Update

11 files changed, 125 insertions, 159 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 7ffa6f52c891..69d27a2af2c2 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = sagemath-git
 	pkgdesc = Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab
-	pkgver = 8.2.rc2.r0.g303efaa461
+	pkgver = 8.3.beta0.r0.g8bdc326ba5
 	pkgrel = 1
 	url = http://www.sagemath.org
 	arch = x86_64
@@ -88,6 +88,7 @@ pkgbase = sagemath-git
 	optdepends = latte-integrale: integral point count in polyhedra
 	optdepends = polymake: polymake backend for polyhedral computations
 	optdepends = shared_meataxe: faster matrix arithmetic over finite fields
+	optdepends = openblas: faster linear algebra
 	optdepends = sirocco: for computing the fundamental group of the complement of a plane curve
 	optdepends = three.js: alternative 3D plots engine
 	source = git://git.sagemath.org/sage.git#branch=develop
@@ -100,30 +101,26 @@ pkgbase = sagemath-git
 	source = r-no-readline.patch
 	source = fes02.patch
 	source = sagemath-threejs.patch
-	source = pari-stackwarn.patch
-	source = sagemath-detect-igraph.patch
+	source = sagemath-ignore-warnings.patch
 	source = sagemath-networkx2.patch
 	source = sagemath-scipy-1.0.patch
-	source = sagemath-lrs.patch
 	source = sagemath-singular-4.1.1.patch
 	source = sagemath-lcalc-c++11.patch
 	source = pari-ratpoints.patch::https://github.com/sagemath/sage/commit/83458400.patch
 	sha256sums = SKIP
-	sha256sums = 39b76a189365464998cab9355d177581bc2b15dff10858f316faa85f2efa0426
-	sha256sums = c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107
+	sha256sums = 6f95ef6960acb3b368bc6245783d88fcadaa63537e1bf9f41d8d91b28e95ddf9
+	sha256sums = 9e3c998e0ca8dcbf7ad9f5a8d591f2bc4cb792be14708e064594046081e9b60d
 	sha256sums = 0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a
 	sha256sums = 2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646
 	sha256sums = 962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f
-	sha256sums = ef94908d4ab28d13af622e6e58ec191aa78817d17e4466c7bb6f64ee72a813b9
+	sha256sums = 18edeafb01cc1ed7270c2dfb41a58717918680c98e8eada1858736acd65d92ba
 	sha256sums = afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7
 	sha256sums = 7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94
-	sha256sums = 514135b920a43f999571a15e97b41e14f5bed59f65b19643864dc23555a7b830
-	sha256sums = e4a2f1de73dc3a6deedc1a05d716facd94afc9fe98239c4300e1b67375f95fc1
-	sha256sums = 28d7789b8d777922ab8871ca43b6afab751428cae875c0343d3962e6a2030b88
-	sha256sums = 1024f3a6a9a1a6ae96d9962bb7d1f5842f4a4a5ff5098afad81a60188b7d5160
+	sha256sums = 2d13b15ad2d1511bb3d752a261497060a8901882b1c2fa9813219781b7a71d83
+	sha256sums = a4a6c87b46ff23b89608aca66d00427334502e8bfb5dfe68b94497d19be1c7ae
+	sha256sums = 8253730940687992dd29d90d95bea7e2685bb4854db004090c8196ce92859b64
 	sha256sums = 17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a
-	sha256sums = c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c
-	sha256sums = cc679321c2968d5e74b0ec060979c74019df2995857906bdd1397695b1f24c5c
+	sha256sums = 369f1483e0364031d73d43d9e63b7bf2b0929c8a1d470c1596f98f9f1aa80750
 	sha256sums = 5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0
 	sha256sums = e24ad879f6b2eb970778fc5e867bcbe0a6d393feca8f11f5cb8d07da1f024be9
 
@@ -152,6 +149,7 @@ pkgname = sagemath-git
 	optdepends = latte-integrale: integral point count in polyhedra
 	optdepends = polymake: polymake backend for polyhedral computations
 	optdepends = shared_meataxe: faster matrix arithmetic over finite fields
+	optdepends = openblas: faster linear algebra
 	optdepends = sirocco: for computing the fundamental group of the complement of a plane curve
 	optdepends = three.js: alternative 3D plots engine
 	optdepends = sagemath-jupyter: Jupyter kernel
diff --git a/PKGBUILD b/PKGBUILD
index 5989dc8cbf86..9884e29cb8fb 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -8,7 +8,7 @@
 
 pkgbase=sagemath-git
 pkgname=(sagemath-git sagemath-jupyter-git)
-pkgver=8.2.rc2.r0.g303efaa461
+pkgver=8.3.beta0.r0.g8bdc326ba5
 pkgrel=1
 pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
 arch=(x86_64)
@@ -29,33 +29,30 @@ optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cyt
   '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' 'polymake: polymake backend for polyhedral computations'
-  'shared_meataxe: faster matrix arithmetic over finite fields'
+  'shared_meataxe: faster matrix arithmetic over finite fields' 'openblas: faster linear algebra'
   'sirocco: for computing the fundamental group of the complement of a plane curve'
   'three.js: alternative 3D plots engine')
 makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco
   mcqd coxeter bliss-graphs tdlib python2-pkgconfig shared_meataxe libfes git)
 source=(git://git.sagemath.org/sage.git#branch=develop
         sagemath-env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch
-        r-no-readline.patch fes02.patch sagemath-threejs.patch pari-stackwarn.patch
-        sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-scipy-1.0.patch sagemath-lrs.patch
-        sagemath-singular-4.1.1.patch sagemath-lcalc-c++11.patch
+        r-no-readline.patch fes02.patch sagemath-threejs.patch sagemath-ignore-warnings.patch
+        sagemath-networkx2.patch sagemath-scipy-1.0.patch sagemath-singular-4.1.1.patch sagemath-lcalc-c++11.patch
         pari-ratpoints.patch::"https://github.com/sagemath/sage/commit/83458400.patch")
 sha256sums=('SKIP'
-            '39b76a189365464998cab9355d177581bc2b15dff10858f316faa85f2efa0426'
-            'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107'
+            '6f95ef6960acb3b368bc6245783d88fcadaa63537e1bf9f41d8d91b28e95ddf9'
+            '9e3c998e0ca8dcbf7ad9f5a8d591f2bc4cb792be14708e064594046081e9b60d'
             '0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a'
             '2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646'
             '962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f'
-            'ef94908d4ab28d13af622e6e58ec191aa78817d17e4466c7bb6f64ee72a813b9'
+            '18edeafb01cc1ed7270c2dfb41a58717918680c98e8eada1858736acd65d92ba'
             'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7'
             '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94'
-            '514135b920a43f999571a15e97b41e14f5bed59f65b19643864dc23555a7b830'
-            'e4a2f1de73dc3a6deedc1a05d716facd94afc9fe98239c4300e1b67375f95fc1'
-            '28d7789b8d777922ab8871ca43b6afab751428cae875c0343d3962e6a2030b88'
-            '1024f3a6a9a1a6ae96d9962bb7d1f5842f4a4a5ff5098afad81a60188b7d5160'
+            '2d13b15ad2d1511bb3d752a261497060a8901882b1c2fa9813219781b7a71d83'
+            'a4a6c87b46ff23b89608aca66d00427334502e8bfb5dfe68b94497d19be1c7ae'
+            '8253730940687992dd29d90d95bea7e2685bb4854db004090c8196ce92859b64'
             '17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a'
-            'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c'
-            'cc679321c2968d5e74b0ec060979c74019df2995857906bdd1397695b1f24c5c'
+            '369f1483e0364031d73d43d9e63b7bf2b0929c8a1d470c1596f98f9f1aa80750'
             '5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0'
             'e24ad879f6b2eb970778fc5e867bcbe0a6d393feca8f11f5cb8d07da1f024be9')
 
@@ -82,19 +79,12 @@ prepare(){
   patch -p1 -i ../latte-count.patch
 # make 'sage -notebook=jupyter' work with our python3 jupyter-notebook package
   patch -p1 -i ../sagemath-python3-notebook.patch
-# fix Cremona database detection
-  sed -e "s|is_package_installed('database_cremona_ellcurve')|os.path.exists('/usr/share/cremona/cremona.db')|" \
-   -i src/sage/databases/cremona.py
-# fix python-igraph detection
-  patch -p1 -i ../sagemath-detect-igraph.patch
-# fix lrs detection
-  patch -p1 -i ../sagemath-lrs.patch
 # adapt to networkx 2 changes
   patch -p1 -i ../sagemath-networkx2.patch
 # fix three.js plotting backend
   patch -p1 -i ../sagemath-threejs.patch
-# don't show PARI stack size increase warnings during doctesting (Debian)
-  patch -p1 -i ../pari-stackwarn.patch
+# don't show PARI stack size increase or GLPK warnings during doctesting (Debian)
+  patch -p1 -i ../sagemath-ignore-warnings.patch
 # remove deprecated scipy parameters
   patch -p1 -i ../sagemath-scipy-1.0.patch
 # fix build with Singular 4.1.1
@@ -109,20 +99,15 @@ prepare(){
   patch -p1 -i ../fes02.patch
 
 # use python2
-  sed -e 's|#!/usr/bin/env sage-python23|#!/usr/bin/env python2|' -e 's|\<#!/usr/bin/env sage-python\>|#!/usr/bin/env python2|' \
-    -e 's|\<exec python\>|exec python2|' -i src/bin/*
+  sed -e 's|#!/usr/bin/env sage-python23|#!/usr/bin/env python2|' -e 's|#!/usr/bin/env python\b|#!/usr/bin/env python2|' \
+    -e 's|exec python\b|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|exec ipython\b|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
-  autoreconf -vi
-  ./configure --prefix=/usr || true
-
-  cd src
+  cd sage/src
 
   export SAGE_ROOT="$PWD"
   export SAGE_SRC="$PWD"
@@ -145,7 +130,7 @@ package_sagemath-git() {
 
   mkdir -p "$pkgdir"/usr/bin
   cp bin/sage "$pkgdir"/usr/bin
-  for _i in arch-env cachegrind callgrind cleaner coverage coverageall cython env env-config eval grep grepdoc inline-fortran \
+  for _i in 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
diff --git a/package.patch b/package.patch
index 62e1e3df57a1..152786f0c523 100644
--- a/package.patch
+++ b/package.patch
@@ -1,8 +1,8 @@
 --- 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
-@@ -320,7 +320,7 @@
-         sage: for pkg in list_packages('pip', local=True):
-         ....:     assert not is_package_installed(pkg)
+@@ -329,7 +329,7 @@
+         Use the framework provided by :mod:`sage.features` to check
+         whether a library is installed and functional.
      """
 -    return any(p.split('-')[0] == package for p in installed_packages(exclude_pip))
 +    return True
@@ -13,17 +13,18 @@
 +++ 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
+ from sage.misc.package import list_packages
  
 -all_packages = list_packages(local=True)
 -
  
  class CythonizeExtension(Extension):
      """
-@@ -76,14 +74,7 @@
+@@ -76,15 +74,7 @@
          condition = kwds.pop("condition")
      except KeyError:
          pkg = kwds.pop("package")
+-        from sage.misc.package import is_package_installed
 -        try:
 -            pkginfo = all_packages[pkg]
 -        except KeyError:
diff --git a/sagemath-detect-igraph.patch b/sagemath-detect-igraph.patch
deleted file mode 100644
index dc6babe49ac5..000000000000
--- a/sagemath-detect-igraph.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-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
-@@ -8188,10 +8188,12 @@ 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/sagemath-env.patch b/sagemath-env.patch
index ff08bd0fc63a..906d3efafeca 100644
--- a/sagemath-env.patch
+++ b/sagemath-env.patch
@@ -41,29 +41,57 @@
 -fi
 +NEW_SAGE_ROOT="/usr"
  
- # Display the Sage startup banner, used in src/bin/sage
- sage_banner() {
-@@ -185,6 +185,7 @@
+ 
+ # Don't execute the commands more than once for the same version of
+@@ -174,33 +174,9 @@
  export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION
  
  export SAGE_ROOT="$NEW_SAGE_ROOT"
 +export SAGE_LOCAL='/usr'
++export SAGE_SCRIPTS_DIR='/usr/bin'
  
+-
+-# sage-env must know where the Sage's script files are.
+-# Note that SAGE_SCRIPTS_DIR is only used here, so it does not need to
+-# be exported.
+-if [ -z "$SAGE_SCRIPTS_DIR" ]; then
+-    if [ -n "$SAGE_LOCAL" ] && [ -f "$SAGE_LOCAL/bin/sage-env-config" ]; then
+-        SAGE_SCRIPTS_DIR="$SAGE_LOCAL/bin"
+-    elif [ -f "$SAGE_ROOT/src/bin/sage-env-config" ]; then
+-        SAGE_SCRIPTS_DIR="$SAGE_ROOT/src/bin"
+-    else
+-        echo >&2 "Error: You must set either the SAGE_LOCAL or SAGE_SCRIPTS_DIR environment variable to run this"
+-        return 1
+-    fi
+-elif [ ! -f "$SAGE_SCRIPTS_DIR/sage-env-config" ]; then
+-    echo >&2 "Error: SAGE_SCRIPTS_DIR is set to a bad value:"
+-    echo >&2 "SAGE_SCRIPTS_DIR=$SAGE_SCRIPTS_DIR"
+-    echo >&2 "You must correct it or erase it and rerun this script"
+-    return 1
+-fi
+-
+-# Set environment variables (like SAGE_LOCAL) depending on ./configure
+-. "$SAGE_SCRIPTS_DIR/sage-env-config"
+-if [ $? -ne 0 ]; then
+-    echo >&2 "Error: failed to source $SAGE_SCRIPTS_DIR/sage-env-config"
+-    return 1
+-fi
  
- # sage-env must know where the Sage's script files are.
-@@ -307,8 +307,9 @@
+ # The compilers are set in order of priority by
+ # 1) environment variables
+@@ -296,8 +296,9 @@
  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_SRC="$SAGE_LOCAL/lib/python2.7/site-packages"
 +export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
  export SAGE_DOC="$SAGE_SHARE/doc/sage"
  
  if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
-@@ -414,6 +414,9 @@
+@@ -403,6 +403,9 @@
      export SAGE_STARTUP_FILE
  fi
  
@@ -73,7 +101,7 @@
  if [ "$PYTHON_EGG_CACHE" = "" ]; then
      PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs"
      export PYTHON_EGG_CACHE
-@@ -499,7 +499,6 @@
+@@ -488,7 +488,6 @@
          fi
      fi
  fi
@@ -81,7 +109,7 @@
  
  PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
  
-@@ -619,9 +619,6 @@
+@@ -608,9 +608,6 @@
      LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
  fi
  
@@ -93,7 +121,7 @@
  # First, figure out the right values for SAGE_NUM_THREADS (default
 --- src/sage/env.py.orig       2017-12-07 19:51:25.554281539 +0000
 +++ src/sage/env.py    2017-12-07 19:51:42.787654650 +0000
-@@ -117,8 +117,8 @@
+@@ -117,13 +117,13 @@
  _add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid())
  
  # bunch of sage directories and files
@@ -104,4 +132,18 @@
  _add_variable_or_fallback('SAGE_ETC',        opj('$SAGE_LOCAL', 'etc'))
  _add_variable_or_fallback('SAGE_INC',        opj('$SAGE_LOCAL', 'include'))
  _add_variable_or_fallback('SAGE_SHARE',      opj('$SAGE_LOCAL', 'share'))
-
+ 
+-_add_variable_or_fallback('SAGE_SRC',        opj('$SAGE_ROOT', 'src'))
++_add_variable_or_fallback('SAGE_SRC',        opj('$SAGE_LOCAL', 'lib', 'python2.7', 'site-packages'))
+ 
+ try:
+     sitepackages_dirs = site.getsitepackages()
+@@ -163,7 +163,7 @@
+ _add_variable_or_fallback('GRAPHS_DATA_DIR',  opj('$SAGE_SHARE','graphs'))
+ _add_variable_or_fallback('ELLCURVE_DATA_DIR',opj('$SAGE_SHARE','ellcurves'))
+ _add_variable_or_fallback('POLYTOPE_DATA_DIR',opj('$SAGE_SHARE','reflexive_polytopes'))
+-_add_variable_or_fallback('GAP_ROOT_DIR',     opj('$SAGE_LOCAL','gap','latest'))
++_add_variable_or_fallback('GAP_ROOT_DIR',     opj('$SAGE_LOCAL','lib','gap'))
+ _add_variable_or_fallback('THEBE_DIR',        opj('$SAGE_SHARE','thebe'))
+ 
+ # locate singular shared object
diff --git a/pari-stackwarn.patch b/sagemath-ignore-warnings.patch
index b01e1c90f30f..c1094d844bc5 100644
--- a/pari-stackwarn.patch
+++ b/sagemath-ignore-warnings.patch
@@ -5,19 +5,21 @@ Description: Ignore warnings of PARI increasing the stack size when parsing doct
 Author: Tobias Hansen <thansen@debian.org>
 --- sage/src/sage/doctest/parsing.py
 +++ sage/src/sage/doctest/parsing.py
-@@ -40,6 +40,7 @@
+@@ -40,6 +40,8 @@
  
  float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)')
  optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))')
 +pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.')
++glpk_simplex_warning_regex = re.compile(r'(Long-step dual simplex will be used)')
  find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M)
  find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M)
  random_marker = re.compile('.*random', re.I)
-@@ -881,6 +882,7 @@
-             u'you'
+@@ -935,6 +936,8 @@
+             <type 'float'>
          """
          got = self.human_readable_escape_sequences(got)
 +        got = pari_stack_warning_regex.sub('', got)
++        got = glpk_simplex_warning_regex.sub('', got)
          if isinstance(want, MarkedOutput):
              if want.random:
                  return True
diff --git a/sagemath-lrs.patch b/sagemath-lrs.patch
deleted file mode 100644
index f0e5ea4eac8d..000000000000
--- a/sagemath-lrs.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py
-index 2115de6800..da94aa5d45 100644
---- a/src/sage/game_theory/normal_form_game.py
-+++ b/src/sage/game_theory/normal_form_game.py
-@@ -621,6 +621,7 @@ from sage.matrix.constructor import vector
- from sage.misc.package import is_package_installed, PackageNotFoundError
- from sage.misc.temporary_file import tmp_filename
- from sage.numerical.mip import MixedIntegerLinearProgram
-+import os
- 
- try:
-     from gambit import Game
-@@ -1636,7 +1637,7 @@ class NormalFormGame(SageObject, MutableMapping):
-         if not algorithm:
-             if self.is_constant_sum():
-                 algorithm = "lp"
--            elif is_package_installed('lrslib'):
-+            elif os.path.exists('/usr/bin/lrsnash'):
-                 algorithm = "lrs"
-             else:
-                 algorithm = "enumeration"
-
diff --git a/sagemath-networkx2.patch b/sagemath-networkx2.patch
index 0b4ca5cf54c5..8090add150ce 100644
--- a/sagemath-networkx2.patch
+++ b/sagemath-networkx2.patch
@@ -28,7 +28,7 @@ index ff1d02900a..bad4a18539 100644
  
          """
          import networkx
-@@ -1158,7 +1156,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
+@@ -1154,7 +1152,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
          import networkx
          try:
              if self._nxg.is_multigraph():
@@ -37,7 +37,7 @@ index ff1d02900a..bad4a18539 100644
                      if d.get('weight',None) == l:
                          self._nxg.remove_edge(u,v,k)
                          break
-@@ -1227,7 +1225,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
+@@ -1223,7 +1221,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
          """
          cdef dict E
          try:
@@ -46,7 +46,7 @@ index ff1d02900a..bad4a18539 100644
          except KeyError:
              from networkx import NetworkXError
              raise NetworkXError("Edge (%s,%s) requested via get_edge_label does not exist."%(u,v))
-@@ -1416,7 +1414,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
+@@ -1412,7 +1410,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
              sage: G.iterator_nbrs(0)
              <dictionary-keyiterator object at ...>
          """
@@ -68,7 +68,7 @@ index 003a8d6bcb..986137a9b0 100644
          elif format == 'igraph':
              if not data.is_directed():
                  raise ValueError("A *directed* igraph graph was expected. To "+
-@@ -2844,7 +2844,7 @@ class DiGraph(GenericGraph):
+@@ -2846,7 +2846,7 @@ class DiGraph(GenericGraph):
          Using the NetworkX implementation ::
  
              sage: D.topological_sort(implementation = "NetworkX")
@@ -77,7 +77,7 @@ index 003a8d6bcb..986137a9b0 100644
  
          Using the NetworkX recursive implementation ::
  
-@@ -2870,9 +2870,7 @@ class DiGraph(GenericGraph):
+@@ -2872,9 +2872,7 @@ class DiGraph(GenericGraph):
                sage: D = DiGraph({ 0:[1,2,3], 4:[2,5], 1:[8], 2:[7], 3:[7],
                ....:   5:[6,7], 7:[8], 6:[9], 8:[10], 9:[10] })
                sage: N = D.networkx_graph()
@@ -88,7 +88,7 @@ index 003a8d6bcb..986137a9b0 100644
                [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10]
  
          TESTS:
-@@ -2895,10 +2893,7 @@ class DiGraph(GenericGraph):
+@@ -2897,10 +2895,7 @@ class DiGraph(GenericGraph):
  
          elif implementation == "NetworkX" or implementation == "recursive":
              import networkx
@@ -100,28 +100,6 @@ index 003a8d6bcb..986137a9b0 100644
              if S is None:
                  raise TypeError('Digraph is not acyclic; there is no topological sort.')
              else:
-diff --git a/src/sage/graphs/generators/basic.py b/src/sage/graphs/generators/basic.py
-index 8777b95c4b..28ef7e48f2 100644
---- a/src/sage/graphs/generators/basic.py
-+++ b/src/sage/graphs/generators/basic.py
-@@ -437,7 +437,7 @@ def CompleteBipartiteGraph(n1, n2):
- 
-     Compare the plotting::
- 
--        sage: n = networkx.complete_bipartite_graph(11,17)
-+        sage: n = networkx.complete_bipartite_graph(11r,17r)
-         sage: spring_med = Graph(n)
-         sage: posdict_med = graphs.CompleteBipartiteGraph(11,17)
- 
-@@ -469,7 +469,7 @@ def CompleteBipartiteGraph(n1, n2):
-         sage: g = []
-         sage: j = []
-         sage: for i in range(9):
--        ....:     spr = networkx.complete_bipartite_graph(i+1,4)
-+        ....:     spr = networkx.complete_bipartite_graph(int(i+1),4r)
-         ....:     k = Graph(spr)
-         ....:     g.append(k)
-         sage: for i in range(3):
 diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
 index 8f81333685..1540ec0dcc 100644
 --- a/src/sage/graphs/generators/families.py
@@ -149,15 +127,6 @@ diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py
 index 3550f990ef..490813e619 100644
 --- a/src/sage/graphs/graph.py
 +++ b/src/sage/graphs/graph.py
-@@ -108,7 +108,7 @@ examples are covered here.
-    ::
- 
-        sage: import networkx
--       sage: K = networkx.complete_bipartite_graph(12,7)
-+       sage: K = networkx.complete_bipartite_graph(12r,7r)
-        sage: G = Graph(K)
-        sage: G.degree()
-        [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12]
 @@ -1199,7 +1199,7 @@ class Graph(GenericGraph):
              self.allow_loops(loops, check=False)
              self.allow_multiple_edges(multiedges, check=False)
@@ -167,7 +136,7 @@ index 3550f990ef..490813e619 100644
          elif format == 'igraph':
              if data.is_directed():
                  raise ValueError("An *undirected* igraph graph was expected. "+
-@@ -4600,7 +4600,7 @@ class Graph(GenericGraph):
+@@ -4621,7 +4621,7 @@ class Graph(GenericGraph):
  
              sage: g = Graph([(0,1,0), (1,2,999), (2,3,-5)])
              sage: g.matching(use_edge_labels=True)
@@ -176,16 +145,25 @@ index 3550f990ef..490813e619 100644
              sage: g.matching(algorithm="LP", use_edge_labels=True)
              [(1, 2, 999)]
  
-@@ -6288,7 +6288,7 @@ class Graph(GenericGraph):
+@@ -4671,7 +4671,7 @@ class Graph(GenericGraph):
+             else:
+                 for u, v in L:
+                     g.add_edge(u, v)
+-            d = networkx.max_weight_matching(g)
++            d = dict(networkx.max_weight_matching(g).union(t[::-1] for t in networkx.max_weight_matching(g)))
+             if value_only:
+                 if use_edge_labels:
+                     return sum(W[u, v] for u, v in six.iteritems(d) if u < v)
+@@ -6305,7 +6305,7 @@ class Graph(GenericGraph):
          return networkx.number_of_cliques(self.networkx_graph(copy=False), vertices, cliques)
  
      @doc_index("Clique-related methods")
 -    def cliques_get_max_clique_graph(self, name=''):
 +    def cliques_get_max_clique_graph(self):
          """
-         Returns a graph constructed with maximal cliques as vertices, and
-         edges between maximal cliques with common members in the original
-@@ -6317,7 +6317,7 @@ class Graph(GenericGraph):
+         Return the clique graph.
+ 
+@@ -6336,7 +6336,7 @@ class Graph(GenericGraph):
              sage: (G.cliques_get_max_clique_graph()).show(figsize=[2,2])
          """
          import networkx
@@ -194,3 +172,4 @@ index 3550f990ef..490813e619 100644
  
      @doc_index("Clique-related methods")
      def cliques_get_clique_bipartite(self, **kwds):
+
diff --git a/sagemath-singular-4.1.1.patch b/sagemath-singular-4.1.1.patch
index 3c925458521b..5e5d3ba38d2a 100644
--- a/sagemath-singular-4.1.1.patch
+++ b/sagemath-singular-4.1.1.patch
@@ -2,7 +2,7 @@ diff --git a/src/sage/libs/singular/decl.pxd b/src/sage/libs/singular/decl.pxd
 index 676544ab1e..5c8639d362 100644
 --- a/src/sage/libs/singular/decl.pxd
 +++ b/src/sage/libs/singular/decl.pxd
-@@ -188,7 +188,7 @@ cdef extern from "singular/Singular/libsingular.h":
+@@ -170,7 +170,7 @@ cdef extern from "singular/Singular/libsingular.h":
  
      int n_NumberOfParameters(const n_Procs_s* r)
  
@@ -11,7 +11,7 @@ index 676544ab1e..5c8639d362 100644
          poly *next
          number *coef
          unsigned long exp[1]
-@@ -650,7 +650,7 @@ cdef extern from "singular/Singular/libsingular.h":
+@@ -632,7 +632,7 @@ cdef extern from "singular/Singular/libsingular.h":
  
      # divide monomial p by monomial q, p,q const
  
@@ -24,7 +24,7 @@ diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sa
 index 089524d6b4..ce6d58fc6f 100644
 --- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
 +++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
-@@ -188,8 +188,8 @@ from sage.libs.singular.decl cimport (
+@@ -190,8 +190,8 @@ from sage.libs.singular.decl cimport (
      n_IsUnit, n_Invers,
      p_ISet, rChangeCurrRing, p_Copy, p_Init, p_SetCoeff, p_Setm, p_SetExp, p_Add_q,
      p_NSet, p_GetCoeff, p_Delete, p_GetExp, pNext, rRingVar, omAlloc0, omStrDup,
@@ -35,7 +35,7 @@ index 089524d6b4..ce6d58fc6f 100644
      p_IsUnit, p_Series, p_Head, idInit, fast_map_common_subexp, id_Delete,
      p_IsHomogeneous, p_Homogen, p_Totaldegree,pLDeg1_Totaldegree, singclap_pdivide, singclap_factorize,
      idLift, IDELEMS, On, Off, SW_USE_CHINREM_GCD, SW_USE_EZGCD,
-@@ -1690,8 +1695,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic):
+@@ -1692,8 +1697,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic):
          if not g._poly:
              raise ZeroDivisionError
  
@@ -46,7 +46,7 @@ index 089524d6b4..ce6d58fc6f 100644
          if coeff:
              if r.cf.type == n_unknown or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf):
                  n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf)
-@@ -1850,8 +1855,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic):
+@@ -1852,8 +1857,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic):
                     and (<MPolynomial_libsingular>g) \
                     and g.parent() is self \
                     and p_LmDivisibleBy((<MPolynomial_libsingular>g)._poly, m, r):
@@ -57,7 +57,7 @@ index 089524d6b4..ce6d58fc6f 100644
                  #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<MPolynomial_libsingular>g)._poly, r), r), r)
                  p_SetCoeff(flt, n_Init(1, r), r)
                  return new_MP(self,flt), g
-@@ -4046,10 +4051,10 @@ cdef class MPolynomial_libsingular(MPolynomial):
+@@ -4049,10 +4054,10 @@ cdef class MPolynomial_libsingular(MPolynomial):
              if _right.is_monomial():
                  p = _self._poly
                  quo = p_ISet(0,r)
diff --git a/sagemath-threejs.patch b/sagemath-threejs.patch
index ec9453c03e67..a837db7ea2cc 100644
--- a/sagemath-threejs.patch
+++ b/sagemath-threejs.patch
@@ -5,7 +5,7 @@
          if online:
              from sage.misc.package import installed_packages
 -            version = installed_packages()['threejs']
-+            version = 'r80'
++            version = 'r90'
              return """
  <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/build/three.min.js"></script>
  <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/examples/js/controls/OrbitControls.js"></script>
diff --git a/test-optional.patch b/test-optional.patch
index 1fae8b4962cc..891f8181dc02 100644
--- a/test-optional.patch
+++ b/test-optional.patch
@@ -1,6 +1,6 @@
 --- 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
-@@ -320,22 +320,6 @@
+@@ -326,24 +326,6 @@
              if "all" in options.optional:
                  # Special case to run all optional tests
                  options.optional = True
@@ -20,6 +20,8 @@
 -                for o in options.optional:
 -                    if not optionaltag_regex.search(o):
 -                        raise ValueError('invalid optional tag {!r}'.format(o))
- 
+-
+-                options.optional |= auto_optional_tags
+
          self.options = options
          self.files = args