11535
Comment: mention user installed python library

← Revision 168 as of 20150306 07:23:29 ⇥
11535
Update info foor Singular 4

Deletions are marked like this.  Additions are marked like this. 
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 [[http://anonscm.debian.org/gitweb/?p=debianscience/packages/singular.git;a=summarysingular]]  [[https://packages.qa.debian.org/s/singular.htmlPTS]]   singular 3.1.6 is packaged in debianscience's git and Sage >= 6.2 has also 3.1.6; an ITP has been filled to package singular 4.0.1, see DebianBug:764475.    [[http://anonscm.debian.org/gitweb/?p=debianscience/packages/singular.git;a=summarysingular]]  [[https://packages.qa.debian.org/s/singular.htmlPTS]]   singular 3.1.6 is packaged in debianscience's git and Sage >= 6.2 has also 3.1.6; a package for singular 4.0.1 is in the NEW queue, see DebianBug:764475.  
Some people within DebianScience would like to package again Sage for Debian. An old version of Sage got packaged long time ago by Tim Abbott, but, because of lack of maintainance, it became totally unusable and was removed from Debian. The status pages (master branch, develop branch) give an overview about package versions in Sage and Debian. If you want to help out, pick one of the open tasks or issues below and get going. Or contact us via the mailing list or in #debianscience on irc.oftc.net.
Steps to get an uptodate Sage standard suite in Debian
Building Sage with Debian packages
We have a git repository (sagemath, also see README) to document the steps we currently do to experiment with building Sage against Debian packages. Important elements are the build dependencies of Sage, patches for Sage and a script called "pruner" that uses automake to determine if the necessary packages are installed (see also this mail).
It is recommended to do these steps one by one:
git clone recursive url/to/sagemath.git 
Recursive git clone to also get sage which is included as a git submodule. 
sudo mkbuilddeps install debian/control 
Install build dependencies that are in unstable (requires Debian unstable). 
quilt push a 
Apply patches to Sage. 
debian/rules prune 
Run the pruner script. 
debian/rules build 
Build sage and run the test suite (includes pruning if necessary, but not patching). 
The output of the pruner tells you in the end which dependencies were not found on the machine. These will be downloaded and built in the build step, before Sage itself is built. In the moment the pruner should output something like the following, and it is for now recommended to use these four packages from Sage.
libgap will not come from debian! cddlib will not come from debian! singular will not come from debian! jmol will not come from debian! 95 system packages will be used
The following commands clean everything up properly.
debian/rules clean 
Clean up after prune and build. 
quilt pop a 
Unapply patches. 
cd sage && git clean dfx 
Clean sage folder (git does not show untracked files from the built due to .gitignore). 
rm rf ~/.local/lib/python2.7/sitepackages/sage* 
Remove sage python library that is installed during the build process. 
Finally, there are still dependencies that cannot yet be satisfied with packages from unstable. This changes frequently. For now (the sagemath git repository currently uses sage 6.5) the following packages should be installed from git:
singular (use the tag debian/316+dfsg1, Sage will use its own singular but this is needed anyway)
Some Debian packages have to be rebuilt to include patches:
With these changes the compilation of Sage 6.5 should finish and one can concentrate on fixing failing doctests.
For compiling Sage 6.6 one should also update the gap and cython packages to newer versions.
New build system for Sage (the distribution)
this is slightly out of date, also, Sage (the community) is not interested in using packages that another distribution provides.
The Sage library is getting an autotools build system in the course of a Google Summer of Code project. With the new build system, it can be built against system libraries. There are tarballs with the code at http://tool.em.cs.unifrankfurt.de/~felix/sage/. (There is also a git repository but the tarballs are recommended). Note that this is work in progress and problems are expected, but we are happy about testers. The transition of this work into Sage is coordinated via a bunch of Sage tickets. We have a Debian package sagelib that currently builds metapackages that help installing the build dependencies of Sage. To test building Sage against Debian packages, one should consult the control file. The dependencies of the metapackage sagelibbuilddepsgit still need special treatment and can't be just installed from Debian.
The following Debian packages should be installed from the git repositories:
For the remaining packages where the Debian package is missing or is missing features required by Sage, it is currently most convenient to use the versions from Sage. This is done by configuring with
../configure \ disableall \ enable{boehm_gc,cython,ecl,flintqs,genus2reduction,maxima,pari,pexpect,pynac,rubiks,sagelib,sagetex,tachyon} \ withgmp
New build system for Sage (the library)
There is some work in progress trying to make sagelib work on top of any software distribution. we use autotools to sort out dependencies, run time paths and provide standard build/installation routines. unlike the first approach, this is heading towards a fork and will likely not play well with the current upstream development process. Experimental tarballs are available at http://tool.em.cs.unifrankfurt.de/~felix/sagelib/, there is no public git repo yet.
Open tasks
Package 
Bug / Link 
Assigned 
Comments 
Packages that need a new maintainer and an upload to Debian: 

jmol 


There is a request for help, see 719330 
pexpect 2.0 


(Debian pkg: pythonpexpect): Debian ships version 2.4, but Sage requires version 2.0 (though one of the necessary patches is already in 2.4). Plotting in the notebook is likely to break with newer versions that are in Debian; and >2.0 is reported to be slow. There is a new upstream version so Sage might update, see this sage bug. 

singular 3.1.6 is packaged in debianscience's git and Sage >= 6.2 has also 3.1.6; a package for singular 4.0.1 is in the NEW queue, see 764475. 

Sage components that need a new maintainer and an upload to Debian: 



the dependencies should be in Debian now (691509, 703541, 703531, 703533, 703534, 703535 and 703536) 

sagetex 



Softwares that need to be packaged: 

4ti2 


Singular 4 depends on 4ti2; a package is in the NEW queue, see 769997 
normaliz 


Singular 4 depends on normaliz; an ITP has been filled to package normaliz 2.12.2, see 776019 
surfalggeo 


Singular 4 depends on surf; an ITP has been filled to package surfalggeo 1.0.6, see 777132 
Packages that are (hopefully) not needed: 

cephes 


The Cephes Mathematical Library is only needed for systems where the libc doesn't provide appropriate mathematical functions (cygwin and FreeBSD) and so is not required for Debian. 
iconv 


is part of the libc 
libgap 


Will most likely be replaced by a wrapper for GAP. 

mpir is supposed to be ABIcompatible with gmp. A lot of math packages use gmp and we hope we can have a purely gmp based Sage in Debian. Combining the two will most likely lead to conflicts, using mpir we would need an extra mpir version of many packages. 
Other known or suspected issues
ECL has a strange bug in debian (see 777473).
 sage expects to use both ecl and maxima, together, but maxima in debian is using gcl and has no support for ecl ; Snark has fixes for that, but some things (like the above ECL problem) need to clear out before they can be pushed in debian.
pari in sage's latest has a patch and uses a header file which aren't in the debian package, so one currently needs to modify a few things by hand to get going (see 777237)
cddlib in sage is a fork so the current debian package won't replace it even if the versions match (see this sage bug)
Information bits that are no issues
Sage upstream would like to get rid of flintqs since some recent versions of flint ship with a quadratic sieve (see this ticket, but it hasn't been done yet). This mail of William Hart tells more about the state of the quadratic sieve code in both flint and flint2. flintqs was uploaded to Debian for the meantime (but blocked in unstable).
Old sagemath package
The old, buggy sagemath Debian package source code is available at http://snapshot.debian.org/package/sagemath/3.0.5dfsg5.1/