eLyXer has several options for Math output:
 http://elyxer.nongnu.org/userguide.html#sub:Math Sadly, none of them is 
 MathML, since at
 the time eLyXer was conceived it was not very widely supported, and I have 
 not found the
 time to add it.
 
 Hope this helps,
 
 Alex Fernández.
 
 Hi, Alex,
 
 Thanks for the comments and for the great tool. It does what it claims to 
 to, convert LyX to 
 HTML, with lots of math options. The default conversion looks great in a 
 browser.
 
 I tried your --html suggestion and indeed Word opens it, and displays it 
 much as a browser 
 does. Unfortunately, the HTML limitations are apparent; this is probably as 
 good as a
 HTML-only conversion can get.
 
 In my slow-witted way, I'm starting to understand why Word will not open the 
 various XML 
 formats that I'm throwing at it. (I also played with TeXht today (and the 
 Mac GUI over it, 
 SimpleTeXht. This method also makes XML in some variations, and .odt.) So 
 Word isn't 
 broken—it's just not made to recognize this particular kind of XML. (I want 
 to use the word 
 schema but don't really know what I'm talking about.) So What is missing, 
 as has been
 stated in previous threads, is a converter from the XML that we're seeing to 
 .docx, it
 seems.
 
 check pandoc - I am using pandoc to convert xhtml to docx and odt - works 
 perfect for me. I
 just

Ups - should have been:
###
I just added the following converter:

\converter xhtml msdocx pandoc -o $$o $$i 
\converter xhtml odt lo pandoc -o $$o $$i 
###

 
 \converter xhtml msdocx pandoc -o $$o $$i  \converter xhtml odt 
 lo pandoc -o $$o
 $$i added the following converter:
 
 You have to play with the LyX xhtml or the eLyXer xhtml - I used LyXHTRML 
 because it workded 
 better in my case.
 
 I really think that pandoc should be detected automatically by LyX (when 
 doing reconfigure)
 and added as it provides very usable conversions.
 
 
 Cheers,
 
 Rainer
 
 
 Jerry
 
 



Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Liviu Andronic
Rainer,


On Fri, Jan 18, 2013 at 9:44 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 \converter xhtml msdocx pandoc -o $$o $$i 
 \converter xhtml odt lo pandoc -o $$o $$i 
 ###

Would you mind pasting all the pandoc-related converter and format
definitions that work for you to http://www.lyx.org/trac/ticket/6042 ?
If you include working configs there and others can test them and
confirm they indeed work, then chances are that they would get
included in base LyX.

Liviu


Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Rainer M Krug
On 18/01/13 10:58, Liviu Andronic wrote:
 Rainer,
 
 
 On Fri, Jan 18, 2013 at 9:44 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 \converter xhtml msdocx pandoc -o $$o $$i  \converter xhtml odt 
 lo pandoc -o $$o
 $$i  ###
 
 Would you mind pasting all the pandoc-related converter and format 
 definitions that work for
 you to http://www.lyx.org/trac/ticket/6042 ? If you include working configs 
 there and others
 can test them and confirm they indeed work, then chances are that they would 
 get included in
 base LyX.

Done - thanks for reminding me.

Rainer

 
 Liviu
 


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys.
(Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :   +33 - (0)9 53 10 27 44
Cell:   +33 - (0)6 85 62 59 98
Fax :   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug


SOLVED: Text in certain colours

2013-01-18 Thread Rainer M Krug
On 17/01/13 17:37, Rainer M Krug wrote:
 On 17/01/13 17:18, Alex Vergara Gil wrote:
 Hi
 
 I have line graphs generated in R, where each line is in a different colour 
 (the colours
 are generated in R by using rainbow(8)).
 
 Due to space problems in the graph, I can not put the legend into the 
 grapgh itself, but
 want to put it into the caption. Therefore I would like to reproduce the 
 colours in LaTeX.
 I know how to set the text colour via LyX to one of the pre-defined 
 colours, but hjow can I
 set them to these specific colours?
 
 In addition, I would like to have the colours as filled squares in the text 
 - any 
 suggestions?
 
 
 
 Oh you mean by adding \textcolor{yourcolor}{$\blacksquare$yourcaption} in an 
 ERT
 
 Perfect - thanks.
 
 Now I just have to figure out how to translate the colour codes in R into 
 LaTeX readable. The 
 eight colours in R are:
 
 #FFFF #FFBF00FF #80FF00FF #00FF40FF #00FF #0040 
 #8000
 #FF00BFFF

Solved:

I just have to leave out the last two characters, as the first 6 represent the 
rgb colors in hex.
so #FFFF translates into:

[[ \textcolor[HTML]{FF}{$\blacksquare$ ]] my caption [[ } ]]

where [[  ]] stands for ERT.

And I have a filled square in the text and the caption in the colour used in R 
for plotting.

Thanks,

Rainer

 
 Thanks,
 
 Rainer
 
 
 Regards
 
 Alex
 
 


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys.
(Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :   +33 - (0)9 53 10 27 44
Cell:   +33 - (0)6 85 62 59 98
Fax :   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug


Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Steve Litt
On Thu, 17 Jan 2013 21:17:28 -0700, Jerry said:
 
 On Jan 17, 2013, at 2:30 AM, Alex Fernandez wrote:
 
  Hi Jerry,
  
  I am the primary author of eLyXer.
  
  On Thu, Jan 17, 2013 at 4:49 AM, Jerry lancebo...@qwest.net wrote:
  Thanks for that tip. I checked it out. It's just a Python thing so
  it works fine on OS X, and LyX picked it up as advertised.
  
  Yes, I can confirm that OS X is fully supported.
   
  The output on my simple test case does look nice in a browser, but
  I get the same error opening with Word as I first described: The
  XML file bla bla bla cannot be opened... etc. I thought maybe my
  copy of Word was broken but it reads other HTML files fine--I'm
  guessing they don't have the XML stuff in them, however.
  
  Word does not like XHTML very much; you need to export to HTML 4,
  using the --html option.
  http://elyxer.nongnu.org/userguide.html#sub:HTML-Code If you are
  doing the conversion inside LyX, instead of on the command line,
  you have to add the --html in the conversion interface. I checked
  the HTML file that eLyXer made with the W3C page and got: The
  uploaded document - was successfully checked as XHTML 1.0
  Transitional.
  
  Yes, eLyXer outputs pure XHTML.
   
  Also--eLyXer does not appear to use MathML so I don't think there
  is any hope of getting editable math into Word using this method.
  (But I haven't read all of the eLyXer docs.)
  
  eLyXer has several options for Math output:
http://elyxer.nongnu.org/userguide.html#sub:Math
  Sadly, none of them is MathML, since at the time eLyXer was
  conceived it was not very widely supported, and I have not found
  the time to add it.
  
  Hope this helps,
  
  Alex Fernández.
  
 Hi, Alex,
 
 Thanks for the comments and for the great tool. It does what it
 claims to to, convert LyX to HTML, with lots of math options. The
 default conversion looks great in a browser.
 
 I tried your --html suggestion and indeed Word opens it, and displays
 it much as a browser does. Unfortunately, the HTML limitations are
 apparent; this is probably as good as a HTML-only conversion can get.
 
 In my slow-witted way, I'm starting to understand why Word will not
 open the various XML formats that I'm throwing at it. (I also played
 with TeXht today (and the Mac GUI over it, SimpleTeXht. This method
 also makes XML in some variations, and .odt.) So Word isn't
 broken—it's just not made to recognize this particular kind of XML.
 (I want to use the word schema but don't really know what I'm
 talking about.) So What is missing, as has been stated in previous
 threads, is a converter from the XML that we're seeing to .docx, it
 seems.
 
 Jerry

Hi Jerry,

Did you ever consider trying to open the LyXML or whatever it's called
in LibreOffice, and then from LibreOffice exporting it to MSWord
format? That just might work.

Thanks

SteveT

Steve Litt*  http://www.troubleshooters.com/
  *  http://twitter.com/stevelitt
Troubleshooting Training  *  Human Performance



Paste under 2.0.5.1

2013-01-18 Thread Eran Kaplinsky
After installing the latest (using the Installer-1 binary on a Win 7
system) paste is broken.
Content copied from a browser cannot be pasted, as the paste options
in the edit menu are all greyed out.
Text copied from LyX can only be pasted using paste recent, even if
never pasted before.


Advice welcome.





--
Dr. Eran S. Kaplinsky
Faculty of Law
University of Alberta
447 Law Centre
Edmonton · AB · T6G 2H5
C A N A D A

Tel: (780) 492-2941
Fax: (780) 492-4924


Re: moderncv

2013-01-18 Thread Gregory Jefferis

On 14 Jan 2013, at 18:35, Hansen, Glenn J. wrote:

 Thank you in advance for the help. I am new to lyx/tex.
 
 I have been trying to get my cv moved to lyx/tex format and have ran into a 
 problem that I am not able to solve. I have nearly everything done but 
 getting a multiple sectioned bibliography to work(e.g., section for journal 
 articles and conference papers). I get the following error:
 
 ! Package bibtopic Error: Found unknown `thebibliography' environment. 

The error message includes the additional information:

You should either use a package providing a known bibliography
environment (such as natbib), or use the `defaultbib' package
option as a workaround; please see the section about `Warnings
and error messages' in `bibtopic.dvi' for details.

If you go to: Document ... Settings ... Document Class ... 

and then edit the Custom field to add

defaultbib

then as far as I can see things should work. 

Best,

Greg.


--
Gregory Jefferis, PhD  
Division of Neurobiology   
MRC Laboratory of Molecular Biology,   
Hills Road,
Cambridge, CB2 0QH, UK.

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://www.neuroscience.cam.ac.uk/directory/profile.php?gsxej2
http://flybrain.stanford.edu



pLyX system: find replace LyX format code

2013-01-18 Thread Andrew Parsloe
The pLyX system (see http://wiki.lyx.org/Examples/Examples) provides a 
means of launching python scripts at the click of a few toolbar buttons; 
these scripts modify the current document. Given the speed of modern 
computers, the whole process feels built-in -- the document changes 
almost immediately in front of one's eyes.


As part of this system, I've attached a find--replace script for LyX's 
native file format,  associated files:


findrepl.py -- the script that does the finding  replacing.
findrepl_help.py  -- a help script.
pLyXFindReplace(compressed).lyx -- an explanatory LyX document that 
needs to be saved in uncompressed format for the examples in it to work.


In the document I show how the script can be used to tackle some queries 
that have appeared on the users list over the past year:


document-wide changing the width of figures
document-wide centering of figures
converting chemical formulae written in math insets (for the sake of 
sub- and superscripts) to \mathrm
clearing up debris after importing documents from, e.g., OpenOffice or 
Abiword, that have been exported as LaTeX (in other words getting rid of 
all those irritating left  right braces in ERT insets).


One way of tackling such problems is to open the document in a text 
editor and make appropriate changes there. The find--replace script 
means that is no longer necessary. It can be done from the comfort of 
the LyX GUI. There are usually other ways of tackling such matters (and 
perhaps more insightful in a LaTeX sense) but for someone pressed for 
time, this may provide a convenient fallback.


The script has a simple mode capable of finding  replacing possibly 
multiple lines of native LyX format code, and a powerful regular 
expression mode similarly capable, but also of condensing multiple 
simple searches into one regexp search (and, of course, with a health 
warning about crashing LyX, given the obscurity of regexps, but it's 
great fun).


Andrew
# Find  replace elements of the LyX source.
# Part of the pLyX.py system.
#
# Andrew Parsloe (apars...@clear.net.nz)
# version 0.1 (19 November 2012)
#
# findrepl.py 
#
import argparse, re, sys

re_backslash = re.compile(r'\n?\\backslash\n')

flex_fr = r'\begin_inset Flex .find  repl'
flex_arg = r'\begin_inset Flex .[argument]'
begin_layout = r'\begin_layout'
end_layout = r'\end_layout'
begin_std = r'\begin_layout Standard'
begin_inset = r'\begin_inset'
end_inset = r'\end_inset'
begin_note = r'\begin_inset Note'
st_open = 'status open\n'
st_coll = 'status collapsed\n'
end_body = r'\end_body'
end_document = r'\end_document'
backslash = r'\backslash'

begin_msg = r'''\begin_inset Note Note
status open
\begin_layout Plain Layout
'''
end_msg = r'''
\end_layout
\end_inset
'''

##
def main(infl, outfl, options, guff):

def strip_outers(stuff):
'''Strip enclosing layout statements.'''
stuff = stuff.partition('\n')[2]
stuff = stuff.rpartition(end_layout)[0]
return stuff

def inset_contents():
'''Get contents of inset minus LyX paragraphing.'''

contents = lines = ''
layouts, insets = 0, 1
status = True
newpara = False

for line in infl:
lines += line
if line == '\n':
continue
# assumes status open|collapsed is last status line
elif status:
if st_open == line or st_coll == line:
status = False
continue
elif begin_layout in line:
# exclude LyX paragraphing of contents
layouts += 1
if layouts  1:
contents += line
else:
newpara = True
elif begin_inset in line:
insets += 1
contents += line
elif backslash in line:
if newpara:
contents += '\n' + line
else:
contents += line
elif end_layout in line:
newpara = False
# exclude LyX paragraphing of contents
if layouts  1:
contents += line
layouts -= 1
elif end_inset in line:
newpara = False
insets -= 1
if insets == 0:
return contents, lines
else:
contents += line
else:
newpara = False
contents += line

def get_lines(n):
temp = ''
i = 0
if n == 0:
return ''
else:
for line in infl:
if line != '\n':
temp += line
i += 1
if i == n:
break
return temp

def write_msg(msg):
'''Write a yellow 

Re: Vancouver style options -changed to: almost soved

2013-01-18 Thread Julien Rioux

On 18/01/2013 3:19 AM, Wolfgang Engelmann wrote:

Am Dienstag, 15. Januar 2013, 14:39:07 schrieb Wolfgang Engelmann:

Hi,

still not done with Vancouver style

I tried for quite some time but can't find the option for references, in
which more than 2 authors are referenced as
author1 et al

Wolfgang


I found out how to solve it:

in vancouver.bst
(which is in my case in home/wolfgang/texlive/2012/texmf-dist/bibtex/bst/)

change
nameptr #6
to
nameptr #2

and
numname #6
to
numname #2

I saved this changed vancouver.bst to vancouver2etal.bst
in order not to interfere with the original file
and added this to documentsettings  bibliography styledefault style
WHICH DID NOT WORK
however, if I changed vancouver2etal.bst to vancouver.bst
(by saving the original vancouver.bst preliminary as vancouverOrig.bst)
IT WORKED
namely, only maximally 2 authors in the bibliography, if more: et al after
the second one

My question:
why was vancouver2etal in bibliography styledefault style not recognized?
I did a reconfigure before.

Wolfgang



This is new in LyX 2.1:
For the Default style defined in document settings to be used, the style 
in the BibTeX-generated bibliography dialog must be set to default. 
Note that this isn't completely ironed out, but the intention behind 
this document-wide setting is for citation engine that define the style 
in the preamble, e.g. biblatex.


For now, I would recommend to use the LyX 2.0 way:
Just set the bibliography style you want from the BibTeX-generated 
bibliography dialog.


Regards,
Julien


Re: Endnote number size/position

2013-01-18 Thread Julien Rioux

On 16/12/2012 4:48 PM, Maria Gouskova wrote:

On Wed, Nov 14, 2012 at 2:03 PM, Richard Heck rgh...@lyx.org wrote:

On 10/22/2012 04:19 PM, Maria Gouskova wrote:


Thanks, Richard--example file attached! It works when everything in
the preamble is commented out, but the endnote numbers appear as
superscripts in the Notes section (which is not what I want; I need
them to be on the main line in normal size, followed by periods and
then the note text).


The right command to change is: \@makeenmark, with the @.


(Sorry about the late response!)

I replaced the preamble line

\renewcommand\makeenmark{\theenmark. }

with

\renewcommand\@makeenmark{\theenmark. }

and the result is an Undefined control sequence error:

  \footnote{
A footnote/endnote A footnote/endnote A footnote/endnote A fo...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.


Maria




The attached seems to work for me. Is this what you are after?

Regards,
Julien


aendnote_test_file-1.lyx
Description: application/lyx


Re: Trouble with track changes appearing in pdflatex views

2013-01-18 Thread Julien Rioux

On 28/11/2012 9:19 AM, Richard Heck wrote:

On 11/27/2012 03:01 PM, Allen Wilkinson wrote:

My problem is that if I want to show tracked changes in PDF view or
output I get these errors:

Package xcolor Error: Undefined color `LYXDELETED'.
Package xcolor Error: Undefined color `LYXADDED'.
...
+++
after a modest finite extent of the document is processed.

If I delete changed and unchanged text from the document such that the
document is small enough, then PDF output with tracked changes works.

This is true whether I use Lyx PDF viewing, or run OS' pdflatex
compiler on exported .tex file.

If I disable 'show changes in output', then PDF output occurs without
errors.

Can anyone help me resolve this problem?


Odd that the undefined color is in all caps. Is LyX exporting this wrong?

I think we can only answer this with a test file that causes the problem.

rh




The headers from that document class must be all caps. A similar error 
happened with changes in section titles with the revtex document class, 
which use all caps section titles. For some reason latex thinks that it 
should also capitalize the color names. A workaround is to also define 
the colors with capitalized names! c.f. http://www.lyx.org/trac/ticket/4625


Regards,
Julien


Re: Two Column Article - Text rows vertically misaligned

2013-01-18 Thread Julien Rioux

On 17/12/2012 9:06 PM, TB L wrote:

Hey everyone,

just tried to typeset an article with two-column layout and am now faced
with the problem that the text rows on the right hand are not vertically
aligned to the one on the left hand (probably because of section titles?).

Is there any option to force Lyx / Latex to ensure that the text rows are
correctly aligned on both sides with respect to each other? This would look
a lot more professional. Would be really thankful for your support [image:
:)]

Tim



Apparently, (la)tex wasn't designed with left- and right-column line 
matching in mind at all, and accomplishing this after the fact is 
challenging. That said, if you find a way to make this work in latex, 
please post your result. We could look how difficult it would be to have 
it implemented in LyX.


Regards,
Julien


Re: References appear with et instead of and between authors

2013-01-18 Thread Julien Rioux

On 07/05/2012 3:41 PM, ChiPro wrote:

Hi all,

I'm using BibDesk as my reference package in Lyx. I have set the Lyx options
(Documents  Settings) to Natbib: Author-year and the citation style to
[author1] and [author2] ([year]).

Unfortunately, when I produce my PDF file, the reference appears as


[Author1] et [Author2] (2000)


instead of the desired


[Author1] and [Author2] (2000).


Any help would be appreciated.

Thanks,
CP




Which style file (.bst) are you using?

--
Julien


Re: problem with natbib numbering

2013-01-18 Thread Julien Rioux

On 16/06/2012 9:39 AM, julien.babinot wrote:

Hello,

I am currently writing my PhD thesis on Lyx, and i have one problem with
my bibliography.
I am using multiple bibliography, with a separate bib file for each
chapter (these are included in a main document thesis.lyx).
As advised in the advanced options document, i use \begin{btUnit}and
\end{btUnit}at the beginning and end of my chapter to allow the multiple
bibliography.
I want to use a numbered style, in superscript, and numbered in the
order of citation. But my problem is that references are listed in the
alphabetical order of authors, thus generating numbering like 5, 23, 6
 and not 1,2,3
Here is the Latex code generated by Lyx:

%% LyX 2.0.3 created this file. For more info, see http://www.lyx.org/.

%% Do not edit unless you really know what you are doing.

\documentclass[oneside,english,french]{thl3i}

\usepackage[T1]{fontenc}

\usepackage[utf8x]{inputenc}

\setcounter{secnumdepth}{1}

\setcounter{tocdepth}{1}

\usepackage{array}

\usepackage{float}

\usepackage{textcomp}

\usepackage{multirow}

\usepackage{amsthm}

\usepackage{amsmath}

\usepackage{graphicx}

\usepackage{setspace}

\usepackage[dot]{bibtopic}

\PassOptionsToPackage{normalem}{ulem}

\usepackage{ulem}

\onehalfspacing

\makeatletter

%% LyX specific LaTeX commands.

\DeclareRobustCommand{\greektext}{%

\fontencoding{LGR}\selectfont\def\encodingdefault{LGR}}

\DeclareRobustCommand{\textgreek}[1]{\leavevmode{\greektext #1}}

\DeclareFontEncoding{LGR}{}{}

\DeclareTextSymbol{\~}{LGR}{126}

%% Because html converters don't know tabularnewline

\providecommand{\tabularnewline}{\\}

%% A simple dot to overcome graphicx limitations

\newcommand{\lyxdot}{.}

%% Textclass specific LaTeX commands.

\numberwithin{equation}{section}

\newcommand{\lyxaddress}[1]{

\par {\raggedright #1

\vspace{1.4em}

\noindent\par}

}

%% User specified LaTeX commands.

\usepackage[numbers,super,sortcompress]{natbib}

\bibliographystyle{unsrtnat}

\makeatother

\usepackage{babel}

\addto\extrasfrench{%

\providecommand{\og}{\leavevmode\flqq~}%

\providecommand{\fg}{\ifdim\lastskip\z@\unskip\fi~\frqq}%

}

\begin{document}

\titreLogoUn{}

\titreLogoDeux{}

\subject{}

\title{}

\author{\textbf{\large }\\

}

\date{xx/xx/2012}

\Rapporteurs{Rapporteur 1Université 1\\

Rapporteur 2Université 2}

\Examinateurs{Examinateur 1Université 3\\

Examinateur 2Université 4}

\Directeur{Directeur 1Université 5}

\Encadrant{Encadrant 1Université 6}

\Encadrant{Invité 1Université 7}

\titreBasDePage{}

\maketitle

\address{%

\begin{minipage}[t][1\textheight]{1\columnwidth}%

\begin{center}

\includegraphics[width=3cm]{Logos/Financeur}

\par\end{center}

\vspace{1cm}

\begin{tabular}{rll}

\emph{Thèse réalisée au}  \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{Web :}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

\emph{Sous la direction de }  \tabularnewline

  \tabularnewline

\emph{Co-encadrement}  \tabularnewline

  \tabularnewline

\end{tabular}

\begin{center}

\cleardoublepage

\par\end{center}

\begin{center}

\par\end{center}%

\end{minipage}}

\frontmatter

\include{Remerciements}\include{Résumé}

\include{Abstract}

\tableofcontents{}

\listoffigures

\listoftables

\include{abreviations}

\mainmatter

\include{Introduction}

\include{Chapitre1}

\include{Chapitre2}

\include{Chapitre3}

\include{Chapitre4}

\include{Chapitre5}

\include{Chapitre6}

\include{Conclusion}

\include{Annexes}

\backmatter

\end{document}


What i don't understand is that my bibliography is actually numbered in
superscript but not sorted by order of citation?! unsrtnat is not
supposed to do so?

I would extremely appreciate any help.

Thanks,

Julien






Did you figure it out? Although unsrtnat won't sort, bibtopic might 
interfering?


--
Julien


Re: Relative path to bib source doesn't work in lyx (but does work when exported as .tex)

2013-01-18 Thread Julien Rioux

On 27/11/2012 6:47 PM, stefano franchi wrote:

On Tue, Nov 27, 2012 at 5:34 PM, Roey Angel angel.r...@gmail.com wrote:

So, a bug or a 'feature'?



Feature, p/h? It has a great educational value: it forces you to understand
how lyx uses the latex (and biber, texindy, etc) backends ;-)

Cheers,

Stefano




There's an enhancement request that might solve this, eventually (don't 
hold your breath, it's 7 year old): http://www.lyx.org/trac/ticket/2645


--
Julien


Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Rainer M Krug
On 18/01/13 05:17, Jerry wrote:
 
 On Jan 17, 2013, at 2:30 AM, Alex Fernandez wrote:
 
 Hi Jerry,
 
 I am the primary author of eLyXer.
 
 On Thu, Jan 17, 2013 at 4:49 AM, Jerry lancebo...@qwest.net 
 mailto:lancebo...@qwest.net
 wrote:
 
 Thanks for that tip. I checked it out. It's just a Python thing so it works 
 fine on OS X,
 and LyX picked it up as advertised.
 
 
 Yes, I can confirm that OS X is fully supported.
 
 
 The output on my simple test case does look nice in a browser, but I get the 
 same error 
 opening with Word as I first described: The XML file bla bla bla cannot be 
 opened... etc.
 I thought maybe my copy of Word was broken but it reads other HTML files 
 fine--I'm guessing
 they don't have the XML stuff in them, however.
 
 
 Word does not like XHTML very much; you need to export to HTML 4, using the 
 --html option. 
 http://elyxer.nongnu.org/userguide.html#sub:HTML-Code If you are doing the 
 conversion inside
 LyX, instead of on the command line, you have to add the --html in the 
 conversion interface.
 
 
 I checked the HTML file that eLyXer made with the W3C page and got: The 
 uploaded document
 - was successfully checked as XHTML 1.0 Transitional.
 
 
 Yes, eLyXer outputs pure XHTML.
 
 
 Also--eLyXer does not appear to use MathML so I don't think there is any 
 hope of getting 
 editable math into Word using this method. (But I haven't read all of the 
 eLyXer docs.)
 
 
 eLyXer has several options for Math output: 
 http://elyxer.nongnu.org/userguide.html#sub:Math 
 Sadly, none of them is MathML, since at the time eLyXer was conceived it was 
 not very widely 
 supported, and I have not found the time to add it.
 
 Hope this helps,
 
 Alex Fernández.
 
 Hi, Alex,
 
 Thanks for the comments and for the great tool. It does what it claims to to, 
 convert LyX to
 HTML, with lots of math options. The default conversion looks great in a 
 browser.
 
 I tried your --html suggestion and indeed Word opens it, and displays it much 
 as a browser
 does. Unfortunately, the HTML limitations are apparent; this is probably as 
 good as a HTML-only
 conversion can get.
 
 In my slow-witted way, I'm starting to understand why Word will not open the 
 various XML
 formats that I'm throwing at it. (I also played with TeXht today (and the Mac 
 GUI over it,
 SimpleTeXht. This method also makes XML in some variations, and .odt.) So 
 Word isn't
 broken—it's just not made to recognize this particular kind of XML. (I want 
 to use the word
 schema but don't really know what I'm talking about.) So What is missing, 
 as has been stated
 in previous threads, is a converter from the XML that we're seeing to .docx, 
 it seems.

check pandoc - I am using pandoc to convert xhtml to docx and odt - works 
perfect for me. I just

\converter xhtml msdocx pandoc -o $$o $$i 
\converter xhtml odt lo pandoc -o $$o $$i added the following converter:

You have to play with the LyX xhtml or the eLyXer xhtml - I used LyXHTRML 
because it workded
better in my case.

I really think that pandoc should be detected automatically by LyX (when doing 
reconfigure) and
added as it provides very usable conversions.


Cheers,

Rainer

 
 Jerry



Re: Vancouver style options -changed to: almost soved

2013-01-18 Thread Wolfgang Engelmann
Am Dienstag, 15. Januar 2013, 14:39:07 schrieb Wolfgang Engelmann:
 Hi,
 
 still not done with Vancouver style
 
 I tried for quite some time but can't find the option for references, in
 which more than 2 authors are referenced as
 author1 et al
 
 Wolfgang

I found out how to solve it:

in vancouver.bst
(which is in my case in home/wolfgang/texlive/2012/texmf-dist/bibtex/bst/)

change
nameptr #6
to
nameptr #2

and 
numname #6
to
numname #2

I saved this changed vancouver.bst to vancouver2etal.bst
in order not to interfere with the original file 
and added this to documentsettings  bibliography styledefault style
WHICH DID NOT WORK
however, if I changed vancouver2etal.bst to vancouver.bst
(by saving the original vancouver.bst preliminary as vancouverOrig.bst)
IT WORKED
namely, only maximally 2 authors in the bibliography, if more: et al after 
the second one

My question:
why was vancouver2etal in bibliography styledefault style not recognized? 
I did a reconfigure before.

Wolfgang


Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Rainer M Krug
On 18/01/13 09:10, Rainer M Krug wrote:
 On 18/01/13 05:17, Jerry wrote:
 
 On Jan 17, 2013, at 2:30 AM, Alex Fernandez wrote:
 
 Hi Jerry,
 
 I am the primary author of eLyXer.
 
 On Thu, Jan 17, 2013 at 4:49 AM, Jerry lancebo...@qwest.net
 mailto:lancebo...@qwest.net wrote:
 
 Thanks for that tip. I checked it out. It's just a Python thing so it works 
 fine on OS X, 
 and LyX picked it up as advertised.
 
 
 Yes, I can confirm that OS X is fully supported.
 
 
 The output on my simple test case does look nice in a browser, but I get 
 the same error 
 opening with Word as I first described: The XML file bla bla bla cannot be 
 opened...
 etc. I thought maybe my copy of Word was broken but it reads other HTML 
 files fine--I'm
 guessing they don't have the XML stuff in them, however.
 
 
 Word does not like XHTML very much; you need to export to HTML 4, using the 
 --html option.
  http://elyxer.nongnu.org/userguide.html#sub:HTML-Code If you are doing the 
 conversion
 inside LyX, instead of on the command line, you have to add the --html in 
 the conversion
 interface.
 
 
 I checked the HTML file that eLyXer made with the W3C page and got: The 
 uploaded document 
 - was successfully checked as XHTML 1.0 Transitional.
 
 
 Yes, eLyXer outputs pure XHTML.
 
 
 Also--eLyXer does not appear to use MathML so I don't think there is any 
 hope of getting 
 editable math into Word using this method. (But I haven't read all of the 
 eLyXer docs.)
 
 
 eLyXer has several options for Math output:
 http://elyxer.nongnu.org/userguide.html#sub:Math Sadly, none of them is 
 MathML, since at
 the time eLyXer was conceived it was not very widely supported, and I have 
 not found the
 time to add it.
 
 Hope this helps,
 
 Alex Fernández.
 
 Hi, Alex,
 
 Thanks for the comments and for the great tool. It does what it claims to 
 to, convert LyX to 
 HTML, with lots of math options. The default conversion looks great in a 
 browser.
 
 I tried your --html suggestion and indeed Word opens it, and displays it 
 much as a browser 
 does. Unfortunately, the HTML limitations are apparent; this is probably as 
 good as a
 HTML-only conversion can get.
 
 In my slow-witted way, I'm starting to understand why Word will not open the 
 various XML 
 formats that I'm throwing at it. (I also played with TeXht today (and the 
 Mac GUI over it, 
 SimpleTeXht. This method also makes XML in some variations, and .odt.) So 
 Word isn't 
 broken—it's just not made to recognize this particular kind of XML. (I want 
 to use the word 
 schema but don't really know what I'm talking about.) So What is missing, 
 as has been
 stated in previous threads, is a converter from the XML that we're seeing to 
 .docx, it
 seems.
 
 check pandoc - I am using pandoc to convert xhtml to docx and odt - works 
 perfect for me. I
 just

Ups - should have been:
###
I just added the following converter:

\converter xhtml msdocx pandoc -o $$o $$i 
\converter xhtml odt lo pandoc -o $$o $$i 
###

 
 \converter xhtml msdocx pandoc -o $$o $$i  \converter xhtml odt 
 lo pandoc -o $$o
 $$i added the following converter:
 
 You have to play with the LyX xhtml or the eLyXer xhtml - I used LyXHTRML 
 because it workded 
 better in my case.
 
 I really think that pandoc should be detected automatically by LyX (when 
 doing reconfigure)
 and added as it provides very usable conversions.
 
 
 Cheers,
 
 Rainer
 
 
 Jerry
 
 



Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Liviu Andronic
Rainer,


On Fri, Jan 18, 2013 at 9:44 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 \converter xhtml msdocx pandoc -o $$o $$i 
 \converter xhtml odt lo pandoc -o $$o $$i 
 ###

Would you mind pasting all the pandoc-related converter and format
definitions that work for you to http://www.lyx.org/trac/ticket/6042 ?
If you include working configs there and others can test them and
confirm they indeed work, then chances are that they would get
included in base LyX.

Liviu


Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Rainer M Krug
On 18/01/13 10:58, Liviu Andronic wrote:
 Rainer,
 
 
 On Fri, Jan 18, 2013 at 9:44 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 \converter xhtml msdocx pandoc -o $$o $$i  \converter xhtml odt 
 lo pandoc -o $$o
 $$i  ###
 
 Would you mind pasting all the pandoc-related converter and format 
 definitions that work for
 you to http://www.lyx.org/trac/ticket/6042 ? If you include working configs 
 there and others
 can test them and confirm they indeed work, then chances are that they would 
 get included in
 base LyX.

Done - thanks for reminding me.

Rainer

 
 Liviu
 


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys.
(Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :   +33 - (0)9 53 10 27 44
Cell:   +33 - (0)6 85 62 59 98
Fax :   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug


SOLVED: Text in certain colours

2013-01-18 Thread Rainer M Krug
On 17/01/13 17:37, Rainer M Krug wrote:
 On 17/01/13 17:18, Alex Vergara Gil wrote:
 Hi
 
 I have line graphs generated in R, where each line is in a different colour 
 (the colours
 are generated in R by using rainbow(8)).
 
 Due to space problems in the graph, I can not put the legend into the 
 grapgh itself, but
 want to put it into the caption. Therefore I would like to reproduce the 
 colours in LaTeX.
 I know how to set the text colour via LyX to one of the pre-defined 
 colours, but hjow can I
 set them to these specific colours?
 
 In addition, I would like to have the colours as filled squares in the text 
 - any 
 suggestions?
 
 
 
 Oh you mean by adding \textcolor{yourcolor}{$\blacksquare$yourcaption} in an 
 ERT
 
 Perfect - thanks.
 
 Now I just have to figure out how to translate the colour codes in R into 
 LaTeX readable. The 
 eight colours in R are:
 
 #FFFF #FFBF00FF #80FF00FF #00FF40FF #00FF #0040 
 #8000
 #FF00BFFF

Solved:

I just have to leave out the last two characters, as the first 6 represent the 
rgb colors in hex.
so #FFFF translates into:

[[ \textcolor[HTML]{FF}{$\blacksquare$ ]] my caption [[ } ]]

where [[  ]] stands for ERT.

And I have a filled square in the text and the caption in the colour used in R 
for plotting.

Thanks,

Rainer

 
 Thanks,
 
 Rainer
 
 
 Regards
 
 Alex
 
 


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys.
(Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :   +33 - (0)9 53 10 27 44
Cell:   +33 - (0)6 85 62 59 98
Fax :   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug


Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Steve Litt
On Thu, 17 Jan 2013 21:17:28 -0700, Jerry said:
 
 On Jan 17, 2013, at 2:30 AM, Alex Fernandez wrote:
 
  Hi Jerry,
  
  I am the primary author of eLyXer.
  
  On Thu, Jan 17, 2013 at 4:49 AM, Jerry lancebo...@qwest.net wrote:
  Thanks for that tip. I checked it out. It's just a Python thing so
  it works fine on OS X, and LyX picked it up as advertised.
  
  Yes, I can confirm that OS X is fully supported.
   
  The output on my simple test case does look nice in a browser, but
  I get the same error opening with Word as I first described: The
  XML file bla bla bla cannot be opened... etc. I thought maybe my
  copy of Word was broken but it reads other HTML files fine--I'm
  guessing they don't have the XML stuff in them, however.
  
  Word does not like XHTML very much; you need to export to HTML 4,
  using the --html option.
  http://elyxer.nongnu.org/userguide.html#sub:HTML-Code If you are
  doing the conversion inside LyX, instead of on the command line,
  you have to add the --html in the conversion interface. I checked
  the HTML file that eLyXer made with the W3C page and got: The
  uploaded document - was successfully checked as XHTML 1.0
  Transitional.
  
  Yes, eLyXer outputs pure XHTML.
   
  Also--eLyXer does not appear to use MathML so I don't think there
  is any hope of getting editable math into Word using this method.
  (But I haven't read all of the eLyXer docs.)
  
  eLyXer has several options for Math output:
http://elyxer.nongnu.org/userguide.html#sub:Math
  Sadly, none of them is MathML, since at the time eLyXer was
  conceived it was not very widely supported, and I have not found
  the time to add it.
  
  Hope this helps,
  
  Alex Fernández.
  
 Hi, Alex,
 
 Thanks for the comments and for the great tool. It does what it
 claims to to, convert LyX to HTML, with lots of math options. The
 default conversion looks great in a browser.
 
 I tried your --html suggestion and indeed Word opens it, and displays
 it much as a browser does. Unfortunately, the HTML limitations are
 apparent; this is probably as good as a HTML-only conversion can get.
 
 In my slow-witted way, I'm starting to understand why Word will not
 open the various XML formats that I'm throwing at it. (I also played
 with TeXht today (and the Mac GUI over it, SimpleTeXht. This method
 also makes XML in some variations, and .odt.) So Word isn't
 broken—it's just not made to recognize this particular kind of XML.
 (I want to use the word schema but don't really know what I'm
 talking about.) So What is missing, as has been stated in previous
 threads, is a converter from the XML that we're seeing to .docx, it
 seems.
 
 Jerry

Hi Jerry,

Did you ever consider trying to open the LyXML or whatever it's called
in LibreOffice, and then from LibreOffice exporting it to MSWord
format? That just might work.

Thanks

SteveT

Steve Litt*  http://www.troubleshooters.com/
  *  http://twitter.com/stevelitt
Troubleshooting Training  *  Human Performance



Paste under 2.0.5.1

2013-01-18 Thread Eran Kaplinsky
After installing the latest (using the Installer-1 binary on a Win 7
system) paste is broken.
Content copied from a browser cannot be pasted, as the paste options
in the edit menu are all greyed out.
Text copied from LyX can only be pasted using paste recent, even if
never pasted before.


Advice welcome.





--
Dr. Eran S. Kaplinsky
Faculty of Law
University of Alberta
447 Law Centre
Edmonton · AB · T6G 2H5
C A N A D A

Tel: (780) 492-2941
Fax: (780) 492-4924


Re: moderncv

2013-01-18 Thread Gregory Jefferis

On 14 Jan 2013, at 18:35, Hansen, Glenn J. wrote:

 Thank you in advance for the help. I am new to lyx/tex.
 
 I have been trying to get my cv moved to lyx/tex format and have ran into a 
 problem that I am not able to solve. I have nearly everything done but 
 getting a multiple sectioned bibliography to work(e.g., section for journal 
 articles and conference papers). I get the following error:
 
 ! Package bibtopic Error: Found unknown `thebibliography' environment. 

The error message includes the additional information:

You should either use a package providing a known bibliography
environment (such as natbib), or use the `defaultbib' package
option as a workaround; please see the section about `Warnings
and error messages' in `bibtopic.dvi' for details.

If you go to: Document ... Settings ... Document Class ... 

and then edit the Custom field to add

defaultbib

then as far as I can see things should work. 

Best,

Greg.


--
Gregory Jefferis, PhD  
Division of Neurobiology   
MRC Laboratory of Molecular Biology,   
Hills Road,
Cambridge, CB2 0QH, UK.

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://www.neuroscience.cam.ac.uk/directory/profile.php?gsxej2
http://flybrain.stanford.edu



pLyX system: find replace LyX format code

2013-01-18 Thread Andrew Parsloe
The pLyX system (see http://wiki.lyx.org/Examples/Examples) provides a 
means of launching python scripts at the click of a few toolbar buttons; 
these scripts modify the current document. Given the speed of modern 
computers, the whole process feels built-in -- the document changes 
almost immediately in front of one's eyes.


As part of this system, I've attached a find--replace script for LyX's 
native file format,  associated files:


findrepl.py -- the script that does the finding  replacing.
findrepl_help.py  -- a help script.
pLyXFindReplace(compressed).lyx -- an explanatory LyX document that 
needs to be saved in uncompressed format for the examples in it to work.


In the document I show how the script can be used to tackle some queries 
that have appeared on the users list over the past year:


document-wide changing the width of figures
document-wide centering of figures
converting chemical formulae written in math insets (for the sake of 
sub- and superscripts) to \mathrm
clearing up debris after importing documents from, e.g., OpenOffice or 
Abiword, that have been exported as LaTeX (in other words getting rid of 
all those irritating left  right braces in ERT insets).


One way of tackling such problems is to open the document in a text 
editor and make appropriate changes there. The find--replace script 
means that is no longer necessary. It can be done from the comfort of 
the LyX GUI. There are usually other ways of tackling such matters (and 
perhaps more insightful in a LaTeX sense) but for someone pressed for 
time, this may provide a convenient fallback.


The script has a simple mode capable of finding  replacing possibly 
multiple lines of native LyX format code, and a powerful regular 
expression mode similarly capable, but also of condensing multiple 
simple searches into one regexp search (and, of course, with a health 
warning about crashing LyX, given the obscurity of regexps, but it's 
great fun).


Andrew
# Find  replace elements of the LyX source.
# Part of the pLyX.py system.
#
# Andrew Parsloe (apars...@clear.net.nz)
# version 0.1 (19 November 2012)
#
# findrepl.py 
#
import argparse, re, sys

re_backslash = re.compile(r'\n?\\backslash\n')

flex_fr = r'\begin_inset Flex .find  repl'
flex_arg = r'\begin_inset Flex .[argument]'
begin_layout = r'\begin_layout'
end_layout = r'\end_layout'
begin_std = r'\begin_layout Standard'
begin_inset = r'\begin_inset'
end_inset = r'\end_inset'
begin_note = r'\begin_inset Note'
st_open = 'status open\n'
st_coll = 'status collapsed\n'
end_body = r'\end_body'
end_document = r'\end_document'
backslash = r'\backslash'

begin_msg = r'''\begin_inset Note Note
status open
\begin_layout Plain Layout
'''
end_msg = r'''
\end_layout
\end_inset
'''

##
def main(infl, outfl, options, guff):

def strip_outers(stuff):
'''Strip enclosing layout statements.'''
stuff = stuff.partition('\n')[2]
stuff = stuff.rpartition(end_layout)[0]
return stuff

def inset_contents():
'''Get contents of inset minus LyX paragraphing.'''

contents = lines = ''
layouts, insets = 0, 1
status = True
newpara = False

for line in infl:
lines += line
if line == '\n':
continue
# assumes status open|collapsed is last status line
elif status:
if st_open == line or st_coll == line:
status = False
continue
elif begin_layout in line:
# exclude LyX paragraphing of contents
layouts += 1
if layouts  1:
contents += line
else:
newpara = True
elif begin_inset in line:
insets += 1
contents += line
elif backslash in line:
if newpara:
contents += '\n' + line
else:
contents += line
elif end_layout in line:
newpara = False
# exclude LyX paragraphing of contents
if layouts  1:
contents += line
layouts -= 1
elif end_inset in line:
newpara = False
insets -= 1
if insets == 0:
return contents, lines
else:
contents += line
else:
newpara = False
contents += line

def get_lines(n):
temp = ''
i = 0
if n == 0:
return ''
else:
for line in infl:
if line != '\n':
temp += line
i += 1
if i == n:
break
return temp

def write_msg(msg):
'''Write a yellow 

Re: Vancouver style options -changed to: almost soved

2013-01-18 Thread Julien Rioux

On 18/01/2013 3:19 AM, Wolfgang Engelmann wrote:

Am Dienstag, 15. Januar 2013, 14:39:07 schrieb Wolfgang Engelmann:

Hi,

still not done with Vancouver style

I tried for quite some time but can't find the option for references, in
which more than 2 authors are referenced as
author1 et al

Wolfgang


I found out how to solve it:

in vancouver.bst
(which is in my case in home/wolfgang/texlive/2012/texmf-dist/bibtex/bst/)

change
nameptr #6
to
nameptr #2

and
numname #6
to
numname #2

I saved this changed vancouver.bst to vancouver2etal.bst
in order not to interfere with the original file
and added this to documentsettings  bibliography styledefault style
WHICH DID NOT WORK
however, if I changed vancouver2etal.bst to vancouver.bst
(by saving the original vancouver.bst preliminary as vancouverOrig.bst)
IT WORKED
namely, only maximally 2 authors in the bibliography, if more: et al after
the second one

My question:
why was vancouver2etal in bibliography styledefault style not recognized?
I did a reconfigure before.

Wolfgang



This is new in LyX 2.1:
For the Default style defined in document settings to be used, the style 
in the BibTeX-generated bibliography dialog must be set to default. 
Note that this isn't completely ironed out, but the intention behind 
this document-wide setting is for citation engine that define the style 
in the preamble, e.g. biblatex.


For now, I would recommend to use the LyX 2.0 way:
Just set the bibliography style you want from the BibTeX-generated 
bibliography dialog.


Regards,
Julien


Re: Endnote number size/position

2013-01-18 Thread Julien Rioux

On 16/12/2012 4:48 PM, Maria Gouskova wrote:

On Wed, Nov 14, 2012 at 2:03 PM, Richard Heck rgh...@lyx.org wrote:

On 10/22/2012 04:19 PM, Maria Gouskova wrote:


Thanks, Richard--example file attached! It works when everything in
the preamble is commented out, but the endnote numbers appear as
superscripts in the Notes section (which is not what I want; I need
them to be on the main line in normal size, followed by periods and
then the note text).


The right command to change is: \@makeenmark, with the @.


(Sorry about the late response!)

I replaced the preamble line

\renewcommand\makeenmark{\theenmark. }

with

\renewcommand\@makeenmark{\theenmark. }

and the result is an Undefined control sequence error:

  \footnote{
A footnote/endnote A footnote/endnote A footnote/endnote A fo...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.


Maria




The attached seems to work for me. Is this what you are after?

Regards,
Julien


aendnote_test_file-1.lyx
Description: application/lyx


Re: Trouble with track changes appearing in pdflatex views

2013-01-18 Thread Julien Rioux

On 28/11/2012 9:19 AM, Richard Heck wrote:

On 11/27/2012 03:01 PM, Allen Wilkinson wrote:

My problem is that if I want to show tracked changes in PDF view or
output I get these errors:

Package xcolor Error: Undefined color `LYXDELETED'.
Package xcolor Error: Undefined color `LYXADDED'.
...
+++
after a modest finite extent of the document is processed.

If I delete changed and unchanged text from the document such that the
document is small enough, then PDF output with tracked changes works.

This is true whether I use Lyx PDF viewing, or run OS' pdflatex
compiler on exported .tex file.

If I disable 'show changes in output', then PDF output occurs without
errors.

Can anyone help me resolve this problem?


Odd that the undefined color is in all caps. Is LyX exporting this wrong?

I think we can only answer this with a test file that causes the problem.

rh




The headers from that document class must be all caps. A similar error 
happened with changes in section titles with the revtex document class, 
which use all caps section titles. For some reason latex thinks that it 
should also capitalize the color names. A workaround is to also define 
the colors with capitalized names! c.f. http://www.lyx.org/trac/ticket/4625


Regards,
Julien


Re: Two Column Article - Text rows vertically misaligned

2013-01-18 Thread Julien Rioux

On 17/12/2012 9:06 PM, TB L wrote:

Hey everyone,

just tried to typeset an article with two-column layout and am now faced
with the problem that the text rows on the right hand are not vertically
aligned to the one on the left hand (probably because of section titles?).

Is there any option to force Lyx / Latex to ensure that the text rows are
correctly aligned on both sides with respect to each other? This would look
a lot more professional. Would be really thankful for your support [image:
:)]

Tim



Apparently, (la)tex wasn't designed with left- and right-column line 
matching in mind at all, and accomplishing this after the fact is 
challenging. That said, if you find a way to make this work in latex, 
please post your result. We could look how difficult it would be to have 
it implemented in LyX.


Regards,
Julien


Re: References appear with et instead of and between authors

2013-01-18 Thread Julien Rioux

On 07/05/2012 3:41 PM, ChiPro wrote:

Hi all,

I'm using BibDesk as my reference package in Lyx. I have set the Lyx options
(Documents  Settings) to Natbib: Author-year and the citation style to
[author1] and [author2] ([year]).

Unfortunately, when I produce my PDF file, the reference appears as


[Author1] et [Author2] (2000)


instead of the desired


[Author1] and [Author2] (2000).


Any help would be appreciated.

Thanks,
CP




Which style file (.bst) are you using?

--
Julien


Re: problem with natbib numbering

2013-01-18 Thread Julien Rioux

On 16/06/2012 9:39 AM, julien.babinot wrote:

Hello,

I am currently writing my PhD thesis on Lyx, and i have one problem with
my bibliography.
I am using multiple bibliography, with a separate bib file for each
chapter (these are included in a main document thesis.lyx).
As advised in the advanced options document, i use \begin{btUnit}and
\end{btUnit}at the beginning and end of my chapter to allow the multiple
bibliography.
I want to use a numbered style, in superscript, and numbered in the
order of citation. But my problem is that references are listed in the
alphabetical order of authors, thus generating numbering like 5, 23, 6
 and not 1,2,3
Here is the Latex code generated by Lyx:

%% LyX 2.0.3 created this file. For more info, see http://www.lyx.org/.

%% Do not edit unless you really know what you are doing.

\documentclass[oneside,english,french]{thl3i}

\usepackage[T1]{fontenc}

\usepackage[utf8x]{inputenc}

\setcounter{secnumdepth}{1}

\setcounter{tocdepth}{1}

\usepackage{array}

\usepackage{float}

\usepackage{textcomp}

\usepackage{multirow}

\usepackage{amsthm}

\usepackage{amsmath}

\usepackage{graphicx}

\usepackage{setspace}

\usepackage[dot]{bibtopic}

\PassOptionsToPackage{normalem}{ulem}

\usepackage{ulem}

\onehalfspacing

\makeatletter

%% LyX specific LaTeX commands.

\DeclareRobustCommand{\greektext}{%

\fontencoding{LGR}\selectfont\def\encodingdefault{LGR}}

\DeclareRobustCommand{\textgreek}[1]{\leavevmode{\greektext #1}}

\DeclareFontEncoding{LGR}{}{}

\DeclareTextSymbol{\~}{LGR}{126}

%% Because html converters don't know tabularnewline

\providecommand{\tabularnewline}{\\}

%% A simple dot to overcome graphicx limitations

\newcommand{\lyxdot}{.}

%% Textclass specific LaTeX commands.

\numberwithin{equation}{section}

\newcommand{\lyxaddress}[1]{

\par {\raggedright #1

\vspace{1.4em}

\noindent\par}

}

%% User specified LaTeX commands.

\usepackage[numbers,super,sortcompress]{natbib}

\bibliographystyle{unsrtnat}

\makeatother

\usepackage{babel}

\addto\extrasfrench{%

\providecommand{\og}{\leavevmode\flqq~}%

\providecommand{\fg}{\ifdim\lastskip\z@\unskip\fi~\frqq}%

}

\begin{document}

\titreLogoUn{}

\titreLogoDeux{}

\subject{}

\title{}

\author{\textbf{\large }\\

}

\date{xx/xx/2012}

\Rapporteurs{Rapporteur 1Université 1\\

Rapporteur 2Université 2}

\Examinateurs{Examinateur 1Université 3\\

Examinateur 2Université 4}

\Directeur{Directeur 1Université 5}

\Encadrant{Encadrant 1Université 6}

\Encadrant{Invité 1Université 7}

\titreBasDePage{}

\maketitle

\address{%

\begin{minipage}[t][1\textheight]{1\columnwidth}%

\begin{center}

\includegraphics[width=3cm]{Logos/Financeur}

\par\end{center}

\vspace{1cm}

\begin{tabular}{rll}

\emph{Thèse réalisée au}  \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

 \multicolumn{2}{l}{Web :}\tabularnewline

 \multicolumn{2}{l}{}\tabularnewline

\emph{Sous la direction de }  \tabularnewline

  \tabularnewline

\emph{Co-encadrement}  \tabularnewline

  \tabularnewline

\end{tabular}

\begin{center}

\cleardoublepage

\par\end{center}

\begin{center}

\par\end{center}%

\end{minipage}}

\frontmatter

\include{Remerciements}\include{Résumé}

\include{Abstract}

\tableofcontents{}

\listoffigures

\listoftables

\include{abreviations}

\mainmatter

\include{Introduction}

\include{Chapitre1}

\include{Chapitre2}

\include{Chapitre3}

\include{Chapitre4}

\include{Chapitre5}

\include{Chapitre6}

\include{Conclusion}

\include{Annexes}

\backmatter

\end{document}


What i don't understand is that my bibliography is actually numbered in
superscript but not sorted by order of citation?! unsrtnat is not
supposed to do so?

I would extremely appreciate any help.

Thanks,

Julien






Did you figure it out? Although unsrtnat won't sort, bibtopic might 
interfering?


--
Julien


Re: Relative path to bib source doesn't work in lyx (but does work when exported as .tex)

2013-01-18 Thread Julien Rioux

On 27/11/2012 6:47 PM, stefano franchi wrote:

On Tue, Nov 27, 2012 at 5:34 PM, Roey Angel angel.r...@gmail.com wrote:

So, a bug or a 'feature'?



Feature, p/h? It has a great educational value: it forces you to understand
how lyx uses the latex (and biber, texindy, etc) backends ;-)

Cheers,

Stefano




There's an enhancement request that might solve this, eventually (don't 
hold your breath, it's 7 year old): http://www.lyx.org/trac/ticket/2645


--
Julien


Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Rainer M Krug
On 18/01/13 05:17, Jerry wrote:
> 
> On Jan 17, 2013, at 2:30 AM, Alex Fernandez wrote:
> 
>> Hi Jerry,
>> 
>> I am the primary author of eLyXer.
>> 
>> On Thu, Jan 17, 2013 at 4:49 AM, Jerry > >
>> wrote:
>> 
>> Thanks for that tip. I checked it out. It's just a Python thing so it works 
>> fine on OS X,
>> and LyX picked it up as advertised.
>> 
>> 
>> Yes, I can confirm that OS X is fully supported.
>> 
>> 
>> The output on my simple test case does look nice in a browser, but I get the 
>> same error 
>> opening with Word as I first described: "The XML file bla bla bla cannot be 
>> opened..." etc.
>> I thought maybe my copy of Word was broken but it reads other HTML files 
>> fine--I'm guessing
>> they don't have the XML stuff in them, however.
>> 
>> 
>> Word does not like XHTML very much; you need to export to HTML 4, using the 
>> --html option. 
>> http://elyxer.nongnu.org/userguide.html#sub:HTML-Code If you are doing the 
>> conversion inside
>> LyX, instead of on the command line, you have to add the --html in the 
>> conversion interface.
>> 
>> 
>> I checked the HTML file that eLyXer made with the W3C page and got: "The 
>> uploaded document
>> "-" was successfully checked as XHTML 1.0 Transitional."
>> 
>> 
>> Yes, eLyXer outputs pure XHTML.
>> 
>> 
>> Also--eLyXer does not appear to use MathML so I don't think there is any 
>> hope of getting 
>> editable math into Word using this method. (But I haven't read all of the 
>> eLyXer docs.)
>> 
>> 
>> eLyXer has several options for Math output: 
>> http://elyxer.nongnu.org/userguide.html#sub:Math 
>> Sadly, none of them is MathML, since at the time eLyXer was conceived it was 
>> not very widely 
>> supported, and I have not found the time to add it.
>> 
>> Hope this helps,
>> 
>> Alex Fernández.
>> 
> Hi, Alex,
> 
> Thanks for the comments and for the great tool. It does what it claims to to, 
> convert LyX to
> HTML, with lots of math options. The default conversion looks great in a 
> browser.
> 
> I tried your --html suggestion and indeed Word opens it, and displays it much 
> as a browser
> does. Unfortunately, the HTML limitations are apparent; this is probably as 
> good as a HTML-only
> conversion can get.
> 
> In my slow-witted way, I'm starting to understand why Word will not open the 
> various XML
> formats that I'm throwing at it. (I also played with TeXht today (and the Mac 
> GUI over it,
> SimpleTeXht. This method also makes XML in some variations, and .odt.) So 
> Word isn't
> broken—it's just not made to recognize this particular kind of XML. (I want 
> to use the word
> "schema" but don't really know what I'm talking about.) So What is missing, 
> as has been stated
> in previous threads, is a converter from the XML that we're seeing to .docx, 
> it seems.

check pandoc - I am using pandoc to convert xhtml to docx and odt - works 
perfect for me. I just

\converter "xhtml" "msdocx" "pandoc -o $$o $$i" ""
\converter "xhtml" "odt lo" "pandoc -o $$o $$i" ""added the following converter:

You have to play with the LyX xhtml or the eLyXer xhtml - I used LyXHTRML 
because it workded
better in my case.

I really think that pandoc should be detected automatically by LyX (when doing 
reconfigure) and
added as it provides very usable conversions.


Cheers,

Rainer

> 
> Jerry



Re: Vancouver style options -changed to: almost soved

2013-01-18 Thread Wolfgang Engelmann
Am Dienstag, 15. Januar 2013, 14:39:07 schrieb Wolfgang Engelmann:
> Hi,
> 
> still not done with Vancouver style
> 
> I tried for quite some time but can't find the option for references, in
> which more than 2 authors are referenced as
> author1 et al
> 
> Wolfgang

I found out how to solve it:

in vancouver.bst
(which is in my case in home/wolfgang/texlive/2012/texmf-dist/bibtex/bst/)

change
nameptr #6
to
nameptr #2

and 
numname #6
to
numname #2

I saved this changed vancouver.bst to vancouver2etal.bst
in order not to interfere with the original file 
and added this to document>settings  bibliography style>default style
WHICH DID NOT WORK
however, if I changed vancouver2etal.bst to vancouver.bst
(by saving the original vancouver.bst preliminary as vancouverOrig.bst)
IT WORKED
namely, only maximally 2 authors in the bibliography, if more: et al after 
the second one

My question:
why was vancouver2etal in bibliography style>default style not recognized? 
I did a reconfigure before.

Wolfgang


Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Rainer M Krug
On 18/01/13 09:10, Rainer M Krug wrote:
> On 18/01/13 05:17, Jerry wrote:
>> 
>> On Jan 17, 2013, at 2:30 AM, Alex Fernandez wrote:
>> 
>>> Hi Jerry,
>>> 
>>> I am the primary author of eLyXer.
>>> 
>>> On Thu, Jan 17, 2013 at 4:49 AM, Jerry >> > wrote:
>>> 
>>> Thanks for that tip. I checked it out. It's just a Python thing so it works 
>>> fine on OS X, 
>>> and LyX picked it up as advertised.
>>> 
>>> 
>>> Yes, I can confirm that OS X is fully supported.
>>> 
>>> 
>>> The output on my simple test case does look nice in a browser, but I get 
>>> the same error 
>>> opening with Word as I first described: "The XML file bla bla bla cannot be 
>>> opened..."
>>> etc. I thought maybe my copy of Word was broken but it reads other HTML 
>>> files fine--I'm
>>> guessing they don't have the XML stuff in them, however.
>>> 
>>> 
>>> Word does not like XHTML very much; you need to export to HTML 4, using the 
>>> --html option.
>>>  http://elyxer.nongnu.org/userguide.html#sub:HTML-Code If you are doing the 
>>> conversion
>>> inside LyX, instead of on the command line, you have to add the --html in 
>>> the conversion
>>> interface.
>>> 
>>> 
>>> I checked the HTML file that eLyXer made with the W3C page and got: "The 
>>> uploaded document 
>>> "-" was successfully checked as XHTML 1.0 Transitional."
>>> 
>>> 
>>> Yes, eLyXer outputs pure XHTML.
>>> 
>>> 
>>> Also--eLyXer does not appear to use MathML so I don't think there is any 
>>> hope of getting 
>>> editable math into Word using this method. (But I haven't read all of the 
>>> eLyXer docs.)
>>> 
>>> 
>>> eLyXer has several options for Math output:
>>> http://elyxer.nongnu.org/userguide.html#sub:Math Sadly, none of them is 
>>> MathML, since at
>>> the time eLyXer was conceived it was not very widely supported, and I have 
>>> not found the
>>> time to add it.
>>> 
>>> Hope this helps,
>>> 
>>> Alex Fernández.
>>> 
>> Hi, Alex,
>> 
>> Thanks for the comments and for the great tool. It does what it claims to 
>> to, convert LyX to 
>> HTML, with lots of math options. The default conversion looks great in a 
>> browser.
>> 
>> I tried your --html suggestion and indeed Word opens it, and displays it 
>> much as a browser 
>> does. Unfortunately, the HTML limitations are apparent; this is probably as 
>> good as a
>> HTML-only conversion can get.
>> 
>> In my slow-witted way, I'm starting to understand why Word will not open the 
>> various XML 
>> formats that I'm throwing at it. (I also played with TeXht today (and the 
>> Mac GUI over it, 
>> SimpleTeXht. This method also makes XML in some variations, and .odt.) So 
>> Word isn't 
>> broken—it's just not made to recognize this particular kind of XML. (I want 
>> to use the word 
>> "schema" but don't really know what I'm talking about.) So What is missing, 
>> as has been
>> stated in previous threads, is a converter from the XML that we're seeing to 
>> .docx, it
>> seems.
> 
> check pandoc - I am using pandoc to convert xhtml to docx and odt - works 
> perfect for me. I
> just

Ups - should have been:
###
I just added the following converter:

\converter "xhtml" "msdocx" "pandoc -o $$o $$i" ""
\converter "xhtml" "odt lo" "pandoc -o $$o $$i" ""
###

> 
> \converter "xhtml" "msdocx" "pandoc -o $$o $$i" "" \converter "xhtml" "odt 
> lo" "pandoc -o $$o
> $$i" ""added the following converter:
> 
> You have to play with the LyX xhtml or the eLyXer xhtml - I used LyXHTRML 
> because it workded 
> better in my case.
> 
> I really think that pandoc should be detected automatically by LyX (when 
> doing reconfigure)
> and added as it provides very usable conversions.
> 
> 
> Cheers,
> 
> Rainer
> 
>> 
>> Jerry
> 
> 



Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Liviu Andronic
Rainer,


On Fri, Jan 18, 2013 at 9:44 AM, Rainer M Krug  wrote:
> \converter "xhtml" "msdocx" "pandoc -o $$o $$i" ""
> \converter "xhtml" "odt lo" "pandoc -o $$o $$i" ""
> ###
>
Would you mind pasting all the pandoc-related converter and format
definitions that work for you to http://www.lyx.org/trac/ticket/6042 ?
If you include working configs there and others can test them and
confirm they indeed work, then chances are that they would get
included in base LyX.

Liviu


Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Rainer M Krug
On 18/01/13 10:58, Liviu Andronic wrote:
> Rainer,
> 
> 
> On Fri, Jan 18, 2013 at 9:44 AM, Rainer M Krug  wrote:
>> \converter "xhtml" "msdocx" "pandoc -o $$o $$i" "" \converter "xhtml" "odt 
>> lo" "pandoc -o $$o
>> $$i" "" ###
>> 
> Would you mind pasting all the pandoc-related converter and format 
> definitions that work for
> you to http://www.lyx.org/trac/ticket/6042 ? If you include working configs 
> there and others
> can test them and confirm they indeed work, then chances are that they would 
> get included in
> base LyX.

Done - thanks for reminding me.

Rainer

> 
> Liviu
> 


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys.
(Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :   +33 - (0)9 53 10 27 44
Cell:   +33 - (0)6 85 62 59 98
Fax :   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug


SOLVED: Text in certain colours

2013-01-18 Thread Rainer M Krug
On 17/01/13 17:37, Rainer M Krug wrote:
> On 17/01/13 17:18, Alex Vergara Gil wrote:
>>> Hi
>>> 
>>> I have line graphs generated in R, where each line is in a different colour 
>>> (the colours
>>> are generated in R by using rainbow(8)).
>>> 
>>> Due to space problems in the graph, I can not put the legend into the 
>>> grapgh itself, but
>>> want to put it into the caption. Therefore I would like to reproduce the 
>>> colours in LaTeX.
>>> I know how to set the text colour via LyX to one of the pre-defined 
>>> colours, but hjow can I
>>> set them to these specific colours?
>>> 
>>> In addition, I would like to have the colours as filled squares in the text 
>>> - any 
>>> suggestions?
>>> 
>> 
>> 
>> Oh you mean by adding \textcolor{yourcolor}{$\blacksquare$yourcaption} in an 
>> ERT
> 
> Perfect - thanks.
> 
> Now I just have to figure out how to translate the colour codes in R into 
> LaTeX readable. The 
> eight colours in R are:
> 
> "#FFFF" "#FFBF00FF" "#80FF00FF" "#00FF40FF" "#00FF" "#0040" 
> "#8000"
> "#FF00BFFF"

Solved:

I just have to leave out the last two characters, as the first 6 represent the 
rgb colors in hex.
so #FFFF translates into:

[[ \textcolor[HTML]{FF}{$\blacksquare$ ]] my caption [[ } ]]

where [[  ]] stands for ERT.

And I have a filled square in the text and the caption in the colour used in R 
for plotting.

Thanks,

Rainer

> 
> Thanks,
> 
> Rainer
> 
>> 
>> Regards
>> 
>> Alex
>> 
> 


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys.
(Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :   +33 - (0)9 53 10 27 44
Cell:   +33 - (0)6 85 62 59 98
Fax :   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug


Re: Word won't open simplest LyXHTML file

2013-01-18 Thread Steve Litt
On Thu, 17 Jan 2013 21:17:28 -0700, Jerry said:
> 
> On Jan 17, 2013, at 2:30 AM, Alex Fernandez wrote:
> 
> > Hi Jerry,
> > 
> > I am the primary author of eLyXer.
> > 
> > On Thu, Jan 17, 2013 at 4:49 AM, Jerry  wrote:
> > Thanks for that tip. I checked it out. It's just a Python thing so
> > it works fine on OS X, and LyX picked it up as advertised.
> > 
> > Yes, I can confirm that OS X is fully supported.
> >  
> > The output on my simple test case does look nice in a browser, but
> > I get the same error opening with Word as I first described: "The
> > XML file bla bla bla cannot be opened..." etc. I thought maybe my
> > copy of Word was broken but it reads other HTML files fine--I'm
> > guessing they don't have the XML stuff in them, however.
> > 
> > Word does not like XHTML very much; you need to export to HTML 4,
> > using the --html option.
> > http://elyxer.nongnu.org/userguide.html#sub:HTML-Code If you are
> > doing the conversion inside LyX, instead of on the command line,
> > you have to add the --html in the conversion interface. I checked
> > the HTML file that eLyXer made with the W3C page and got: "The
> > uploaded document "-" was successfully checked as XHTML 1.0
> > Transitional."
> > 
> > Yes, eLyXer outputs pure XHTML.
> >  
> > Also--eLyXer does not appear to use MathML so I don't think there
> > is any hope of getting editable math into Word using this method.
> > (But I haven't read all of the eLyXer docs.)
> > 
> > eLyXer has several options for Math output:
> >   http://elyxer.nongnu.org/userguide.html#sub:Math
> > Sadly, none of them is MathML, since at the time eLyXer was
> > conceived it was not very widely supported, and I have not found
> > the time to add it.
> > 
> > Hope this helps,
> > 
> > Alex Fernández.
> > 
> Hi, Alex,
> 
> Thanks for the comments and for the great tool. It does what it
> claims to to, convert LyX to HTML, with lots of math options. The
> default conversion looks great in a browser.
> 
> I tried your --html suggestion and indeed Word opens it, and displays
> it much as a browser does. Unfortunately, the HTML limitations are
> apparent; this is probably as good as a HTML-only conversion can get.
> 
> In my slow-witted way, I'm starting to understand why Word will not
> open the various XML formats that I'm throwing at it. (I also played
> with TeXht today (and the Mac GUI over it, SimpleTeXht. This method
> also makes XML in some variations, and .odt.) So Word isn't
> broken—it's just not made to recognize this particular kind of XML.
> (I want to use the word "schema" but don't really know what I'm
> talking about.) So What is missing, as has been stated in previous
> threads, is a converter from the XML that we're seeing to .docx, it
> seems.
> 
> Jerry

Hi Jerry,

Did you ever consider trying to open the LyXML or whatever it's called
in LibreOffice, and then from LibreOffice exporting it to MSWord
format? That just might work.

Thanks

SteveT

Steve Litt*  http://www.troubleshooters.com/
  *  http://twitter.com/stevelitt
Troubleshooting Training  *  Human Performance



Paste under 2.0.5.1

2013-01-18 Thread Eran Kaplinsky
After installing the latest (using the Installer-1 binary on a Win 7
system) paste is broken.
Content copied from a browser cannot be pasted, as the paste options
in the edit menu are all greyed out.
Text copied from LyX can only be pasted using "paste recent", even if
never pasted before.


Advice welcome.





--
Dr. Eran S. Kaplinsky
Faculty of Law
University of Alberta
447 Law Centre
Edmonton · AB · T6G 2H5
C A N A D A

Tel: (780) 492-2941
Fax: (780) 492-4924


Re: moderncv

2013-01-18 Thread Gregory Jefferis

On 14 Jan 2013, at 18:35, Hansen, Glenn J. wrote:

> Thank you in advance for the help. I am new to lyx/tex.
> 
> I have been trying to get my cv moved to lyx/tex format and have ran into a 
> problem that I am not able to solve. I have nearly everything done but 
> getting a multiple sectioned bibliography to work(e.g., section for journal 
> articles and conference papers). I get the following error:
> 
> "! Package bibtopic Error: Found unknown `thebibliography' environment." 

The error message includes the additional information:

You should either use a package providing a known bibliography
environment (such as natbib), or use the `defaultbib' package
option as a workaround; please see the section about `Warnings
and error messages' in `bibtopic.dvi' for details.

If you go to: Document ... Settings ... Document Class ... 

and then edit the Custom field to add

defaultbib

then as far as I can see things should work. 

Best,

Greg.


--
Gregory Jefferis, PhD  
Division of Neurobiology   
MRC Laboratory of Molecular Biology,   
Hills Road,
Cambridge, CB2 0QH, UK.

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://www.neuroscience.cam.ac.uk/directory/profile.php?gsxej2
http://flybrain.stanford.edu



pLyX system: find & replace LyX format code

2013-01-18 Thread Andrew Parsloe
The pLyX system (see http://wiki.lyx.org/Examples/Examples) provides a 
means of launching python scripts at the click of a few toolbar buttons; 
these scripts modify the current document. Given the speed of modern 
computers, the whole process feels built-in -- the document changes 
almost immediately "in front of one's eyes".


As part of this system, I've attached a find-&-replace script for LyX's 
native file format, & associated files:


findrepl.py -- the script that does the finding & replacing.
findrepl_help.py  -- a help script.
pLyXFindReplace(compressed).lyx -- an explanatory LyX document that 
needs to be saved in uncompressed format for the examples in it to work.


In the document I show how the script can be used to tackle some queries 
that have appeared on the users list over the past year:


document-wide changing the width of figures
document-wide centering of figures
converting chemical formulae written in math insets (for the sake of 
sub- and superscripts) to \mathrm
clearing up "debris" after importing documents from, e.g., OpenOffice or 
Abiword, that have been exported as LaTeX (in other words getting rid of 
all those irritating left & right braces in ERT insets).


One way of tackling such problems is to open the document in a text 
editor and make appropriate changes there. The find-&-replace script 
means that is no longer necessary. It can be done from the comfort of 
the LyX GUI. There are usually other ways of tackling such matters (and 
perhaps more insightful in a LaTeX sense) but for someone pressed for 
time, this may provide a convenient fallback.


The script has a simple mode capable of finding & replacing possibly 
multiple lines of native LyX format code, and a powerful regular 
expression mode similarly capable, but also of condensing multiple 
simple searches into one regexp search (and, of course, with a health 
warning about crashing LyX, given the obscurity of regexps, but it's 
great fun).


Andrew
# Find & replace elements of the LyX source.
# Part of the pLyX.py system.
#
# Andrew Parsloe (apars...@clear.net.nz)
# version 0.1 (19 November 2012)
#
# findrepl.py 
#
import argparse, re, sys

re_backslash = re.compile(r'\n?\\backslash\n')

flex_fr = r'\begin_inset Flex .find & repl'
flex_arg = r'\begin_inset Flex .[argument]'
begin_layout = r'\begin_layout'
end_layout = r'\end_layout'
begin_std = r'\begin_layout Standard'
begin_inset = r'\begin_inset'
end_inset = r'\end_inset'
begin_note = r'\begin_inset Note'
st_open = 'status open\n'
st_coll = 'status collapsed\n'
end_body = r'\end_body'
end_document = r'\end_document'
backslash = r'\backslash'

begin_msg = r'''\begin_inset Note Note
status open
\begin_layout Plain Layout
'''
end_msg = r'''
\end_layout
\end_inset
'''

##
def main(infl, outfl, options, guff):

def strip_outers(stuff):
'''Strip enclosing layout statements.'''
stuff = stuff.partition('\n')[2]
stuff = stuff.rpartition(end_layout)[0]
return stuff

def inset_contents():
'''Get contents of inset minus LyX paragraphing.'''

contents = lines = ''
layouts, insets = 0, 1
status = True
newpara = False

for line in infl:
lines += line
if line == '\n':
continue
# assumes "status open|collapsed" is last status line
elif status:
if st_open == line or st_coll == line:
status = False
continue
elif begin_layout in line:
# exclude LyX paragraphing of contents
layouts += 1
if layouts > 1:
contents += line
else:
newpara = True
elif begin_inset in line:
insets += 1
contents += line
elif backslash in line:
if newpara:
contents += '\n' + line
else:
contents += line
elif end_layout in line:
newpara = False
# exclude LyX paragraphing of contents
if layouts > 1:
contents += line
layouts -= 1
elif end_inset in line:
newpara = False
insets -= 1
if insets == 0:
return contents, lines
else:
contents += line
else:
newpara = False
contents += line

def get_lines(n):
temp = ''
i = 0
if n == 0:
return ''
else:
for line in infl:
if line != '\n':
temp += line
i += 1
if i == n:
break
return temp

def write_msg(msg):

Re: Vancouver style options -changed to: almost soved

2013-01-18 Thread Julien Rioux

On 18/01/2013 3:19 AM, Wolfgang Engelmann wrote:

Am Dienstag, 15. Januar 2013, 14:39:07 schrieb Wolfgang Engelmann:

Hi,

still not done with Vancouver style

I tried for quite some time but can't find the option for references, in
which more than 2 authors are referenced as
author1 et al

Wolfgang


I found out how to solve it:

in vancouver.bst
(which is in my case in home/wolfgang/texlive/2012/texmf-dist/bibtex/bst/)

change
nameptr #6
to
nameptr #2

and
numname #6
to
numname #2

I saved this changed vancouver.bst to vancouver2etal.bst
in order not to interfere with the original file
and added this to document>settings  bibliography style>default style
WHICH DID NOT WORK
however, if I changed vancouver2etal.bst to vancouver.bst
(by saving the original vancouver.bst preliminary as vancouverOrig.bst)
IT WORKED
namely, only maximally 2 authors in the bibliography, if more: et al after
the second one

My question:
why was vancouver2etal in bibliography style>default style not recognized?
I did a reconfigure before.

Wolfgang



This is new in LyX 2.1:
For the Default style defined in document settings to be used, the style 
in the "BibTeX-generated bibliography" dialog must be set to "default". 
Note that this isn't completely ironed out, but the intention behind 
this document-wide setting is for citation engine that define the style 
in the preamble, e.g. biblatex.


For now, I would recommend to use the LyX 2.0 way:
Just set the bibliography style you want from the "BibTeX-generated 
bibliography" dialog.


Regards,
Julien


Re: Endnote number size/position

2013-01-18 Thread Julien Rioux

On 16/12/2012 4:48 PM, Maria Gouskova wrote:

On Wed, Nov 14, 2012 at 2:03 PM, Richard Heck  wrote:

On 10/22/2012 04:19 PM, Maria Gouskova wrote:


Thanks, Richard--example file attached! It works when everything in
the preamble is commented out, but the endnote numbers appear as
superscripts in the Notes section (which is not what I want; I need
them to be on the main line in normal size, followed by periods and
then the note text).


The right command to change is: \@makeenmark, with the @.


(Sorry about the late response!)

I replaced the preamble line

\renewcommand\makeenmark{\theenmark. }

with

\renewcommand\@makeenmark{\theenmark. }

and the result is an Undefined control sequence error:

  \footnote{
A footnote/endnote A footnote/endnote A footnote/endnote A fo...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.


Maria




The attached seems to work for me. Is this what you are after?

Regards,
Julien


aendnote_test_file-1.lyx
Description: application/lyx


Re: Trouble with track changes appearing in pdflatex views

2013-01-18 Thread Julien Rioux

On 28/11/2012 9:19 AM, Richard Heck wrote:

On 11/27/2012 03:01 PM, Allen Wilkinson wrote:

My problem is that if I want to show tracked changes in PDF view or
output I get these errors:

Package xcolor Error: Undefined color `LYXDELETED'.
Package xcolor Error: Undefined color `LYXADDED'.
...
+++
after a modest finite extent of the document is processed.

If I delete changed and unchanged text from the document such that the
document is small enough, then PDF output with tracked changes works.

This is true whether I use Lyx PDF viewing, or run OS' pdflatex
compiler on exported .tex file.

If I disable 'show changes in output', then PDF output occurs without
errors.

Can anyone help me resolve this problem?


Odd that the "undefined color" is in all caps. Is LyX exporting this wrong?

I think we can only answer this with a test file that causes the problem.

rh




The headers from that document class must be all caps. A similar error 
happened with changes in section titles with the revtex document class, 
which use all caps section titles. For some reason latex thinks that it 
should also capitalize the color names. A workaround is to also define 
the colors with capitalized names! c.f. http://www.lyx.org/trac/ticket/4625


Regards,
Julien


Re: Two Column Article - Text rows vertically misaligned

2013-01-18 Thread Julien Rioux

On 17/12/2012 9:06 PM, TB L wrote:

Hey everyone,

just tried to typeset an article with two-column layout and am now faced
with the problem that the text rows on the right hand are not vertically
aligned to the one on the left hand (probably because of section titles?).

Is there any option to force Lyx / Latex to ensure that the text rows are
correctly aligned on both sides with respect to each other? This would look
a lot more professional. Would be really thankful for your support [image:
:)]

Tim



Apparently, (la)tex wasn't designed with left- and right-column line 
matching in mind at all, and accomplishing this after the fact is 
challenging. That said, if you find a way to make this work in latex, 
please post your result. We could look how difficult it would be to have 
it implemented in LyX.


Regards,
Julien


Re: References appear with "et" instead of "and" between authors

2013-01-18 Thread Julien Rioux

On 07/05/2012 3:41 PM, ChiPro wrote:

Hi all,

I'm using BibDesk as my reference package in Lyx. I have set the Lyx options
(Documents > Settings) to "Natbib: Author-year" and the citation style to
"[author1] and [author2] ([year])".

Unfortunately, when I produce my PDF file, the reference appears as


[Author1] et [Author2] (2000)


instead of the desired


[Author1] and [Author2] (2000).


Any help would be appreciated.

Thanks,
CP




Which style file (.bst) are you using?

--
Julien


Re: problem with natbib numbering

2013-01-18 Thread Julien Rioux

On 16/06/2012 9:39 AM, julien.babinot wrote:

Hello,

I am currently writing my PhD thesis on Lyx, and i have one problem with
my bibliography.
I am using multiple bibliography, with a separate bib file for each
chapter (these are included in a main document thesis.lyx).
As advised in the advanced options document, i use \begin{btUnit}and
\end{btUnit}at the beginning and end of my chapter to allow the multiple
bibliography.
I want to use a numbered style, in superscript, and numbered in the
order of citation. But my problem is that references are listed in the
alphabetical order of authors, thus generating numbering like 5, 23, 6
 and not 1,2,3
Here is the Latex code generated by Lyx:

%% LyX 2.0.3 created this file. For more info, see http://www.lyx.org/.

%% Do not edit unless you really know what you are doing.

\documentclass[oneside,english,french]{thl3i}

\usepackage[T1]{fontenc}

\usepackage[utf8x]{inputenc}

\setcounter{secnumdepth}{1}

\setcounter{tocdepth}{1}

\usepackage{array}

\usepackage{float}

\usepackage{textcomp}

\usepackage{multirow}

\usepackage{amsthm}

\usepackage{amsmath}

\usepackage{graphicx}

\usepackage{setspace}

\usepackage[dot]{bibtopic}

\PassOptionsToPackage{normalem}{ulem}

\usepackage{ulem}

\onehalfspacing

\makeatletter

%% LyX specific LaTeX commands.

\DeclareRobustCommand{\greektext}{%

\fontencoding{LGR}\selectfont\def\encodingdefault{LGR}}

\DeclareRobustCommand{\textgreek}[1]{\leavevmode{\greektext #1}}

\DeclareFontEncoding{LGR}{}{}

\DeclareTextSymbol{\~}{LGR}{126}

%% Because html converters don't know tabularnewline

\providecommand{\tabularnewline}{\\}

%% A simple dot to overcome graphicx limitations

\newcommand{\lyxdot}{.}

%% Textclass specific LaTeX commands.

\numberwithin{equation}{section}

\newcommand{\lyxaddress}[1]{

\par {\raggedright #1

\vspace{1.4em}

\noindent\par}

}

%% User specified LaTeX commands.

\usepackage[numbers,super,sort]{natbib}

\bibliographystyle{unsrtnat}

\makeatother

\usepackage{babel}

\addto\extrasfrench{%

\providecommand{\og}{\leavevmode\flqq~}%

\providecommand{\fg}{\ifdim\lastskip>\z@\unskip\fi~\frqq}%

}

\begin{document}

\titreLogoUn{}

\titreLogoDeux{}

\subject{}

\title{}

\author{\textbf{\large }\\

}

\date{xx/xx/2012}

\Rapporteurs{Rapporteur 1é 1\\

Rapporteur 2é 2}

\Examinateurs{Examinateur 1é 3\\

Examinateur 2é 4}

\Directeur{Directeur 1é 5}

\Encadrant{Encadrant 1é 6}

\Encadrant{Invité 1é 7}

\titreBasDePage{}

\maketitle

\address{%

\begin{minipage}[t][1\textheight]{1\columnwidth}%

\begin{center}

\includegraphics[width=3cm]{Logos/Financeur}

\par\end{center}

\vspace{1cm}

\begin{tabular}{rll}

\emph{Thèse réalisée au} & \multicolumn{2}{l}{}\tabularnewline

& \multicolumn{2}{l}{}\tabularnewline

& \multicolumn{2}{l}{}\tabularnewline

& \multicolumn{2}{l}{}\tabularnewline

& \multicolumn{2}{l}{}\tabularnewline

& \multicolumn{2}{l}{}\tabularnewline

& \multicolumn{2}{l}{}\tabularnewline

& \multicolumn{2}{l}{}\tabularnewline

& \multicolumn{2}{l}{Web :}\tabularnewline

& \multicolumn{2}{l}{}\tabularnewline

\emph{Sous la direction de } & \tabularnewline

& & \tabularnewline

\emph{Co-encadrement} & \tabularnewline

& & \tabularnewline

\end{tabular}

\begin{center}

\cleardoublepage

\par\end{center}

\begin{center}

\par\end{center}%

\end{minipage}}

\frontmatter

\include{Remerciements}\include{Résumé}

\include{Abstract}

\tableofcontents{}

\listoffigures

\listoftables

\include{abreviations}

\mainmatter

\include{Introduction}

\include{Chapitre1}

\include{Chapitre2}

\include{Chapitre3}

\include{Chapitre4}

\include{Chapitre5}

\include{Chapitre6}

\include{Conclusion}

\include{Annexes}

\backmatter

\end{document}


What i don't understand is that my bibliography is actually numbered in
superscript but not sorted by order of citation?! unsrtnat is not
supposed to do so?

I would extremely appreciate any help.

Thanks,

Julien






Did you figure it out? Although unsrtnat won't sort, bibtopic might 
interfering?


--
Julien


Re: Relative path to bib source doesn't work in lyx (but does work when exported as .tex)

2013-01-18 Thread Julien Rioux

On 27/11/2012 6:47 PM, stefano franchi wrote:

On Tue, Nov 27, 2012 at 5:34 PM, Roey Angel  wrote:

So, a bug or a 'feature'?



Feature, p/h? It has a great educational value: it forces you to understand
how lyx uses the latex (and biber, texindy, etc) backends ;-)

Cheers,

Stefano




There's an enhancement request that might solve this, eventually (don't 
hold your breath, it's 7 year old): http://www.lyx.org/trac/ticket/2645


--
Julien