Metaticket: clean up SPKGs

[kini]

In the process of working on #13015, we noticed that we have almost 8 MB worth of files in the standard SPKGs, which are not in src/ directories. That is way too much, so this is a metaticket to clean up currently existing SPKGs to make them conform to the standards for SPKGs, which many of them are doubtless breaking.

SPKGs listed by the size of the stuff in them that's not in src nor in .hg in sage-5.1.beta0:

$ du -bsh * | sort -h
4.4K    blas
4.6K    conway_polynomials
4.8K    graphs
5.3K    polytopes_db
5.3K    zodb3
5.5K    docutils
5.6K    freetype
5.8K    jinja2
5.9K    sqlalchemy
6.0K    bzip2
6.0K    cython
6.0K    genus2reduction
6.0K    mpmath
6.7K    gnutls
6.9K    pycrypto
7.0K    zlib
7.3K    gcc
7.7K    libpng
7.7K    sympy
7.8K    libm4rie
8.0K    patch
8.3K    elliptic_curves
8.3K    sagenb
9.3K    scons
11K     glpk
11K     iconv
11K     libm4ri
11K     mpfi
11K     pygments
11K     sagetex
12K     boost-cropped
12K     gd
12K     gsl
12K     lapack
13K     ppl
13K     termcap
14K     gdmodule
14K     ratpoints
15K     eclib
15K     flintqs
15K     ipython
15K     mpc
15K     scipy
15K     sqlite
16K     boehm_gc
16K     mercurial
16K     setuptools
17K     numpy
20K     cliquer
20K     linbox
20K     maxima
23K     pil
23K     sphinx
24K     matplotlib
25K     libgpg_error
25K     symmetrica
26K     networkx
27K     cvxopt
27K     ecl
29K     libfplll
29K     python
30K     readline
31K     opencdk
32K     sympow
35K     lcalc
36K     ecm
38K     flint
42K     rubiks
46K     polybori
49K     givaro
50K     libgcrypt
55K     pari
55K     zn_poly
57K     twisted
61K     cephes
66K     gfan
73K     mpir
76K     ntl
87K     mpfr
99K     tachyon
106K    pexpect
154K    r
191K    palp
231K    python_gnutls
261K    atlas
460K    gap
724K    iml
1.6M    cddlib
3.0M    singular
5.0M    pynac

SPKGs listed by the size of the stuff in the .hg repository (modulo post-merge cleanup operations in git consolidation - see #13015):

fs-boone@zhenghe ~/tmp/csr/out/devel/sage/spkg $ du -bsh * | sort -h
4.4K blas
4.6K conway_polynomials
4.8K graphs
5.3K polytopes_db
5.3K scons
5.3K zodb3
5.4K docutils
5.5K freetype
5.8K jinja2
5.9K bzip2
5.9K cython
5.9K sqlalchemy
6.0K genus2reduction
6.0K mpmath
6.6K gnutls
6.9K pycrypto
6.9K zlib
7.3K gcc
7.6K libm4rie
7.6K libpng
7.6K sympy
7.9K patch
8.1K elliptic_curves
10K sagetex
11K glpk
11K iconv
11K libm4ri
11K mpfi
11K pygments
11K sqlite
12K boost-cropped
12K gd
12K gsl
12K lapack
13K pexpect
13K ppl
13K termcap
14K gdmodule
14K mpc
14K pynac
14K ratpoints
14K scipy
15K eclib
15K flintqs
15K ipython
15K setuptools
16K boehm_gc
16K mercurial
17K numpy
19K linbox
20K cliquer
20K maxima
21K r
23K matplotlib
23K pil
23K sphinx
24K libgpg_error
25K symmetrica
26K ecl
26K networkx
27K cvxopt
29K libfplll
29K python
30K readline
31K opencdk
32K mpfr
32K sympow
35K lcalc
36K ecm
37K flint
42K rubiks
46K polybori
49K givaro
49K libgcrypt
55K pari
55K zn_poly
57K twisted
61K cephes
66K gfan
73K mpir
76K ntl
99K tachyon
191K palp
223K singular
231K python_gnutls
261K atlas
460K gap
724K iml
1.6M cddlib

Tickets:

• Upgrade and clean up cddlib #13026 cddlib
• update iml to the 1.0.3 release + our patches #748 iml

CC: @ohanar @nexttime

Component: packages: standard

Keywords: spkg cleanup

Issue created by migration from https://trac.sagemath.org/ticket/13025

[nexttime]

comment:8

Does anybody update this ticket?

[SnarkBoojum]

comment:12

Let me notice that the current organisation makes it easy to how much upstream sources get modified, by going into build/pkgs, then running du -bsh * | sort -h.

[jdemeyer]

comment:15

Obsolete