Re: Automatic scrolling upon entering math mode inside a caption

[Thomas Coffee]

Uwe Stöhr uwestoehr at web.de writes:
 
 Am 27.09.2010 22:06, schrieb Will:
 
  Hmm, I didn't realize this was important before, but it seems I only
  have this problem when I have View Source open on the bottom of the
  window.
 
 This is because the source window shows you with the default settings 
 only the content of the current paragraph. So depending on the amount 
 your have already in your caption, it needs more space to display the 
 new math code.

This old thread was the only mention I could find of this problem ... but I
still experience this behavior in LyX 2 regardless of what is open or not open
at the bottom of the window (in particular, regardless of whether View Source
is open), so there must be more to the story.

Whenever the cursor enters a math mode element that is inside any kind of box
(Figure caption, LyX note, etc.), via pointing device or arrow keys, the
contents of the editing window are immediately scrolled to place the math mode
element at the top.

I am running LyX 2.0.0 on Ubuntu 11.10 x86_64. I could not find any bug reports
on this topic, so I wonder if any others are having the same problem.

Thomas

Re: Automatic scrolling upon entering math mode inside a caption

[Thomas Coffee]

On Mon, Mar 25, 2013 at 11:08 AM, Thomas Coffee thomasmcof...@gmail.com wrote:
 Whenever the cursor enters a math mode element that is inside any kind of box
 (Figure caption, LyX note, etc.), via pointing device or arrow keys, the
 contents of the editing window are immediately scrolled to place the math mode
 element at the top.

On closer examination, the behavior is actually more complex: it
appears that upon entering or creating a math mode element inside a
box, LyX attempts to scroll the math mode element (if necessary and
possible) such that vertical space appearing below it in the editing
window is greater than or equal to the vertical extent of the box.

(I previously believed it tried to place the math mode element at the
top because all my examples were done inside boxes greater than the
height of the window.)

Can anyone reproduce this?

Thomas

Re: Automatic scrolling upon entering math mode inside a caption

[Thomas Coffee]

Uwe Stöhr uwestoehr at web.de writes:
 
 Am 27.09.2010 22:06, schrieb Will:
 
  Hmm, I didn't realize this was important before, but it seems I only
  have this problem when I have View Source open on the bottom of the
  window.
 
 This is because the source window shows you with the default settings 
 only the content of the current paragraph. So depending on the amount 
 your have already in your caption, it needs more space to display the 
 new math code.

This old thread was the only mention I could find of this problem ... but I
still experience this behavior in LyX 2 regardless of what is open or not open
at the bottom of the window (in particular, regardless of whether View Source
is open), so there must be more to the story.

Whenever the cursor enters a math mode element that is inside any kind of box
(Figure caption, LyX note, etc.), via pointing device or arrow keys, the
contents of the editing window are immediately scrolled to place the math mode
element at the top.

I am running LyX 2.0.0 on Ubuntu 11.10 x86_64. I could not find any bug reports
on this topic, so I wonder if any others are having the same problem.

Thomas

Re: Automatic scrolling upon entering math mode inside a caption

[Thomas Coffee]

On Mon, Mar 25, 2013 at 11:08 AM, Thomas Coffee thomasmcof...@gmail.com wrote:
 Whenever the cursor enters a math mode element that is inside any kind of box
 (Figure caption, LyX note, etc.), via pointing device or arrow keys, the
 contents of the editing window are immediately scrolled to place the math mode
 element at the top.

On closer examination, the behavior is actually more complex: it
appears that upon entering or creating a math mode element inside a
box, LyX attempts to scroll the math mode element (if necessary and
possible) such that vertical space appearing below it in the editing
window is greater than or equal to the vertical extent of the box.

(I previously believed it tried to place the math mode element at the
top because all my examples were done inside boxes greater than the
height of the window.)

Can anyone reproduce this?

Thomas

Re: Automatic scrolling upon entering math mode inside a caption

[Thomas Coffee]

Uwe Stöhr  web.de> writes:
> 
> Am 27.09.2010 22:06, schrieb Will:
> 
> > Hmm, I didn't realize this was important before, but it seems I only
> > have this problem when I have "View Source" open on the bottom of the
> > window.
> 
> This is because the source window shows you with the default settings 
> only the content of the current paragraph. So depending on the amount 
> your have already in your caption, it needs more space to display the 
> new math code.

This old thread was the only mention I could find of this problem ... but I
still experience this behavior in LyX 2 regardless of what is open or not open
at the bottom of the window (in particular, regardless of whether "View Source"
is open), so there must be more to the story.

Whenever the cursor enters a math mode element that is inside any kind of box
(Figure caption, LyX note, etc.), via pointing device or arrow keys, the
contents of the editing window are immediately scrolled to place the math mode
element at the top.

I am running LyX 2.0.0 on Ubuntu 11.10 x86_64. I could not find any bug reports
on this topic, so I wonder if any others are having the same problem.

Thomas

Re: Automatic scrolling upon entering math mode inside a caption

[Thomas Coffee]

On Mon, Mar 25, 2013 at 11:08 AM, Thomas Coffee <thomasmcof...@gmail.com> wrote:
> Whenever the cursor enters a math mode element that is inside any kind of box
> (Figure caption, LyX note, etc.), via pointing device or arrow keys, the
> contents of the editing window are immediately scrolled to place the math mode
> element at the top.

On closer examination, the behavior is actually more complex: it
appears that upon entering or creating a math mode element inside a
box, LyX attempts to scroll the math mode element (if necessary and
possible) such that vertical space appearing below it in the editing
window is greater than or equal to the vertical extent of the box.

(I previously believed it tried to place the math mode element at the
top because all my examples were done inside boxes greater than the
height of the window.)

Can anyone reproduce this?

Thomas

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

button 'View other formats'. I always used this toolbar in stead of
the View menu, and I just didn't think of it (I mean: the menu).

Of course you can post our exchange to the lyx-forum. I think the
combination of LyX - hands down the best text processor I ever worked
with - and Sage opens vast possibilities. It really should get more
publicity.

It seems like a good idea to learn a bit more about the workings of
LyX. Perhaps you can point me to a good source of information about,
e.g., the format and purpose of the various entries in the lyx options
file? Is it dangerous to edit it by hand? (there's a warning not to do
so) Could I e.g. just clear it and build it anew from inside LyX?

Thanks again, Thomas, you have been most helpful.



Hi Dirk,

one improvement I can suggest right away: just eliminate that
one-step process. If its performance gain is indeed minimal, I see no
reason to keep it. I for one was confused as to its purpose.


I agree the annotations about it were confusing ... when I get a
chance to update, I will change this.


The reason the PDF did not open automatically was because I used
the File  Export menu, in stead of the View menu. When I choose View
 etc., the PDF does open automatically. I'm a bit puzzled why the
new format 'PDF (pdflatex + sagetex)' doesn't show up under the
toolbar button 'View other formats'. I always used this toolbar in
stead of the View menu, and I just didn't think of it (I mean: the
menu).


Never noticed that before ... I've filed it as a bug:
http://www.lyx.org/trac/ticket/8550


Of course you can post our exchange to the lyx-forum. I think the
combination of LyX - hands down the best text processor I ever worked
with - and Sage opens vast possibilities. It really should get more
publicity.


In the past I have made extensive use of Mathematica, whose notebook
documents provide a tightly integrated literate programming
environment. However, since my main interest in literate programming
has been for reproducible research, this platform had some severe
limitations (openness, availability to everyone, sophisticated
document features for paper-writing, and extensibility of the
underlying computation system). I am currently using LyX and Sage for
my Ph.D. thesis, and feel like I've finally found the right set of
tools (though of course there's always more to do).


It seems like a good idea to learn a bit more about the workings
of LyX. Perhaps you can point me to a good source of information
about, e.g., the format and purpose of the various entries in the lyx
options file? Is it dangerous to edit it by hand? (there's a warning
not to do so) Could I e.g. just clear it and build it anew from inside
LyX?


I never found a good guide to all of this, though just now I came
across this page that might be a good place to start:
http://www.oak-tree.us/2010/07/13/custom-lyx-modules/ . There's some
information in the Customization manual (Section 5: Installing New
Document Classes, Layouts, and Templates), but not enough to explain
the whole module system. I started from a version of this module
already built by Murat (you can see our discussion here:
http://www.mail-archive.com/lyx-users@lists.lyx.org/msg91798.html ),
so I gradually just figured out how to tweak things to get them to
work.

Everything that we added to the LyX preferences file for purposes of
this module can be changed from within LyX under Tools  Preferences.
If you go there, you'll see the changes we made already appear in the
GUI.


Thanks again, Thomas, you have been most helpful.


My pleasure --- thanks for trying it out!



On Mon, Apr 2, 2012 at 12:31 PM, Thomas Coffee thomasmcof...@gmail.com wrote:
 The attachments on this thread have been posted to the wiki (thanks 
 Christian):

 http://wiki.lyx.org/Layouts/Modules/#toc7
 http://wiki.lyx.org/uploads/Modules/Sage

 Note that if you customize the sage.module file, you can load the
 changes immediately by entering layout-reload in the minibuffer.

 As Murat has done: I hereby grant permission to license my
 contributions to the sage module for LyX under the GNU General Public
 License, version 2 or later.

 - Thomas


 On Sun, Apr 1, 2012 at 12:03 PM, Murat Yildizoglu myi...@gmail.com wrote:
 Good idea, thanks a lot for the suggestion Xu. Here is my statement (I put
 the devel list as CC) :

 I hereby grant permission to license my contributions to the SAGE module for
 LyX under the GNU
 General Public Licence, version 2 or later.

 Murat Yildizoglu


 2012/3/31 Xu Wang xuwang...@gmail.com

 Dear Thomas

 Excellent news! Thank you for your continued work. I have not taken a fine
 look at this yet, but I also use Ubuntu so it looks like it might be useful.

 I'm not sure but I think for your contributions to be used you have to
 give permission explicitly. Look at this email:

 http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html
 You can send something like that to the development list, lyx-devel

Re: SageTeX and LyX

[Thomas Coffee]

Hi Rob,

Sorry I did not see your message last year --- I've been filtering
lyx-users while I finish my thesis.

I just received a private email from someone installing the SageTeX
module, and I've posted the transcript of our conversation to the
existing thread on lyx-users in case it's helpful.

If you're still having issues, I should now hopefully see any messages
addressed to me specifically. Thanks for trying out the module!

- Thomas


On Wed, Oct 3, 2012 at 1:28 PM, Scott Kostyshak skost...@lyx.org wrote:
 Hi Rob,

 I'm CC'ing Thomas Coffee and Murat Yildizoglu, who as the wiki says
 did a lot of work on the SAGE module. They might be interested in your
 experience.

 On Wed, Oct 3, 2012 at 12:11 PM, Rob Oakes lyx-de...@oak-tree.us wrote:
 Hi Scott,

 On Wed, 2012-10-03 at 06:16 -0400, Scott Kostyshak wrote:

 I've been meaning to checkout SAGE + LyX so if no one comes along to
 help you I might take a look.

 I appreciate the offer. After some quality time looking into how the
 module works and how SageTeX processes documents, I was able to get it
 up and running. I found this page to be extremely helpful:
 http://www.sagemath.org/doc/tutorial/sagetex.html

 Great! Good job figuring it out.

 Of course, like all things, I was hoping to get a quick response via the
 list. I decided last year that I wanted to go back to school to improve
 my mechanical engineering skills and was hoping to get Sage working for
 a lab report.

 (Why I decided more education would be desirable is completely beyond
 me. I've forgotten how thoroughly miserable it is to be a student. While
 I frequently have to work late, it's been years since I've had to pull
 an all-night session to finish homework. It's every bit as bad as I
 remember. It might even be worse, if you factor in age.)

 I bet that it's really difficult to do what you're doing. Hopefully
 there are some fun things about being a student again that will
 surprise you. How about coming home after turning your homework in and
 crashing on your bed -- that must have felt nice at least :). Best of
 luck with your challenge!

 How did you install SAGE? In the past
 I've compiled from source which was very smooth but took a while.
 There is also a PPA: https://launchpad.net/~aims/+archive/sagemath

 To get Sage installed, I used the PPA. I thought about compiling from
 source so that I could integrate it with the system Python, and then
 thought better of it. The installation from the PPA was quick and I
 haven't had any issues, so far.

 Glad to hear.

 To install the SageTeX module (which has to be done separately from
 installing Sage), I copied the sagetex folder into my LaTeX path and ran
 texhash.

 Thanks, this is useful for me. I didn't know they were separate.

 Which version do you have installed?

 I'm running version 5.1.

 Does the terminal output or View Messages toolbar give any useful
 output that you could share?

 The output was helpful, but didn't make much sense until I read more
 about how SageTeX works.

 Sage processes files in two steps. You write your document, then you run
 LaTeX (pdflatex, xelatex, lualatex, or regular latex) on it. This
 creates a second file, with the Sage processing instructions in it. This
 has a *.sagetex.sage file extension.

 At this point, you have to run Sage on this secondary file, which
 generates your equations, plots and other elements so that they can be
 incorporated into your original LaTeX file. At that point, you run LaTeX
 on the original file a second time to produce the typeset document.

 The problem I was having is that I was only running LaTeX on my new
 documents. The converters I set up didn't follow the appropriate pathway
 of LaTeX - Sage - LaTeX. Once I added in the Sage processing step,
 everything started to work.

 Thanks for the explanation. It would be nice if the module took care
 of all of this.

 Do you have a minimum working example that you could send or link to?

 Absolutely, attached is a simple example that I'm working up into a
 template.

 I'm just getting started with Sage, but now that it's working, I'm quite
 impressed with what I've seen. For the past 10 years or so, I've been
 using aging copies of Maple for symbolic computation, and this looks
 like it will allow me to modernize. (I don't actually have to do much
 symbolic math, so it hasn't been that big of a deal.)

 Being able to work from within LyX, in a manner very similar to the way
 I work with R code via Knitr/Sweave, is going to be very nice. Knowing
 that it's all open is even better.

 I'm also a big fan of R + Knitr (+ LyX) and I agree with you. I think
 having things integrated is closer to how our minds work and allows
 for a more natural workflow.

 PS, when I get time, I'm going to try and update the instructions on the
 Wiki to make a couple of things clearer. I'll also probably write a blog
 post about it, just so I've got a record of how I got things working. If
 you'd like, I'll send you a link when

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

button 'View other formats'. I always used this toolbar in stead of
the View menu, and I just didn't think of it (I mean: the menu).

Of course you can post our exchange to the lyx-forum. I think the
combination of LyX - hands down the best text processor I ever worked
with - and Sage opens vast possibilities. It really should get more
publicity.

It seems like a good idea to learn a bit more about the workings of
LyX. Perhaps you can point me to a good source of information about,
e.g., the format and purpose of the various entries in the lyx options
file? Is it dangerous to edit it by hand? (there's a warning not to do
so) Could I e.g. just clear it and build it anew from inside LyX?

Thanks again, Thomas, you have been most helpful.



Hi Dirk,

one improvement I can suggest right away: just eliminate that
one-step process. If its performance gain is indeed minimal, I see no
reason to keep it. I for one was confused as to its purpose.


I agree the annotations about it were confusing ... when I get a
chance to update, I will change this.


The reason the PDF did not open automatically was because I used
the File  Export menu, in stead of the View menu. When I choose View
 etc., the PDF does open automatically. I'm a bit puzzled why the
new format 'PDF (pdflatex + sagetex)' doesn't show up under the
toolbar button 'View other formats'. I always used this toolbar in
stead of the View menu, and I just didn't think of it (I mean: the
menu).


Never noticed that before ... I've filed it as a bug:
http://www.lyx.org/trac/ticket/8550


Of course you can post our exchange to the lyx-forum. I think the
combination of LyX - hands down the best text processor I ever worked
with - and Sage opens vast possibilities. It really should get more
publicity.


In the past I have made extensive use of Mathematica, whose notebook
documents provide a tightly integrated literate programming
environment. However, since my main interest in literate programming
has been for reproducible research, this platform had some severe
limitations (openness, availability to everyone, sophisticated
document features for paper-writing, and extensibility of the
underlying computation system). I am currently using LyX and Sage for
my Ph.D. thesis, and feel like I've finally found the right set of
tools (though of course there's always more to do).


It seems like a good idea to learn a bit more about the workings
of LyX. Perhaps you can point me to a good source of information
about, e.g., the format and purpose of the various entries in the lyx
options file? Is it dangerous to edit it by hand? (there's a warning
not to do so) Could I e.g. just clear it and build it anew from inside
LyX?


I never found a good guide to all of this, though just now I came
across this page that might be a good place to start:
http://www.oak-tree.us/2010/07/13/custom-lyx-modules/ . There's some
information in the Customization manual (Section 5: Installing New
Document Classes, Layouts, and Templates), but not enough to explain
the whole module system. I started from a version of this module
already built by Murat (you can see our discussion here:
http://www.mail-archive.com/lyx-users@lists.lyx.org/msg91798.html ),
so I gradually just figured out how to tweak things to get them to
work.

Everything that we added to the LyX preferences file for purposes of
this module can be changed from within LyX under Tools  Preferences.
If you go there, you'll see the changes we made already appear in the
GUI.


Thanks again, Thomas, you have been most helpful.


My pleasure --- thanks for trying it out!



On Mon, Apr 2, 2012 at 12:31 PM, Thomas Coffee thomasmcof...@gmail.com wrote:
 The attachments on this thread have been posted to the wiki (thanks 
 Christian):

 http://wiki.lyx.org/Layouts/Modules/#toc7
 http://wiki.lyx.org/uploads/Modules/Sage

 Note that if you customize the sage.module file, you can load the
 changes immediately by entering layout-reload in the minibuffer.

 As Murat has done: I hereby grant permission to license my
 contributions to the sage module for LyX under the GNU General Public
 License, version 2 or later.

 - Thomas


 On Sun, Apr 1, 2012 at 12:03 PM, Murat Yildizoglu myi...@gmail.com wrote:
 Good idea, thanks a lot for the suggestion Xu. Here is my statement (I put
 the devel list as CC) :

 I hereby grant permission to license my contributions to the SAGE module for
 LyX under the GNU
 General Public Licence, version 2 or later.

 Murat Yildizoglu


 2012/3/31 Xu Wang xuwang...@gmail.com

 Dear Thomas

 Excellent news! Thank you for your continued work. I have not taken a fine
 look at this yet, but I also use Ubuntu so it looks like it might be useful.

 I'm not sure but I think for your contributions to be used you have to
 give permission explicitly. Look at this email:

 http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html
 You can send something like that to the development list, lyx-devel

Re: SageTeX and LyX

[Thomas Coffee]

Hi Rob,

Sorry I did not see your message last year --- I've been filtering
lyx-users while I finish my thesis.

I just received a private email from someone installing the SageTeX
module, and I've posted the transcript of our conversation to the
existing thread on lyx-users in case it's helpful.

If you're still having issues, I should now hopefully see any messages
addressed to me specifically. Thanks for trying out the module!

- Thomas


On Wed, Oct 3, 2012 at 1:28 PM, Scott Kostyshak skost...@lyx.org wrote:
 Hi Rob,

 I'm CC'ing Thomas Coffee and Murat Yildizoglu, who as the wiki says
 did a lot of work on the SAGE module. They might be interested in your
 experience.

 On Wed, Oct 3, 2012 at 12:11 PM, Rob Oakes lyx-de...@oak-tree.us wrote:
 Hi Scott,

 On Wed, 2012-10-03 at 06:16 -0400, Scott Kostyshak wrote:

 I've been meaning to checkout SAGE + LyX so if no one comes along to
 help you I might take a look.

 I appreciate the offer. After some quality time looking into how the
 module works and how SageTeX processes documents, I was able to get it
 up and running. I found this page to be extremely helpful:
 http://www.sagemath.org/doc/tutorial/sagetex.html

 Great! Good job figuring it out.

 Of course, like all things, I was hoping to get a quick response via the
 list. I decided last year that I wanted to go back to school to improve
 my mechanical engineering skills and was hoping to get Sage working for
 a lab report.

 (Why I decided more education would be desirable is completely beyond
 me. I've forgotten how thoroughly miserable it is to be a student. While
 I frequently have to work late, it's been years since I've had to pull
 an all-night session to finish homework. It's every bit as bad as I
 remember. It might even be worse, if you factor in age.)

 I bet that it's really difficult to do what you're doing. Hopefully
 there are some fun things about being a student again that will
 surprise you. How about coming home after turning your homework in and
 crashing on your bed -- that must have felt nice at least :). Best of
 luck with your challenge!

 How did you install SAGE? In the past
 I've compiled from source which was very smooth but took a while.
 There is also a PPA: https://launchpad.net/~aims/+archive/sagemath

 To get Sage installed, I used the PPA. I thought about compiling from
 source so that I could integrate it with the system Python, and then
 thought better of it. The installation from the PPA was quick and I
 haven't had any issues, so far.

 Glad to hear.

 To install the SageTeX module (which has to be done separately from
 installing Sage), I copied the sagetex folder into my LaTeX path and ran
 texhash.

 Thanks, this is useful for me. I didn't know they were separate.

 Which version do you have installed?

 I'm running version 5.1.

 Does the terminal output or View Messages toolbar give any useful
 output that you could share?

 The output was helpful, but didn't make much sense until I read more
 about how SageTeX works.

 Sage processes files in two steps. You write your document, then you run
 LaTeX (pdflatex, xelatex, lualatex, or regular latex) on it. This
 creates a second file, with the Sage processing instructions in it. This
 has a *.sagetex.sage file extension.

 At this point, you have to run Sage on this secondary file, which
 generates your equations, plots and other elements so that they can be
 incorporated into your original LaTeX file. At that point, you run LaTeX
 on the original file a second time to produce the typeset document.

 The problem I was having is that I was only running LaTeX on my new
 documents. The converters I set up didn't follow the appropriate pathway
 of LaTeX - Sage - LaTeX. Once I added in the Sage processing step,
 everything started to work.

 Thanks for the explanation. It would be nice if the module took care
 of all of this.

 Do you have a minimum working example that you could send or link to?

 Absolutely, attached is a simple example that I'm working up into a
 template.

 I'm just getting started with Sage, but now that it's working, I'm quite
 impressed with what I've seen. For the past 10 years or so, I've been
 using aging copies of Maple for symbolic computation, and this looks
 like it will allow me to modernize. (I don't actually have to do much
 symbolic math, so it hasn't been that big of a deal.)

 Being able to work from within LyX, in a manner very similar to the way
 I work with R code via Knitr/Sweave, is going to be very nice. Knowing
 that it's all open is even better.

 I'm also a big fan of R + Knitr (+ LyX) and I agree with you. I think
 having things integrated is closer to how our minds work and allows
 for a more natural workflow.

 PS, when I get time, I'm going to try and update the instructions on the
 Wiki to make a couple of things clearer. I'll also probably write a blog
 post about it, just so I've got a record of how I got things working. If
 you'd like, I'll send you a link when

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

s because I used the
File >> Export menu, in stead of the View menu. When I choose View >>
etc., the PDF does open automatically. I'm a bit puzzled why the new
format 'PDF (pdflatex + sagetex)' doesn't show up under the toolbar
button 'View other formats'. I always used this toolbar in stead of
the View menu, and I just didn't think of it (I mean: the menu).

Of course you can post our exchange to the lyx-forum. I think the
combination of LyX - hands down the best text processor I ever worked
with - and Sage opens vast possibilities. It really should get more
publicity.

It seems like a good idea to learn a bit more about the workings of
LyX. Perhaps you can point me to a good source of information about,
e.g., the format and purpose of the various entries in the lyx options
file? Is it dangerous to edit it by hand? (there's a warning not to do
so) Could I e.g. just clear it and build it anew from inside LyX?

Thanks again, Thomas, you have been most helpful.



Hi Dirk,

one improvement I can suggest right away: just eliminate that
one-step process. If its performance gain is indeed minimal, I see no
reason to keep it. I for one was confused as to its purpose.


I agree the annotations about it were confusing ... when I get a
chance to update, I will change this.


The reason the PDF did not open automatically was because I used
the File >> Export menu, in stead of the View menu. When I choose View
>> etc., the PDF does open automatically. I'm a bit puzzled why the
new format 'PDF (pdflatex + sagetex)' doesn't show up under the
toolbar button 'View other formats'. I always used this toolbar in
stead of the View menu, and I just didn't think of it (I mean: the
menu).


Never noticed that before ... I've filed it as a bug:
http://www.lyx.org/trac/ticket/8550


Of course you can post our exchange to the lyx-forum. I think the
combination of LyX - hands down the best text processor I ever worked
with - and Sage opens vast possibilities. It really should get more
publicity.


In the past I have made extensive use of Mathematica, whose "notebook"
documents provide a tightly integrated literate programming
environment. However, since my main interest in literate programming
has been for reproducible research, this platform had some severe
limitations (openness, availability to everyone, sophisticated
document features for paper-writing, and extensibility of the
underlying computation system). I am currently using LyX and Sage for
my Ph.D. thesis, and feel like I've finally found the right set of
tools (though of course there's always more to do).


It seems like a good idea to learn a bit more about the workings
of LyX. Perhaps you can point me to a good source of information
about, e.g., the format and purpose of the various entries in the lyx
options file? Is it dangerous to edit it by hand? (there's a warning
not to do so) Could I e.g. just clear it and build it anew from inside
LyX?


I never found a good guide to all of this, though just now I came
across this page that might be a good place to start:
http://www.oak-tree.us/2010/07/13/custom-lyx-modules/ . There's some
information in the Customization manual (Section 5: Installing New
Document Classes, Layouts, and Templates), but not enough to explain
the whole module system. I started from a version of this module
already built by Murat (you can see our discussion here:
http://www.mail-archive.com/lyx-users@lists.lyx.org/msg91798.html ),
so I gradually just figured out how to tweak things to get them to
work.

Everything that we added to the LyX preferences file for purposes of
this module can be changed from within LyX under Tools >> Preferences.
If you go there, you'll see the changes we made already appear in the
GUI.


Thanks again, Thomas, you have been most helpful.


My pleasure --- thanks for trying it out!



On Mon, Apr 2, 2012 at 12:31 PM, Thomas Coffee <thomasmcof...@gmail.com> wrote:
> The attachments on this thread have been posted to the wiki (thanks 
> Christian):
>
> http://wiki.lyx.org/Layouts/Modules/#toc7
> http://wiki.lyx.org/uploads/Modules/Sage
>
> Note that if you customize the sage.module file, you can load the
> changes immediately by entering "layout-reload" in the minibuffer.
>
> As Murat has done: I hereby grant permission to license my
> contributions to the sage module for LyX under the GNU General Public
> License, version 2 or later.
>
> - Thomas
>
>
> On Sun, Apr 1, 2012 at 12:03 PM, Murat Yildizoglu <myi...@gmail.com> wrote:
>> Good idea, thanks a lot for the suggestion Xu. Here is my statement (I put
>> the devel list as CC) :
>>
>> I hereby grant permission to license my contributions to the SAGE module for
>> LyX under the GNU
>> General Public Licence, version 2 or later.
>>
>> Murat Yildizoglu
>>
>>
>> 2012/3/31 Xu Wa

Re: SageTeX and LyX

[Thomas Coffee]

Hi Rob,

Sorry I did not see your message last year --- I've been filtering
lyx-users while I finish my thesis.

I just received a private email from someone installing the SageTeX
module, and I've posted the transcript of our conversation to the
existing thread on lyx-users in case it's helpful.

If you're still having issues, I should now hopefully see any messages
addressed to me specifically. Thanks for trying out the module!

- Thomas


On Wed, Oct 3, 2012 at 1:28 PM, Scott Kostyshak <skost...@lyx.org> wrote:
> Hi Rob,
>
> I'm CC'ing Thomas Coffee and Murat Yildizoglu, who as the wiki says
> did a lot of work on the SAGE module. They might be interested in your
> experience.
>
> On Wed, Oct 3, 2012 at 12:11 PM, Rob Oakes <lyx-de...@oak-tree.us> wrote:
>> Hi Scott,
>>
>> On Wed, 2012-10-03 at 06:16 -0400, Scott Kostyshak wrote:
>>
>>> I've been meaning to checkout SAGE + LyX so if no one comes along to
>>> help you I might take a look.
>>
>> I appreciate the offer. After some quality time looking into how the
>> module works and how SageTeX processes documents, I was able to get it
>> up and running. I found this page to be extremely helpful:
>> http://www.sagemath.org/doc/tutorial/sagetex.html
>
> Great! Good job figuring it out.
>
>> Of course, like all things, I was hoping to get a quick response via the
>> list. I decided last year that I wanted to go back to school to improve
>> my mechanical engineering skills and was hoping to get Sage working for
>> a lab report.
>>
>> (Why I decided more education would be desirable is completely beyond
>> me. I've forgotten how thoroughly miserable it is to be a student. While
>> I frequently have to work late, it's been years since I've had to pull
>> an all-night session to finish homework. It's every bit as bad as I
>> remember. It might even be worse, if you factor in age.)
>
> I bet that it's really difficult to do what you're doing. Hopefully
> there are some fun things about being a student again that will
> surprise you. How about coming home after turning your homework in and
> crashing on your bed -- that must have felt nice at least :). Best of
> luck with your challenge!
>
>>> How did you install SAGE? In the past
>>> I've compiled from source which was very smooth but took a while.
>>> There is also a PPA: https://launchpad.net/~aims/+archive/sagemath
>>
>> To get Sage installed, I used the PPA. I thought about compiling from
>> source so that I could integrate it with the system Python, and then
>> thought better of it. The installation from the PPA was quick and I
>> haven't had any issues, so far.
>
> Glad to hear.
>
>> To install the SageTeX module (which has to be done separately from
>> installing Sage), I copied the sagetex folder into my LaTeX path and ran
>> texhash.
>
> Thanks, this is useful for me. I didn't know they were separate.
>
>>> Which version do you have installed?
>>
>> I'm running version 5.1.
>>
>>> Does the terminal output or View Messages toolbar give any useful
>>> output that you could share?
>>
>> The output was helpful, but didn't make much sense until I read more
>> about how SageTeX works.
>>
>> Sage processes files in two steps. You write your document, then you run
>> LaTeX (pdflatex, xelatex, lualatex, or regular latex) on it. This
>> creates a second file, with the Sage processing instructions in it. This
>> has a *.sagetex.sage file extension.
>>
>> At this point, you have to run Sage on this secondary file, which
>> generates your equations, plots and other elements so that they can be
>> incorporated into your original LaTeX file. At that point, you run LaTeX
>> on the original file a second time to produce the typeset document.
>>
>> The problem I was having is that I was only running LaTeX on my new
>> documents. The converters I set up didn't follow the appropriate pathway
>> of LaTeX -> Sage -> LaTeX. Once I added in the Sage processing step,
>> everything started to work.
>
> Thanks for the explanation. It would be nice if the module took care
> of all of this.
>
>>> Do you have a minimum working example that you could send or link to?
>>
>> Absolutely, attached is a simple example that I'm working up into a
>> template.
>>
>> I'm just getting started with Sage, but now that it's working, I'm quite
>> impressed with what I've seen. For the past 10 years or so, I've been
>> using aging copies of Maple for symbolic computation, and this looks
>> like it will allow me to modernize. (I don't a

Re: Scrolling Slowness [Re: keyboard Scrolling Anomaly]

[Thomas Coffee]

I have experienced unbearably sluggish scrolling and typing in LyX that
after much research I attribute to a poor interaction between Qt 4 and my
NVIDIA graphics card driver.

I solved these issues by starting LyX with:

lyx -graphicssystem raster

I have seen this problem described using both GNOME and KDE with NVIDIA
cards (though there also appear to be unrelated scrolling and typing lag
problems out there). The same fallback helps with other Qt-based programs I
run, but beware that it may cause some rendering glitches (though I have
not seen any in LyX).

http://forum.kde.org/viewtopic.php?f=66t=90821
http://www.nvnews.net/vbulletin/showthread.php?t=148778page=2

- Thomas


On Thu, Apr 26, 2012 at 3:17 PM, Richard Heck rgh...@comcast.net wrote:

 On 04/26/2012 11:02 AM, David L. Johnson wrote:

 On 04/26/2012 10:30 AM, Rashif Ray Rahman wrote:

 Hi all

 I've not been a LyX user for long but am going to write a 300-page
 academic paper with it for the final typesetting and formatting. I've
 practised on and off for the past few months but one thing that has always
 troubled me is how I'm unable to scroll with the keyboard (up and down
 arrow keys). I'd like to be rid of the mouse if possible.

 When I hold a particular directional key for up to 20 secs it appears to
 work but as if it's in slow motion. Qt shouldn't be having any such
 scrolling problem, so I haven't been able to troubleshoot this any further.

  I don't see this behavior at all.  The only thing that slows down
 scrolling with the arrows is if the cursor enters a math formula.  Then it
 runs through all the superscripts and subscripts, but still it is
 reasonably fast.

 You also might try using the Pageup and Pagedown keys.

 What system are you using?  Mine is debian testing (a linux variant), on
 a fast machine -- but it works well on even my slow netbook.

  There have been occasional reports of this kind of problem, usually
 connected, as far as we can tell, to interactions issues between LyX and
 certain video drivers. So I'll ask, too: What system is this and, if it's
 Linux, what desktop, what window manager, what X drivers?

 Richard

Re: Scrolling Slowness [Re: keyboard Scrolling Anomaly]

[Thomas Coffee]

I have experienced unbearably sluggish scrolling and typing in LyX that
after much research I attribute to a poor interaction between Qt 4 and my
NVIDIA graphics card driver.

I solved these issues by starting LyX with:

lyx -graphicssystem raster

I have seen this problem described using both GNOME and KDE with NVIDIA
cards (though there also appear to be unrelated scrolling and typing lag
problems out there). The same fallback helps with other Qt-based programs I
run, but beware that it may cause some rendering glitches (though I have
not seen any in LyX).

http://forum.kde.org/viewtopic.php?f=66t=90821
http://www.nvnews.net/vbulletin/showthread.php?t=148778page=2

- Thomas


On Thu, Apr 26, 2012 at 3:17 PM, Richard Heck rgh...@comcast.net wrote:

 On 04/26/2012 11:02 AM, David L. Johnson wrote:

 On 04/26/2012 10:30 AM, Rashif Ray Rahman wrote:

 Hi all

 I've not been a LyX user for long but am going to write a 300-page
 academic paper with it for the final typesetting and formatting. I've
 practised on and off for the past few months but one thing that has always
 troubled me is how I'm unable to scroll with the keyboard (up and down
 arrow keys). I'd like to be rid of the mouse if possible.

 When I hold a particular directional key for up to 20 secs it appears to
 work but as if it's in slow motion. Qt shouldn't be having any such
 scrolling problem, so I haven't been able to troubleshoot this any further.

  I don't see this behavior at all.  The only thing that slows down
 scrolling with the arrows is if the cursor enters a math formula.  Then it
 runs through all the superscripts and subscripts, but still it is
 reasonably fast.

 You also might try using the Pageup and Pagedown keys.

 What system are you using?  Mine is debian testing (a linux variant), on
 a fast machine -- but it works well on even my slow netbook.

  There have been occasional reports of this kind of problem, usually
 connected, as far as we can tell, to interactions issues between LyX and
 certain video drivers. So I'll ask, too: What system is this and, if it's
 Linux, what desktop, what window manager, what X drivers?

 Richard

Re: Scrolling Slowness [Re: keyboard Scrolling Anomaly]

[Thomas Coffee]

I have experienced unbearably sluggish scrolling and typing in LyX that
after much research I attribute to a poor interaction between Qt 4 and my
NVIDIA graphics card driver.

I solved these issues by starting LyX with:

lyx -graphicssystem raster

I have seen this problem described using both GNOME and KDE with NVIDIA
cards (though there also appear to be unrelated scrolling and typing lag
problems out there). The same fallback helps with other Qt-based programs I
run, but beware that it may cause some rendering glitches (though I have
not seen any in LyX).

http://forum.kde.org/viewtopic.php?f=66=90821
http://www.nvnews.net/vbulletin/showthread.php?t=148778=2

- Thomas


On Thu, Apr 26, 2012 at 3:17 PM, Richard Heck  wrote:

> On 04/26/2012 11:02 AM, David L. Johnson wrote:
>
>> On 04/26/2012 10:30 AM, Rashif Ray Rahman wrote:
>>
>>> Hi all
>>>
>>> I've not been a LyX user for long but am going to write a 300-page
>>> academic paper with it for the final typesetting and formatting. I've
>>> practised on and off for the past few months but one thing that has always
>>> troubled me is how I'm unable to scroll with the keyboard (up and down
>>> arrow keys). I'd like to be rid of the mouse if possible.
>>>
>>> When I hold a particular directional key for up to 20 secs it appears to
>>> work but as if it's in slow motion. Qt shouldn't be having any such
>>> scrolling problem, so I haven't been able to troubleshoot this any further.
>>>
>>>  I don't see this behavior at all.  The only thing that slows down
>> scrolling with the arrows is if the cursor enters a math formula.  Then it
>> runs through all the superscripts and subscripts, but still it is
>> reasonably fast.
>>
>> You also might try using the  and  keys.
>>
>> What system are you using?  Mine is debian testing (a linux variant), on
>> a fast machine -- but it works well on even my slow netbook.
>>
>>  There have been occasional reports of this kind of problem, usually
> connected, as far as we can tell, to interactions issues between LyX and
> certain video drivers. So I'll ask, too: What system is this and, if it's
> Linux, what desktop, what window manager, what X drivers?
>
> Richard
>
>
>

Re: Regenerating Lilypond files

[Thomas Coffee]

On GNU/Linux, an easy way to solve it would be to run

touch *.ly

in the directory(ies) containing the Lilypond files to make them appear
modified. Perhaps someone else knows how to do it the right way.

- Thomas


On Sun, Apr 15, 2012 at 4:24 PM, John McKay jzmc...@yahoo.com wrote:

 I am working on a large project involving hundreds of musical examples
 typeset in Lilypond.  So far, LyX has been great in handling them.

 I have run into one issue.  LyX seems to know if a Lilypond file hasn't
 changed since the last output PDF was generated.  If the Lilypond file
 hasn't changed, it doesn't run Lilypond again.

 In most circumstances, I can see how this is desirable.

 However, I need to know how to get LyX to regenerate ALL Lilypond files if
 I want to, even if the file LyX actually sees hasn't changed.

 Basically, since the structure of my musical examples is so complex, I
 have taken to separating some general formatting instructions and the
 actual musical data into separate files.  These are loaded in the header of
 the Lilypond file that LyX actually sees, which is mostly a dummy file that
 sets up the score for the actual LyX example.

 So, if I make changes to the actual notes of my file or to the general
 formatting header file for my examples, the file LyX sees usually doesn't
 change.  Yet, I still need LyX to re-run Lilypond sometimes.

 I don't need this to happen all the time, but is there a command or a way
 to just tell LyX to re-run Lilypond for all external material insets if I
 want a complete wipe?

 (I've noticed various ways of hacking this, like deleting an external
 material insertion and reinstating it in LyX, or adding an unnecessary
 blank comment line to my dummy files so LyX detects a change, but these
 sorts of things are obviously annoying when dealing with hundreds of
 Lilypond files.)

 Thanks for any suggestions!

Re: numbering multi-line formulas

[Thomas Coffee]

Also, pressing Ctrl+Enter in regular math mode will give you eqnarray.


On Sun, Apr 15, 2012 at 9:09 PM, David L. Johnson
david.john...@lehigh.eduwrote:

 On 04/15/2012 06:18 PM, El Merehbi, Ibrahim wrote:

 Hello again,

 I believe I didn't clear it out well. I meant a shortcut for the
 eqnarray not the equation numbering.

 Sorry, I misunderstood.  Add to the shortcuts something like this:

 command-sequence math-mode on; math-mutate eqnarray;

 and link it to your favorite hot-key.  I use F12.

 --

 David L. Johnson

 A mathematician is a machine for turning coffee into theorems.
-- Paul Erdos

 --

Re: Regenerating Lilypond files

[Thomas Coffee]

On GNU/Linux, an easy way to solve it would be to run

touch *.ly

in the directory(ies) containing the Lilypond files to make them appear
modified. Perhaps someone else knows how to do it the right way.

- Thomas


On Sun, Apr 15, 2012 at 4:24 PM, John McKay jzmc...@yahoo.com wrote:

 I am working on a large project involving hundreds of musical examples
 typeset in Lilypond.  So far, LyX has been great in handling them.

 I have run into one issue.  LyX seems to know if a Lilypond file hasn't
 changed since the last output PDF was generated.  If the Lilypond file
 hasn't changed, it doesn't run Lilypond again.

 In most circumstances, I can see how this is desirable.

 However, I need to know how to get LyX to regenerate ALL Lilypond files if
 I want to, even if the file LyX actually sees hasn't changed.

 Basically, since the structure of my musical examples is so complex, I
 have taken to separating some general formatting instructions and the
 actual musical data into separate files.  These are loaded in the header of
 the Lilypond file that LyX actually sees, which is mostly a dummy file that
 sets up the score for the actual LyX example.

 So, if I make changes to the actual notes of my file or to the general
 formatting header file for my examples, the file LyX sees usually doesn't
 change.  Yet, I still need LyX to re-run Lilypond sometimes.

 I don't need this to happen all the time, but is there a command or a way
 to just tell LyX to re-run Lilypond for all external material insets if I
 want a complete wipe?

 (I've noticed various ways of hacking this, like deleting an external
 material insertion and reinstating it in LyX, or adding an unnecessary
 blank comment line to my dummy files so LyX detects a change, but these
 sorts of things are obviously annoying when dealing with hundreds of
 Lilypond files.)

 Thanks for any suggestions!

Re: numbering multi-line formulas

[Thomas Coffee]

Also, pressing Ctrl+Enter in regular math mode will give you eqnarray.


On Sun, Apr 15, 2012 at 9:09 PM, David L. Johnson
david.john...@lehigh.eduwrote:

 On 04/15/2012 06:18 PM, El Merehbi, Ibrahim wrote:

 Hello again,

 I believe I didn't clear it out well. I meant a shortcut for the
 eqnarray not the equation numbering.

 Sorry, I misunderstood.  Add to the shortcuts something like this:

 command-sequence math-mode on; math-mutate eqnarray;

 and link it to your favorite hot-key.  I use F12.

 --

 David L. Johnson

 A mathematician is a machine for turning coffee into theorems.
-- Paul Erdos

 --

Re: Regenerating Lilypond files

[Thomas Coffee]

On GNU/Linux, an easy way to solve it would be to run

touch *.ly

in the directory(ies) containing the Lilypond files to make them appear
modified. Perhaps someone else knows how to do it the "right" way.

- Thomas


On Sun, Apr 15, 2012 at 4:24 PM, John McKay  wrote:

> I am working on a large project involving hundreds of musical examples
> typeset in Lilypond.  So far, LyX has been great in handling them.
>
> I have run into one issue.  LyX seems to "know" if a Lilypond file hasn't
> changed since the last output PDF was generated.  If the Lilypond file
> hasn't changed, it doesn't run Lilypond again.
>
> In most circumstances, I can see how this is desirable.
>
> However, I need to know how to get LyX to regenerate ALL Lilypond files if
> I want to, even if the file LyX actually sees hasn't changed.
>
> Basically, since the structure of my musical examples is so complex, I
> have taken to separating some general formatting instructions and the
> actual musical data into separate files.  These are loaded in the header of
> the Lilypond file that LyX actually sees, which is mostly a dummy file that
> sets up the score for the actual LyX example.
>
> So, if I make changes to the actual notes of my file or to the general
> formatting header file for my examples, the file LyX sees usually doesn't
> change.  Yet, I still need LyX to re-run Lilypond sometimes.
>
> I don't need this to happen all the time, but is there a command or a way
> to just tell LyX to re-run Lilypond for all external material insets if I
> want a complete wipe?
>
> (I've noticed various ways of hacking this, like deleting an external
> material insertion and reinstating it in LyX, or adding an unnecessary
> blank comment line to my dummy files so LyX detects a "change," but these
> sorts of things are obviously annoying when dealing with hundreds of
> Lilypond files.)
>
> Thanks for any suggestions!
>

Re: numbering multi-line formulas

[Thomas Coffee]

Also, pressing Ctrl+Enter in regular math mode will give you eqnarray.


On Sun, Apr 15, 2012 at 9:09 PM, David L. Johnson
wrote:

> On 04/15/2012 06:18 PM, El Merehbi, Ibrahim wrote:
>
>> Hello again,
>>
>> I believe I didn't clear it out well. I meant a shortcut for the
>> "eqnarray" not the equation numbering.
>>
> Sorry, I misunderstood.  Add to the shortcuts something like this:
>
> command-sequence math-mode on; math-mutate eqnarray;
>
> and link it to your favorite hot-key.  I use F12.
>
> --
>
> David L. Johnson
>
> A mathematician is a machine for turning coffee into theorems.
>-- Paul Erdos
>
> --
>
>

Re: LyX as a presentation tool

[Thomas Coffee]

 slides in advance (Also:
 Beamer+Hebrew+LyX is a disaster, so it would force me to turn into OO\MS PP
 or something like that, which is almost as bad)
 * Dynamic -- I can write notes and skip\add steps and lines during the
 class.
 * Slow -- Doing math on slides is bad. Most of the time, the slides are
 too crowded to understand, and fill-up at once, and not character by
 character as one would like on the board. When I'm typing with the class,
 I'm keeping on slow paste, so the can understand the math and follow by it.

 But also some disadvantages:
 * My screen is about 1/4 the size of the whiteboard, and LyX is rather
 lossy in screen-space. So, instead of just pointing into other parts of the
 board, I have to split\scroll.
 * The class's screen reaches to low, So, in order to let the students see
 the all screen, I switch into fullscreen mode, and then add toolbars from
 below in order to push the effective screen upwards.
 * When writing in lyx, one always writes on the bottom part of the screen.
 There is no good way  (after writing more then screen-full of text) to
 start from top, add lines from beneath and then shift to a new screen
 when I fill it.
 * It's rather ugly when I write \latexCommand in red, and just when I'm
 finish its render into symbol.

 Few points one can improve (mostly theoretical. some will demand big many
 expanse from my university, and some are Itches I should scratch when I'll
 have time to code)
 * Create half-slide-mode in lyx: Copy one document into another, character
 by character, When I'm pressing a single key. It will require preparation
 (but anyhow, I prepared the lesson in advance as a lyx document... I don't
 remember all by heart , and anyway, it's still a lot easier then creating
 lyx\beamer slides), but it will save effort and mistakes during the class ,
 while still enable grate flexibility.
 * I wish I had 2 VGA output and 2 projectors, and LyX would switch from
 the end of one screen into the top of a new-clean-page at the other screen
 whenever I fill out the 1st. That would be just perfect :-P.
 * I should get something higher then the teacher's table to put my laptop
 on. For now, I have to bend over it, and my back is not happy.

 Anyway, I'm doing it for a month now,  3 hours a week, and the  experience
 for both me and my students is positive. If you have to teach stuff and
 don't wont to write on a board, you may consider using lyx. it's fun!

 - Ronen.

 --
 __

 Thomas Coffee
 Massachusetts Institute of Technology
 Department of Aeronautics  Astronautics
 Space Systems Laboratory
 617.549.5492

 Please avoid sending attachments in proprietary formats like Word or
 PowerPoint.
 For more information, see
 http://www.gnu.org/philosophy/no-word-attachments.html
 __




lecture 05 excerpt.lyx
Description: application/lyx

Re: LyX as a presentation tool

[Thomas Coffee]

 slides in advance (Also:
 Beamer+Hebrew+LyX is a disaster, so it would force me to turn into OO\MS PP
 or something like that, which is almost as bad)
 * Dynamic -- I can write notes and skip\add steps and lines during the
 class.
 * Slow -- Doing math on slides is bad. Most of the time, the slides are
 too crowded to understand, and fill-up at once, and not character by
 character as one would like on the board. When I'm typing with the class,
 I'm keeping on slow paste, so the can understand the math and follow by it.

 But also some disadvantages:
 * My screen is about 1/4 the size of the whiteboard, and LyX is rather
 lossy in screen-space. So, instead of just pointing into other parts of the
 board, I have to split\scroll.
 * The class's screen reaches to low, So, in order to let the students see
 the all screen, I switch into fullscreen mode, and then add toolbars from
 below in order to push the effective screen upwards.
 * When writing in lyx, one always writes on the bottom part of the screen.
 There is no good way  (after writing more then screen-full of text) to
 start from top, add lines from beneath and then shift to a new screen
 when I fill it.
 * It's rather ugly when I write \latexCommand in red, and just when I'm
 finish its render into symbol.

 Few points one can improve (mostly theoretical. some will demand big many
 expanse from my university, and some are Itches I should scratch when I'll
 have time to code)
 * Create half-slide-mode in lyx: Copy one document into another, character
 by character, When I'm pressing a single key. It will require preparation
 (but anyhow, I prepared the lesson in advance as a lyx document... I don't
 remember all by heart , and anyway, it's still a lot easier then creating
 lyx\beamer slides), but it will save effort and mistakes during the class ,
 while still enable grate flexibility.
 * I wish I had 2 VGA output and 2 projectors, and LyX would switch from
 the end of one screen into the top of a new-clean-page at the other screen
 whenever I fill out the 1st. That would be just perfect :-P.
 * I should get something higher then the teacher's table to put my laptop
 on. For now, I have to bend over it, and my back is not happy.

 Anyway, I'm doing it for a month now,  3 hours a week, and the  experience
 for both me and my students is positive. If you have to teach stuff and
 don't wont to write on a board, you may consider using lyx. it's fun!

 - Ronen.

 --
 __

 Thomas Coffee
 Massachusetts Institute of Technology
 Department of Aeronautics  Astronautics
 Space Systems Laboratory
 617.549.5492

 Please avoid sending attachments in proprietary formats like Word or
 PowerPoint.
 For more information, see
 http://www.gnu.org/philosophy/no-word-attachments.html
 __




lecture 05 excerpt.lyx
Description: application/lyx

Re: LyX as a presentation tool

[Thomas Coffee]

y screen), so I can see them, and they can
> see my face and hear me better.
> * When I have complex illustration, I can just add it to the document..
>
> And over pre-made slides:
> * Saves time -- I do not have to typeset slides in advance (Also:
> Beamer+Hebrew+LyX is a disaster, so it would force me to turn into OO\MS PP
> or something like that, which is almost as bad)
> * Dynamic -- I can write notes and skip\add steps and lines during the
> class.
> * Slow -- Doing math on slides is bad. Most of the time, the slides are
> too crowded to understand, and fill-up at once, and not character by
> character as one would like on the board. When I'm typing with the class,
> I'm keeping on slow paste, so the can understand the math and follow by it.
>
> But also some disadvantages:
> * My screen is about 1/4 the size of the whiteboard, and LyX is rather
> lossy in screen-space. So, instead of just pointing into other parts of the
> board, I have to split\scroll.
> * The class's screen reaches to low, So, in order to let the students see
> the all screen, I switch into fullscreen mode, and then add toolbars from
> below in order to push the effective screen upwards.
> * When writing in lyx, one always writes on the bottom part of the screen.
> There is no good way  (after writing more then screen-full of text) to
> start from top, add lines from beneath and then shift to a "new" screen
> when I fill it.
> * It's rather ugly when I write \latexCommand in red, and just when I'm
> finish its render into symbol.
>
> Few points one can improve (mostly theoretical. some will demand big many
> expanse from my university, and some are "Itches I should scratch when I'll
> have time to code")
> * Create half-slide-mode in lyx: Copy one document into another, character
> by character, When I'm pressing a single key. It will require preparation
> (but anyhow, I prepared the lesson in advance as a lyx document... I don't
> remember all by heart , and anyway, it's still a lot easier then creating
> lyx\beamer slides), but it will save effort and mistakes during the class ,
> while still enable grate flexibility.
> * I wish I had 2 VGA output and 2 projectors, and LyX would switch from
> the end of one screen into the top of a new-clean-page at the other screen
> whenever I fill out the 1st. That would be just perfect :-P.
> * I should get something higher then the teacher's table to put my laptop
> on. For now, I have to bend over it, and my back is not happy.
>
> Anyway, I'm doing it for a month now,  3 hours a week, and the  experience
> for both me and my students is positive. If you have to teach stuff and
> don't wont to write on a board, you may consider using lyx. it's fun!
>
> - Ronen.
>
> --
> __
>
> Thomas Coffee
> Massachusetts Institute of Technology
> Department of Aeronautics & Astronautics
> Space Systems Laboratory
> 617.549.5492
>
> Please avoid sending attachments in proprietary formats like Word or
> PowerPoint.
> For more information, see
> http://www.gnu.org/philosophy/no-word-attachments.html
> __
>
>


lecture 05 excerpt.lyx
Description: application/lyx

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

The attachments on this thread have been posted to the wiki (thanks Christian):

http://wiki.lyx.org/Layouts/Modules/#toc7
http://wiki.lyx.org/uploads/Modules/Sage

Note that if you customize the sage.module file, you can load the
changes immediately by entering layout-reload in the minibuffer.

As Murat has done: I hereby grant permission to license my
contributions to the sage module for LyX under the GNU General Public
License, version 2 or later.

- Thomas


On Sun, Apr 1, 2012 at 12:03 PM, Murat Yildizoglu myi...@gmail.com wrote:
 Good idea, thanks a lot for the suggestion Xu. Here is my statement (I put
 the devel list as CC) :

 I hereby grant permission to license my contributions to the SAGE module for
 LyX under the GNU
 General Public Licence, version 2 or later.

 Murat Yildizoglu


 2012/3/31 Xu Wang xuwang...@gmail.com

 Dear Thomas

 Excellent news! Thank you for your continued work. I have not taken a fine
 look at this yet, but I also use Ubuntu so it looks like it might be useful.

 I'm not sure but I think for your contributions to be used you have to
 give permission explicitly. Look at this email:

 http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html
 You can send something like that to the development list, lyx-devel

 And it could be a good idea for Murat to do the same.

 I'm not sure though.

 In any case, thank you for your continued work. I am appreciative. Xu



 On Sat, Mar 31, 2012 at 3:08 AM, Thomas Coffee thomasmcof...@gmail.com
 wrote:

 Hi Murat and Xu,

 I found your thread in the archives and did some further work on the
 LyX-SageTeX module that Murat posted previously.

 I fixed a few things that did not work for me in the version described
 earlier, and expanded the module specification to provide some
 additional conveniences for including literate Sage code in LyX
 documents. There's still much room for development and customization.

 The attachments comprise a set of files and a shell script setup.sh
 that should largely automate the configuration process on GNU/Linux
 systems.

 *** Help needed:

 For other interested users, I'd like to upload this to
 http://wiki.lyx.org/Layouts/Modules, but I get browser errors for
 links anywhere under the upload path wiki.lyx.org/ipfm. The page
 http://wiki.lyx.org/Site/AboutUploading also tells me I will need
 someone to tell me the upload password. Can anyone assist?

 Thanks,
  Thomas


  Hi Xu,
 
  Thank you for your appreciation. I cannot advance anymore without any
  help
  from Lyx gurus.
  I think I have extracted all the information I can from the help docs.
  If I
  get any answer to my questions, I can construct a little bit smarter
  module
  but the one we have now is already usable. With some supplementary
  tricks
  from the sagetex documentation and through manual executions of the
  latex-sage-latex chain, it is possible to make a lot of computations.
 
  I was also very agreeably surprised that this module can be used for
  conversion to HTML from LyX, with figures and all.
 
  I attach to this message the module in its actual stage and some
  instruction for making the conversion chain functional. I hope this
  would
  already help some of you.
 
  As soon as I have more information, I will try to complete the module
  file.
 
  Best regards,
 
  Murat
 
  2011/10/31 Xu Wang xuwang...@gmail.com
 
   Dear Murat,
  
   This is great! I have been waiting for something like this for a long
   time. I also like the Sweave-like philosophy of this. It's more
   transparent
   and reproducible.
  
   I am looking forward to the final release with much excitement.
  
   Thank you for your work!
  
   Best,
  
   Xu
  
  
   On Mon, Oct 31, 2011 at 12:54 PM, Murat Yildizoglu
   myi...@gmail.comwrote:
  
   Just another mail to correct a problem with the preceding Lyx file
   (see
   the new file attached, and the $ signs in ERT boxes, this is
   connected with
   the problem I describe below) and ask a question about insets again:
  
   What kind of Flex insets can be included in a math mode text? Is
   this
   possible at all? Especially in displayed equation where one would
   like to
   include results from SAge computations?
   I cannot write the following in math mode in Lyx, putting the left
   member
   in a displayed equation and the right member in a sagecode inset
   that would
   be converted to the expression I give
    (\sage{integral(x/(x^2+1),x,0,1))
          \dfrac{\partial^{4}y}{\partial
   x^{4}}=\sage{integral(x/(x^2+1),x,0,1)}
  
   I meet two problems:
   1/ I cannot insert a Flex:sagecommand inset in a displayed equation,
   Lyx
   just goes to the next line before inserting it...
   2/ I cannot type the sagetex instruction (*sage{}  ) by hand,
   because
    x^2 in the right member must not be interpreted by LyX, since
   Sage will
   need it for its computation.
  
   I can of course type everything in an ERT, but this cannot be called
   integration can it? ;-)
  
   I have

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

The attachments on this thread have been posted to the wiki (thanks Christian):

http://wiki.lyx.org/Layouts/Modules/#toc7
http://wiki.lyx.org/uploads/Modules/Sage

Note that if you customize the sage.module file, you can load the
changes immediately by entering layout-reload in the minibuffer.

As Murat has done: I hereby grant permission to license my
contributions to the sage module for LyX under the GNU General Public
License, version 2 or later.

- Thomas


On Sun, Apr 1, 2012 at 12:03 PM, Murat Yildizoglu myi...@gmail.com wrote:
 Good idea, thanks a lot for the suggestion Xu. Here is my statement (I put
 the devel list as CC) :

 I hereby grant permission to license my contributions to the SAGE module for
 LyX under the GNU
 General Public Licence, version 2 or later.

 Murat Yildizoglu


 2012/3/31 Xu Wang xuwang...@gmail.com

 Dear Thomas

 Excellent news! Thank you for your continued work. I have not taken a fine
 look at this yet, but I also use Ubuntu so it looks like it might be useful.

 I'm not sure but I think for your contributions to be used you have to
 give permission explicitly. Look at this email:

 http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html
 You can send something like that to the development list, lyx-devel

 And it could be a good idea for Murat to do the same.

 I'm not sure though.

 In any case, thank you for your continued work. I am appreciative. Xu



 On Sat, Mar 31, 2012 at 3:08 AM, Thomas Coffee thomasmcof...@gmail.com
 wrote:

 Hi Murat and Xu,

 I found your thread in the archives and did some further work on the
 LyX-SageTeX module that Murat posted previously.

 I fixed a few things that did not work for me in the version described
 earlier, and expanded the module specification to provide some
 additional conveniences for including literate Sage code in LyX
 documents. There's still much room for development and customization.

 The attachments comprise a set of files and a shell script setup.sh
 that should largely automate the configuration process on GNU/Linux
 systems.

 *** Help needed:

 For other interested users, I'd like to upload this to
 http://wiki.lyx.org/Layouts/Modules, but I get browser errors for
 links anywhere under the upload path wiki.lyx.org/ipfm. The page
 http://wiki.lyx.org/Site/AboutUploading also tells me I will need
 someone to tell me the upload password. Can anyone assist?

 Thanks,
  Thomas


  Hi Xu,
 
  Thank you for your appreciation. I cannot advance anymore without any
  help
  from Lyx gurus.
  I think I have extracted all the information I can from the help docs.
  If I
  get any answer to my questions, I can construct a little bit smarter
  module
  but the one we have now is already usable. With some supplementary
  tricks
  from the sagetex documentation and through manual executions of the
  latex-sage-latex chain, it is possible to make a lot of computations.
 
  I was also very agreeably surprised that this module can be used for
  conversion to HTML from LyX, with figures and all.
 
  I attach to this message the module in its actual stage and some
  instruction for making the conversion chain functional. I hope this
  would
  already help some of you.
 
  As soon as I have more information, I will try to complete the module
  file.
 
  Best regards,
 
  Murat
 
  2011/10/31 Xu Wang xuwang...@gmail.com
 
   Dear Murat,
  
   This is great! I have been waiting for something like this for a long
   time. I also like the Sweave-like philosophy of this. It's more
   transparent
   and reproducible.
  
   I am looking forward to the final release with much excitement.
  
   Thank you for your work!
  
   Best,
  
   Xu
  
  
   On Mon, Oct 31, 2011 at 12:54 PM, Murat Yildizoglu
   myi...@gmail.comwrote:
  
   Just another mail to correct a problem with the preceding Lyx file
   (see
   the new file attached, and the $ signs in ERT boxes, this is
   connected with
   the problem I describe below) and ask a question about insets again:
  
   What kind of Flex insets can be included in a math mode text? Is
   this
   possible at all? Especially in displayed equation where one would
   like to
   include results from SAge computations?
   I cannot write the following in math mode in Lyx, putting the left
   member
   in a displayed equation and the right member in a sagecode inset
   that would
   be converted to the expression I give
    (\sage{integral(x/(x^2+1),x,0,1))
          \dfrac{\partial^{4}y}{\partial
   x^{4}}=\sage{integral(x/(x^2+1),x,0,1)}
  
   I meet two problems:
   1/ I cannot insert a Flex:sagecommand inset in a displayed equation,
   Lyx
   just goes to the next line before inserting it...
   2/ I cannot type the sagetex instruction (*sage{}  ) by hand,
   because
    x^2 in the right member must not be interpreted by LyX, since
   Sage will
   need it for its computation.
  
   I can of course type everything in an ERT, but this cannot be called
   integration can it? ;-)
  
   I have

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

The attachments on this thread have been posted to the wiki (thanks Christian):

http://wiki.lyx.org/Layouts/Modules/#toc7
http://wiki.lyx.org/uploads/Modules/Sage

Note that if you customize the sage.module file, you can load the
changes immediately by entering "layout-reload" in the minibuffer.

As Murat has done: I hereby grant permission to license my
contributions to the sage module for LyX under the GNU General Public
License, version 2 or later.

- Thomas


On Sun, Apr 1, 2012 at 12:03 PM, Murat Yildizoglu <myi...@gmail.com> wrote:
> Good idea, thanks a lot for the suggestion Xu. Here is my statement (I put
> the devel list as CC) :
>
> I hereby grant permission to license my contributions to the SAGE module for
> LyX under the GNU
> General Public Licence, version 2 or later.
>
> Murat Yildizoglu
>
>
> 2012/3/31 Xu Wang <xuwang...@gmail.com>
>>
>> Dear Thomas
>>
>> Excellent news! Thank you for your continued work. I have not taken a fine
>> look at this yet, but I also use Ubuntu so it looks like it might be useful.
>>
>> I'm not sure but I think for your contributions to be used you have to
>> give permission explicitly. Look at this email:
>>
>> http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html
>> You can send something like that to the development list, lyx-devel
>>
>> And it could be a good idea for Murat to do the same.
>>
>> I'm not sure though.
>>
>> In any case, thank you for your continued work. I am appreciative. Xu
>>
>>
>>
>> On Sat, Mar 31, 2012 at 3:08 AM, Thomas Coffee <thomasmcof...@gmail.com>
>> wrote:
>>>
>>> Hi Murat and Xu,
>>>
>>> I found your thread in the archives and did some further work on the
>>> LyX-SageTeX module that Murat posted previously.
>>>
>>> I fixed a few things that did not work for me in the version described
>>> earlier, and expanded the module specification to provide some
>>> additional conveniences for including literate Sage code in LyX
>>> documents. There's still much room for development and customization.
>>>
>>> The attachments comprise a set of files and a shell script "setup.sh"
>>> that should largely automate the configuration process on GNU/Linux
>>> systems.
>>>
>>> *** Help needed:
>>>
>>> For other interested users, I'd like to upload this to
>>> http://wiki.lyx.org/Layouts/Modules, but I get browser errors for
>>> links anywhere under the upload path wiki.lyx.org/ipfm. The page
>>> http://wiki.lyx.org/Site/AboutUploading also tells me I will need
>>> someone to tell me the upload password. Can anyone assist?
>>>
>>> Thanks,
>>>  Thomas
>>>
>>>
>>> > Hi Xu,
>>> >
>>> > Thank you for your appreciation. I cannot advance anymore without any
>>> > help
>>> > from Lyx gurus.
>>> > I think I have extracted all the information I can from the help docs.
>>> > If I
>>> > get any answer to my questions, I can construct a little bit smarter
>>> > module
>>> > but the one we have now is already usable. With some supplementary
>>> > tricks
>>> > from the sagetex documentation and through manual executions of the
>>> > latex-sage-latex chain, it is possible to make a lot of computations.
>>> >
>>> > I was also very agreeably surprised that this module can be used for
>>> > conversion to HTML from LyX, with figures and all.
>>> >
>>> > I attach to this message the module in its actual stage and some
>>> > instruction for making the conversion chain functional. I hope this
>>> > would
>>> > already help some of you.
>>> >
>>> > As soon as I have more information, I will try to complete the module
>>> > file.
>>> >
>>> > Best regards,
>>> >
>>> > Murat
>>> >
>>> > 2011/10/31 Xu Wang <xuwang...@gmail.com>
>>> >
>>> > > Dear Murat,
>>> > >
>>> > > This is great! I have been waiting for something like this for a long
>>> > > time. I also like the Sweave-like philosophy of this. It's more
>>> > > transparent
>>> > > and reproducible.
>>> > >
>>> > > I am looking forward to the final release with much excitement.
>>> > >
>>> > > Thank you for your work!
>>> > >
>&

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

Hi Xu,

I notice your email shows up in the archive thread but mine does not,
and thus neither do the attachments. Any idea how to change this?

Here is a modified preferences file that preserves a pdflatex-only
update pathway, allowing the user to update the LaTeX only without
updating the Sage computations.

I will try emailing lyx-devel.

Thanks,
 Thomas


On Sat, Mar 31, 2012 at 4:48 AM, Xu Wang xuwang...@gmail.com wrote:
 Dear Thomas

 Excellent news! Thank you for your continued work. I have not taken a fine
 look at this yet, but I also use Ubuntu so it looks like it might be useful.

 I'm not sure but I think for your contributions to be used you have to give
 permission explicitly. Look at this email:

 http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html
 You can send something like that to the development list, lyx-devel

 And it could be a good idea for Murat to do the same.

 I'm not sure though.

 In any case, thank you for your continued work. I am appreciative. Xu



 On Sat, Mar 31, 2012 at 3:08 AM, Thomas Coffee thomasmcof...@gmail.com
 wrote:

 Hi Murat and Xu,

 I found your thread in the archives and did some further work on the
 LyX-SageTeX module that Murat posted previously.

 I fixed a few things that did not work for me in the version described
 earlier, and expanded the module specification to provide some
 additional conveniences for including literate Sage code in LyX
 documents. There's still much room for development and customization.

 The attachments comprise a set of files and a shell script setup.sh
 that should largely automate the configuration process on GNU/Linux
 systems.

 *** Help needed:

 For other interested users, I'd like to upload this to
 http://wiki.lyx.org/Layouts/Modules, but I get browser errors for
 links anywhere under the upload path wiki.lyx.org/ipfm. The page
 http://wiki.lyx.org/Site/AboutUploading also tells me I will need
 someone to tell me the upload password. Can anyone assist?

 Thanks,
  Thomas


  Hi Xu,
 
  Thank you for your appreciation. I cannot advance anymore without any
  help
  from Lyx gurus.
  I think I have extracted all the information I can from the help docs.
  If I
  get any answer to my questions, I can construct a little bit smarter
  module
  but the one we have now is already usable. With some supplementary
  tricks
  from the sagetex documentation and through manual executions of the
  latex-sage-latex chain, it is possible to make a lot of computations.
 
  I was also very agreeably surprised that this module can be used for
  conversion to HTML from LyX, with figures and all.
 
  I attach to this message the module in its actual stage and some
  instruction for making the conversion chain functional. I hope this
  would
  already help some of you.
 
  As soon as I have more information, I will try to complete the module
  file.
 
  Best regards,
 
  Murat
 
  2011/10/31 Xu Wang xuwang...@gmail.com
 
   Dear Murat,
  
   This is great! I have been waiting for something like this for a long
   time. I also like the Sweave-like philosophy of this. It's more
   transparent
   and reproducible.
  
   I am looking forward to the final release with much excitement.
  
   Thank you for your work!
  
   Best,
  
   Xu
  
  
   On Mon, Oct 31, 2011 at 12:54 PM, Murat Yildizoglu
   myi...@gmail.comwrote:
  
   Just another mail to correct a problem with the preceding Lyx file
   (see
   the new file attached, and the $ signs in ERT boxes, this is
   connected with
   the problem I describe below) and ask a question about insets again:
  
   What kind of Flex insets can be included in a math mode text? Is this
   possible at all? Especially in displayed equation where one would
   like to
   include results from SAge computations?
   I cannot write the following in math mode in Lyx, putting the left
   member
   in a displayed equation and the right member in a sagecode inset that
   would
   be converted to the expression I give
    (\sage{integral(x/(x^2+1),x,0,1))
          \dfrac{\partial^{4}y}{\partial
   x^{4}}=\sage{integral(x/(x^2+1),x,0,1)}
  
   I meet two problems:
   1/ I cannot insert a Flex:sagecommand inset in a displayed equation,
   Lyx
   just goes to the next line before inserting it...
   2/ I cannot type the sagetex instruction (*sage{}  ) by hand, because
    x^2 in the right member must not be interpreted by LyX, since Sage
   will
   need it for its computation.
  
   I can of course type everything in an ERT, but this cannot be called
   integration can it? ;-)
  
   I have reread again the help document on layouts and insets, and I
   have
   checked the files that come in the layout folder of LyX, but cannot
   find
   any answer to my question.
  
   Sorry for bothering you again with my problems... I hope that Sage
   integration will interest other people...
  
   Murat
  
   I definitely need the help of a Lyx wizard who understands well the
   insets and their integration in Lyx

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

I'm trying the earlier attachments again from the message that didn't
make it into the archive, minus the binary .pdf file.

- Thomas


On Sat, Mar 31, 2012 at 12:53 PM, Thomas Coffee thomasmcof...@gmail.com wrote:
 Hi Xu,

 I notice your email shows up in the archive thread but mine does not,
 and thus neither do the attachments. Any idea how to change this?

 Here is a modified preferences file that preserves a pdflatex-only
 update pathway, allowing the user to update the LaTeX only without
 updating the Sage computations.

 I will try emailing lyx-devel.

 Thanks,
  Thomas


 On Sat, Mar 31, 2012 at 4:48 AM, Xu Wang xuwang...@gmail.com wrote:
 Dear Thomas

 Excellent news! Thank you for your continued work. I have not taken a fine
 look at this yet, but I also use Ubuntu so it looks like it might be useful.

 I'm not sure but I think for your contributions to be used you have to give
 permission explicitly. Look at this email:

 http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html
 You can send something like that to the development list, lyx-devel

 And it could be a good idea for Murat to do the same.

 I'm not sure though.

 In any case, thank you for your continued work. I am appreciative. Xu



 On Sat, Mar 31, 2012 at 3:08 AM, Thomas Coffee thomasmcof...@gmail.com
 wrote:

 Hi Murat and Xu,

 I found your thread in the archives and did some further work on the
 LyX-SageTeX module that Murat posted previously.

 I fixed a few things that did not work for me in the version described
 earlier, and expanded the module specification to provide some
 additional conveniences for including literate Sage code in LyX
 documents. There's still much room for development and customization.

 The attachments comprise a set of files and a shell script setup.sh
 that should largely automate the configuration process on GNU/Linux
 systems.

 *** Help needed:

 For other interested users, I'd like to upload this to
 http://wiki.lyx.org/Layouts/Modules, but I get browser errors for
 links anywhere under the upload path wiki.lyx.org/ipfm. The page
 http://wiki.lyx.org/Site/AboutUploading also tells me I will need
 someone to tell me the upload password. Can anyone assist?

 Thanks,
  Thomas


  Hi Xu,
 
  Thank you for your appreciation. I cannot advance anymore without any
  help
  from Lyx gurus.
  I think I have extracted all the information I can from the help docs.
  If I
  get any answer to my questions, I can construct a little bit smarter
  module
  but the one we have now is already usable. With some supplementary
  tricks
  from the sagetex documentation and through manual executions of the
  latex-sage-latex chain, it is possible to make a lot of computations.
 
  I was also very agreeably surprised that this module can be used for
  conversion to HTML from LyX, with figures and all.
 
  I attach to this message the module in its actual stage and some
  instruction for making the conversion chain functional. I hope this
  would
  already help some of you.
 
  As soon as I have more information, I will try to complete the module
  file.
 
  Best regards,
 
  Murat
 
  2011/10/31 Xu Wang xuwang...@gmail.com
 
   Dear Murat,
  
   This is great! I have been waiting for something like this for a long
   time. I also like the Sweave-like philosophy of this. It's more
   transparent
   and reproducible.
  
   I am looking forward to the final release with much excitement.
  
   Thank you for your work!
  
   Best,
  
   Xu
  
  
   On Mon, Oct 31, 2011 at 12:54 PM, Murat Yildizoglu
   myi...@gmail.comwrote:
  
   Just another mail to correct a problem with the preceding Lyx file
   (see
   the new file attached, and the $ signs in ERT boxes, this is
   connected with
   the problem I describe below) and ask a question about insets again:
  
   What kind of Flex insets can be included in a math mode text? Is this
   possible at all? Especially in displayed equation where one would
   like to
   include results from SAge computations?
   I cannot write the following in math mode in Lyx, putting the left
   member
   in a displayed equation and the right member in a sagecode inset that
   would
   be converted to the expression I give
    (\sage{integral(x/(x^2+1),x,0,1))
          \dfrac{\partial^{4}y}{\partial
   x^{4}}=\sage{integral(x/(x^2+1),x,0,1)}
  
   I meet two problems:
   1/ I cannot insert a Flex:sagecommand inset in a displayed equation,
   Lyx
   just goes to the next line before inserting it...
   2/ I cannot type the sagetex instruction (*sage{}  ) by hand, because
    x^2 in the right member must not be interpreted by LyX, since Sage
   will
   need it for its computation.
  
   I can of course type everything in an ERT, but this cannot be called
   integration can it? ;-)
  
   I have reread again the help document on layouts and insets, and I
   have
   checked the files that come in the layout folder of LyX, but cannot
   find
   any answer to my question.
  
   Sorry

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

Hi Xu,

I notice your email shows up in the archive thread but mine does not,
and thus neither do the attachments. Any idea how to change this?

Here is a modified preferences file that preserves a pdflatex-only
update pathway, allowing the user to update the LaTeX only without
updating the Sage computations.

I will try emailing lyx-devel.

Thanks,
 Thomas


On Sat, Mar 31, 2012 at 4:48 AM, Xu Wang xuwang...@gmail.com wrote:
 Dear Thomas

 Excellent news! Thank you for your continued work. I have not taken a fine
 look at this yet, but I also use Ubuntu so it looks like it might be useful.

 I'm not sure but I think for your contributions to be used you have to give
 permission explicitly. Look at this email:

 http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html
 You can send something like that to the development list, lyx-devel

 And it could be a good idea for Murat to do the same.

 I'm not sure though.

 In any case, thank you for your continued work. I am appreciative. Xu



 On Sat, Mar 31, 2012 at 3:08 AM, Thomas Coffee thomasmcof...@gmail.com
 wrote:

 Hi Murat and Xu,

 I found your thread in the archives and did some further work on the
 LyX-SageTeX module that Murat posted previously.

 I fixed a few things that did not work for me in the version described
 earlier, and expanded the module specification to provide some
 additional conveniences for including literate Sage code in LyX
 documents. There's still much room for development and customization.

 The attachments comprise a set of files and a shell script setup.sh
 that should largely automate the configuration process on GNU/Linux
 systems.

 *** Help needed:

 For other interested users, I'd like to upload this to
 http://wiki.lyx.org/Layouts/Modules, but I get browser errors for
 links anywhere under the upload path wiki.lyx.org/ipfm. The page
 http://wiki.lyx.org/Site/AboutUploading also tells me I will need
 someone to tell me the upload password. Can anyone assist?

 Thanks,
  Thomas


  Hi Xu,
 
  Thank you for your appreciation. I cannot advance anymore without any
  help
  from Lyx gurus.
  I think I have extracted all the information I can from the help docs.
  If I
  get any answer to my questions, I can construct a little bit smarter
  module
  but the one we have now is already usable. With some supplementary
  tricks
  from the sagetex documentation and through manual executions of the
  latex-sage-latex chain, it is possible to make a lot of computations.
 
  I was also very agreeably surprised that this module can be used for
  conversion to HTML from LyX, with figures and all.
 
  I attach to this message the module in its actual stage and some
  instruction for making the conversion chain functional. I hope this
  would
  already help some of you.
 
  As soon as I have more information, I will try to complete the module
  file.
 
  Best regards,
 
  Murat
 
  2011/10/31 Xu Wang xuwang...@gmail.com
 
   Dear Murat,
  
   This is great! I have been waiting for something like this for a long
   time. I also like the Sweave-like philosophy of this. It's more
   transparent
   and reproducible.
  
   I am looking forward to the final release with much excitement.
  
   Thank you for your work!
  
   Best,
  
   Xu
  
  
   On Mon, Oct 31, 2011 at 12:54 PM, Murat Yildizoglu
   myi...@gmail.comwrote:
  
   Just another mail to correct a problem with the preceding Lyx file
   (see
   the new file attached, and the $ signs in ERT boxes, this is
   connected with
   the problem I describe below) and ask a question about insets again:
  
   What kind of Flex insets can be included in a math mode text? Is this
   possible at all? Especially in displayed equation where one would
   like to
   include results from SAge computations?
   I cannot write the following in math mode in Lyx, putting the left
   member
   in a displayed equation and the right member in a sagecode inset that
   would
   be converted to the expression I give
    (\sage{integral(x/(x^2+1),x,0,1))
          \dfrac{\partial^{4}y}{\partial
   x^{4}}=\sage{integral(x/(x^2+1),x,0,1)}
  
   I meet two problems:
   1/ I cannot insert a Flex:sagecommand inset in a displayed equation,
   Lyx
   just goes to the next line before inserting it...
   2/ I cannot type the sagetex instruction (*sage{}  ) by hand, because
    x^2 in the right member must not be interpreted by LyX, since Sage
   will
   need it for its computation.
  
   I can of course type everything in an ERT, but this cannot be called
   integration can it? ;-)
  
   I have reread again the help document on layouts and insets, and I
   have
   checked the files that come in the layout folder of LyX, but cannot
   find
   any answer to my question.
  
   Sorry for bothering you again with my problems... I hope that Sage
   integration will interest other people...
  
   Murat
  
   I definitely need the help of a Lyx wizard who understands well the
   insets and their integration in Lyx

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

I'm trying the earlier attachments again from the message that didn't
make it into the archive, minus the binary .pdf file.

- Thomas


On Sat, Mar 31, 2012 at 12:53 PM, Thomas Coffee thomasmcof...@gmail.com wrote:
 Hi Xu,

 I notice your email shows up in the archive thread but mine does not,
 and thus neither do the attachments. Any idea how to change this?

 Here is a modified preferences file that preserves a pdflatex-only
 update pathway, allowing the user to update the LaTeX only without
 updating the Sage computations.

 I will try emailing lyx-devel.

 Thanks,
  Thomas


 On Sat, Mar 31, 2012 at 4:48 AM, Xu Wang xuwang...@gmail.com wrote:
 Dear Thomas

 Excellent news! Thank you for your continued work. I have not taken a fine
 look at this yet, but I also use Ubuntu so it looks like it might be useful.

 I'm not sure but I think for your contributions to be used you have to give
 permission explicitly. Look at this email:

 http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html
 You can send something like that to the development list, lyx-devel

 And it could be a good idea for Murat to do the same.

 I'm not sure though.

 In any case, thank you for your continued work. I am appreciative. Xu



 On Sat, Mar 31, 2012 at 3:08 AM, Thomas Coffee thomasmcof...@gmail.com
 wrote:

 Hi Murat and Xu,

 I found your thread in the archives and did some further work on the
 LyX-SageTeX module that Murat posted previously.

 I fixed a few things that did not work for me in the version described
 earlier, and expanded the module specification to provide some
 additional conveniences for including literate Sage code in LyX
 documents. There's still much room for development and customization.

 The attachments comprise a set of files and a shell script setup.sh
 that should largely automate the configuration process on GNU/Linux
 systems.

 *** Help needed:

 For other interested users, I'd like to upload this to
 http://wiki.lyx.org/Layouts/Modules, but I get browser errors for
 links anywhere under the upload path wiki.lyx.org/ipfm. The page
 http://wiki.lyx.org/Site/AboutUploading also tells me I will need
 someone to tell me the upload password. Can anyone assist?

 Thanks,
  Thomas


  Hi Xu,
 
  Thank you for your appreciation. I cannot advance anymore without any
  help
  from Lyx gurus.
  I think I have extracted all the information I can from the help docs.
  If I
  get any answer to my questions, I can construct a little bit smarter
  module
  but the one we have now is already usable. With some supplementary
  tricks
  from the sagetex documentation and through manual executions of the
  latex-sage-latex chain, it is possible to make a lot of computations.
 
  I was also very agreeably surprised that this module can be used for
  conversion to HTML from LyX, with figures and all.
 
  I attach to this message the module in its actual stage and some
  instruction for making the conversion chain functional. I hope this
  would
  already help some of you.
 
  As soon as I have more information, I will try to complete the module
  file.
 
  Best regards,
 
  Murat
 
  2011/10/31 Xu Wang xuwang...@gmail.com
 
   Dear Murat,
  
   This is great! I have been waiting for something like this for a long
   time. I also like the Sweave-like philosophy of this. It's more
   transparent
   and reproducible.
  
   I am looking forward to the final release with much excitement.
  
   Thank you for your work!
  
   Best,
  
   Xu
  
  
   On Mon, Oct 31, 2011 at 12:54 PM, Murat Yildizoglu
   myi...@gmail.comwrote:
  
   Just another mail to correct a problem with the preceding Lyx file
   (see
   the new file attached, and the $ signs in ERT boxes, this is
   connected with
   the problem I describe below) and ask a question about insets again:
  
   What kind of Flex insets can be included in a math mode text? Is this
   possible at all? Especially in displayed equation where one would
   like to
   include results from SAge computations?
   I cannot write the following in math mode in Lyx, putting the left
   member
   in a displayed equation and the right member in a sagecode inset that
   would
   be converted to the expression I give
    (\sage{integral(x/(x^2+1),x,0,1))
          \dfrac{\partial^{4}y}{\partial
   x^{4}}=\sage{integral(x/(x^2+1),x,0,1)}
  
   I meet two problems:
   1/ I cannot insert a Flex:sagecommand inset in a displayed equation,
   Lyx
   just goes to the next line before inserting it...
   2/ I cannot type the sagetex instruction (*sage{}  ) by hand, because
    x^2 in the right member must not be interpreted by LyX, since Sage
   will
   need it for its computation.
  
   I can of course type everything in an ERT, but this cannot be called
   integration can it? ;-)
  
   I have reread again the help document on layouts and insets, and I
   have
   checked the files that come in the layout folder of LyX, but cannot
   find
   any answer to my question.
  
   Sorry

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

Hi Xu,

I notice your email shows up in the archive thread but mine does not,
and thus neither do the attachments. Any idea how to change this?

Here is a modified preferences file that preserves a pdflatex-only
update pathway, allowing the user to update the LaTeX only without
updating the Sage computations.

I will try emailing lyx-devel.

Thanks,
 Thomas


On Sat, Mar 31, 2012 at 4:48 AM, Xu Wang <xuwang...@gmail.com> wrote:
> Dear Thomas
>
> Excellent news! Thank you for your continued work. I have not taken a fine
> look at this yet, but I also use Ubuntu so it looks like it might be useful.
>
> I'm not sure but I think for your contributions to be used you have to give
> permission explicitly. Look at this email:
>
> http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html
> You can send something like that to the development list, lyx-devel
>
> And it could be a good idea for Murat to do the same.
>
> I'm not sure though.
>
> In any case, thank you for your continued work. I am appreciative. Xu
>
>
>
> On Sat, Mar 31, 2012 at 3:08 AM, Thomas Coffee <thomasmcof...@gmail.com>
> wrote:
>>
>> Hi Murat and Xu,
>>
>> I found your thread in the archives and did some further work on the
>> LyX-SageTeX module that Murat posted previously.
>>
>> I fixed a few things that did not work for me in the version described
>> earlier, and expanded the module specification to provide some
>> additional conveniences for including literate Sage code in LyX
>> documents. There's still much room for development and customization.
>>
>> The attachments comprise a set of files and a shell script "setup.sh"
>> that should largely automate the configuration process on GNU/Linux
>> systems.
>>
>> *** Help needed:
>>
>> For other interested users, I'd like to upload this to
>> http://wiki.lyx.org/Layouts/Modules, but I get browser errors for
>> links anywhere under the upload path wiki.lyx.org/ipfm. The page
>> http://wiki.lyx.org/Site/AboutUploading also tells me I will need
>> someone to tell me the upload password. Can anyone assist?
>>
>> Thanks,
>>  Thomas
>>
>>
>> > Hi Xu,
>> >
>> > Thank you for your appreciation. I cannot advance anymore without any
>> > help
>> > from Lyx gurus.
>> > I think I have extracted all the information I can from the help docs.
>> > If I
>> > get any answer to my questions, I can construct a little bit smarter
>> > module
>> > but the one we have now is already usable. With some supplementary
>> > tricks
>> > from the sagetex documentation and through manual executions of the
>> > latex-sage-latex chain, it is possible to make a lot of computations.
>> >
>> > I was also very agreeably surprised that this module can be used for
>> > conversion to HTML from LyX, with figures and all.
>> >
>> > I attach to this message the module in its actual stage and some
>> > instruction for making the conversion chain functional. I hope this
>> > would
>> > already help some of you.
>> >
>> > As soon as I have more information, I will try to complete the module
>> > file.
>> >
>> > Best regards,
>> >
>> > Murat
>> >
>> > 2011/10/31 Xu Wang <xuwang...@gmail.com>
>> >
>> > > Dear Murat,
>> > >
>> > > This is great! I have been waiting for something like this for a long
>> > > time. I also like the Sweave-like philosophy of this. It's more
>> > > transparent
>> > > and reproducible.
>> > >
>> > > I am looking forward to the final release with much excitement.
>> > >
>> > > Thank you for your work!
>> > >
>> > > Best,
>> > >
>> > > Xu
>> > >
>> > >
>> > > On Mon, Oct 31, 2011 at 12:54 PM, Murat Yildizoglu
>> > > <myi...@gmail.com>wrote:
>> > >
>> > >> Just another mail to correct a problem with the preceding Lyx file
>> > >> (see
>> > >> the new file attached, and the $ signs in ERT boxes, this is
>> > >> connected with
>> > >> the problem I describe below) and ask a question about insets again:
>> > >>
>> > >> What kind of Flex insets can be included in a math mode text? Is this
>> > >> possible at all? Especially in displayed equation where one would
>> > >> like to
>> > >> include results from SAge c

Re: Examples of integration between Lyx, Sage computations, and PDFLateX

[Thomas Coffee]

I'm trying the earlier attachments again from the message that didn't
make it into the archive, minus the binary .pdf file.

- Thomas


On Sat, Mar 31, 2012 at 12:53 PM, Thomas Coffee <thomasmcof...@gmail.com> wrote:
> Hi Xu,
>
> I notice your email shows up in the archive thread but mine does not,
> and thus neither do the attachments. Any idea how to change this?
>
> Here is a modified preferences file that preserves a pdflatex-only
> update pathway, allowing the user to update the LaTeX only without
> updating the Sage computations.
>
> I will try emailing lyx-devel.
>
> Thanks,
>  Thomas
>
>
> On Sat, Mar 31, 2012 at 4:48 AM, Xu Wang <xuwang...@gmail.com> wrote:
>> Dear Thomas
>>
>> Excellent news! Thank you for your continued work. I have not taken a fine
>> look at this yet, but I also use Ubuntu so it looks like it might be useful.
>>
>> I'm not sure but I think for your contributions to be used you have to give
>> permission explicitly. Look at this email:
>>
>> http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html
>> You can send something like that to the development list, lyx-devel
>>
>> And it could be a good idea for Murat to do the same.
>>
>> I'm not sure though.
>>
>> In any case, thank you for your continued work. I am appreciative. Xu
>>
>>
>>
>> On Sat, Mar 31, 2012 at 3:08 AM, Thomas Coffee <thomasmcof...@gmail.com>
>> wrote:
>>>
>>> Hi Murat and Xu,
>>>
>>> I found your thread in the archives and did some further work on the
>>> LyX-SageTeX module that Murat posted previously.
>>>
>>> I fixed a few things that did not work for me in the version described
>>> earlier, and expanded the module specification to provide some
>>> additional conveniences for including literate Sage code in LyX
>>> documents. There's still much room for development and customization.
>>>
>>> The attachments comprise a set of files and a shell script "setup.sh"
>>> that should largely automate the configuration process on GNU/Linux
>>> systems.
>>>
>>> *** Help needed:
>>>
>>> For other interested users, I'd like to upload this to
>>> http://wiki.lyx.org/Layouts/Modules, but I get browser errors for
>>> links anywhere under the upload path wiki.lyx.org/ipfm. The page
>>> http://wiki.lyx.org/Site/AboutUploading also tells me I will need
>>> someone to tell me the upload password. Can anyone assist?
>>>
>>> Thanks,
>>>  Thomas
>>>
>>>
>>> > Hi Xu,
>>> >
>>> > Thank you for your appreciation. I cannot advance anymore without any
>>> > help
>>> > from Lyx gurus.
>>> > I think I have extracted all the information I can from the help docs.
>>> > If I
>>> > get any answer to my questions, I can construct a little bit smarter
>>> > module
>>> > but the one we have now is already usable. With some supplementary
>>> > tricks
>>> > from the sagetex documentation and through manual executions of the
>>> > latex-sage-latex chain, it is possible to make a lot of computations.
>>> >
>>> > I was also very agreeably surprised that this module can be used for
>>> > conversion to HTML from LyX, with figures and all.
>>> >
>>> > I attach to this message the module in its actual stage and some
>>> > instruction for making the conversion chain functional. I hope this
>>> > would
>>> > already help some of you.
>>> >
>>> > As soon as I have more information, I will try to complete the module
>>> > file.
>>> >
>>> > Best regards,
>>> >
>>> > Murat
>>> >
>>> > 2011/10/31 Xu Wang <xuwang...@gmail.com>
>>> >
>>> > > Dear Murat,
>>> > >
>>> > > This is great! I have been waiting for something like this for a long
>>> > > time. I also like the Sweave-like philosophy of this. It's more
>>> > > transparent
>>> > > and reproducible.
>>> > >
>>> > > I am looking forward to the final release with much excitement.
>>> > >
>>> > > Thank you for your work!
>>> > >
>>> > > Best,
>>> > >
>>> > > Xu
>>> > >
>>> > >
>>> > > On Mon, Oct 31, 2011 at 12:54 PM, Murat Yildizoglu