[sage-devel] Re: Problem installing sagecell

[Andrey Novoseltsev]

On Tuesday, 25 February 2014 22:37:45 UTC-7, Andrey Novoseltsev wrote:
>
> in the end installing sagecell spkg still fails (don't recall the error), 
> but it gets installed well enough to pull the fresh version from the github 
> and run make again.
>

Actually, I get exactly the same error and the reason is that current 
sagenb is at a different version than back in August. But as I said, that's 
just fine for doing

cd sagecell
git pull origin master
../sage -sh -c "make -B"

which in my script is followed by

cd ..
chown -R :sagecell .
chmod -R g+r local # Why are there such issues???

I never figured out what is going wrong with permissions, but there are 
some files that are not group readable and so Sage cannot be used by the 
worker account otherwise.

Andrey 

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[sage-devel] Re: Problem installing sagecell

[Andrey Novoseltsev]

Hello,

I managed to install sagecell on Debian, although I am running a backported 
kernel and had to enable testing for several packages.

A couple of bugs (or features) that I had to deal with in the process while 
following vm scripts from sagecell repository:

ln -s /usr/bin/nodejs /usr/bin/node # Because node.js is called nodejs but 
expected to be node somewhere

and something goes wrong with extra installs in python, but this helps from 
the $SAGEROOT:

# looks like we need to upgrade setuptools first
# ./sage -sh -c "easy_install -U setuptools"
# which does not quite work so let's try
rm local/bin/easy_install*
wget http://python-distribute.org/distribute_setup.py
./sage -sh -c "python distribute_setup.py"
rm distribute*
./sage -sh -c "easy_install pip"
./sage -i http://boxen.math.washington.edu/home/jason/zeromq-4.0.3.spkg
./sage -i pyzmq
# we need a more recent pyzmq than Sage provides
./sage -sh -c "pip install -U pyzmq"

in the end installing sagecell spkg still fails (don't recall the error), 
but it gets installed well enough to pull the fresh version from the github 
and run make again.

Hope this helps!
Andrey

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Re: [sage-devel] GSOC 2014 iOS App

[Ivan Andrus]

On Feb 25, 2014, at 2:42 AM, Aditya Makkar  wrote:

> Hi,
> I am Aditya and I am interested in getting involved in Google Summer of Code 
> with Sage. I am just finishing my second year at Indian Institute of 
> Technology, Delhi doing B.Tech in Mechanical Engineering. I have good 
> knowledge of C++, Python and Objective-C. I have some experience in iOS app 
> development, mainly through the course "CS 193P iPhone Application 
> Development", which I am currently doing. I have the Sage app on iPad and I 
> have downloaded the code from here(Bitbucket).

> So I would really love if I could be a contributor to Sage and work on this 
> project in my summers.

Cool!  My suggestion at this stage is to use the iOS app (which I assume you 
are) and come up with ideas for improvements.  I think it looks really good on 
your GSOC application if you've already submitted a pull request or otherwise 
had a patch accepted (even a fairly trivial one) since that shows that shows 
that you've been in communication and such.

I know there is lots of room for improvement on the iPad version.  I have some 
ideas, but you'll probably come up with better ones.

> Thank You
> Aditya Makkar
> 
> PS: I am sorry if this not the right place to post this, since I could not 
> post it in sage-gsoc google group.

Feel free to contact me directly (or via bitbucket) if you have questions 
specific to the iOS app.

-Ivan

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[sage-devel] Re: Sage accepted for GSoC 2014

[Dima Pasechnik]

On 2014-02-25, mmarco  wrote:
> I would be happy to mentor a student in a knot theory related project in 
> sage. I had mainly two ideas:
>
> First idea is to write a class for knots/links. This class should be able 
> to translate between the different possible representations of links (Gauss 
> codes, 3d curves, braid closure...) and compute some of their invariants 
> (the usual polynomials, Seifert forms, fundamental groups...). It should 
> also produce pictures of knot diagrams and 3d representations of the 
> knot/link. Some (or most) of this features can be either written from 
> scratch, or just wrap external code (like the mentioned SnapPy).

perhaps one can try to incorporate parts of knotscape into Sage.
Well, it's kind of old, but still works:
https://github.com/dimpase/knotscap
(incidentally, a colleague wanted to use knotscape on a modern Linux
system, so I did these small fixes for him)


>
> Another idea, closely related to the previous one, is to write a javascript 
> editor for knots and links, following what knotplot [1] does. This can be 
> part of the same project or a separated one, if someone else writes the 
> backend (although i think that it should be possible to write the editor 
> and a simple backend in a single gsoc project, but that can be discussed). 
> An important part of this editor would be the algorithm for dynamically 
> relaxing the link. In particular, such an algorithm is explained in chapter 
> 7 of Scharein's thesis [1].
>
> [1] http://www.knotplot.com/thesis/thesis.html
>

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Re: [sage-devel] Re: Sage accepted for GSoC 2014

[Amit Jamadagni]

I have been going through the implementation Knot Atlas, as per my
understanding they have stored the knots in a table and have inputted it to
get various results, I would like to know whether we will be using tables
to input or any other way to input. I have seen through Vogel's algorithm
 which takes in the oriented gauss code and ends up giving out the braid
word [1] from which we can construct the knot(as it is closed braid) and
from the braid word we can calculate the Alexander polynomial from the
Burau's representation(which is currently implemented in braid in Sage) (I
have heard is not true for strings greater than 5). I have been reading
through [2] which mentions how to calculate Seifert matrix from a braid
representation which can be again used to represent knots. I have been
searching for algorithms which would relate the Seifert matrix and various
invariants. It would be really helpful if I could get more reference to the
algorithms that could be implemented. I have just started the
implementation details mentioned in [3].

[1] http://magma.maths.usyd.edu.au/~danr/site/talks/20070531.pdf
[2] http://www.maths.ed.ac.uk/~jcollins/SeifertMatrix/SeifertMatrix.pdf
[3] http://www.layer8.co.uk/maths/braids/braid-user-documentation.html

On Tue, Feb 25, 2014 at 7:16 PM, kcrisman  wrote:

>
>>
>> [2] http://legacy.earlham.edu/~peters/knotlink.htm#software
>>
>>
> *"June 2, 2004*. Unfortunately I no longer have time to update *Knots on
> the Web*. I know it conntains many dead links and omits many good, new
> sites. "
>
> And my understanding is that the Knot Atlas
> http://katlas.math.toronto.edu/wiki/Main_Page and the Mathematica package
> creating it is the state of the art.  Does SnapPy now really have all that
> combinatorial stuff?  I think that at the very least a good wrapper
> allowing for use of *any* robust backend for knots would be a great
> contribution to Sage.  mmarco seems to have a good sense of what would
> actually be needed to do this.  It's definitely a significant hole in Sage.
> - one might even wonder whether the authors of the Mma package would be
> willing to license their package in such a way that the algorithms for
> computing various invariants etc. could be used/{P,C}ythonized in Sage, if
> some people know them http://katlas.math.toronto.edu/wiki/Acknowledgement
>
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Re: [sage-devel] Re: Building sage-6.1.1 fail with Error installing package ecm-6.4.4

[Jeroen Demeyer]

On 2014-02-25 19:56, Volker Braun wrote:

This looks like a compiler error, try

export SAGE_INSTALL_GCC=yes
make


No, the problem is the assembler, i.e. binutils.

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Re: [sage-devel] Building sage-6.1.1 fail with Error installing package ecm-6.4.4

[Jeroen Demeyer]

Try upgrading binutils.

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[sage-devel] Building sage-6.1.1 fail with Error installing package ecm-6.4.4

[Sergio Rojas]

Hello all,

Trying to building sage on a laptop having Intel(R) Core(TM) i7-4700MQ CPU @ 
2.40GH, sage make finished with a Error installing package ecm-6.4.4.

I am including below the full log file in the hope the developer team can identi
fy and help to fix this problem.

Is it possible to skip the installation of the ecm-6.4.4 package?

Thanks in advance,

Sergio 

$ more ecm-6.4.4.log
Found local metadata for ecm-6.4.4
Found local sources at /opt/Sage/sage-6.1.1/upstream/ecm-6.4.4.tar.bz2
Checksum: 97a6f9fc68337d8dadebc4754a61fdfe97bb0136 vs 97a6f9fc68337d8dadebc4754a
61fdfe97bb0136
ecm-6.4.4

Setting up build directory for ecm-6.4.4
Finished set up

Host system:
Linux wsci 3.11.0-17-generic #31~precise1-Ubuntu SMP Tue Feb 4 21:25:43 UTC 2014
 x86_64 x86_64 x86_64 GNU/Linux

C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubu
ntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages
=c,c++,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.6 --enable-shared 
--enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-incl
uded-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 
--libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-li
bstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-pl
ugin --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic -
-enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --targ
et=x86_64-linux-gnu
Thread model: posix
gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) 

Adding '-fPIC' to CFLAGS since we don't (also) build a shared library.
Using additional host-specific CFLAGS: -march=native

Settings from SAGE_LOCAL/include/gmp.h:
  CC=gcc -std=gnu99
  CFLAGS=-m64 -O2 -march=k8 -mtune=k8  -g 
Finally using:
  CC=gcc
  CFLAGS=-march=native -g -O3  -fPIC
  CPP=
  CPPFLAGS=
  LDFLAGS=
  ABI=
  M4=
(These settings may still get overridden by 'configure' or Makefiles.)

Now configuring GMP-ECM with the following options:
  --prefix="/opt/Sage/sage-6.1.1/local"
  --libdir="/opt/Sage/sage-6.1.1/local/lib"
  --with-gmp="/opt/Sage/sage-6.1.1/local"
You can set ECM_CONFIGURE to pass additional parameters,
e.g. "--enable-shared" to also build a *shared* library,
or "--disable-sse2" if you encounter problems on a Pentium III system.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for a sed that does not truncate output... /bin/sed
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking dependency style of gcc... (cached) gcc3
checking dependency style of gcc... gcc3
checking whether gcc and cc understand -c and -o together... yes
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... ld
checking if the linker (ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 3458764513820540925
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-li
nux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format.
.. func_convert_file_noop
checking for ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
che

[sage-devel] Re: Saving .show() Output as a Vector Graphic

[Evan Oman]

Interesting, it must have something to do with my sage install on Ubuntu then? 
Are the packages loaded to the cloud version the same as the standard local 
install?

I used the Ubuntu PPA to install and the only additional package I installed 
was Pandas. 

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Re: [sage-devel] Re: Sage accepted for GSoC 2014

[kcrisman]

>
>
>
> [2] http://legacy.earlham.edu/~peters/knotlink.htm#software 
>
>
*"June 2, 2004*. Unfortunately I no longer have time to update *Knots on 
the Web*. I know it conntains many dead links and omits many good, new 
sites. "

And my understanding is that the Knot 
Atlas http://katlas.math.toronto.edu/wiki/Main_Page and the Mathematica 
package creating it is the state of the art.  Does SnapPy now really have 
all that combinatorial stuff?  I think that at the very least a good 
wrapper allowing for use of *any* robust backend for knots would be a great 
contribution to Sage.  mmarco seems to have a good sense of what would 
actually be needed to do this.  It's definitely a significant hole in Sage. 
- one might even wonder whether the authors of the Mma package would be 
willing to license their package in such a way that the algorithms for 
computing various invariants etc. could be used/{P,C}ythonized in Sage, if 
some people know them http://katlas.math.toronto.edu/wiki/Acknowledgement

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[sage-devel] Re: drop future first-class SPARC support?

[Jean-Pierre Flori]

Dear all,

On Saturday, February 22, 2014 10:00:30 AM UTC+1, Ralf Stephan wrote:
>
> Ticket #14780 (allow embedding Python tuples in symbolic expressions) 
> cannot be resolved because it's buggy on SPARC only and, frankly, I 
> wouldn't touch that iron with a long stick. It blocks #14801 (piecewise 
> functions) and with it  #11225 , 
> #1773 , 
> #8994, 
> and #8603 , as well as #14802 
> (dynamic attributes of SE). These in turn are needed for #2516 (generalized 
> hypergeometric 
> functions)
>  
> and finally #14896 (symbolic confluent hypergeometric functions). Probably 
> more.
>
> Quite a lot of optional packages don't compile on SPARC, too, so I'm 
> asking myself if this is really needed. 
>

> If you (yes you!) really need SPARC support, are you willing to fix 
> #14780? Then please post here---I'm sure Volker can give details about 
> #14780.
>
> I am willing to fix this, whether we drop *first-class* support or not.
I don't really care about *first-class* support on sparc, I just compile 
Sage on such hardware from time to time *for fun* and because it can expose 
ugly bugs which wouldn't happen as frequently on different hardware.

But first I'd like to get confirmation that the problem mentioned on #14780 
is actually occurring on a sparc machine.
>From what I've read there it's happening on an x86_64 machine and I have 
tested  it without problem on a sparc/solaris machine (could test 
sparc/debian as well)...

It would also be great to fix the NaN's in matplotlib (that requires some 
work for sure, and none of us has illimited time to devote to such things, 
but I think contributing back to software Sage use is a very good idea), or 
fix the way they get handled afterward, but I don't think I have the 
capabilities to take care of that.

Best,
JP

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[sage-devel] Re: Problem installing sagecell

[Jason Grout]

On 2/25/14 5:46 AM, Jesus Escribano wrote:

make: *** No hay ninguna regla para construir el objetivo 
`/home/sagecell/sage/local/lib/python/site-packages/sagenb-0.10.4-py2.7.egg/sagenb/data/sage/js/canvas3d_lib.js',
 necesario para `static/all.js'.  Alto.


It's looking for the file it mentions.  Is that file where it is looking?

I think those instructions are slightly out of date now, but they're 
probably basically correct still.


Thanks,

Jason


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[sage-devel] Problem installing sagecell

[Jesus Escribano]

Hello
I am installing a sagecell server following the instructions at
http://ufrmeca.univ-lyon1.fr/~buffat/sagecell.html
I have a problem in step 

8. Install SageCell
# sagecell
./sage -i 
http://sage.math.washington.edu/home/jason/sagecell-spkg/sagecell-2013-08-13.spkg

My data: Linux 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64

The error:

Running make in sagecell
if git submodule status | grep -q ^[+-]; then git submodule update --init > 
/dev/null; fi
gcc -o submodules/jsmin-bin submodules/jsmin/jsmin.c
cat /home/sagecell/sage/ipython/IPython/html/static//base/js/events.js 
/home/sagecell/sage/ipython/IPython/html/static//base/js/utils.js 
/home/sagecell/sage/ipython/IPython/html/static//services/kernels/js/kernel.js 
static/jquery-ui/js/jquery-ui-1.10.2.custom.min.js 
submodules/jquery-ui-touch-punch/jquery.ui.touch-punch.min.js \
static/colorpicker/js/colorpicker.js > static/wrap.js
python ./fix-js.py static/wrap.js
make: *** No hay ninguna regla para construir el objetivo 
`/home/sagecell/sage/local/lib/python/site-packages/sagenb-0.10.4-py2.7.egg/sagenb/data/sage/js/canvas3d_lib.js',
 necesario para `static/all.js'.  Alto.
Error minifying javascript and CSS.

real0m13.659s
user0m3.204s
sys 0m1.824s

Error installing package sagecell-2013-08-13


Any idea? 
Thank you very much.

Jesus Escribano
Universidad Complutense de Madrid.

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[sage-devel] GSOC 2014 iOS App

[Aditya Makkar]

Hi,
I am Aditya and I am interested in getting involved in Google Summer of 
Code with Sage. I am just finishing my second year at Indian Institute of 
Technology, Delhi doing B.Tech in Mechanical Engineering. I have good 
knowledge of C++, Python and Objective-C. I have some experience in iOS app 
development, mainly through the course "CS 193P iPhone Application 
Development", which I am currently doing. I have the Sage app on iPad and I 
have downloaded the code from 
here(Bitbucket)
.
So I would really love if I could be a contributor to Sage and work on this 
project in my summers.

Thank You
Aditya Makkar

PS: I am sorry if this not the right place to post this, since I could not 
post it in sage-gsoc google group.

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[sage-devel] Re: Sage accepted for GSoC 2014

[mmarco]

I would be happy to mentor a student in a knot theory related project in 
sage. I had mainly two ideas:

First idea is to write a class for knots/links. This class should be able 
to translate between the different possible representations of links (Gauss 
codes, 3d curves, braid closure...) and compute some of their invariants 
(the usual polynomials, Seifert forms, fundamental groups...). It should 
also produce pictures of knot diagrams and 3d representations of the 
knot/link. Some (or most) of this features can be either written from 
scratch, or just wrap external code (like the mentioned SnapPy).

Another idea, closely related to the previous one, is to write a javascript 
editor for knots and links, following what knotplot [1] does. This can be 
part of the same project or a separated one, if someone else writes the 
backend (although i think that it should be possible to write the editor 
and a simple backend in a single gsoc project, but that can be discussed). 
An important part of this editor would be the algorithm for dynamically 
relaxing the link. In particular, such an algorithm is explained in chapter 
7 of Scharein's thesis [1].

[1] http://www.knotplot.com/thesis/thesis.html

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Re: [sage-devel] Re: Sage accepted for GSoC 2014

[Amit Jamadagni]

Hello Volker,
   Thanks for the reply. As I have posted in the recent
threads, I would like to discuss this project and have created a thread for
the same on the sage-gsoc group. I hope you've had a look at it (
https://groups.google.com/forum/#!topic/sage-gsoc/tb2O7zEoUx0) , it would
be really great if you could comment on it as it would provide me with an
idea of the implementation that can be done. Thanks.


On Tue, Feb 25, 2014 at 4:06 PM, Volker Braun  wrote:

> We certainly could to use some of the SnapPy parts, like look at the
> Tcl/Tk link editor. But thats not going to integrate into the notebook.
> Also, link plots could look imho better. Apart from the GUI side, we need
> something that we can interface with more research-y codes written in GAP
> or Singular which SnapPy can't do.
>
>
>
> On Tuesday, February 25, 2014 8:35:39 AM UTC+1, vdelecroix wrote:
>>
>> There are already plenty of math software for knot theory. One very
>> active is SnapPy [1]
>>
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Re: [sage-devel] Re: Sage accepted for GSoC 2014

[Volker Braun]

We certainly could to use some of the SnapPy parts, like look at the Tcl/Tk 
link editor. But thats not going to integrate into the notebook. Also, link 
plots could look imho better. Apart from the GUI side, we need something 
that we can interface with more research-y codes written in GAP or Singular 
which SnapPy can't do.

 

On Tuesday, February 25, 2014 8:35:39 AM UTC+1, vdelecroix wrote:
>
> There are already plenty of math software for knot theory. One very 
> active is SnapPy [1] 
>

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Re: [sage-devel] Re: Sage accepted for GSoC 2014

[Amit Jamadagni]

Hello Vincent,
   Thanks for the reply. I wanted to work on the implementation as
it was mentioned in the ideas page(
https://docs.google.com/document/d/15v7lXZR1U4H2pT21d2fyPduYGb74JAFjkXJ6CWYmYfw/pub).
 I have introduced myself and posted about the same on the sage-gsoc google
group. I wanted to know whether I need to forward the discussion to the
possible mentors mentioned on the ideas page or whether it was sufficient
just to post on that group. Coming back to the implementation I will look
through SnapPy and its integration with Sage and get back in touch with you
as soon as possible. Thanks for all the help and guidance.

Amit.


On Tue, Feb 25, 2014 at 1:05 PM, Vincent Delecroix <
20100.delecr...@gmail.com> wrote:

> Hello Amit,
>
> > I am a student and I would like to participate in SoC. I have
> > already posted about my interest on working about the implementation of
> > Knot Theory. Is it necessary that the message be forwarded to mentors or
> > any other mailing list other than this one ??  Thanks.
>
> There are already plenty of math software for knot theory. One very
> active is SnapPy [1] but you can find several lists of softwares on
> the web such as [2]. SnapPy is licensed GPLv2+ so it should be
> compatible with Sage. SnapPy is already packaged for Sage [3] but the
> integration could be smoother (in particular the package might be
> available from sagemath.org website).
> If you are interested in knot theory, one option is to contact authors
> of SnapPy (Marc Culler and Nathan Dunfield from Chicago) and see if
> they can mentor you for a Sage related project. You can mention my
> name to them and if needed I could also possibly do part of the
> mentoring.
> In any case do not start from scratch implementing knots in Sage. It
> would be a waste of time.
>
> All best,
> Vincent Delecroix (from France)
>
> [1] http://www.math.uic.edu/t3m/SnapPy/
> [2] http://legacy.earlham.edu/~peters/knotlink.htm#software
> [3] http://www.math.uic.edu/t3m/SnapPy/installing.html#sage
>
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