SIGs/SciTech/SAGE: Difference between revisions

Revision as of 02:21, 15 November 2012

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/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/

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

Packages that need changes to work with sagemath

(these are required for the work in progress sagemath-5.3)

Fedora package	Upstream	Request for Enhancement / status
python-matplotlib	matplotlib	#837156 Requires
libmpc	mpc	#855599 Build 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/

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)

Some of those may or may not be worth packaging as separate SRPMs.

@@ Line 94: / Line 94: @@
 |[http://admin.fedoraproject.org/pkgdb/acls/name/givaro givaro ]||[http://ljk.imag.fr/CASYS/LOGICIELS/givaro/ Givaro]||[https://bugzilla.redhat.com/show_bug.cgi?id=475065 Review Request Completed, in Fedora]||
 |-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-networkx python-networkx]||[https://networkx.lanl.gov/wiki NetworkX] || [https://bugzilla.redhat.com/show_bug.cgi?id=476350 Review Request Complete, in Fedora]||1.2.p2
+|[http://admin.fedoraproject.org/pkgdb/acls/name/python-networkx python-networkx]||[https://networkx.lanl.gov/wiki NetworkX] || [https://bugzilla.redhat.com/show_bug.cgi?id=476350 Review Request Complete, in Fedora]||1.6
 |-
-|[http://admin.fedoraproject.org/pkgdb/acls/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]||1.1.4.p1
+|[http://admin.fedoraproject.org/pkgdb/acls/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]||1.1.5
 |-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/flint flint]||[http://www.flintlib.org/ Flint]||[https://bugzilla.redhat.com/show_bug.cgi?id=473744 Review Request Completed, in Fedora]||[http://www.sagemath.org/packages/standard/flint-1.5.2.p0.spkg flint-1.5.2.p0]
+|[http://admin.fedoraproject.org/pkgdb/acls/name/flint flint]||[http://www.flintlib.org/ Flint]||[https://bugzilla.redhat.com/show_bug.cgi?id=473744 Review Request Completed, in Fedora]||[http://www.sagemath.org/packages/standard/flint-1.5.2.p2.spkg flint-1.5.2.p2]
 |-
 |[http://admin.fedoraproject.org/pkgdb/acls/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]||3.0.12.p2
@@ Line 108: / Line 108: @@
 |[http://admin.fedoraproject.org/pkgdb/acls/name/ghmm ghmm]||[http://ghmm.sourceforge.net/ GHMM]||[https://bugzilla.redhat.com/show_bug.cgi?id=491490 Review Request Complete, in Fedora]||
 |-
-|[http://admin.fedoraproject.org/pkgdb/acls/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]||6.3.p7
+|[http://admin.fedoraproject.org/pkgdb/acls/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]||6.3.p8
 |-
 |[http://admin.fedoraproject.org/pkgdb/acls/name/iml iml]||[http://www.cs.uwaterloo.ca/%7Ez4chen/iml.html IML]||[https://bugzilla.redhat.com/show_bug.cgi?id=466692 Review Request Completed, in Fedora]||1.0.1.p14
 |-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-jinja jinja]||[http://jinja.pocoo.org/1/ Jinja]||Already in Fedora||1.2
+|[http://admin.fedoraproject.org/pkgdb/acls/name/jmol jmol]||[http://jmol.sourceforge.net/ Jmol]||Already in Fedora: 11.6-8.10506svn||12.3.27.p3
-|-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/jmol jmol]||[http://jmol.sourceforge.net/ Jmol]||Already in Fedora: 11.6-8.10506svn||12.2.21.p0
 |-
 |[http://admin.fedoraproject.org/pkgdb/acls/name/L-function L-function]||[http://pmmac03.math.uwaterloo.ca/%7Emrubinst/L_function_public/CODE/ L-function]||[https://bugzilla.redhat.com/show_bug.cgi?id=470702 Review Request Completed, in Fedora]||1.23.p10
@@ Line 120: / Line 118: @@
 |[http://admin.fedoraproject.org/pkgdb/acls/name/linbox linbox]||[http://www.linalg.org/ Linbox]||[https://bugzilla.redhat.com/show_bug.cgi?id=476299 Review Request Completed, in Fedora]||
 |-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/m4ri m4ri]||[http://m4ri.sagemath.org/ M4RI]||[https://bugzilla.redhat.com/show_bug.cgi?id=470173 Review Request complete, in Fedora]||20111004
+|[http://admin.fedoraproject.org/pkgdb/acls/name/m4ri m4ri]||[http://m4ri.sagemath.org/ M4RI]||[https://bugzilla.redhat.com/show_bug.cgi?id=470173 Review Request complete, in Fedora]||20120613
 |-
 |[http://admin.fedoraproject.org/pkgdb/acls/name/mpfi mpfi]||[http://perso.ens-lyon.fr/nathalie.revol/software.html MPFI]||[https://bugzilla.redhat.com/show_bug.cgi?id=466688 Review Request Completed, in Fedora]||1.5.1
 |-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/palp palp]||[http://hep.itp.tuwien.ac.at/%7Ekreuzer/CY/CYpalp.html PALP]||[https://bugzilla.redhat.com/show_bug.cgi?id=476351 Review Request Completed, in Fedora]||2.1.p1
+|[http://admin.fedoraproject.org/pkgdb/acls/name/palp palp]||[http://hep.itp.tuwien.ac.at/%7Ekreuzer/CY/CYpalp.html PALP]||[https://bugzilla.redhat.com/show_bug.cgi?id=476351 Review Request Completed, in Fedora]||2.1.p0
 |-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/pynac pynac]||[http://pynac.sagemath.org/ pynac]||[https://bugzilla.redhat.com/show_bug.cgi?id=529198 Review Request Completed, Fedora]||0.2.4
+|[http://admin.fedoraproject.org/pkgdb/acls/name/pynac pynac]||[http://pynac.sagemath.org/ pynac]||[https://bugzilla.redhat.com/show_bug.cgi?id=529198 Review Request Completed, Fedora]||0.2.5
 |-
 |[http://admin.fedoraproject.org/pkgdb/acls/name/python-crypto python-crypto]||[http://www.dlitz.net/software/pycrypto/ PyCrypto] || Already packaged in Fedora (python-crypto)||2.1.0
 |-
-|[http://admin.fedoraproject.org/pkgdb/acls/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/acls/name/python-polybori python-polybori]||[http://polybori.sourceforge.net/ PolyBoRi]||[https://bugzilla.redhat.com/show_bug.cgi?id=476346 Review Request Complete, in Fedora]||0.8.2
-|-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-polybori python-polybori]||[http://polybori.sourceforge.net/ PolyBoRi]||[https://bugzilla.redhat.com/show_bug.cgi?id=476346 Review Request Complete, in Fedora]||0.8.1.p10
-|-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-ZConfig python-ZConfig]||[http://pypi.python.org/pypi/ZConfig/ python-ZConfig]||[https://bugzilla.redhat.com/show_bug.cgi?id=476528 Review Request Completed, in Fedora 12]||
-|-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-zdaemon python-zdaemon]||[http://pypi.python.org/pypi/zdaemon/ python-zdaemon]||[https://bugzilla.redhat.com/show_bug.cgi?id=476527 Review Request Complete, in Fedora 12]||
 |-
 |[http://admin.fedoraproject.org/pkgdb/acls/name/python-ZODB3 python-ZODB3]||[http://www.zope.org/Wikis/ZODB/ python-ZODB3]||[https://bugzilla.redhat.com/show_bug.cgi?id=476600 Review Request Complete, in Fedora]||
-|-
-|[http://admin.fedoraproject.org/pkgdb/scls/name/python-zope-filesystem python-zope-filesystem]||||[https://bugzilla.redhat.com/show_bug.cgi?id=476475 Review Request Completed, in Fedora]||
-|-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-zope-interface python-zope-interface]||python-zope-interface||||
-|-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-zope-proxy python-zope-proxy]||[http://pypi.python.org/pypi/zope.proxy/ python-zope-proxy]||[https://bugzilla.redhat.com/show_bug.cgi?id=476523 Review Request Completed, in Fedora]||
-|-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-zope-testing python-zope-testing ]||[http://pypi.python.org/pypi/zope.testing/ python-zope-testing]||[https://bugzilla.redhat.com/show_bug.cgi?id=476524 Review Request Completed, in Fedora 12]||
 |-
 |[http://admin.fedoraproject.org/pkgdb/acls/name/surf-geometry surf]||[http://surf.sourceforge.net/ Surf]||[https://bugzilla.redhat.com/show_bug.cgi?id=840244 Review Request Completed, in Fedora]||1.1.0
@@ Line 157: / Line 141: @@
 |-
 |[http://admin.fedoraproject.org/pkgdb/acls/name/sympow sympow]||[http://www.maths.bris.ac.uk/%7Emamjw/ Sympow]||[https://bugzilla.redhat.com/show_bug.cgi?id=476406 Review Request Complete, in Fedora]||1.018.1.p11
-|-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-sphinx sphinx]||[http://sphinx.pocoo.org/ Sphinx]||[https://bugzilla.redhat.com/show_bug.cgi?id=439337 Review Request Complete, in Fedora]||
-|-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-pygments pygments]||[http://pygments.org/ Pygments]||[https://bugzilla.redhat.com/show_bug.cgi?id=246312 Review Request Complete, in Fedora]||
-|-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-zc-lockfile python-zc-lockfile]||[http://pypi.python.org/pypi/zc.lockfile/ zc-lockfile]||[https://bugzilla.redhat.com/show_bug.cgi?id=476525 Review Request Complete, in Fedora]||
-|-
-|[http://admin.fedoraproject.org/pkgdb/acls/name/python-zope-event python-zope-event]||[http://pypi.python.org/pypi/zope.event/ python-zope-event]||[https://bugzilla.redhat.com/show_bug.cgi?id=476526 Review Request Complete, in Fedora]||
 |}

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