Differences between revisions 18 and 44 (spanning 26 versions)
⇤ ← Revision 18 as of 2015-09-10 05:28:03 →
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Editor: jdemeyer
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← Revision 44 as of 2018-07-25 20:04:17 → ⇥
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Editor: chapoton
Comment:
Deletions are marked like this. Additions are marked like this.
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that). that). See [[http://files.sagemath.org/spkg/index.html]] for the packages.
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 * nzmath  * nzmath (pip installable)
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 * pyx (pip installable)
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 * dvipng
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 * meataxe
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 * polymake
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   * openmpi
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   * dvipng
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   * PyVTK
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 * coxeter3 [[http://trac.sagemath.org/ticket/19178|#19178]]  * chomp [[http://trac.sagemath.org/ticket/15202|#15202]]
 * fes [[http://trac.sagemath.org/ticket/15209|#15209]]

Packages that have a Sage interface, so these are likely of interest:
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 * database_jones_numfield [[http://trac.sagemath.org/ticket/19174|#19174]]
 * database_mutation_class (new name of cluster_seed) [[http://trac.sagemath.org/ticket/19177|#19177]]
 * fes [[http://trac.sagemath.org/ticket/15209|#15209]]
 * lie [[http://trac.sagemath.org/ticket/19176|#19176]]
 * ore_algebra [[http://trac.sagemath.org/ticket/19175|#19175]]
 * p_group_cohomology (see discussion at [[http://trac.sagemath.org/ticket/18514|#18514]])
 * patchbot [[http://trac.sagemath.org/ticket/18937|#18937]]

Packages that have a Sage interface, so these are likely of interest:

 * chomp # a possible issue is that chomp was completely rewritten since then, hence it is likely that our old interface will not work with the newer versions of chomp
 * database_kohel # partially superseded by PARI: precisely those parts that are interfaced by Sage can now be computed by PARI
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Here is the list of old-style packages which are documented
somewhere in Sage as being Sage packages
(this is orthogonal to there being a proper Sage interface).
If we stop supporting these packages,
we should adjust the documentation.		 Here is the list of old-style packages which appear in the [[http://doc.sagemath.org/html/en/thematic_tutorials/numerical_sage/index.html|Numerical Computing tutorial]], see also [[http://trac.sagemath.org/ticket/19198|#19198]]:
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 * mpi4py (pip installable)  * openmpi
 * python-2.5.1-framework [[http://trac.sagemath.org/ticket/3924|#3924]]
 * PyVTK
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 * surf # package for Singular


=== Packages that are easily pip installable (hence can be removed) ===

Here are the old-style optional/experimental packages that do not need to be
repackaged since they are easily installable via `sage -pip install` command.


 * beautifulsoup
 * biopython
 * brian
 * guppy
 * mpi4py
 * pybtex
 * pyx
 * sip
 * pynifti (superseeded by NiBabel pip-installable package)
 * trac


=== Superseeded packages ===

Here are mathematical packages for which we found another way, hence can be removed.

 * gnuplotpy # we have our own interface
 * qhull # we already have two copies coming from the standard packages matplotlib and scipy
 * numarray # numpy
 * numeric # numpy
 * pygsl # we have our own interface
 * lrs # there is now lrslib
  * VTK (archived package!)

=== Superseded packages ===

Here are packages for which we found another way, hence can be removed.

 * gd # renamed to libgd
 * gdmodule # no longer needed
 * genus2reduction # superseded by PARI
 * gnuplotpy # we have our own interface
 * numarray # numpy
 * numeric # numpy
 * pil # replaced by pillow
 * pygsl # we have our own interface
 * lrs # there is now lrslib

=== Superseded packages with no replacement yet ===

This is installable via `pip`, but it is also outdated:

 * pynifti (superseded by NiBabel pip-installable package)
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 * beautifulsoup [[http://trac.sagemath.org/ticket/19187|#19187]]
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 * biopython [[http://trac.sagemath.org/ticket/19187|#19187]]
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 * brian [[http://trac.sagemath.org/ticket/19187|#19187]]
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 * coxeter3 [[http://trac.sagemath.org/ticket/19178|#19178]]
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 * database_jones_numfield [[http://trac.sagemath.org/ticket/19174|#19174]]
 * database_kohel
 * database_mutation_class (new name of cluster_seed) [[http://trac.sagemath.org/ticket/19177|#19177]]
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 * guppy [[http://trac.sagemath.org/ticket/19187|#19187]]
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 * lie [[http://trac.sagemath.org/ticket/19176|#19176]]
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 * meataxe [[http://trac.sagemath.org/ticket/12103| #12103]]
 * mercurial [[http://trac.sagemath.org/ticket/19187|#19187]]
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 * mpi4py [[http://trac.sagemath.org/ticket/19187|#19187]]
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 * ore_algebra (see [[http://trac.sagemath.org/ticket/19175|#19175]])
 * p_group_cohomology (see [[http://trac.sagemath.org/ticket/18514|#18514]])
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 * patchbot
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 * polymake
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 * pybtex [[http://trac.sagemath.org/ticket/19187|#19187]]
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 * pyopenssl [[http://trac.sagemath.org/ticket/19187|#19187]]
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 * qhull
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 * sip (experimental)
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 * sqlalchemy [[http://trac.sagemath.org/ticket/19187|#19187]]
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 * surf (experimental)
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 * trac [[http://trac.sagemath.org/ticket/19187|#19187]]

This page aims at moving forward in the decision not to rely on old-style packaging system (therefore cleaning up all the Sage code that deals with that). See http://files.sagemath.org/spkg/index.html for the packages.

Packages that still require a decision

optional packages that still need to be classified

Here is the list of old-style optional packages for which it is not clear what to do (ignore, new-style repackage), they must eventually get moved to one of the classified lists.

  • extra_docs
  • java3d
  • nzmath (pip installable)
  • pycryptoplus
  • pyx (pip installable)

unclassified experimental packages

Here is the list of old-style expermiental packages for which it is not clear whether they can be forgotten.

Since most of those packages are broken anyway, do not move them into some "please repackage me" section (unless you know how to let this happen and open a ticket for that).

  • asymptote
  • cadabra
  • clapack
  • dvipng
  • gnofract4d
  • gnuplot
  • graphviz
  • openopt
  • phcpack
  • qasm2circ
  • quantlib, quantlib_swig
  • reallib3
  • sandpile
  • semigroupe
  • simpqs
  • superlu

unclassified non-mathematical packages

Here are non-mathematical packages that are not directly related to Sage.

  • optional
  • experimental
    • bison
    • clisp
    • ets
    • flex
    • libcprops
    • libjpeg
    • libsigsegv
    • modglue
    • mpich2
    • pcre
    • processing
    • pygame
    • pygtk
    • pyqt

    • PyQt4

    • pyrexembed
    • QScintilla2
    • soya
    • soya_cvs
    • wxPython
    • vtk_meta
    • yafray
    • yassl

Classified packages

packages that need to be new-style packaged

Put here the old-style packages from above that are interesting from the Sage perspective, do not put useless stuff here, only those you think are useful.

Packages that have a Sage interface, so these are likely of interest:

  • cunningham_tables
  • ginv
  • kash3
  • macaulay2
  • phc
  • polytopes_db_4d

packages appearing in Sage documentation

Here is the list of old-style packages which appear in the Numerical Computing tutorial, see also #19198:

  • mayavi
  • openmpi

  • python-2.5.1-framework #3924

  • PyVTK
  • scitools++
  • VTK (archived package!)

Superseded packages

Here are packages for which we found another way, hence can be removed.

  • gd # renamed to libgd
  • gdmodule # no longer needed
  • genus2reduction # superseded by PARI
  • gnuplotpy # we have our own interface
  • numarray # numpy
  • numeric # numpy
  • pil # replaced by pillow
  • pygsl # we have our own interface
  • lrs # there is now lrslib

Superseded packages with no replacement yet

This is installable via pip, but it is also outdated:

  • pynifti (superseded by NiBabel pip-installable package)

Already migrated to new style

Here are the packages that are already migrated new-style

  • 4ti2
  • arb
  • atlas
  • autotools
  • backports_ssl_match_hostname

  • beautifulsoup #19187

  • benzene

  • biopython #19187

  • bliss
  • boehm_gc
  • boost_cropped

  • brian #19187

  • buckygen
  • bzip2
  • cbc
  • ccache
  • cddlib
  • cephes
  • certifi
  • cliquer
  • cmake
  • combinatorial_designs
  • compilerwrapper
  • configure
  • conway_polynomials

  • coxeter3 #19178

  • cryptominisat
  • csdp
  • cvxopt
  • cython
  • d3js
  • database_cremona_ellcurve
  • database_gap

  • database_jones_numfield #19174

  • database_kohel

  • database_mutation_class (new name of cluster_seed) #19177

  • database_odlyzko_zeta
  • database_pari
  • database_stein_watkins
  • database_stein_watkins_mini
  • database_symbolic_data
  • dateutil
  • docutils
  • dot2tex
  • ecl
  • eclib
  • ecm
  • elliptic_curves
  • fflas_ffpack
  • flint
  • flintqs
  • freetype
  • fricas
  • gambit
  • gap
  • gap_packages
  • gcc
  • gdb
  • gf2x
  • gfan
  • giac
  • giacpy
  • git
  • git_trac
  • givaro
  • glpk
  • gmp
  • graphs
  • gsl

  • guppy #19187

  • iconv
  • iml
  • ipython
  • jinja2
  • jmol
  • jsonschema
  • latte_int
  • lcalc
  • libfplll
  • libgap
  • libgd
  • libogg
  • libpng
  • libtheora
  • lidia

  • lie #19176

  • linbox
  • lrcalc
  • lrslib
  • m4ri
  • m4rie
  • markupsafe
  • mathjax
  • matplotlib
  • maxima
  • mcqd

  • meataxe #12103

  • mercurial #19187

  • mistune
  • modular_decomposition
  • mpc
  • mpfi
  • mpfr

  • mpi4py #19187

  • mpir
  • mpmath
  • nauty
  • ncurses
  • networkx
  • normaliz
  • nose
  • ntl
  • numpy
  • openssl

  • ore_algebra (see #19175)

  • p_group_cohomology (see #18514)

  • palp
  • pari
  • pari_galdata
  • pari_seadata_small
  • patch
  • patchbot
  • pexpect
  • pillow
  • pip
  • pkgconf
  • pkgconfig
  • planarity
  • plantri
  • polybori
  • polymake
  • polytopes_db
  • ppl

  • pybtex #19187

  • pycrypto
  • pygments
  • pynac

  • pyopenssl #19187

  • pyparsing
  • python2
  • python3
  • pyzmq
  • qhull

  • saclib and qepcad #10224

  • r
  • ratpoints
  • readline
  • rpy2
  • rubiks
  • rw
  • sage_mode
  • sagenb
  • sagetex
  • scipy
  • scons
  • setuptools
  • singular
  • sip (experimental)
  • six
  • sphinx

  • sqlalchemy #19187

  • sqlite
  • surf (experimental)
  • symmetrica
  • sympow
  • sympy
  • tachyon
  • termcap
  • threejs
  • tides
  • topcom
  • tornado

  • trac #19187

  • valgrind
  • zeromq
  • zlib
  • zn_poly