SIGs/SciTech/SAGE

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__TOC__
 
__TOC__
== Fedora and other community efforts ==
+
== People ==
  
 
People interested helping in packaging/reviewing:
 
People interested helping in packaging/reviewing:
Line 19: Line 19:
 
* ...add your name here...
 
* ...add your name here...
  
Cross-distribution efforts:
+
== sagemath-5.4 Fedora review request ==
 +
The "package SAGE itself" goal has been reached!
  
* Debian: [http://qa.debian.org/developer.php?login=tabbott@mit.edu Tim Abbott's list of SAGE-related Debian packages].  Some of these Debian packages may include some patches for the dependencies that may be required for SAGE that have not yet been pushed upstream  (older unmaintained wiki page  http://wiki.sagemath.org/devel/DebianSage)
+
https://bugzilla.redhat.com/show_bug.cgi?id=877651
* PcLinuxOS: http://www.mypclinuxos.com/forum/index.php?topic=1509.msg13532#msg13532
+
* Mandriva: http://svn.mandriva.com/cgi-bin/viewvc.cgi/packages/cooker/sagemath/
+
  
On fedora-devel KevinKofler points out that:
+
It is now possible to build sagemath in rawhide, with minor efforts in f18,
 +
and there is a private x86_64 f17 repository at:
  
<pre>
+
http://pcpa.fedorapeople.org/sagemath/f17/
One problem will be that they're bundling many third-party components which should
+
be packaged separately:</pre> http://sage.math.washington.edu/sage/doc/html/inst/intro.html
+
  
<pre>So the first step is to track down which of these dependencies are in Fedora
+
You need this in /etc/yum.repos.d
already, whether they need any patches to work with SAGE, whether they are
+
http://pcpa.fedorapeople.org/sagemath/sagemath-f17.repo
build-time (BuildRequires) dependencies, run-time (Requires) dependencies or
+
both, whether they're required or optional and package those which are not in
+
Fedora yet.
+
</pre>
+
  
He suggests the following order:
+
(Note that this backports a very large amount of rawhide packages and will not be maintained once f18 is released)
 
+
#package required build-time dependencies
+
#package required run-time dependencies
+
#package as many optional build-time dependencies as possible
+
#package SAGE itself
+
#package optional run-time dependencies (and decide on a case by case basis whether it makes sense to add them as actual Requires: dependencies to the package or not)
+
 
+
''Required'' components that SAGE ships with: http://sagemath.org/packages/standard/
+
 
+
''Optional'' components that SAGE ships with: http://sagemath.org/packages/optional/
+
 
+
(a manual list with descriptions which may vary somewhat with respect to the above is at http://sagemath.org/links-components.html) (See also: http://wiki.sagemath.org/days6/sprint/debian)
+
  
 
== Dependencies (for which there is a separate upstream) ==
 
== Dependencies (for which there is a separate upstream) ==
Line 60: Line 42:
 
{|
 
{|
 
!Fedora package||Upstream||Review request / status
 
!Fedora package||Upstream||Review request / status
 +
|-
 +
 +
|cliquer || [http://users.tkk.fi/pat/cliquer.html cliquer] || [https://bugzilla.redhat.com/show_bug.cgi?id=825494 #825494] Missing in f18
 
|-
 
|-
  
Line 72: Line 57:
  
 
|[http://admin.fedoraproject.org/pkgdb/acls/name/python-matplotlib python-matplotlib] || [http://sourceforge.net/projects/matplotlib matplotlib] || [https://bugzilla.redhat.com/show_bug.cgi?id=837156 #837156] Requires
 
|[http://admin.fedoraproject.org/pkgdb/acls/name/python-matplotlib python-matplotlib] || [http://sourceforge.net/projects/matplotlib matplotlib] || [https://bugzilla.redhat.com/show_bug.cgi?id=837156 #837156] Requires
 +
|-
 +
 +
|[http://admin.fedoraproject.org/pkgdb/acls/name/numpy numpy] || [http://numeric.scipy.org scipy] || [https://bugzilla.redhat.com/show_bug.cgi?id=868585 #868585] Requires
 
|-
 
|-
  
Line 142: Line 130:
  
 
== Packages for which SAGE is upstream ==
 
== Packages for which SAGE is upstream ==
Latest versions found in http://www.sagemath.org/packages/standard/
+
Latest versions found in http://www.sagemath.org/packages/standard/ that may be worth packaging as separate SRPMS or different subpackages:
* sage
+
{|
* sage_scripts
+
| sage || could be named python-sagemath for %{python_sitearch}/sage contents but may not be fully functional without a few "system overrides" in $SAGE_ROOT/site-packages
* rubiks
+
|-
* doc
+
 
* examples
+
| sage_scripts || the main sagemath package requiring all python modules
* extcode
+
|-
* elliptic_curves, conway_polynomials, graphs, polytopes_db (ZoDB databases used internally by SAGE)
+
 
* flintqs (upstream because original upstream deprecated it)
+
| rubiks || there are 3 solvers, but only 2 with functional upstream link, therefore should use sagemath spkg
Some of those may or may not be worth packaging as separate SRPMs.
+
|-
 +
 
 +
| doc || can be made optional in a sagemath-doc package for users that would prefer to access documentation from elsewhere or are good enough with the python docstrings
 +
|-
 +
 
 +
| extcode || interfaces to other systems or customizations, could/should be made an optional, but a very small package
 +
|-
 +
 
 +
| notebook || %{python_sitearch}/sagenb contents, needs some testing, but may be useful if one wants only the command line interface
 +
|-
 +
 
 +
| elliptic_curves, conway_polynomials, graphs, polytopes_db || ZoDB databases used internally by SAGE
 +
|-
 +
 
 +
| flintqs || upstream because original upstream deprecated it
 +
|-
 +
|}
 +
 
 +
==Cross-distribution efforts==
 +
* Debian: [http://qa.debian.org/developer.php?login=tabbott@mit.edu Tim Abbott's list of SAGE-related Debian packages].  Some of these Debian packages may include some patches for the dependencies that may be required for SAGE that have not yet been pushed upstream  (older unmaintained wiki page  http://wiki.sagemath.org/devel/DebianSage)
 +
* PcLinuxOS: http://www.mypclinuxos.com/forum/index.php?topic=1509.msg13532#msg13532
 +
* Mandriva: http://svn.mandriva.com/cgi-bin/viewvc.cgi/packages/cooker/sagemath/
 +
 
 +
==Historical discussion==
 +
On fedora-devel KevinKofler points out that:
 +
 
 +
<pre>
 +
One problem will be that they're bundling many third-party components which should
 +
be packaged separately:</pre> http://sage.math.washington.edu/sage/doc/html/inst/intro.html
 +
 
 +
<pre>So the first step is to track down which of these dependencies are in Fedora
 +
already, whether they need any patches to work with SAGE, whether they are
 +
build-time (BuildRequires) dependencies, run-time (Requires) dependencies or
 +
both, whether they're required or optional and package those which are not in
 +
Fedora yet.
 +
</pre>
 +
 
 +
He suggests the following order:
 +
 
 +
#package required build-time dependencies
 +
#package required run-time dependencies
 +
#package as many optional build-time dependencies as possible
 +
#package SAGE itself
 +
#package optional run-time dependencies (and decide on a case by case basis whether it makes sense to add them as actual Requires: dependencies to the package or not)
 +
 
 +
''Required'' components that SAGE ships with: http://sagemath.org/packages/standard/
 +
 
 +
''Optional'' components that SAGE ships with: http://sagemath.org/packages/optional/
 +
 
 +
(a manual list with descriptions which may vary somewhat with respect to the above is at http://sagemath.org/links-components.html) (See also: http://wiki.sagemath.org/days6/sprint/debian)
  
 
[[Category:SciTech_SIG|SAGE]]
 
[[Category:SciTech_SIG|SAGE]]

Revision as of 16:09, 29 November 2012

This is to help document the process to get SAGE (http://sagemath.org/), the open-source computer algebra/mathematics framework into Fedora.

Contents

People

People interested helping in packaging/reviewing:

sagemath-5.4 Fedora review request

The "package SAGE itself" goal has been reached!

https://bugzilla.redhat.com/show_bug.cgi?id=877651

It is now possible to build sagemath in rawhide, with minor efforts in f18, and there is a private x86_64 f17 repository at:

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

You need this in /etc/yum.repos.d

http://pcpa.fedorapeople.org/sagemath/sagemath-f17.repo

(Note that this backports a very large amount of rawhide packages and will not be maintained once f18 is released)

Dependencies (for which there is a separate upstream)

Missing required components

(If you are working on packaging a component or have filed a review request bug, please note it or link to something here.)

Fedora package Upstream Review request / status
cliquer cliquer #825494 Missing in f18

Packages that need changes to work with sagemath

Fedora package Upstream Request for Enhancement / status
python-matplotlib matplotlib #837156 Requires
numpy scipy #868585 Requires

Completed (reviewed and built) required components

Fedora package Upstream Review request / status Version in SAGE
cddlib Cddlib Review Request Completed, in Fedora 094f.p11
cliquer Cliquer Review Request Completed, in Fedora 1.2.p11
cudd CUDD Review Request Completed, in Fedora
eclib EClib Review Request Completed, in Fedora
givaro Givaro Review Request Completed, in Fedora
python-networkx NetworkX Review Request Complete, in Fedora 1.6
python-cvxopt CVXOPT Review Request Completed, in Fedora 1.1.5
flint Flint Review Request Completed, in Fedora flint-1.5.2.p2
libfpll FpLLL Review Request Completed, in Fedora 3.0.12.p2
genus2reduction Genus2reduction Review Request Completed, in Fedora genus2reduction-0.3.p8
gfan Gfan Review Request Completed, in Fedora 0.4plus.p3
ghmm GHMM Review Request Complete, in Fedora
gmp-ecm GMP-ECM Review Request completed, in Fedora 6.3.p8
iml IML Review Request Completed, in Fedora 1.0.1.p14
jmol Jmol Already in Fedora: 11.6-8.10506svn 12.3.27.p3
L-function L-function Review Request Completed, in Fedora 1.23.p10
linbox Linbox Review Request Completed, in Fedora
m4ri M4RI Review Request complete, in Fedora 20120613
mpfi MPFI Review Request Completed, in Fedora 1.5.1
palp PALP Review Request Completed, in Fedora 2.1.p0
pynac pynac Review Request Completed, Fedora 0.2.5
python-crypto PyCrypto Already packaged in Fedora (python-crypto) 2.1.0
python-polybori PolyBoRi Review Request Complete, in Fedora 0.8.2
python-ZODB3 python-ZODB3 Review Request Complete, in Fedora
surf Surf Review Request Completed, in Fedora 1.1.0
symmetrica Symmetrica Review Request Completed, in Fedora 2.0.p7
sympy Sympy Review Request Completed, in Fedora 0.7.1.p0
scipy Weave Already in scipy. 0.9.p1
sympow Sympow Review Request Complete, in Fedora 1.018.1.p11

Packages for which SAGE is upstream

Latest versions found in http://www.sagemath.org/packages/standard/ that may be worth packaging as separate SRPMS or different subpackages:

sage could be named python-sagemath for %{python_sitearch}/sage contents but may not be fully functional without a few "system overrides" in $SAGE_ROOT/site-packages
sage_scripts the main sagemath package requiring all python modules
rubiks there are 3 solvers, but only 2 with functional upstream link, therefore should use sagemath spkg
doc can be made optional in a sagemath-doc package for users that would prefer to access documentation from elsewhere or are good enough with the python docstrings
extcode interfaces to other systems or customizations, could/should be made an optional, but a very small package
notebook  %{python_sitearch}/sagenb contents, needs some testing, but may be useful if one wants only the command line interface
elliptic_curves, conway_polynomials, graphs, polytopes_db ZoDB databases used internally by SAGE
flintqs upstream because original upstream deprecated it

Cross-distribution efforts

Historical discussion

On fedora-devel KevinKofler points out that:

One problem will be that they're bundling many third-party components which should
be packaged separately:
http://sage.math.washington.edu/sage/doc/html/inst/intro.html
So the first step is to track down which of these dependencies are in Fedora
already, whether they need any patches to work with SAGE, whether they are
build-time (BuildRequires) dependencies, run-time (Requires) dependencies or
both, whether they're required or optional and package those which are not in
Fedora yet.

He suggests the following order:

  1. package required build-time dependencies
  2. package required run-time dependencies
  3. package as many optional build-time dependencies as possible
  4. package SAGE itself
  5. package optional run-time dependencies (and decide on a case by case basis whether it makes sense to add them as actual Requires: dependencies to the package or not)

Required components that SAGE ships with: http://sagemath.org/packages/standard/

Optional components that SAGE ships with: http://sagemath.org/packages/optional/

(a manual list with descriptions which may vary somewhat with respect to the above is at http://sagemath.org/links-components.html) (See also: http://wiki.sagemath.org/days6/sprint/debian)