SIGs/SciTech/SAGE: Difference between revisions

Revision as of 08:22, 19 February 2009

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

Fedora and other community efforts

People interested helping in packaging/reviewing:

Cross-distribution efforts:

Debian: 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/DebianSAGE)
PcLinuxOS: http://www.mypclinuxos.com/forum/index.php?topic=1509.msg13532#msg13532

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:

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)

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
[1]	EClib	Review Request
[2]	Flint	Review Request
	G95	Not needed, we can use gcc-gfortran instead. ^[1]
	GAP	This is large (they claim you need 500M of disk)
[3]	Genus2reduction	Review Request
[4]	Givaro	Review Request
	JsMath
[5]	Lcalc	Review Request
[6]	Linbox	Review Request
	NetworkX	Review Request
[7]	PolyBoRi	Review Request
[8]	python-ZConfig	Review Request
[9]	python-zc-lockfile	Review Request
[10]	python-zdaemon	Review Request
[11]	python-ZODB3	Review Request
[12]	python-zope-event	Review Request
[13]	python-zope-proxy	Review Request
[14]	python-zope-testing	Review Request
[15]	Qd	Review Request [may removed from SAGE soon]
	Singular	I'm also working on this (konradm) and some deps.
[16]	Sympow	Review Request
	ghmm, jinja, jmol, sphinx, pynac, pygments	[recently added to SAGE, need to check status]

Completed (reviewed and built) required components

Fedora package	Upstream	Review request / status
cddlib	Cddlib	Review Request Completed, in Fedora
cudd	CUDD	Review Request Completed, in Fedora
python-cvxopt	CVXOPT	Review Request Completed, in Fedora
libfpll	FpLLL	Review Request Completed, in Fedora
gfan	Gfan	Review Request Completed, in Fedora
gmp-ecm	GMP-ECM	Review Request completed, in Fedora
iml	IML	Review Request Completed, in Fedora
m4ri	M4RI	Review Request complete, in Fedora
mpfi	MPFI	Review Request Completed, in Fedora
palp	PALP	Review Request Completed, in Fedora
python-crypto	PyCrypto	Already packaged in Fedora (python-crypto)
python-transaction	python-transaction	Review Request Completed, in Fedora
python-zope-filesystem		Review Request Completed, in Fedora
python-zope-interface	python-zope-interface
symmetrica	Symmetrica	Review Request Completed, in Fedora
sympy	Sympy	Review Request Completed, in Fedora
scipy	Weave	Already in scipy.

Packages for which SAGE is upstream

Latest versions found in http://www.sagemath.org/packages/standard/

sage
sage_scripts
rubiks
doc
examples
extcode
elliptic_curves, conway_polynomials, graphs, polytopes_db (ZoDB databases used internally by SAGE)
flintqs (upstream because original upstream deprecated it)

References

↑ From upstream's readme.txt: "If you're using Fortran on a platform without g95 binaries included with Sage, e.g., Itanium, you must use a system-wide gfortran.". So they support gfortran and even system-wide installations of it.

[1] From upstream's readme.txt: "If you're using Fortran on a platform without g95 binaries included with Sage, e.g., Itanium, you must use a system-wide gfortran.". So they support gfortran and even system-wide installations of it.

[1]

@@ Line 64: / Line 64: @@
 |-
 |[http://admin.fedoraproject.org/pkgdb/packages/name/ ]||[http://www.math.u-bordeaux.fr/%7Eliu/G2R/ Genus2reduction]||[https://bugzilla.redhat.com/show_bug.cgi?id=475322 Review Request]
-|-
-|[http://admin.fedoraproject.org/pkgdb/packages/name/ ]||[http://www.math.tu-berlin.de/%7Ejensen/software/gfan/gfan.html Gfan]||[https://bugzilla.redhat.com/show_bug.cgi?id=475055 Review Request]
 |-
 |[http://admin.fedoraproject.org/pkgdb/packages/name/ ]||[http://ljk.imag.fr/CASYS/LOGICIELS/givaro/ Givaro]||[https://bugzilla.redhat.com/show_bug.cgi?id=475065 Review Request]
@@ Line 78: / Line 76: @@
 |-
 |[http://admin.fedoraproject.org/pkgdb/packages/name/ ]||[http://polybori.sourceforge.net/ PolyBoRi]||[https://bugzilla.redhat.com/show_bug.cgi?id=476346 Review Request]
-|-
-|[http://admin.fedoraproject.org/pkgdb/packages/name/ ]||[http://pypi.python.org/pypi/transaction python-transaction]||[https://bugzilla.redhat.com/show_bug.cgi?id=476599 Review Request]
 |-
 |[http://admin.fedoraproject.org/pkgdb/packages/name/ ]||[http://pypi.python.org/pypi/ZConfig/ python-ZConfig]||[https://bugzilla.redhat.com/show_bug.cgi?id=476528 Review Request]
@@ Line 109: / Line 105: @@
 !Fedora package||Upstream||Review request / status
 |-
-|[http://admin.fedoraproject.org/pkgdb/packages/name/cddlib cddlib]||[http://www.ifor.math.ethz.ch/%7Efukuda/cdd_home Cddlib]||[https://bugzilla.redhat.com/show_bug.cgi?id=464074 Review Request]
+|[http://admin.fedoraproject.org/pkgdb/packages/name/cddlib cddlib]||[http://www.ifor.math.ethz.ch/%7Efukuda/cdd_home Cddlib]||[https://bugzilla.redhat.com/show_bug.cgi?id=464074 Review Request Completed, in Fedora]
 |-
-|[http://admin.fedoraproject.org/pkgdb/packages/name/cudd cudd]||[http://vlsi.colorado.edu/~fabio/CUDD/ CUDD]||[https://bugzilla.redhat.com/show_bug.cgi?id=476329 Review Request]
+|[http://admin.fedoraproject.org/pkgdb/packages/name/cudd cudd]||[http://vlsi.colorado.edu/~fabio/CUDD/ CUDD]||[https://bugzilla.redhat.com/show_bug.cgi?id=476329 Review Request Completed, in Fedora]
 |-
-|[http://admin.fedoraproject.org/pkgdb/packages/name/python-cvxopt python-cvxopt]||[http://abel.ee.ucla.edu/cvxopt CVXOPT]||[https://bugzilla.redhat.com/show_bug.cgi?id=466717 Review Request]
+|[http://admin.fedoraproject.org/pkgdb/packages/name/python-cvxopt python-cvxopt]||[http://abel.ee.ucla.edu/cvxopt CVXOPT]||[https://bugzilla.redhat.com/show_bug.cgi?id=466717 Review Request Completed, in Fedora]
 |-
 |[http://admin.fedoraproject.org/pkgdb/packages/name/libfplll libfpll]||[http://perso.ens-lyon.fr/damien.stehle/english.html#software FpLLL]||[https://bugzilla.redhat.com/show_bug.cgi?id=466655 Review Request Completed, in Fedora]
+|-
+|[http://admin.fedoraproject.org/pkgdb/packages/name/gfan gfan]||[http://www.math.tu-berlin.de/%7Ejensen/software/gfan/gfan.html Gfan]||[https://bugzilla.redhat.com/show_bug.cgi?id=475055 Review Request Completed, in Fedora]
 |-
 |[http://admin.fedoraproject.org/pkgdb/packages/name/gmp-ecm gmp-ecm]||[http://gforge.inria.fr/projects/ecm/ GMP-ECM]||[https://bugzilla.redhat.com/show_bug.cgi?id=473330 Review Request completed, in Fedora]
@@ Line 128: / Line 126: @@
 |-
 |[http://admin.fedoraproject.org/pkgdb/packages/name/python-crypto python-crypto]||[http://www.dlitz.net/software/pycrypto/ PyCrypto] || Already packaged in Fedora (python-crypto)
+|-
+|[http://admin.fedoraproject.org/pkgdb/packages/name/python-transaction python-transaction]||[http://pypi.python.org/pypi/transaction python-transaction]||[https://bugzilla.redhat.com/show_bug.cgi?id=468222 Review Request Completed, in Fedora]
 |-
 |[http://admin.fedoraproject.org/pkgdb/packages/name/python-zope-filesystem python-zope-filesystem]||||[https://bugzilla.redhat.com/show_bug.cgi?id=476475 Review Request Completed, in Fedora]

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