sagemath x86_64 f17 repository

[Paulo César Pereira de Andrade]

  Rdieter suggested me to make an experimental repository for
early adopters, so, my first fedora repository has been created :-)

  To enable it, run something like:

#  su
# cd /etc/yum.repos.d
# wget http://fedorapeople.org/~pcpa/sagemath/sagemath-f17.repo

and then:

# yum install sagemath

  There is no guarantee that nothing will break in dependencies.
It should install cleanly in a fedora 17 using the kde "scientific"
iso image. You can look at the contents of the repository at:

http://fedorapeople.org/~pcpa/sagemath/f17/x86_64/

  Note that it will update pari, libmpc, maxima, givaro, numpy, etc
what may cause issues with updates of other packages later.

  Please report any issues. But remember this is the first
prototype/package for fedora.

  I will later make a repository for f18, that should have very
few dependencies as most are already in f18.

Thanks,
Paulo

PS: If you are on it, please also, if you have any comments
about my experimental/prototype packages at:
http://fedorapeople.org/~pcpa/coinor/
I would like any feedback

[Vedran Miletić]

2012/9/30 Paulo César Pereira de Andrade
<paulo.cesar.pereira.de.andrade(a)gmail.com&gt;:
>    Rdieter suggested me to make an experimental repository for
>  early adopters, so, my first fedora repository has been created :-)
>
>    To enable it, run something like:
>
>  #  su
>  # cd /etc/yum.repos.d
>  # wget http://fedorapeople.org/~pcpa/sagemath/sagemath-f17.repo
>
>  and then:
>
>  # yum install sagemath
>
>    There is no guarantee that nothing will break in dependencies.
>  It should install cleanly in a fedora 17 using the kde "scientific"
>  iso image. You can look at the contents of the repository at:
>
>  http://fedorapeople.org/~pcpa/sagemath/f17/x86_64/
>
>    Note that it will update pari, libmpc, maxima, givaro, numpy, etc
>  what may cause issues with updates of other packages later.
>
>    Please report any issues. But remember this is the first
>  prototype/package for fedora.
>  
I haven't tested it thoroughly, but it works. Running sage installed
via a package manager gives a good feeling indeed.

Thanks for your effort.

Regards,
Vedran Miletić

>    I will later make a repository for f18, that should have very
>  few dependencies as most are already in f18.
>
>  Thanks,
>  Paulo
>
>  PS: If you are on it, please also, if you have any comments
>  about my experimental/prototype packages at:
>  http://fedorapeople.org/~pcpa/coinor/
>  I would like any feedback

[José Abílio Matos]

On 10/04/2012 07:23 AM, Vedran Miletić wrote:
>  I haven't tested it thoroughly, but it works. Running sage
> installed
>  via a package manager gives a good feeling indeed.
>
>  Thanks for your effort.
>
>  Regards,
>  Vedran Miletić 
I agree, thanks for your persistence Paulo. :-)

-- 
José Matos

[Paulo César Pereira de Andrade]

2012/10/4 José Matos <jamatos(a)fc.up.pt&gt;:
>  On 10/04/2012 07:23 AM, Vedran Miletić wrote:
> > I haven't tested it thoroughly, but it works. Running sage installed
> > via a package manager gives a good feeling indeed.
> >
> > Thanks for your effort.
> >
> > Regards,
> > Vedran Miletić
>
>  I agree, thanks for your persistence Paulo. :-) 
  :-)

  I just updated the f17 repository to provide sagemath 5.4.beta1

  There is also an updated numpy package with the patches from
https://github.com/numpy/numpy/issues/291

  For rawhide there is not yet a proper repository, but besides
also providing a pre built numpy (that should not be required
soon, as the patches are in the main numpy branch), I also
added fplll patches, that I also posted at
http://trac.sagemath.org/sage_trac/ticket/12835

  One issue that was working flawlessly previously was
the jmol interface, that now is not fully functional, I got it
to work by using the JmolData.jar in the jmol tarball, but
that is cheating as it would use a prebuilt jar. I almost got
it to work by patching like this:

---%<---
diff -up sage-5.4.beta1/spkg/build/sage-5.4.beta1/sage/interfaces/jmoldata.py.orig
sage-5.4.beta1/spkg/build/sage-5.4.beta1/sage/interfaces/jmoldata.py
--- sage-5.4.beta1/spkg/build/sage-5.4.beta1/sage/interfaces/jmoldata.py.orig	2012-10-20
13:09:00.932379141 -0300
+++ sage-5.4.beta1/spkg/build/sage-5.4.beta1/sage/interfaces/jmoldata.py	2012-10-20
16:39:46.791863395 -0300
@@ -86,7 +86,7 @@ class JmolData(SageObject):
             sage_makedirs(jmolscratch)
         scratchout = os.path.join(jmolscratch,"jmolout.txt")
         jout=open(scratchout,'w')
-        testjavapath = os.path.join(SAGE_LOCAL, "share", "jmol",
"testjava.sh")
+        testjavapath = os.path.join(SAGE_LOCAL, "bin",
"testjava.sh")
         result = subprocess.call([testjavapath],stdout=jout)
         jout.close()
         if (result == 0):
@@ -185,7 +185,7 @@ class JmolData(SageObject):
             scratchout = os.path.join(jmolscratch,"jmolout.txt")
             jout=open(scratchout,'w')
             #now call the java application and write the file.
-            result =
subprocess.call(["java","-Xmx512m","-Djava.awt.headless=true","-jar",jmolpath,"-iox","-g",sizeStr,"-J",launchscript,"-j",imagescript],stdout=jout)
+            result =
subprocess.call(["java","-Xmx512m","-Djava.awt.headless=true","-classpath","/usr/share/java/Jmol.jar:/usr/share/java/vecmath.jar:/usr/share/java/apache-commons-cli.jar","org.openscience.jmol.app.JmolData","-iox","-g",sizeStr,"-J",launchscript,"-j",imagescript],stdout=jout)
             jout.close()
         else:
             errStr = "Java Virtual Machine not available.\n"
---%<---

but it was failing with a null pointer exception when loading
the interface to export a png image, and I could not get
enough backtrace information to try to figure out what jar
file was missing, and preventing it from generating a
"quick" thumbnail of the plot...
It would also require rebuilding jmol anyway, to either build
JmolData.java and add JmolData.class to Jmol.jar, or install
JmolUnsignedF.jar as JmolData.jar.
So, for now the jmol interface wil show a harmless error
message (due to not installing testjava.sh actually), and
have a button to start an interactive plot. The new "advanced
controls" work.

>  --
>  José Matos 
Paulo

[Paulo César Pereira de Andrade]

[...]

  I just updated the sagemath x86_64 f17 repository, now correcting
several issues, and adding a workaround to the previous issue of
the jmol interface not properly working.

  Sample jmol related screenshots from my f17 notebook:

http://pcpa.fedorapeople.org/f17-sagemath-notebook1.png
[after pressing the "evaluate" button, shows a preview]

http://pcpa.fedorapeople.org/f17-sagemath-notebook2.png
[after pressing the "Make Interactive" button;
 the plot becomes interactive :-)]

http://pcpa.fedorapeople.org/f17-sagemath-notebook3.png
[after pressing the "Toggle Advanced Controls" button;
 as far as I could test, everything is fully functional]

http://pcpa.fedorapeople.org/f17-sagemath-notebook4.png
[popup after pressing the "Help for Jmol 3-D Viewer" button]

  It does not properly work with konqueror, known to work is firefox
and chromium-browser, but now I changed it to force using
firefox, it sets "export SAGE_BROWSER=firefox" in /usr/bin/sage

  Another change was to add pt translation, but there are others:

$ ls /usr/share/sagemath/doc/output/html
de  en  fr  pt  ru  tr

and a screenshot :-)
http://pcpa.fedorapeople.org/f17-sagemath-notebook5.png

Paulo