Re: Recommended third-party tools

2012-02-22 Thread Russell D Brunelle 
I'd like to thank everyone who offered suggestions for this guide. I've 
implemented almost all of them, and anyone who wants to take this thing and 
make something more official out of it is welcome to.

I remain of the opinion that a simple, one-page guide which takes the user 
step-by-step not only through installing LyX, but also through installing at 
least one good example of each of the main types of supporting tools, would be 
a boon for beginners.

Although one of the strengths of open source software is the amount of choice 
you get, I also believe it's helpful to be able to say to a beginner, "You are 
welcome and encouraged to try everything and see what best suits you, but for 
purpose X, right now package Y (or perhaps package Z) would be an excellent 
place to start."

Not only does this make LyX more attractive through showing the power of the 
entire software ecosystem, but it raises the odds that the user actually *will* 
end up using some sort of software for purpose X instead of nothing (a great 
example of this is reference management software like jabref or pybliographer 
which seems to me to be woefully underutilized).

Anyway, thank you again for all the suggestions. I've always loved LyX and hope 
in some small way this contribution was worthwhile.

Russell

> http://russellb.livejournal.com/1335718.html
> 
> I believe a simplified guide such as this could be very helpful for students 
> about to enter college to study one of the sciences

Re: Recommended third-party tools

2012-02-21 Thread Wolfgang Engelmann 
Am Sonntag, 19. Februar 2012, 00:45:52 schrieb Russell D Brunelle:
> I'm working on creating the "perfect" step-by-step procedure for setting
> up a Linux workstation for scientific writing, based on LyX and with an
> emphasis on selecting the best available FOSS tools for creating
> graphics and performing computations.  Whenever possible I wanted to
> select tools which are in common use, so that the skills being gained
> might have lasting value.
> 
> Here's the draft I have so far, which builds on something I mentioned on
> this list a while ago: http://russellb.livejournal.com/1335718.html
> 
> I believe a simplified guide such as this could be very helpful for
> students about to enter college to study one of the sciences, and I'm
> hoping members of this list might be able to offer suggestions for
> additional third-party tools, or enhancements to LyX, which may have
> been left out.  I don't consider myself a LyX expert, but I do believe
> there is a need for something like this, and I gave this my best shot
> in the hopes of getting the ball rolling.
> 
> Russell

Thanks for that. A few questions:

Your point 3 re compose key refers to lyx or the PC setting? 
Is latex2rtf and rcs contained in texlife? 

I would add jabref as an alternative to Pybliographer

As a scientist I need often to extract diagrams from publications for my 
books. I scan them and use engauge to digitize the data. To plot them I 
like pyxplot on the command line which is easy to learn and use. The 
handbook is well written. However, it would be very handy to have a 
frontend program in the way lyx is for latex, i.e. some way to handle the 
plot items graphically. I do realize it is a major job...

Wolfgang

Re: Recommended third-party tools

2012-02-21 Thread Pavel Sanda 
Yihui Xie wrote:
> Yes, knitr is beyond beta state now. I appreciate if someone can add a
> description item below Sweave:

Added. P

Re: Recommended third-party tools

2012-02-20 Thread Yihui Xie 
Yes, knitr is beyond beta state now. I appreciate if someone can add a
description item below Sweave:

 http://yihui.name/knitr/"; class="urllink">knitr -
literate programming. A comprehensive R package derived from
Sweave with a different design that includes code formatting,
highlighting, caching, fine control of graphics, conditional
evaluation, multiple markup formats and other features. 

Regards,
Yihui
--
Yihui Xie 
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA



On Mon, Feb 20, 2012 at 12:24 PM, Pavel Sanda  wrote:
> Russell D Brunelle wrote:
>> left out.  I don't consider myself a LyX expert, but I do believe there is
>> a need for something like this, and I gave this my best shot in the hopes
>> of getting the ball rolling.
>
> You may want to check http://www.lyx.org/AdditionalSoftware
>
> Yihui Xie wrote:
>> The topic of the original post is too broad for me to comment on, but
>> if it comes down to statistical computing and graphics, I certainly
>> recommend R. Here are some sample documents created in LyX with R
>> literate programming modules:
>>
>> https://github.com/downloads/yihui/lyx/sweave.pdf
>> https://github.com/downloads/yihui/knitr/knitr-manual.pdf
>> https://github.com/downloads/yihui/knitr/knitr-graphics.pdf
>
>
> Our description currently says:
> Sweave - literate programming. Tool that allows to embed the R code for 
> complete data analyses in latex documents.
>
> Is there something new to be added WRT knitr (is it beyond beta state)?
>
> Pavel

Re: Recommended third-party tools

2012-02-20 Thread Pavel Sanda 
Russell D Brunelle wrote:
> left out.  I don't consider myself a LyX expert, but I do believe there is 
> a need for something like this, and I gave this my best shot in the hopes 
> of getting the ball rolling.

You may want to check http://www.lyx.org/AdditionalSoftware

Yihui Xie wrote:
> The topic of the original post is too broad for me to comment on, but
> if it comes down to statistical computing and graphics, I certainly
> recommend R. Here are some sample documents created in LyX with R
> literate programming modules:
> 
> https://github.com/downloads/yihui/lyx/sweave.pdf
> https://github.com/downloads/yihui/knitr/knitr-manual.pdf
> https://github.com/downloads/yihui/knitr/knitr-graphics.pdf


Our description currently says:
Sweave - literate programming. Tool that allows to embed the R code for 
complete data analyses in latex documents. 

Is there something new to be added WRT knitr (is it beyond beta state)?

Pavel

Re: New LyX Personal Package Archive: was Recommended third-party tools

2012-02-19 Thread Liviu Andronic 
On Sun, Feb 19, 2012 at 9:13 PM, Steve Litt  wrote:
>> [1] https://launchpad.net/~lyx-devel/+archive/release
>
> You should shout this from the rooftops. This should be on the LyX
> Wiki's home page in +3 bold typesize. If this Personal Package Archive
> (PPA) actually yields working LyXes, it changes everything.
>
I am doing my best. In any case, the packaging 'debian' dir is taken
from Maverick and slightly tweaked to account for (some) changes in
packaging in Oneiric.


> From my perspective, a working PPA means no more stains on my
> desk from the tears that I shed trying to ./configure;make;make install
> and getting slapped down by dependencies at every turn. A working PPA
> means an end to the annual pilgrimages to Xforms' gravestone, upon
> which I placed flowers and mourned the hours lost to a particularly bad
> Qt4 dependency way back in the early 1.6.x's.
>
I am glad if this can change your life (and spare you some flower expenses). :)


> All this could mean I regularly have a modern and working LyX.
>
Please let me know how it works for you. Cheers
Liviu



> Maybe some day the PPA could encompass Red Hat and other types of
> packages. This is really cool. Thank you!
>
> SteveT



-- 
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http://www.alienetworks.com/srtest.cfm
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New LyX Personal Package Archive: was Recommended third-party tools

2012-02-19 Thread Steve Litt 
On Sun, 19 Feb 2012 19:48:53 +0100
Liviu Andronic  wrote:

> On Sun, Feb 19, 2012 at 2:12 AM, Steve Litt
[clip]

> > On the other hand, Debian's more likely to
> > have a *working* LyX :-)
> >
> This is hopefully changing. Now we have a PPA containing up-to-date
> releases of LyX. [1] I will announce it on the list shortly. (The PPA
> is still considered 'experimental' until more people test it and
> provide positive feedback. Please do backups.)
> 
> Liviu
> 
> [1] https://launchpad.net/~lyx-devel/+archive/release

Liviu,

You should shout this from the rooftops. This should be on the LyX
Wiki's home page in +3 bold typesize. If this Personal Package Archive
(PPA) actually yields working LyXes, it changes everything.

From my perspective, a working PPA means no more stains on my
desk from the tears that I shed trying to ./configure;make;make install
and getting slapped down by dependencies at every turn. A working PPA
means an end to the annual pilgrimages to Xforms' gravestone, upon
which I placed flowers and mourned the hours lost to a particularly bad
Qt4 dependency way back in the early 1.6.x's.

All this could mean I regularly have a modern and working LyX.

Maybe some day the PPA could encompass Red Hat and other types of
packages. This is really cool. Thank you!

SteveT

Re: Recommended third-party tools

2012-02-19 Thread Yihui Xie 
Liviu,

This is really great news! I've been longing for such a PPA. Thanks!

Regards,
Yihui
--
Yihui Xie 
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA



On Sun, Feb 19, 2012 at 12:48 PM, Liviu Andronic  wrote:
> This is hopefully changing. Now we have a PPA containing up-to-date
> releases of LyX. [1] I will announce it on the list shortly. (The PPA
> is still considered 'experimental' until more people test it and
> provide positive feedback. Please do backups.)
>
> Liviu
>
> [1] https://launchpad.net/~lyx-devel/+archive/release

Re: Recommended third-party tools

2012-02-19 Thread Liviu Andronic 
On Sun, Feb 19, 2012 at 2:12 AM, Steve Litt  wrote:
>> I'm working on creating the "perfect" step-by-step procedure for
>> setting up a Linux workstation for scientific writing, based on LyX
>
It would be nice if you could use *bold* for each of the apps included
in that page. This should improve the readability of the article.


> 1) I'd recommend Ubuntu over Debian for two reasons: A) Ubuntu is
> easier to get working with random hardware, and B) Ubuntu is likely to
> have a newer LyX. On the other hand, Debian's more likely to have a
> *working* LyX :-)
>
This is hopefully changing. Now we have a PPA containing up-to-date
releases of LyX. [1] I will announce it on the list shortly. (The PPA
is still considered 'experimental' until more people test it and
provide positive feedback. Please do backups.)

Liviu

[1] https://launchpad.net/~lyx-devel/+archive/release

Re: Recommended third-party tools

2012-02-19 Thread Liviu Andronic 
On Sun, Feb 19, 2012 at 4:56 AM, Les Denham  wrote:
> Firstly, the version of Linux is not all that important. I've had good
> experiences with Ubuntu in the past, but thanks to some idiotic (in my
> opinion) decisions recently by the maintainers of both Gnome and KDE
> and by Ubuntu for its default desktop, I've given up on Ubuntu, Gnome,
> and KDE, all three of which I have used happily in the past. For the
> average user now I would recommend Linux Mint (which just works even
> more smoothly than Ubuntu) and, for those willing to learn a little or a
> lot about what is behind the pretty windows, either Sabayon or Gentoo.
> Whichever distro you choose, change the window manager to XFCE or LXDE.
>
It was somewhat implied, but to make it explicit, there is no need to
drop Ubuntu because of the recent Gnome3/Unity fiasco: you can always
change to Xubuntu (or Lubuntu). Personally I've been using Xfce for
the past 5-7 years and I always found it---as far as the core apps are
concerned---superior to Gnome 2.


> If you are using "PDF for everything else" you definitely need
> pdfimages (part of the Poppler library) and pdftk.
>
Another suggestion would be PDF Chain [1], a nice GUI interface to pdftk.

Liviu

[1] http://alternativeto.net/software/pdf-chain/

Re: Recommended third-party tools

2012-02-19 Thread stefano franchi 
On Sun, Feb 19, 2012 at 9:14 AM, David L. Johnson
 wrote:
> On 02/18/2012 10:56 PM, Les Denham wrote:
>>
>>
>> Firstly, the version of Linux is not all that important. I've had good
>> experiences with Ubuntu in the past, but thanks to some idiotic (in my
>> opinion) decisions recently by the maintainers of both Gnome and KDE
>> and by Ubuntu for its default desktop, I've given up on Ubuntu, Gnome,
>> and KDE, all three of which I have used happily in the past. For the
>> average user now I would recommend Linux Mint (which just works even
>> more smoothly than Ubuntu) and, for those willing to learn a little or a
>> lot about what is behind the pretty windows, either Sabayon or Gentoo.
>> Whichever distro you choose, change the window manager to XFCE or LXDE.
>
>
> Amen to that.  Gnome has, IMNSHO, shot themselves in the foot with a bloated
> interface that doesn't work on a lot of hardware with their version 3.  For
> that reason, you do need to be careful to not use a distribution that only
> uses Gnome.  It was a long annoying process for me to switch over after an
> upgrade dumped me into Gnome 3.  Xfce is fine, though, so and distribution
> that allows you to choose will be good.  Frankly, I don't know what Kde did,
> but my advice is to avoid Gnome.
>

This is starting to be more and more off-topic, but here are my 2
cents on distros:

I'm very happy with KDE and have been using it since version 3.4.
However, Kubuntu (Kde-based ubuntu distribution) is terrible and will
probably get worse now that Canonical has moved the only fully paid
maintainer to other projects. By "terrible" i mean that the twice
yearly major upgrades would routinely break my X11 setup, which meant
manually tweaking the xorg.conf file every time. Definitely not fun
(http://xkcd.com/963/  pretty much describes my life under kubuntu).

Switching to Archlinux solved all my problems, however. Kde is
rock-solid and fast (even on not so recent hardware). I never had any
problems

Stefano


> --
>
> David L. Johnson
>
> When you are up to your ass in alligators, it's hard to remember that
> your initial objective was to drain the swamp.
>                -- LBJ
>



-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic Studies            Ph:   +1 (979) 845-2125
Texas A&M University                          Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Recommended third-party tools

2012-02-19 Thread David L. Johnson 

On 02/18/2012 10:56 PM, Les Denham wrote:


Firstly, the version of Linux is not all that important. I've had good
experiences with Ubuntu in the past, but thanks to some idiotic (in my
opinion) decisions recently by the maintainers of both Gnome and KDE
and by Ubuntu for its default desktop, I've given up on Ubuntu, Gnome,
and KDE, all three of which I have used happily in the past. For the
average user now I would recommend Linux Mint (which just works even
more smoothly than Ubuntu) and, for those willing to learn a little or a
lot about what is behind the pretty windows, either Sabayon or Gentoo.
Whichever distro you choose, change the window manager to XFCE or LXDE.


Amen to that.  Gnome has, IMNSHO, shot themselves in the foot with a 
bloated interface that doesn't work on a lot of hardware with their 
version 3.  For that reason, you do need to be careful to not use a 
distribution that only uses Gnome.  It was a long annoying process for 
me to switch over after an upgrade dumped me into Gnome 3.  Xfce is 
fine, though, so and distribution that allows you to choose will be 
good.  Frankly, I don't know what Kde did, but my advice is to avoid Gnome.


--

David L. Johnson

When you are up to your ass in alligators, it's hard to remember that
your initial objective was to drain the swamp.
-- LBJ

Re: Recommended third-party tools

2012-02-18 Thread Les Denham 
On Sat, 18 Feb 2012 15:45:52 -0800
Russell D Brunelle  wrote:

> Here's the draft I have so far, which builds on something I mentioned
> on this list a while ago: http://russellb.livejournal.com/1335718.html

I'm sure everyone has different preferences, but here are some of my
preferences.

Firstly, the version of Linux is not all that important. I've had good
experiences with Ubuntu in the past, but thanks to some idiotic (in my
opinion) decisions recently by the maintainers of both Gnome and KDE
and by Ubuntu for its default desktop, I've given up on Ubuntu, Gnome,
and KDE, all three of which I have used happily in the past. For the
average user now I would recommend Linux Mint (which just works even
more smoothly than Ubuntu) and, for those willing to learn a little or a
lot about what is behind the pretty windows, either Sabayon or Gentoo.
Whichever distro you choose, change the window manager to XFCE or LXDE.

For attractive graphics, I would generally agree. You have left out two
tools I find very versatile and useful: for easy publication-quality
data plotting I think xmgrace (which has a graphical interface, but can
also be used on the command line and in scripts) is easier to use than
gnuplot; and if maps of any kind are needed, you need GMT (Generic
Mapping Tools).

If you are using "PDF for everything else" you definitely need
pdfimages (part of the Poppler library) and pdftk.

And for things like the title pages Steve Litt says you need to do with
something other than LyX, you need Scribus.

Finally, if you want to make your document into an ebook, you need
Calibre.

Les

Re: Recommended third-party tools

2012-02-18 Thread Yihui Xie 
The topic of the original post is too broad for me to comment on, but
if it comes down to statistical computing and graphics, I certainly
recommend R. Here are some sample documents created in LyX with R
literate programming modules:

https://github.com/downloads/yihui/lyx/sweave.pdf
https://github.com/downloads/yihui/knitr/knitr-manual.pdf
https://github.com/downloads/yihui/knitr/knitr-graphics.pdf

I write almost all my documents in LyX (homework, reports, papers,
...). The good thing about literate programming is you do not have to
copy and paste; all results are generated dynamically by executing
code (R code in this case).

Just my 2 cents.

Regards,
Yihui
--
Yihui Xie 
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA

Re: Recommended third-party tools

2012-02-18 Thread Steve Litt 
On Sat, 18 Feb 2012 15:45:52 -0800
Russell D Brunelle  wrote:

> I'm working on creating the "perfect" step-by-step procedure for
> setting up a Linux workstation for scientific writing, based on LyX
> and with an emphasis on selecting the best available FOSS tools for
> creating graphics and performing computations.  Whenever possible I
> wanted to select tools which are in common use, so that the skills
> being gained might have lasting value.
> 
> Here's the draft I have so far, which builds on something I mentioned
> on this list a while ago: http://russellb.livejournal.com/1335718.html
> 
> I believe a simplified guide such as this could be very helpful for 
> students about to enter college to study one of the sciences, and I'm 
> hoping members of this list might be able to offer suggestions for 
> additional third-party tools, or enhancements to LyX, which may have
> been left out.  I don't consider myself a LyX expert, but I do
> believe there is a need for something like this, and I gave this my
> best shot in the hopes of getting the ball rolling.
> 
> Russell

OUTstanding Russell. Very thorough and *very* much needed. I'm so glad
you recognized the value of dia as diagramming software -- most
remember only its lower quality past and not its current
spectacularism. I also like the fact that you recommended both Gimp and
Inkscape -- both are necessary to my business. And congrats on
recommending Gnumeric -- it just works, and works, and works, and never
crashes.

Life would be boring if everyone agreed, so here are some of the points
I would have diverged had I been the author:

1) I'd recommend Ubuntu over Debian for two reasons: A) Ubuntu is
easier to get working with random hardware, and B) Ubuntu is likely to
have a newer LyX. On the other hand, Debian's more likely to have a
*working* LyX :-)

On the subject of recommending distros, I can find you at least fifty
people to tell you that Ubuntu sux, and having used it for five years,
I can't argue with them because I see their point, but for me it's still
the best.

2) I'd either stay away from recommending an email client at all, or
I'd expand it to discuss the different types, PIMs, fat email clients,
and webmail. Some people, me for instance, run screaming from email
acting like a PIM, so I doubt I'll ever use Evolution. More on email in
another post...

3) As long as you're listing specialized products like R, Sweave, SPSS
and the like, you might consider listing one or two circuit analysis
softwares.

The blogpost you just wrote is *very* necessary for the LyX biosphere.
There's a LyX wiki somewhere where you can put URLs of LyX docs. You
should find it and include the URL to your blogpost.

Thanks for the great job!

SteveT

Re: Recommended third-party tools

2012-02-18 Thread Rich Shepard 

On Sat, 18 Feb 2012, Russell D Brunelle wrote:


I'm working on creating the "perfect" step-by-step procedure for setting
up a Linux workstation for scientific writing, based on LyX and with an
emphasis on selecting the best available FOSS tools for creating graphics
and performing computations.  Whenever possible I wanted to select tools
which are in common use, so that the skills being gained might have
lasting value.


  For vector graphics, PSTricks . For raster
graphics The GIMP. For data analyses and statistical computing, R
.

  Of course, 'perfect' and 'best available' is highly individualistic.
What's perfect and best available to me might not be for you. I prefer emacs
and others prefer vi. I prefer the CLI and others perfer the GUI. And so it
goes. Unlike Microsoft, linux and the *BSDs offer a plethora of choices and
flame wars over what's 'best' used to rage out of control.

  Pick what you find comfortable for your work, learn the tools inside-out,
and stick with them ignoring what others think are 'best' or 'perfect.'


I believe a simplified guide such as this could be very helpful for
students about to enter college to study one of the sciences, and I'm
hoping members of this list might be able to offer suggestions for
additional third-party tools, or enhancements to LyX, which may have been
left out.  I don't consider myself a LyX expert, but I do believe there is
a need for something like this, and I gave this my best shot in the hopes
of getting the ball rolling.


  Teach them to explore choices and pick what suits them the best. Each
individual will settle on a different suite of tools.

Rich

--
Richard B. Shepard, Ph.D.  |   Integrity - Credibility - Innovation
Applied Ecosystem Services, Inc.   |Helping Ensure Our Clients' Futures
 Voice: 503-667-4517  Fax: 503-667-8863

Recommended third-party tools

2012-02-18 Thread Russell D Brunelle 
I'm working on creating the "perfect" step-by-step procedure for setting 
up a Linux workstation for scientific writing, based on LyX and with an 
emphasis on selecting the best available FOSS tools for creating graphics 
and performing computations.  Whenever possible I wanted to select tools 
which are in common use, so that the skills being gained might have 
lasting value.


Here's the draft I have so far, which builds on something I mentioned on 
this list a while ago: http://russellb.livejournal.com/1335718.html


I believe a simplified guide such as this could be very helpful for 
students about to enter college to study one of the sciences, and I'm 
hoping members of this list might be able to offer suggestions for 
additional third-party tools, or enhancements to LyX, which may have been 
left out.  I don't consider myself a LyX expert, but I do believe there is 
a need for something like this, and I gave this my best shot in the hopes 
of getting the ball rolling.


Russell