Diff for "Classify old-style packages"

Differences between revisions 1 and 31 (spanning 30 versions)

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
pycryptoplus
pyx
sip (also experimental)

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
meataxe
openopt
phcpack
polymake
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
- gdbm
- knoboo
- PyQt
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.

chomp #15202
coxeter3 #19178
database_jones_numfield #19174
database_mutation_class (new name of cluster_seed) #19177
fes #15209
lie #19176
ore_algebra #19175
p_group_cohomology (see discussion at #18514)
patchbot #18937

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

cunningham_tables
database_kohel (partially superseded by PARI: precisely those parts that are interfaced by Sage can now be computed by PARI)
ginv
kash3
macaulay2
phc
polytopes_db_4d

packages appearing in Sage documentation

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.

pyopenssl #19187
surf (package for Singular)

These appear only in the Numerical Computing tutorial, see also #19198:

mayavi
mpi4py #19187
openmpi
python-2.5.1-framework #3924
PyVTK
scitools++
VTK (archived package!)

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.

With #19187, they can even be installed with the usual sage -i PKGNAME command.

beautifulsoup
biopython
brian
guppy
mpi4py
mercurial
pybtex
pynifti (superseeded by NiBabel pip-installable package)
sqlalchemy
trac

Superseeded 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
qhull # we already have two copies coming from the standard packages matplotlib and scipy
numarray # numpy
numeric # numpy
pil # replaced by pillow
pygsl # we have our own interface
lrs # there is now lrslib

Already migrated to new style

Here are the packages that are already migrated new-style

4ti2
arb
atlas
autotools
backports_ssl_match_hostname
benzene
bliss
boehm_gc
boost_cropped
buckygen
bzip2
cbc
ccache
cddlib
cephes
certifi
cliquer
cmake
combinatorial_designs
compilerwrapper
configure
conway_polynomials
cryptominisat
csdp
cvxopt
cython
d3js
database_cremona_ellcurve
database_gap
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
iconv
iml
ipython
jinja2
jmol
jsonschema
latte_int
lcalc
libfplll
libgap
libgd
libogg
libpng
libtheora
lidia
linbox
lrcalc
lrslib
m4ri
m4rie
markupsafe
mathjax
matplotlib
maxima
mcqd
mistune
modular_decomposition
mpc
mpfi
mpfr
mpir
mpmath
nauty
ncurses
networkx
normaliz
nose
ntl
numpy
openssl
palp
pari
pari_galdata
pari_seadata_small
patch
pexpect
pillow
pip
pkgconf
pkgconfig
planarity
plantri
polybori
polytopes_db
ppl
pycrypto
pygments
pynac
pyparsing
python2
python3
pyzmq
saclib and qepcad #10224
r
ratpoints
readline
rpy2
rubiks
rw
sage_mode
sagenb
sagetex
scipy
scons
setuptools
singular
six
sphinx
sqlite
symmetrica
sympow
sympy
tachyon
termcap
threejs
tides
topcom
tornado
valgrind
zeromq
zlib
zn_poly

-  ⇤ ← Revision 1 as of 2015-08-04 13:49:11 → 
  Size: 5084
  Editor: tmonteil
  Comment:
+   ← Revision 31 as of 2015-09-13 07:56:20 → ⇥
  Size: 6884
  Editor: jdemeyer
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
-that).
+that). See [[http://files.sagemath.org/spkg/index.html]] for the packages.
 Line 14:
- * chomp
 * cluster_seed
 * coxeter3
 * cunningham_tables
 * database_jones_numfield
 * database_kohel
-Line 22:
+Line 15:
- * ginv
-Line 24:
+Line 16:
- * kash3
 * lie
 * lrs
-Line 28:
+Line 17:
- * ore_algebra         the spkg is directly maintained upstream
 * phc
-Line 31:
+Line 18:
+ * pyx
 * sip (also experimental)
-Line 45:
+Line 33:
- * fes
+ * dvipng
-Line 49:
+Line 37:
- * macaulay2
 * mayavi
-Line 59:
+Line 45:
- * scitools++
-Line 63:
+Line 48:
- * surf


== Classified packages ==


=== Optional 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.

 * p_group_cohomology
 * patchbot
 * qepcad (was experimental, but can become optional new-style with #10224
  (needs review))


=== 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 pip install command.


 * beautifulsoup
 * biopython
 * brian
 * guppy
 * mpi4py
 * pybtex
 * pyx
 * sip

pynifti (superseeded by NiBabel pip-installable package)


=== 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



=== Unrelated packages ===

Here are non-mathematical packages that are not directly related to Sage and were not needed for a while.
+=== unclassified non-mathematical packages ===

Here are non-mathematical packages that are not directly related to Sage.
-Line 117:
+Line 56:
-   * openmpi
-Line 119:
+Line 57:
-   * trac
-Line 124:
+Line 61:
-   * cmake
   * dvipng
-Line 140:
+Line 75:
-   * PyVTK
-Line 148:
+Line 82:
+== 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.

 * chomp [[http://trac.sagemath.org/ticket/15202|#15202]]
 * coxeter3 [[http://trac.sagemath.org/ticket/19178|#19178]]
 * 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:

 * cunningham_tables
 * database_kohel  (partially superseded by PARI: precisely those parts that are interfaced by Sage can now be computed by PARI)
 * ginv
 * kash3
 * macaulay2
 * phc
 * polytopes_db_4d


=== packages appearing in Sage documentation ===

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.

 * pyopenssl [[http://trac.sagemath.org/ticket/19187|#19187]]
 * surf  (package for Singular)

These appear only 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]]:

 * mayavi
 * mpi4py [[http://trac.sagemath.org/ticket/19187|#19187]]
 * openmpi
 * python-2.5.1-framework [[http://trac.sagemath.org/ticket/3924|#3924]]
 * PyVTK
 * scitools++
 * VTK (archived package!)

=== 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.

With [[http://trac.sagemath.org/ticket/19187|#19187]], they can even be installed with the usual `sage -i PKGNAME` command.

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


=== Superseeded 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
 * qhull             # we already have two copies coming from the standard packages matplotlib and scipy
 * numarray          # numpy
 * numeric           # numpy
 * pil               # replaced by pillow
 * pygsl             # we have our own interface
 * lrs               # there is now lrslib
-Line 171:
+Line 190:
+ * cmake
-Line 277:
+Line 297:
+ * saclib and qepcad [[http://trac.sagemath.org/ticket/10224|#10224]]
-Line 283:
+Line 304:
- * saclib