Diff for "Classify old-style packages"

Differences between revisions 4 and 44 (spanning 40 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 (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
- 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
fes #15209

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Superseded packages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genus2reduction # superseded by PARI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Superseded packages with no replacement yet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

-  ⇤ ← Revision 4 as of 2015-08-04 14:12:39 → 
  Size: 5126
  Editor: tmonteil
  Comment:
+   ← Revision 44 as of 2018-07-25 20:04:17 → ⇥
  Size: 6609
  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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- * chomp
 * cluster_seed
 * coxeter3
 * cunningham_tables
 * database_jones_numfield
 * database_kohel
-Line 22:
+Line 15:
- * ginv
-Line 24:
+Line 16:
- * kash3
 * lie
 * nzmath
 * ore_algebra         # note that the spkg is directly maintained upstream
 * phc
+ * nzmath (pip installable)
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+Line 18:
+ * pyx (pip installable)
-Line 44:
+Line 32:
- * fes
+ * dvipng
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+Line 36:
- * macaulay2
 * mayavi
 * meataxe
-Line 53:
+Line 38:
- * polymake
-Line 58:
+Line 42:
- * scitools++
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+Line 45:
- * 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
 * lrs         # there is now lrslib


=== 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 115:
+Line 53:
-   * openmpi
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+Line 54:
-   * trac
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+Line 58:
-   * cmake
   * dvipng
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+Line 72:
-   * PyVTK
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+Line 81:
+== 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]]
 * fes [[http://trac.sagemath.org/ticket/15209|#15209]]

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 [[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
 * openmpi
 * python-2.5.1-framework [[http://trac.sagemath.org/ticket/3924|#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)
-Line 157:
+Line 142:
+ * beautifulsoup [[http://trac.sagemath.org/ticket/19187|#19187]]
-Line 158:
+Line 144:
+ * biopython [[http://trac.sagemath.org/ticket/19187|#19187]]
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+Line 148:
+ * brian [[http://trac.sagemath.org/ticket/19187|#19187]]
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+Line 157:
+ * cmake
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+Line 162:
+ * coxeter3 [[http://trac.sagemath.org/ticket/19178|#19178]]
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+Line 170:
+ * 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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+Line 206:
+ * guppy [[http://trac.sagemath.org/ticket/19187|#19187]]
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+Line 222:
+ * lie [[http://trac.sagemath.org/ticket/19176|#19176]]
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+Line 233:
+ * meataxe [[http://trac.sagemath.org/ticket/12103| #12103]]
 * mercurial [[http://trac.sagemath.org/ticket/19187|#19187]]
-Line 243:
+Line 240:
+ * mpi4py [[http://trac.sagemath.org/ticket/19187|#19187]]
-Line 253:
+Line 251:
+ * ore_algebra (see [[http://trac.sagemath.org/ticket/19175|#19175]])
 * p_group_cohomology (see [[http://trac.sagemath.org/ticket/18514|#18514]])
 Line 258:
+ * patchbot
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+Line 267:
+ * polymake
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+Line 270:
+ * pybtex [[http://trac.sagemath.org/ticket/19187|#19187]]
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+Line 274:
+ * pyopenssl [[http://trac.sagemath.org/ticket/19187|#19187]]
-Line 275:
+Line 279:
+ * qhull
 * saclib and qepcad [[http://trac.sagemath.org/ticket/10224|#10224]]
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+Line 287:
- * saclib
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+Line 294:
+ * sip (experimental)
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+Line 297:
+ * sqlalchemy [[http://trac.sagemath.org/ticket/19187|#19187]]
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+Line 299:
+ * surf (experimental)
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+Line 309:
+ * trac [[http://trac.sagemath.org/ticket/19187|#19187]]