Difference between revisions of "SIGs/SciTech/SAGE"

Revision as of 17:55, 15 February 2017

This is to help document the process to get SageMath (also colloquially called Sage; SAGE is a retired name) (http://www.sagemath.org/), the open-source computer algebra/mathematics framework into Fedora.

People

People interested helping in packaging/reviewing:

Sagemath Fedora package

The package "sagemath" is now available for Fedora 18 or newer.

Name	Upstream	Review Request	Status
`sagemath`	sagemath	#877651	pass

Dependencies (for which there is a separate upstream)

SageMath calls the packages they integrate an "spkg" (Sage package). Since the goal of the project is to integrate as many third-party products as possible, dependencies aren't always updated along with 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.)

Name	Upstream	Review Request
lrcalc	lrcalc	#909510 Build Requires
coin-or-CoinUtils	CoinUtils	#894585 Build Requires
coin-or-Osi	Osi	#894586 Build Requires
coin-or-Clp	Clp	#894587 Build Requires
coin-or-Cgl	Cgl	#894588 Build Requires
coin-or-Cbc	Cbc	#894597 Build Requires
fes	fes	#914936 (Optional) Build Requires

Packages that need changes to work with sagemath

Fedora package	Upstream	Request for Enhancement / status

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 https://git.sagemath.org/sage.git/tree/build/pkgs 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	spkg because original upstream deprecated it

Cross-distribution efforts

Debian: Tim Abbott's list of SAGE-related Debian packages. Abbot told User:Mrennekamp that he stopped working on Debian in 2010. However, it seems that a person within the SageMath project is working on providing SageMath in its own live distro: https://wiki.sagemath.org/SageDebianLive.
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:

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)

A wiki for included SageMath packages is at https://wiki.sagemath.org/spkg. (See also: http://wiki.sagemath.org/days6/sprint/debian)

@@ Line 1: / Line 1: @@
-This is to help document the process to get SAGE (http://sagemath.org/), the open-source computer algebra/mathematics framework into Fedora.
+This is to help document the process to get SageMath (also colloquially called Sage; SAGE is a retired name) (http://www.sagemath.org/), the open-source computer algebra/mathematics framework into Fedora.
 __TOC__
@@ Line 17: / Line 17: @@
 * [[User:fpmurphy|Finnbarr P. Murphy]]
 * [[User:pcpa|Paulo Andrade]]
+* [[User:Cicku|Christopher Meng]]
+* [[User:lupinix|Christian Dersch]]
+* [[User:Mrennekamp|Matthew Rennekamp]]
 * ...add your name here...
-== sagemath-5.5 Fedora review request ==
+== Sagemath Fedora package ==
-The "package SAGE itself" goal has been reached!
+'''The package "{{package|sagemath}}" is now available for Fedora 18 or newer.
+'''
+{|border="2" cellpadding="2" cellspacing="0"
+!Name||Upstream||Review Request || Status
+|-
+| {{package|sagemath}} || [http://sagemath.org sagemath] || [https://bugzilla.redhat.com/show_bug.cgi?id=877651 #877651] || {{result|pass}}
+|-
+|}
-https://bugzilla.redhat.com/show_bug.cgi?id=877651
+== Dependencies (for which there is a separate upstream) ==
+SageMath calls the packages they integrate an "spkg" (Sage package). Since the goal of the project is to integrate as many third-party products as possible, dependencies aren't always updated along with upstream.
+===Missing required components===
-It is now possible to build sagemath in rawhide and in f18,
+(If you are working on packaging a component or have filed a review request bug, please note it or link to something here.)
-and there is a private x86_64 f18 repository at:
- http://pcpa.fedorapeople.org/sagemath/f18/
+{|border="2" cellpadding="2" cellspacing="0"
+!Name||Upstream||Review Request || Status
+|-
-You need this in /etc/yum.repos.d
+<!-- |cliquer || [http://users.tkk.fi/pat/cliquer.html cliquer] || [https://bugzilla.redhat.com/show_bug.cgi?id=825494 #825494] Missing in f18 -->
- http://pcpa.fedorapeople.org/sagemath/sagemath-f18.repo
+|-
-----
+|lrcalc || [http://math.rutgers.edu/~asbuch/lrcalc lrcalc] || [https://bugzilla.redhat.com/show_bug.cgi?id=909510 #909510] Build Requires
-If you were using the previous f17 private repository, a suggested
+|-
-update method to f18 is:
-  $ sudo yum erase sagemath
+|coin-or-CoinUtils || [http://projects.coin-or.org/CoinUtils CoinUtils] || [https://bugzilla.redhat.com/show_bug.cgi?id=894585 #894585] Build Requires
-  $ sudo yum update yum
+|-
-  $ sudo yum clean all
-  $ sudo yum --releasever=18 --disableplugin=presto distro-sync
-  $ sudo rpm --rebuilddb
-(you may need to erase other packages thay may cause conflicts,
+|coin-or-Osi || [http://projects.coin-or.org/Osi Osi] || [https://bugzilla.redhat.com/show_bug.cgi?id=894586 #894586] Build Requires
-usually packages from rpmfusion or elsewhere, possibly f15
+|-
-packages, but that is out of scope of this cheat sheet)
-After that, remove the sagemath-f17.repo from /etc/yum.repos.d and add
+|coin-or-Clp || [http://projects.coin-or.org/Clp Clp] || [https://bugzilla.redhat.com/show_bug.cgi?id=894587 #894587] Build Requires
-the new sagemath-f18.repo there.
+|-
-== 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.)
+|coin-or-Cgl || [http://projects.coin-or.org/Cgl Cgl] || [https://bugzilla.redhat.com/show_bug.cgi?id=894588 #894588] Build Requires
-{|
-!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 -->
+|coin-or-Cbc || [http://projects.coin-or.org/Cbc Cbc] || [https://bugzilla.redhat.com/show_bug.cgi?id=894597 #894597] Build Requires
 |-
-<!-- |python-flask-autoindex || [http://github.com/sublee/flask-autoindex/ Flask-AutoIndex] || [https://bugzilla.redhat.com/show_bug.cgi?id=839097 #839097] Requires -->
+|fes || [http://www.lifl.fr/~bouillag/download fes] || [https://bugzilla.redhat.com/show_bug.cgi?id=914936 #914936] (Optional) Build Requires
 |-
 |}
@@ Line 72: / Line 73: @@
 <!-- |[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=896311 #896311] Requires
 |-
@@ Line 81: / Line 79: @@
 ===Completed (reviewed and built) required components===
-{|
+{|border="2" cellpadding="2" cellspacing="0"
 |-
 !Fedora package||Upstream||Review request / status||Version in SAGE
@@ Line 145: / Line 143: @@
 == 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:
+Latest versions found in https://git.sagemath.org/sage.git/tree/build/pkgs that may be worth packaging as separate SRPMS or different subpackages:
-{|
+{|border="2" cellpadding="2" cellspacing="0"
 | 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
 |-
@@ Line 168: / Line 166: @@
 |-
-| flintqs || upstream because original upstream deprecated it
+| flintqs || spkg 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)
+* Debian: [http://qa.debian.org/developer.php?login=tabbott@mit.edu Tim Abbott's list of SAGE-related Debian packages]. Abbot told [[User:Mrennekamp]] that he stopped working on Debian in 2010. However, it seems that a person within the SageMath project is working on providing SageMath in its own live distro: https://wiki.sagemath.org/SageDebianLive.
 * PcLinuxOS: http://www.mypclinuxos.com/forum/index.php?topic=1509.msg13532#msg13532
 * Mandriva: http://svn.mandriva.com/cgi-bin/viewvc.cgi/packages/cooker/sagemath/
@@ Line 183: / Line 181: @@
 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
@@ Line 199: / Line 196: @@
 #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/
+A wiki for included SageMath packages is at https://wiki.sagemath.org/spkg.
+(See also: http://wiki.sagemath.org/days6/sprint/debian)
-''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]]

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