Removing sagemath: This package is in [community] repo

16 files changed, 0 insertions, 1130 deletions

diff --git a/libre/sagemath/PKGBUILD b/libre/sagemath/PKGBUILD
deleted file mode 100644
index 32e892716..000000000
--- a/libre/sagemath/PKGBUILD
+++ /dev/null
@@ -1,150 +0,0 @@
-# $Id: PKGBUILD 219758 2017-03-28 19:08:08Z arojas $
-# Maintainer (Arch): Evgeniy Alekseev <arcanis.arch at gmail dot com>
-# Maintainer (Arch): Antonio Rojas <arojas@archlinux.org>
-# Contributor (Arch): Daniel Wallace <danielwallace at gtmanfred dot com>
-# Contributor (Arch): Thomas Dziedzic <gostrc at gmail dot com>
-# Contributor (Arch): Osman Ugus <ugus11 at yahoo dot com>
-# Contributor (Arch): Stefan Husmann <stefan-husmann at t-online dot de>
-# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD
-# Maintainer: Omar Vega Ramos <ovruni@gnu.org.pe>
-# Maintainer: André Silva <emulatorman@parabola.nu>
-
-pkgname=sagemath
-pkgver=7.6
-pkgrel=2.parabola1
-pkgdesc="Free Mathematics Software, free software replacement of Magma, Maple, Mathematica, and Matlab, without nonfree nauty support"
-arch=(i686 x86_64 armv7h)
-url="http://www.sagemath.org"
-license=(GPL)
-depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow python2-rpy2 python2-fpylll python2-psutil
-  python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future libgap flintqs lcalc lrcalc arb
-  eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox rubiks pari-galdata pari-seadata-small planarity rankwidth
-  sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials)
-optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cython code'
-  'jmol: 3D plots' 'sage-notebook: Browser-based (flask) notebook interface'
-  'sagemath-doc: Documentation and inline help' 'python2-igraph: igraph backend for graph theory'
-  'coin-or-cbc: COIN backend for numerical computations' 'coin-or-csdp: for computing Lovász theta-function of graphs'
-  'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
-  'modular_decomposition: modular decomposition of graphs' 'ffmpeg: to export animations to video' 'imagemagick: to show animations'
-  'coxeter3: Coxeter groups implementation' 'cryptominisat2: SAT solver' 'gap-data: for computing Galois groups'
-  'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
-  'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups'
-  'libfes: exhaustive search of solutions for boolean equations' 'python2-pynormaliz: Normaliz backend for polyhedral computations'
-  'latte-integrale: integral point count in polyhedra'
-  'three.js: alternative 3D plots engine' 'tachyon: alternative 3D plots engine'
-  'sagemath-jupyter: Jupyter kernel')
-makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding
-  mcqd coxeter3 cryptominisat2 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe libfes)
-conflicts=(sage-mathematics)
-replaces=(sage-mathematics)
-provides=(sage-mathematics)
-source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
-        env.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch latte-count.patch
-        jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch ecm-7.patch increase-rtol.patch r-no-readline.patch
-        sagemath-planarity3.patch fes02.patch sagemath-singular-4.1.0.p2.patch)
-sha256sums=('e6e0729ab25446e7c922058db0eee4b0b294b32c196e34842e843ea9fae41423'
-            '9dba04ff13626a7b6c338a8b18a6c27d343f68a547a218533cf773af3dae6635'
-            'b02b3d2d5620ca20f96adb62b6fef05e4676c0a60983310a1450fdf3d923cb04'
-            'ff7e034d08ab084fdb193484f7fe3a659ebcd8ab33a2b7177237d65b26de7872'
-            'd60fb0fbd27991ce9496ca035a54b03334b5b53f244227a8d6e13f3327ce75d2'
-            '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212'
-            'b816c71d345fb1188c3faa01c4e75cfa04ba6506080231d5d2c303a2288e9b50'
-            '775051aa9076ebf631c8a291af38b6ec4a13c904740dc9da831641d592d8bcd8'
-            '27aa73d427d92aeb2c181a233aa3a574a4158cd7dee33832808f69edaec55ea2'
-            '81d08c6a760f171f3381455b66a6c84789c9f0eefddbe6ca5794075514ad8c3a'
-            '65ad84c83d5f956fde8eab961f2caad56d64044324c4abc0e56bcd9f44061cb6'
-            'be925eefeac3f28e639794ddc20d64e6faafd7181804e29417a510224d19ccc7'
-            'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf'
-            'a1c562ebe4538d672404ca3ac2e954a3c955afeb7463f7b4fe6eaa6fa74fe5c7'
-            'a39da083c038ada797ffc5bedc9ba47455a3f77057d42f86484ae877ef9172ea'
-            'e1912afec58b834fac3b9161c2d5a1794bb618126c6bd7a4be85c834231360e7')
-
-prepare(){
-  cd sage-$pkgver
-
-# Parabola-specific patches
-# assume all optional packages are installed
-  patch -p0 -i ../package.patch
-# set env variables
-  patch -p0 -i ../env.patch
-# skip checking build status
-  patch -p0 -i ../skip-check.patch
-# don't list optional packages when running tests
-  patch -p0 -i ../test-optional.patch
-# set jupyter path
-  patch -p0 -i ../jupyter-path.patch
-# search system paths for cython includes
-  patch -p1 -i ../cython-sys-path.patch
-# fix regressions with ECM 7
-  patch -p1 -i ../ecm-7.patch
-# increase numerical tolerance, needed by scipy 0.18
-  patch -p1 -i ../increase-rtol.patch
-# fix freezes in R interface with readline 7 (Debian)
-  patch -p1 -i ../r-no-readline.patch
-# fix build with planarity 3 (Debian)
-  patch -p2 -i ../sagemath-planarity3.patch
-# fix build with Singular 4.1.0-p2
-  patch -p0 -i ../sagemath-singular-4.1.0.p2.patch
-# use correct latte-count binary name
-  patch -p1 -i ../latte-count.patch
-# make 'sage -notebook=jupyter' work with our python3 jupyter-notebook package
-  patch -p1 -i ../sagemath-python3-notebook.patch
-
-# Upstream patches  
-# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
-  patch -p1 -i ../fes02.patch
-# replace is_package_installed usage http://trac.sagemath.org/ticket/20377
-  patch -p1 -i ../is-package-installed.patch
-
-# use python2
-  sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
-  sed -e 's|cython {OPT}|cython2 {OPT}|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py
-  sed -e 's|exec ipython|exec ipython2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage
-  sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
-  sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env
-}
-
-
-build() {
-  cd sage-$pkgver/src
-
-  export SAGE_LOCAL="/usr"
-  export SAGE_ROOT="$PWD"
-  export SAGE_SRC="$PWD"
-  export CC=gcc
-
-  python2 setup.py build
-}
-
-package() {
-  cd sage-$pkgver/src
-
-  export SAGE_ROOT="$PWD"
-  export SAGE_LOCAL="/usr"
-  export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
-
-  python2 setup.py install --root="$pkgdir" --optimize=1 --skip-build
-
-  mkdir -p "$pkgdir"/usr/bin
-  cp bin/sage "$pkgdir"/usr/bin
-  for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran ipython \
-    massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run run-cython runtests startuptime.py \
-    sws2rst valgrind version.sh
-  do
-    cp bin/sage-$_i "$pkgdir"/usr/bin
-  done
-  cp bin/math-readline "$pkgdir"/usr/bin
-  
-  mkdir -p "$pkgdir"/usr/share/sage
-  cp -r ext "$pkgdir"/usr/share/sage
-  
-# Create SAGE_SRC, needed for the notebook and help
-  mkdir "$pkgdir"/usr/share/sage/source
-  ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc
-
-# Remove sage_setup
-  rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
-
-# Split jupyter kernel
-  rm -r "$pkgdir"/usr/share/jupyter
-}
diff --git a/libre/sagemath/cython-sys-path.patch b/libre/sagemath/cython-sys-path.patch
deleted file mode 100644
index 7ec63e20b..000000000
--- a/libre/sagemath/cython-sys-path.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- sage-7.1/src/setup.py.orig	2016-04-08 16:59:24.691349473 +0000
-+++ sage-7.1/src/setup.py	2016-04-08 17:03:03.847153796 +0000
-@@ -414,6 +414,7 @@
-             build_dir=SAGE_CYTHONIZED,
-             force=force,
-             aliases=aliases,
-+            include_path=sys.path,
-             compiler_directives={
-                 'autotestdict': False,
-                 'cdivision': True,
diff --git a/libre/sagemath/ecm-7.patch b/libre/sagemath/ecm-7.patch
deleted file mode 100644
index 617e18d98..000000000
--- a/libre/sagemath/ecm-7.patch
+++ /dev/null
@@ -1,79 +0,0 @@
---- a/src/sage/interfaces/ecm.py.orig	2016-05-16 22:18:03.894827738 +0200
-+++ b/src/sage/interfaces/ecm.py	2016-05-16 22:19:14.674904932 +0200
-@@ -140,9 +140,6 @@
-         - ``ve`` -- integer `n`. Verbosely show short (`< n`
-           character) expressions on each loop
- 
--        - ``cofdec`` -- boolean. Force cofactor output in decimal
--          (even if expressions are used )
--
-         - ``B2scale`` -- integer. Multiplies the default B2 value
- 
-         - ``go`` -- integer. Preload with group order val, which can
-@@ -395,15 +392,15 @@
-             if m is not None:
-                 factor = m.group('factor')
-                 primality = m.group('primality')
--                assert primality in ['probable prime', 'composite']
--                result += [(ZZ(factor), primality == 'probable prime')]
-+                assert primality in ['prime', 'composite']
-+                result += [(ZZ(factor), primality == 'prime')]
-                 continue  # cofactor on the next line
-             m = self._found_cofactor_re.match(line)
-             if m is not None:
-                 cofactor = m.group('cofactor')
-                 primality = m.group('primality')
--                assert primality in ['Probable prime', 'Composite']
--                result += [(ZZ(cofactor), primality == 'Probable prime')]
-+                assert primality in ['Prime', 'Composite']
-+                result += [(ZZ(cofactor), primality == 'Prime')]
-                 # assert len(result) == 2
-                 return result
-         raise ValueError('failed to parse ECM output')
-@@ -501,7 +498,6 @@
-         if factor_digits is not None:
-             B1 = self.recommended_B1(factor_digits)
-         kwds['one'] = True
--        kwds['cofdec'] = True
-         cmd = self._make_cmd(B1, None, kwds)
-         out = self._run_ecm(cmd, n)
-         return self._parse_output(n, out)
-@@ -828,8 +828,8 @@
- Step 1 took 12ms
- Step 2 took 17ms
- ********** Factor found in step 2: 79792266297612017
--Found probable prime factor of 17 digits: 79792266297612017
--Probable prime cofactor 6366805760909027985741435139224233 has 34 digits
-+Found prime factor of 17 digits: 79792266297612017
-+Prime cofactor 6366805760909027985741435139224233 has 34 digits
- """
- 
- TEST_ECM_OUTPUT_2 = """
-@@ -839,8 +839,8 @@
- Step 1 took 2ms
- Step 2 took 3ms
- ********** Factor found in step 2: 179424673
--Found probable prime factor of  9 digits: 179424673
--Probable prime cofactor 179424673 has 9 digits
-+Found prime factor of  9 digits: 179424673
-+Prime cofactor 179424673 has 9 digits
- """
- 
- TEST_ECM_OUTPUT_3 = """
-@@ -858,7 +858,7 @@
- Step 1 took 5ms
- Step 2 took 4ms
- ********** Factor found in step 2: 197002597249
--Found probable prime factor of 12 digits: 197002597249
-+Found prime factor of 12 digits: 197002597249
- Composite cofactor 339872432034468861533158743041639097889948066859 has 48 digits
- """
- 
-@@ -870,5 +870,5 @@
- Step 2 took 2ms
- ********** Factor found in step 2: 265748496095531068869578877937
- Found composite factor of 30 digits: 265748496095531068869578877937
--Probable prime cofactor 251951573867253012259144010843 has 30 digits
-+Prime cofactor 251951573867253012259144010843 has 30 digits
- """
-
diff --git a/libre/sagemath/env.patch b/libre/sagemath/env.patch
deleted file mode 100644
index fc37e00db..000000000
--- a/libre/sagemath/env.patch
+++ /dev/null
@@ -1,94 +0,0 @@
---- src/bin/sage-env.orig	2015-01-06 10:46:04.469687605 +0100
-+++ src/bin/sage-env	2015-01-06 10:49:59.547762019 +0100
-@@ -110,41 +110,7 @@
- }
- 
- 
--# New value for SAGE_ROOT: either SAGE_ROOT (if given)
--# or a guessed value based on pwd.
--if [ -n "$SAGE_ROOT" ]; then
--    NEW_SAGE_ROOT="$SAGE_ROOT"
--elif [ -f sage -a -d build ]; then
--    NEW_SAGE_ROOT="."
--elif [ -f ../../sage -a -d ../../build ]; then
--    NEW_SAGE_ROOT="../.."
--else
--    # No idea what SAGE_ROOT should be...
--    echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this"
--    echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory."
--    return 1
--fi
--
--# Make NEW_SAGE_ROOT absolute
--NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P`
--
--# Sanity check NEW_SAGE_ROOT
--if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then
--    :
--else
--    echo >&2 "Error: SAGE_ROOT is set to a bad value:"
--    echo >&2 "SAGE_ROOT=$SAGE_ROOT"
--    echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT"
--    echo >&2 "or SAGE_ROOT/local/bin/ directory."
--    return 1
--fi
--
--# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT
--if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then
--    echo >&2 "Warning: overwriting SAGE_ROOT environment variable:"
--    echo >&2 "Old SAGE_ROOT=$SAGE_ROOT"
--    echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT"
--fi
-+NEW_SAGE_ROOT="/usr"
- 
- # Display the Sage startup banner, used in src/bin/sage
- sage_banner() {
-@@ -187,7 +187,7 @@
- 
- # SAGE_LOCAL is the installation prefix and can be customized
- if [ -z "$SAGE_LOCAL" ]; then
--    export SAGE_LOCAL="$SAGE_ROOT/local"
-+    export SAGE_LOCAL="/usr"
- fi
- 
- # sage-env must know where the Sage's script files are
-@@ -233,8 +233,9 @@
- export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
- export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
- export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
--export SAGE_SRC="$SAGE_ROOT/src"
--export SAGE_DOC_SRC="$SAGE_SRC/doc"
-+export GAP_ROOT_DIR="/usr/lib/gap"
-+export SAGE_SRC="$SAGE_SHARE/sage/source"
-+export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
- export SAGE_DOC="$SAGE_SHARE/doc/sage"
- 
- if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
-@@ -374,6 +337,9 @@
-     export SAGE_STARTUP_FILE
- fi
- 
-+export LIBMTX="$DOT_SAGE/meataxe"
-+[[ -d $LIBMTX ]] || mkdir $LIBMTX # Create meataxe data dir
-+
- if [ -z "$IPYTHONDIR" ]; then
-     # We hardcode a version number in the directory name. The idea is
-     # that we keep using the same version number as long as that is
-@@ -468,7 +400,6 @@
-         fi
-     fi
- fi
--export MAXIMA_PREFIX="$SAGE_LOCAL"
- 
- PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
- 
-@@ -629,9 +608,6 @@
-     LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
- fi
- 
--# See trac 7186 -- this is needed if ecl is moved
--ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR
--
- # Handle parallel building/testing/...
- # See Trac Ticket #12016
- # First, figure out the right values for SAGE_NUM_THREADS (default
diff --git a/libre/sagemath/fes02.patch b/libre/sagemath/fes02.patch
deleted file mode 100644
index 155d114b1..000000000
--- a/libre/sagemath/fes02.patch
+++ /dev/null
@@ -1,57 +0,0 @@
-From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001
-From: Charles Bouillaguet <charles.bouillaguet@lifl.fr>
-Date: Thu, 19 Sep 2013 10:31:11 +0200
-Subject: updating the libFES binding to match a change in the interface
-
----
- src/sage/libs/fes.pyx | 12 +++++++-----
- 1 file changed, 7 insertions(+), 5 deletions(-)
-
-diff --git a/src/sage/libs/fes.pyx b/src/sage/libs/fes.pyx
-index 40b9c23..d188cf0 100644
---- a/src/sage/libs/fes.pyx
-+++ b/src/sage/libs/fes.pyx
-@@ -1,17 +1,19 @@
- """
--Binding for the FES library.
-+Binding for the libFES library.
- 
- Finding solutions of systems of boolean equations by exhaustive
- search, via the fes library. This is usually (much) faster than
- computing a Groebner basis, except in special cases where the latter
- is particularly easy.
- 
--The FES library is presently only able to deal with polynomials in 64
-+More information is available at [http://www.lifl.fr/~bouillag/fes].
-+
-+The libFES library is presently only able to deal with polynomials in 64
- variables. Performing a full exhaustive search over 64 variables will
- take a **long** time. The number of variables can be artificially
- reduced to 64 by specializing some of them.
- 
--Note that the FES library **requires** at least of the equations to be
-+Note that the libFES library **requires** at least of the equations to be
- non-linear.
- 
- AUTHORS:
-@@ -71,7 +73,7 @@ from libc.stdint cimport uint64_t
- cdef extern from "fes_interface.h":
-     ctypedef int (*solution_callback_t)(void *, uint64_t)
- 
--    void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose)
-+    void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T)
- 
- 
- include 'sage/ext/interrupt.pxi'  #sig_on(), sig_off()
-@@ -219,7 +221,7 @@ def exhaustive_search(eqs,  max_sols=Infinity, verbose=False):
- 
-     # ------- runs the library
-     sig_on()
--    exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose)
-+    exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose, 0)
-     sig_off()
- 
-     # ------- frees memory occupied by the dense representation of the equations
--- 
-cgit v1.0-1-gd88e
-
diff --git a/libre/sagemath/increase-rtol.patch b/libre/sagemath/increase-rtol.patch
deleted file mode 100644
index dc0ff8799..000000000
--- a/libre/sagemath/increase-rtol.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-diff -ru sage-7.3.orig/src/sage/coding/code_bounds.py sage-7.3/src/sage/coding/code_bounds.py
---- sage-7.3.orig/src/sage/coding/code_bounds.py        2016-08-05 20:26:10.033204091 +0200
-+++ sage-7.3/src/sage/coding/code_bounds.py     2016-08-05 20:32:27.276579565 +0200
-@@ -554,7 +554,7 @@
-     if q < 2:   # Here we check that q is actually at least 2
-         raise ValueError("The value q must be an integer greater than 1")
- 
--    eps  = 4.5e-16 # find_root has about this as the default xtol
-+    eps  = 4.5e-15 # find_root has about this as the default xtol
-     ymax = 1 - 1/q
-     if x <= eps:
-         return 0
-diff -ru sage-7.3.orig/src/sage/numerical/optimize.py sage-7.3/src/sage/numerical/optimize.py
---- sage-7.3.orig/src/sage/numerical/optimize.py        2016-08-05 20:26:10.816536625 +0200
-+++ sage-7.3/src/sage/numerical/optimize.py     2016-08-05 20:32:21.449907130 +0200
-@@ -15,7 +15,7 @@
- from sage.rings.real_double import RDF
- 
- 
--def find_root(f, a, b, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
-+def find_root(f, a, b, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
-     """
-     Numerically find a root of ``f`` on the closed interval `[a,b]`
-     (or `[b,a]`) if possible, where ``f`` is a function in the one variable.
-diff -ru sage-7.3.orig/src/sage/symbolic/expression.pyx sage-7.3/src/sage/symbolic/expression.pyx
---- sage-7.3.orig/src/sage/symbolic/expression.pyx      2016-08-05 20:26:11.333202767 +0200
-+++ sage-7.3/src/sage/symbolic/expression.pyx   2016-08-05 20:32:14.236566826 +0200
-@@ -10884,7 +10884,7 @@
-             ret = ret[0]
-         return ret
- 
--    def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
-+    def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
-         """
-         Numerically find a root of self on the closed interval [a,b] (or
-         [b,a]) if possible, where self is a function in the one variable.
-
diff --git a/libre/sagemath/is-package-installed.patch b/libre/sagemath/is-package-installed.patch
deleted file mode 100644
index 9a52ac5ff..000000000
--- a/libre/sagemath/is-package-installed.patch
+++ /dev/null
@@ -1,328 +0,0 @@
-diff --git a/src/sage/databases/cremona.py b/src/sage/databases/cremona.py
-index 0a5f794..2969d92 100644
---- a/src/sage/databases/cremona.py
-+++ b/src/sage/databases/cremona.py
-@@ -53,7 +53,6 @@ from sage.misc.prandom import randint
- 
- import sage.schemes.elliptic_curves.constructor as elliptic
- from .sql_db import SQLDatabase, verify_column
--from sage.misc.package import is_package_installed
- from sage.env import SAGE_SHARE
- from sage.misc.all import walltime
- 
-@@ -824,7 +823,7 @@ class MiniCremonaDatabase(SQLDatabase):
-             if N < self.largest_conductor():
-                 message = "There is no elliptic curve with label " + label \
-                     + " in the database"
--            elif is_package_installed('database_cremona_ellcurve'):
-+            elif os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
-                 message = "There is no elliptic curve with label " + label \
-                     + " in the currently available databases"
-             else:
-@@ -1673,7 +1672,7 @@ def CremonaDatabase(name=None,mini=None,set_global=None):
-     if name is None and not set_global:
-         return _db
-     if set_global and name is None:
--        if is_package_installed('database_cremona_ellcurve'):
-+        if os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
-             name = 'cremona'
-         else:
-             name = 'cremona mini'
-diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py
-index b917d2a..80fb20c 100644
---- a/src/sage/game_theory/normal_form_game.py
-+++ b/src/sage/game_theory/normal_form_game.py
-@@ -614,8 +614,9 @@ from sage.rings.all import QQ
- from sage.structure.sage_object import SageObject
- from sage.matrix.constructor import matrix
- from sage.matrix.constructor import vector
--from sage.misc.package import is_package_installed
- from sage.misc.temporary_file import tmp_filename
-+import os
-+from sage.env import SAGE_LOCAL
- 
- try:
-     from gambit import Game
-@@ -1317,13 +1318,13 @@ class NormalFormGame(SageObject, MutableMapping):
-             raise ValueError("utilities have not been populated")
- 
-         if not algorithm:
--            if is_package_installed('lrslib'):
-+            if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
-                 algorithm = "lrs"
-             else:
-                 algorithm = "enumeration"
- 
-         if algorithm == "lrs":
--            if not is_package_installed('lrslib'):
-+            if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
-                 raise NotImplementedError("lrslib is not installed")
- 
-             return self._solve_lrs(maximization)
-diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py
-index 2f58d8b..eb519a2 100644
---- a/src/sage/geometry/polyhedron/base.py
-+++ b/src/sage/geometry/polyhedron/base.py
-@@ -21,7 +21,6 @@ import six
- from sage.structure.element import Element, coerce_binop, is_Vector
- 
- from sage.misc.all import cached_method, prod
--from sage.misc.package import is_package_installed
- 
- from sage.rings.all import QQ, ZZ
- from sage.rings.real_double import RDF
-@@ -3691,7 +3690,9 @@ class Polyhedron_base(Element):
- 
-              David Avis's lrs program.
-         """
--        if not is_package_installed('lrslib'):
-+        import os
-+        from sage.env import SAGE_LOCAL
-+        if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')) != True:
-             raise NotImplementedError('You must install the optional lrslib package '
-                                        'for this function to work')
- 
-diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
-index e80f2a5..04cd9ce 100644
---- a/src/sage/graphs/generators/classical_geometries.py
-+++ b/src/sage/graphs/generators/classical_geometries.py
-@@ -1287,10 +1287,9 @@ def CossidentePenttilaGraph(q):
-         raise ValueError('q(={}) must be an odd prime power'.format(q))
- 
-     from sage.libs.gap.libgap import libgap
--    from sage.misc.package import is_package_installed, PackageNotFoundError
-+    from sage.interfaces.gap import gap
- 
--    if not is_package_installed('gap_packages'):
--        raise PackageNotFoundError('gap_packages')
-+    gap.load_package("grape")
- 
-     adj_list=libgap.function_factory("""function(q)
-         local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
-diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
-index 252984f..ce19682 100644
---- a/src/sage/graphs/generic_graph.py
-+++ b/src/sage/graphs/generic_graph.py
-@@ -7858,7 +7858,6 @@ class GenericGraph(GenericGraph_pyx):
-            sage: abs(flow_ff-flow_igraph) < 0.00001         # optional python_igraph
-            True
-         """
--        from sage.misc.package import is_package_installed
-         self._scream_if_not_simple(allow_loops=True)
-         if vertex_bound and algorithm in ["FF", "igraph"]:
-             raise ValueError("This method does not support both " +
-@@ -7876,10 +7875,12 @@ class GenericGraph(GenericGraph_pyx):
-         if algorithm is None:
-             if vertex_bound:
-                 algorithm = "LP"
--            elif is_package_installed("python_igraph"):
--                algorithm = "igraph"
-             else:
--                algorithm = "FF"
-+                algorithm = "igraph"
-+                try:
-+                    import igraph
-+                except ImportError:
-+                    algorithm = "FF"
- 
-         if (algorithm == "FF"):
-             return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels)
-diff --git a/src/sage/graphs/graph_generators.py b/src/sage/graphs/graph_generators.py
-index 5919ab3..1766796 100644
---- a/src/sage/graphs/graph_generators.py
-+++ b/src/sage/graphs/graph_generators.py
-@@ -1195,8 +1195,9 @@ class GraphGenerators():
-         .. [buckygen] \G. Brinkmann, J. Goedgebeur and B.D. McKay, Generation of Fullerenes,
-           Journal of Chemical Information and Modeling, 52(11):2910-2918, 2012.
-         """
--        from sage.misc.package import is_package_installed
--        if not is_package_installed("buckygen"):
-+        import os
-+        from sage.env import SAGE_LOCAL
-+        if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'buckygen')):
-             raise TypeError("the optional buckygen package is not installed")
- 
-         # number of vertices should be positive
-@@ -1280,8 +1281,9 @@ class GraphGenerators():
-         .. [benzene] \G. Brinkmann, G. Caporossi and P. Hansen, A Constructive Enumeration of Fusenes and Benzenoids,
-           Journal of Algorithms, 45:155-166, 2002.
-         """
--        from sage.misc.package import is_package_installed
--        if not is_package_installed("benzene"):
-+        import os
-+        from sage.env import SAGE_LOCAL
-+        if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'benzene')):
-             raise TypeError("the optional benzene package is not installed")
- 
-         # number of hexagons should be positive
-@@ -1433,8 +1435,9 @@ class GraphGenerators():
-         .. [plantri] \G. Brinkmann and B.D. McKay, Fast generation of planar graphs,
-            MATCH-Communications in Mathematical and in Computer Chemistry, 58(2):323-357, 2007.
-         """
--        from sage.misc.package import is_package_installed
--        if not is_package_installed("plantri"):
-+        import os
-+        from sage.env import SAGE_LOCAL
-+        if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
-             raise TypeError("the optional plantri package is not installed")
- 
-         # number of vertices should be positive
-@@ -1632,8 +1635,9 @@ class GraphGenerators():
-             sage: [g.size() for g in graphs.triangulations(6, minimum_connectivity=3)] # optional plantri
-             [12, 12]
-         """
--        from sage.misc.package import is_package_installed
--        if not is_package_installed("plantri"):
-+        import os
-+        from sage.env import SAGE_LOCAL
-+        if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
-             raise TypeError("the optional plantri package is not installed")
- 
-         # number of vertices should be positive
-@@ -1786,8 +1790,9 @@ class GraphGenerators():
-             sage: [len(g) for g in graphs.quadrangulations(12, no_nonfacial_quadrangles=True, dual=True)]  # optional plantri
-             [10, 10]
-         """
--        from sage.misc.package import is_package_installed
--        if not is_package_installed("plantri"):
-+        import os
-+        from sage.env import SAGE_LOCAL
-+        if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
-             raise TypeError("the optional plantri package is not installed")
- 
-         # number of vertices should be positive
-diff --git a/src/sage/graphs/lovasz_theta.py b/src/sage/graphs/lovasz_theta.py
-index 0d345c9..60948d2 100644
---- a/src/sage/graphs/lovasz_theta.py
-+++ b/src/sage/graphs/lovasz_theta.py
-@@ -65,10 +65,9 @@ def lovasz_theta(graph):
-     from sage.misc.temporary_file import tmp_filename
-     import os, subprocess
-     from sage.env import SAGE_LOCAL
--    from sage.misc.package import is_package_installed, PackageNotFoundError
- 
--    if not is_package_installed('csdp'):
--        raise PackageNotFoundError("csdp")
-+    if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'theta')):
-+        raise NotImplementedError("You must install csdp before using this function")
- 
-     g = graph.relabel(inplace=False, perm=range(1,n+1)).networkx_graph()
-     tf_name = tmp_filename()
-diff --git a/src/sage/groups/generic.py b/src/sage/groups/generic.py
-index c801636..f43e6d9 100644
---- a/src/sage/groups/generic.py
-+++ b/src/sage/groups/generic.py
-@@ -1400,15 +1400,15 @@ def structure_description(G, latex=False):
-         sage: groups.matrix.GL(4,2).structure_description() # optional - database_gap
-         'A8'
-     """
--    import re
--    from sage.misc.package import is_package_installed
-+    import re, os
-+    from sage.env import SAGE_LOCAL
-     def correct_dihedral_degree(match):
-         return "%sD%d" % (match.group(1), int(match.group(2))/2)
- 
-     try:
-         description = str(G._gap_().StructureDescription())
-     except RuntimeError:
--        if not is_package_installed('database_gap'):
-+	if not os.path.isfile(os.path.join(SAGE_LOCAL, "lib", "gap", "small", "readsml.g")):
-             raise RuntimeError("You must install the optional database_gap package first.")
-         raise
- 
-diff --git a/src/sage/groups/perm_gps/permgroup.py b/src/sage/groups/perm_gps/permgroup.py
-index e42db61..d4d5684 100644
---- a/src/sage/groups/perm_gps/permgroup.py
-+++ b/src/sage/groups/perm_gps/permgroup.py
-@@ -145,7 +145,6 @@ from sage.groups.perm_gps.permgroup_element import PermutationGroupElement, stan
- from sage.groups.abelian_gps.abelian_group import AbelianGroup
- from sage.misc.cachefunc import cached_method
- from sage.groups.class_function import ClassFunction
--from sage.misc.package import is_package_installed
- from sage.sets.finite_enumerated_set import FiniteEnumeratedSet
- from sage.categories.all import FiniteEnumeratedSets
- from sage.groups.conjugacy_classes import ConjugacyClassGAP
-@@ -190,8 +189,6 @@ def hap_decorator(f):
-     """
-     @wraps(f)
-     def wrapped(self, n, p=0):
--        if not is_package_installed('gap_packages'):
--            raise RuntimeError("You must install the optional gap_packages package.")
-         load_hap()
-         from sage.arith.all import is_prime
-         if not (p == 0 or is_prime(p)):
-@@ -1682,9 +1679,7 @@ class PermutationGroup_generic(group.FiniteGroup):
-         try:
-             return [Integer(n) for n in self._gap_().IdGroup()]
-         except RuntimeError:
--            if not is_package_installed('database_gap'):
--                raise RuntimeError("You must install the optional database_gap package first.")
--            raise
-+            raise RuntimeError("You must install the optional gap_packages package.")
- 
-     def id(self):
-         """
-@@ -1735,9 +1730,7 @@ class PermutationGroup_generic(group.FiniteGroup):
-         try:
-             return Integer(self._gap_().PrimitiveIdentification())
-         except RuntimeError:
--            if not is_package_installed('database_gap'):
--                raise RuntimeError("You must install the optional database_gap package first.")
--            raise
-+            raise RuntimeError("You must install the optional gap_packages package.")
- 
-     def center(self):
-         """
-@@ -4113,8 +4106,6 @@ class PermutationGroup_generic(group.FiniteGroup):
-         - David Joyner and Graham Ellis
- 
-         """
--        if not is_package_installed('gap_packages'):
--            raise RuntimeError("You must install the optional gap_packages package.")
-         load_hap()
-         from sage.arith.all import is_prime
-         if not (p == 0 or is_prime(p)):
-diff --git a/src/sage/misc/all.py b/src/sage/misc/all.py
-index 90e6985..21daeb0 100644
---- a/src/sage/misc/all.py
-+++ b/src/sage/misc/all.py
-@@ -53,10 +53,6 @@ from fpickle import pickle_function, unpickle_function
- 
- from .dist import install_scripts
- 
--from .package import (installed_packages, is_package_installed,
--        standard_packages, optional_packages, experimental_packages,
--        package_versions)
--
- from .pager import pager
- 
- lazy_import('sage.misc.sagedoc', ['browse_sage_doc',
-diff --git a/src/sage/rings/polynomial/multi_polynomial_sequence.py b/src/sage/rings/polynomial/multi_polynomial_sequence.py
-index da41cb0..49cae0b 100644
---- a/src/sage/rings/polynomial/multi_polynomial_sequence.py
-+++ b/src/sage/rings/polynomial/multi_polynomial_sequence.py
-@@ -163,7 +163,6 @@ from sage.misc.cachefunc import cached_method
- 
- from types import GeneratorType
- from sage.misc.converting_dict import KeyConvertingDict
--from sage.misc.package import is_package_installed
- 
- from sage.structure.sequence import Sequence, Sequence_generic
- 
-@@ -1433,10 +1432,11 @@ class PolynomialSequence_gf2(PolynomialSequence_generic):
- 
-         if S != []:
-             if algorithm == "exhaustive_search":
--                if not is_package_installed('fes'):
--                    from sage.misc.package import PackageNotFoundError
--                    raise PackageNotFoundError("fes")
--                from sage.libs.fes import exhaustive_search
-+                try:
-+                    from sage.libs.fes import exhaustive_search
-+                except ImportError:
-+                    raise RuntimeError("You must install the optional fes package.")
-+
-                 solutions = exhaustive_search(S, max_sols=n, verbose=verbose, **kwds)
- 
-             elif algorithm == "polybori":
diff --git a/libre/sagemath/jupyter-path.patch b/libre/sagemath/jupyter-path.patch
deleted file mode 100644
index 3eec99a89..000000000
--- a/libre/sagemath/jupyter-path.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- src/sage/repl/ipython_kernel/install.py.orig	2015-10-23 19:23:39.728456590 +0000
-+++ src/sage/repl/ipython_kernel/install.py	2015-10-23 19:24:00.965018978 +0000
-@@ -13,8 +13,7 @@
-     SAGE_ROOT, SAGE_DOC, SAGE_LOCAL, SAGE_EXTCODE,
-     SAGE_VERSION
- )
--from jupyter_core.paths import ENV_JUPYTER_PATH
--JUPYTER_PATH = ENV_JUPYTER_PATH[0]
-+JUPYTER_PATH = os.environ.get('JUPYTER_PATH') 
- 
- class SageKernelSpec(object):
-
-@@ -208,7 +208,7 @@
-             sage: spec._symlink_resources()    # not tested
-         """
-         path = os.path.join(SAGE_EXTCODE, 'notebook-ipython')
--        for filename in os.listdir(path):
-+        for filename in os.listdir('ext/notebook-ipython'):
-             self.symlink(
-                 os.path.join(path, filename),
-                 os.path.join(self.kernel_dir, filename)
-
diff --git a/libre/sagemath/latte-count.patch b/libre/sagemath/latte-count.patch
deleted file mode 100644
index 623259294..000000000
--- a/libre/sagemath/latte-count.patch
+++ /dev/null
@@ -1,84 +0,0 @@
-diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py
-index 50d99f99e4..3a3a8cb214 100644
---- a/src/sage/geometry/polyhedron/base.py
-+++ b/src/sage/geometry/polyhedron/base.py
-@@ -4629,7 +4629,7 @@ class Polyhedron_base(Element):
-             ...
-             RuntimeError: LattE integrale program failed (exit code 1):
-             ...
--            Invocation: count '--redundancy-check=none' --cdd /dev/stdin
-+            Invocation: latte-count '--redundancy-check=none' --cdd /dev/stdin
-             ...
-             Parse error in CDD-style input file /dev/stdin
-             sage: Q.integral_points_count(verbose=True) # optional - latte_int
-diff --git a/src/sage/geometry/polyhedron/base_ZZ.py b/src/sage/geometry/polyhedron/base_ZZ.py
-index 268af9db0d..70d41dfa30 100644
---- a/src/sage/geometry/polyhedron/base_ZZ.py
-+++ b/src/sage/geometry/polyhedron/base_ZZ.py
-@@ -228,7 +228,7 @@ class Polyhedron_ZZ(Polyhedron_base):
-             sage: p = P.ehrhart_polynomial(maxdet=5, verbose=True)  # optional - latte_int
-             This is LattE integrale ...
-             ...
--            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin
-+            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin
-             ...
-             sage: p    # optional - latte_int
-             1/2*t^2 + 3/2*t + 1
-@@ -236,7 +236,7 @@ class Polyhedron_ZZ(Polyhedron_base):
-             sage: p = P.ehrhart_polynomial(dual=True, verbose=True)  # optional - latte_int
-             This is LattE integrale ...
-             ...
--            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin
-+            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin
-             ...
-             sage: p   # optional - latte_int
-             1/2*t^2 + 3/2*t + 1
-@@ -244,7 +244,7 @@ class Polyhedron_ZZ(Polyhedron_base):
-             sage: p = P.ehrhart_polynomial(irrational_primal=True, verbose=True)   # optional - latte_int
-             This is LattE integrale ...
-             ...
--            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin
-+            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin
-             ...
-             sage: p   # optional - latte_int
-             1/2*t^2 + 3/2*t + 1
-@@ -252,7 +252,7 @@ class Polyhedron_ZZ(Polyhedron_base):
-             sage: p = P.ehrhart_polynomial(irrational_all_primal=True, verbose=True)  # optional - latte_int
-             This is LattE integrale ...
-             ...
--            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin
-+            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin
-             ...
-             sage: p   # optional - latte_int
-             1/2*t^2 + 3/2*t + 1
-@@ -264,7 +264,7 @@ class Polyhedron_ZZ(Polyhedron_base):
-             ...
-             RuntimeError: LattE integrale program failed (exit code 1):
-             ...
--            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin
-+            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin
-             Unknown command/option --bim-bam-boum=19
-         """
-         if self.is_empty():
-diff --git a/src/sage/interfaces/latte.py b/src/sage/interfaces/latte.py
-index 066cedd401..302b39910d 100644
---- a/src/sage/interfaces/latte.py
-+++ b/src/sage/interfaces/latte.py
-@@ -86,7 +86,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False,
-         sage: n = count(cddin, cdd=True, verbose=True, raw_output=True)  # optional - latte_int
-         This is LattE integrale ...
-         ...
--        Invocation: count '--redundancy-check=none' --cdd /dev/stdin
-+        Invocation: latte-count '--redundancy-check=none' --cdd /dev/stdin
-         ...
-         Total Unimodular Cones: ...
-         Maximum number of simplicial cones in memory at once: ...
-@@ -106,7 +106,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False,
-     from sage.misc.misc import SAGE_TMP
-     from sage.rings.integer import Integer
- 
--    args = ['count']
-+    args = ['latte-count']
-     if ehrhart_polynomial and multivariate_generating_function:
-         raise ValueError
-     if ehrhart_polynomial:
diff --git a/libre/sagemath/package.patch b/libre/sagemath/package.patch
deleted file mode 100644
index 0139f4b15..000000000
--- a/libre/sagemath/package.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- src/sage/misc/package.py.orig	2014-11-23 15:58:13.000000000 +0100
-+++ src/sage/misc/package.py	2015-01-22 20:32:25.651383902 +0100
-@@ -343,7 +343,7 @@
-         sage: for pkg in list_packages('pip', local=True):
-         ....:     assert not is_package_installed(pkg)
-     """
--    return any(p.split('-')[0] == package for p in installed_packages(exclude_pip))
-+    return True
- 
- def package_versions(package_type, local=False):
-     r"""
---- src/sage_setup/optional_extension.py.orig  2016-10-19 18:35:10.092577510 +0000
-+++ src/sage_setup/optional_extension.py       2016-10-19 18:38:13.514765366 +0000
-@@ -21,8 +21,6 @@
- from distutils.extension import Extension
- from sage.misc.package import is_package_installed, list_packages
- 
--all_packages = list_packages(local=True)
--
- 
- class CythonizeExtension(Extension):
-     """
-@@ -76,14 +74,7 @@
-         condition = kwds.pop("condition")
-     except KeyError:
-         pkg = kwds.pop("package")
--        try:
--            pkginfo = all_packages[pkg]
--        except KeyError:
--            # Might be an installed old-style package
--            condition = is_package_installed(pkg)
--        else:
--            condition = (pkginfo["installed_version"] == pkginfo["remote_version"])
--
-+        condition = True
-     if condition:
-         return Extension(*args, **kwds)
-     else:
diff --git a/libre/sagemath/r-no-readline.patch b/libre/sagemath/r-no-readline.patch
deleted file mode 100644
index 001d34f65..000000000
--- a/libre/sagemath/r-no-readline.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/sage/interfaces/r.py
-+++ b/src/sage/interfaces/r.py
-@@ -331,7 +331,7 @@
-                   prompt = '> ', #default, later comes the change
- 
-                   # This is the command that starts up your program
--                  command = "R --vanilla --quiet",
-+                  command = "R --no-readline --vanilla --quiet",
- 
-                   server=server,
-                   server_tmpdir=server_tmpdir,
diff --git a/libre/sagemath/sagemath-planarity3.patch b/libre/sagemath/sagemath-planarity3.patch
deleted file mode 100644
index 607600879..000000000
--- a/libre/sagemath/sagemath-planarity3.patch
+++ /dev/null
@@ -1,113 +0,0 @@
-Author: Ximin Luo <infinity0@debian.org>
-Bug: https://trac.sagemath.org/ticket/21774
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/sage/src/sage/graphs/planarity.pyx
-+++ b/sage/src/sage/graphs/planarity.pyx
-@@ -3,13 +3,19 @@
- """
- 
- cdef extern from "planarity/graph.h":
--    ctypedef struct graphNode:
--        int v
-+    ctypedef struct vertexRec:
-         int link[2]
--    ctypedef graphNode * graphNodeP
-+        int index
-+    ctypedef vertexRec * vertexRecP
-+
-+    ctypedef struct edgeRec:
-+        int link[2]
-+        int neighbor
-+    ctypedef edgeRec * edgeRecP
- 
-     ctypedef struct BM_graph:
--        graphNodeP G
-+        vertexRecP V
-+        edgeRecP E
-         int N
-     ctypedef BM_graph * graphP
- 
-@@ -93,15 +99,16 @@
-             g._pos = { u: [0,0], v: [0,1] }
-         return (True, None) if kuratowski else True
- 
--    # create to and from mappings to relabel vertices to the set {0,...,n-1}
-+    # create to and from mappings to relabel vertices to the set {1,...,n}
-+    # (planarity 3 uses 1-based array indexing, with 0 representing NIL)
-     cdef int i
-     listto = g.vertices()
-     ffrom = {}
-     for vvv in listto:
--        ffrom[vvv] = listto.index(vvv)
-+        ffrom[vvv] = listto.index(vvv) + 1
-     to = {}
-     for i from 0 <= i < len(listto):
--        to[i] = listto[i]
-+        to[i + 1] = listto[i]
-     g.relabel(ffrom)
- 
-     cdef graphP theGraph
-@@ -125,7 +132,7 @@
-     status = gp_Embed(theGraph, EMBEDFLAGS_PLANAR)
-     gp_SortVertices(theGraph)
- 
--    # use to and from mappings to relabel vertices back from the set {0,...,n-1}
-+    # use to and from mappings to relabel vertices back from the set {1,...,n}
-     g.relabel(to)
- 
-     if status == NOTOK:
-@@ -134,12 +141,12 @@
-         # Kuratowski subgraph isolator
-         g_dict = {}
-         from sage.graphs.graph import Graph
--        for i from 0 <= i < theGraph.N:
-+        for i from 0 < i <= theGraph.N:
-             linked_list = []
--            j = theGraph.G[i].link[1]
--            while j >= theGraph.N:
--                linked_list.append(to[theGraph.G[j].v])
--                j = theGraph.G[j].link[1]
-+            j = theGraph.V[i].link[1]
-+            while j:
-+                linked_list.append(to[theGraph.E[j].neighbor])
-+                j = theGraph.E[j].link[1]
-             if len(linked_list) > 0:
-                 g_dict[to[i]] = linked_list
-         G = Graph(g_dict)
-@@ -153,12 +160,12 @@
-             if set_embedding:
-                 emb_dict = {}
-                 #for i in range(theGraph.N):
--                for i from 0 <= i < theGraph.N:
-+                for i from 0 < i <= theGraph.N:
-                     linked_list = []
--                    j = theGraph.G[i].link[1]
--                    while j >= theGraph.N:
--                        linked_list.append(to[theGraph.G[j].v])
--                        j = theGraph.G[j].link[1]
-+                    j = theGraph.V[i].link[1]
-+                    while j:
-+                        linked_list.append(to[theGraph.E[j].neighbor])
-+                        j = theGraph.E[j].link[1]
-                     emb_dict[to[i]] = linked_list
-                 g._embedding = emb_dict
-             if set_pos:
-@@ -174,12 +181,12 @@
- 
-                 emb_dict = {}
-                 #for i in range(theGraph.N):
--                for i from 0 <= i < theGraph.N:
-+                for i from 0 < i <= theGraph.N:
-                     linked_list = []
--                    j = theGraph.G[i].link[0]
--                    while j >= theGraph.N:
--                        linked_list.append(to[theGraph.G[j].v])
--                        j = theGraph.G[j].link[0]
-+                    j = theGraph.V[i].link[0]
-+                    while j:
-+                        linked_list.append(to[theGraph.E[j].neighbor])
-+                        j = theGraph.E[j].link[0]
-                     emb_dict[to[i]] = linked_list
-                 g._embedding = emb_dict
-         gp_Free(&theGraph)
diff --git a/libre/sagemath/sagemath-python3-notebook.patch b/libre/sagemath/sagemath-python3-notebook.patch
deleted file mode 100644
index cae225615..000000000
--- a/libre/sagemath/sagemath-python3-notebook.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-diff --git a/src/bin/sage-notebook b/src/bin/sage-notebook
-index 74192da240..0ede281aad 100755
---- a/src/bin/sage-notebook
-+++ b/src/bin/sage-notebook
-@@ -96,8 +96,7 @@ class NotebookJupyter(object):
-         if not have_prerequisites():
-             print(self.PREREQUISITE_ERROR)
-             raise SystemExit(1)
--        from notebook.notebookapp import main
--        main(argv)
-+        os.execvp('jupyter-notebook', ['jupyter-notebook'] + argv)
- 
- 
- class SageNBExport(NotebookJupyter):
-diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py
-index 3912b8cdf5..bd40cdadda 100644
---- a/src/sage/repl/ipython_kernel/install.py
-+++ b/src/sage/repl/ipython_kernel/install.py
-@@ -281,7 +281,6 @@ def have_prerequisites(debug=True):
-         True
-     """
-     try:
--        from notebook.notebookapp import NotebookApp
-         return True
-     except ImportError:
-         if debug:
-
diff --git a/libre/sagemath/sagemath-singular-4.1.0.p2.patch b/libre/sagemath/sagemath-singular-4.1.0.p2.patch
deleted file mode 100644
index b1a74a091..000000000
--- a/libre/sagemath/sagemath-singular-4.1.0.p2.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- src/sage/libs/singular/decl.pxd.orig	2017-02-21 07:58:27.088118954 +0000
-+++ src/sage/libs/singular/decl.pxd	2017-02-21 07:59:01.794846500 +0000
-@@ -484,8 +484,8 @@
- 
-     ring *rDefault(int char , int nvars, char **names)
-     ring *rDefault(const n_Procs_s* cf, int nvars, char **names)
--    ring *rDefault(int ch             , int nvars, char **names,int ord_size, int *ord, int *block0, int *block1, int **wvhdl)
--    ring *rDefault(const n_Procs_s* cf, int nvars, char **names,int ord_size, int *ord, int *block0, int *block1, int **wvhdl)
-+    ring *rDefault(int ch             , int nvars, char **names,int ord_size, rRingOrder_t *ord, int *block0, int *block1, int **wvhdl)
-+    ring *rDefault(const n_Procs_s* cf, int nvars, char **names,int ord_size, rRingOrder_t *ord, int *block0, int *block1, int **wvhdl)
- 
- 
- 
---- src/sage/libs/singular/ring.pyx.orig	2017-02-21 07:24:23.197906897 +0000
-+++ src/sage/libs/singular/ring.pyx	2017-02-21 07:29:23.731763098 +0000
-@@ -21,7 +21,7 @@
- from sage.libs.singular.decl cimport number, poly, ring, currRing
- from sage.libs.singular.decl cimport rChangeCurrRing, rCopy0, rComplete, rDelete, idInit
- from sage.libs.singular.decl cimport omAlloc0, omStrDup, omAlloc, omAlloc0Bin,  sip_sring_bin, rnumber_bin
--from sage.libs.singular.decl cimport ringorder_dp, ringorder_Dp, ringorder_lp, ringorder_rp, ringorder_ds, ringorder_Ds, ringorder_ls, ringorder_M, ringorder_C, ringorder_wp, ringorder_Wp, ringorder_ws, ringorder_Ws, ringorder_a
-+from sage.libs.singular.decl cimport ringorder_dp, ringorder_Dp, ringorder_lp, ringorder_rp, ringorder_ds, ringorder_Ds, ringorder_ls, ringorder_M, ringorder_C, ringorder_wp, ringorder_Wp, ringorder_ws, ringorder_Ws, ringorder_a, rRingOrder_t
- from sage.libs.singular.decl cimport p_Copy, prCopyR
- from sage.libs.singular.decl cimport n_unknown,  n_Zp,  n_Q,   n_R,   n_GF,  n_long_R,  n_algExt,n_transExt,n_long_C,   n_Z,   n_Zn,  n_Znm,  n_Z2m,  n_CF
- from sage.libs.singular.decl cimport n_coeffType, cfInitCharProc
-@@ -165,7 +165,7 @@
-     ##         q    q : GF(q=p^n)       *names         TRUE              (todo)
- 
-     _wvhdl  = <int **>omAlloc0((nblcks + 2) * sizeof(int *))
--    _order  = <int *>omAlloc0((nblcks + 2) * sizeof(int))
-+    _order  = <rRingOrder_t *>omAlloc0((nblcks + 2) * sizeof(int))
-     _block0 = <int *>omAlloc0((nblcks + 2) * sizeof(int))
-     _block1 = <int *>omAlloc0((nblcks + 2) * sizeof(int))
- 
diff --git a/libre/sagemath/skip-check.patch b/libre/sagemath/skip-check.patch
deleted file mode 100644
index 48cac24b7..000000000
--- a/libre/sagemath/skip-check.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- src/bin/sage.orig	2014-12-18 09:47:27.354829070 +0100
-+++ src/bin/sage	2014-12-18 09:48:00.041563401 +0100
-@@ -352,18 +352,6 @@
- 
- # Prepare for running Sage, either interactively or non-interactively.
- sage_setup() {
--    # Check that we're not in a source tarball which hasn't been built yet (#13561).
--    if [ ! -d "$SAGE_LOCAL/lib/python/site-packages/sage" ]; then
--        echo >&2 '************************************************************************'
--        echo >&2 'It seems that you are attempting to run Sage from an unpacked source'
--        echo >&2 'tarball, but you have not compiled it yet (or maybe the build has not'
--        echo >&2 'finished). You should run `make` in the Sage root directory first.'
--        echo >&2 'If you did not intend to build Sage from source, you should download'
--        echo >&2 'a binary tarball instead. Read README.txt for more information.'
--        echo >&2 '************************************************************************'
--        exit 1
--    fi
--
-     # Display the startup banner (unless SAGE_BANNER is explictly "no")
-     if [ "$SAGE_BANNER" != "no" ]; then
-         # can be 'bare', or 'yes', or unspecified
-
diff --git a/libre/sagemath/test-optional.patch b/libre/sagemath/test-optional.patch
deleted file mode 100644
index 1918cbe5d..000000000
--- a/libre/sagemath/test-optional.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- src/sage/doctest/control.py.orig       2016-10-20 19:39:53.714618246 +0200
-+++ src/sage/doctest/control.py    2016-10-20 19:40:15.158049920 +0200
-@@ -307,22 +307,6 @@
-             if "all" in options.optional:
-                 # Special case to run all optional tests
-                 options.optional = True
--            else:
--                # We replace the 'optional' tag by all optional
--                # packages for which the installed version matches the
--                # latest available version (this implies in particular
--                # that the package is actually installed).
--                if 'optional' in options.optional:
--                    options.optional.discard('optional')
--                    from sage.misc.package import list_packages
--                    for pkg in list_packages('optional', local=True).values():
--                        if pkg['installed_version'] == pkg['remote_version']:
--                            options.optional.add(pkg['name'])
--
--                # Check that all tags are valid
--                for o in options.optional:
--                    if not optionaltag_regex.search(o):
--                        raise ValueError('invalid optional tag {!r}'.format(o))
- 
-         self.options = options
-         self.files = args