[arch-commits] Commit in sagemath/trunk (10 files)

Antonio Rojas arojas at archlinux.org
Thu Jun 27 05:59:51 UTC 2019


    Date: Thursday, June 27, 2019 @ 05:59:51
  Author: arojas
Revision: 484664

Update to 8.8

Modified:
  sagemath/trunk/PKGBUILD
  sagemath/trunk/latte-count.patch
  sagemath/trunk/package.patch
  sagemath/trunk/sagemath-env.patch
  sagemath/trunk/sagemath-python3-notebook.patch
  sagemath/trunk/sagemath-threejs.patch
  sagemath/trunk/test-optional.patch
Deleted:
  sagemath/trunk/sagemath-gap-4.10.1.patch
  sagemath/trunk/sagemath-sphinx-1.8.patch
  sagemath/trunk/sagemath-threejs-100.patch

---------------------------------+
 PKGBUILD                        |   60 ++---
 latte-count.patch               |   20 -
 package.patch                   |    2 
 sagemath-env.patch              |   18 -
 sagemath-gap-4.10.1.patch       |  381 --------------------------------------
 sagemath-python3-notebook.patch |    2 
 sagemath-sphinx-1.8.patch       |   28 --
 sagemath-threejs-100.patch      |   52 -----
 sagemath-threejs.patch          |    4 
 test-optional.patch             |   13 -
 10 files changed, 52 insertions(+), 528 deletions(-)

Modified: PKGBUILD
===================================================================
--- PKGBUILD	2019-06-27 03:36:32 UTC (rev 484663)
+++ PKGBUILD	2019-06-27 05:59:51 UTC (rev 484664)
@@ -7,8 +7,8 @@
 
 pkgbase=sagemath
 pkgname=(sagemath sagemath-jupyter)
-pkgver=8.7
-pkgrel=5
+pkgver=8.8
+pkgrel=1
 pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
 arch=(x86_64)
 url="http://www.sagemath.org"
@@ -27,7 +27,7 @@
   'coxeter: Coxeter groups implementation'
   'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
   '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'
+  'latte-integrale: integral point count in polyhedra' 'python2-jupymake: polymake backend for polyhedral computations'
   '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' 'primecount: faster prime_pi implementation'
   'dot2tex: for displaying some diagrams' 'cryptominisat5: SAT solver' 'python2-pycosat: picosat SAT solver'
@@ -43,26 +43,20 @@
         fes02.patch
         sagemath-threejs.patch
         sagemath-cremona.patch
-        sagemath-sphinx-1.8.patch
         sagemath-singular-4.1.2.patch
         sagemath-ecl-sigfpe.patch
-        sagemath-gap-4.10.1.patch
-        sagemath-threejs-100.patch
         sagemath-linbox-1.6.patch)
-sha256sums=('263c3b3fc956b8bebc532f3b51e68c1b0d559d3b7e7c9fadffdfc0f4dbae18ab'
-            'e0e36f2a39b634a76e1c3ad9a31f9ab60e734dd53b43203557b76613277d53b9'
-            'b1068a8d5750051c2b5cfcb89d3d5870cf4233ab445e71c398543fb8b1e6281a'
-            'b66d5bb692159910cec83c80262c43a687d3a678010c7ae4c7070f7cf3a0d5cb'
-            '12cd410035ae644c2495b0dcd3a5138133a471ecc07912d37114c46ee837eb0e'
-            'f12bd2a53ad51549015093aacc89978f4d796d9ab5bcd3d737aa0d57a5815b54'
+sha256sums=('d012ff4f0f34e086fcaf576e25220fc647826116c69b62b887bc0b8ced5c1e9f'
+            '1c2a2d750e81ac65a1dc07094f086ba07f4862288c935a1cd009cdd62bcfc23c'
+            '328e45e78065b5f6527174bda48cfff6828acbf107c2535b0a9a92c3ceb35842'
+            '596d03daf53a76b04029b120619253250b0e58d530d69f14afa169e27e06f446'
+            '7be9f88975079d671eb3cde78e752e74741bcc29ba9b323bab5cddf50ce6dec9'
+            '1f2a34e15bf732ec8687c467a52e897615505dc3ddd792d811e8b6a7e19f1517'
             '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94'
-            'd3c50256cfcf84a90336647f8a1164386b6b8034f47c45361d57be487e92d2c1'
+            'a8c1409f4b4f1553b4f7602d4a6f0f3c6297ed258feed079f6560b0ec2dc62c6'
             '4c6df9e4e5a7b29ecf6189eda3e5a79f69b6e1b4d29c1b9559663149b8c0af96'
-            '22f5e44a42c8276025b8512f45cac1c36d576c29c7fd9d36fde8b19ff87867d8'
             '961bfb5694b67d425d21240d71490cb71714b5207c23448c89be0966512ff8f9'
             'a42f3b152b1aedb8abf16bc70971419919d1fe30328574e7fef8305f9d07d938'
-            '9ec56a3788e32c54f35abeaeedf7cadf6670fa10d39007050b23b93d3c35278e'
-            '3ee624bb47f757516a860799d817168fe9cf74e603416e18e70c93c692259242'
             '81fc39e39e8508f742ccc784efd0492fd04474cee75edf7bd3cbea43edd49b2e')
 
 prepare(){
@@ -79,12 +73,8 @@
   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 three.js plotting backend
+# use correct online three.js version
   patch -p1 -i ../sagemath-threejs.patch
-# fix introspection with sphinx 1.8
-  patch -p1 -i ../sagemath-sphinx-1.8.patch
-# port to GAP 4.10.1 API changes
-  patch -p1 -i ../sagemath-gap-4.10.1.patch
 
 # Upstream patches  
 # fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
@@ -95,17 +85,13 @@
   patch -p1 -i ../sagemath-singular-4.1.2.patch
 # Fix SIGFPE crashes with ecl 16.1.3 https://trac.sagemath.org/ticket/22191
   patch -p1 -i ../sagemath-ecl-sigfpe.patch
-# Fix rendering with three.js r100 https://trac.sagemath.org/ticket/26718
-  patch -p1 -i ../sagemath-threejs-100.patch
 # fix build with linbox 1.6 https://trac.sagemath.org/ticket/26932
   patch -p1 -i ../sagemath-linbox-1.6.patch
 
 # use python2
   sed -e 's|sage-python23|python2|' -e 's|#!/usr/bin/env python\b|#!/usr/bin/env 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\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|"python"|"python2"|' -i src/sage/env.py
 }
 
 
@@ -112,10 +98,10 @@
 build() {
   cd sage-$pkgver/src
 
-  export CC=gcc
-  export SAGE_ROOT="$PWD"
-  export SAGE_SRC="$PWD"
-  export SAGE_NUM_THREADS=10
+  export CC=gcc \
+         SAGE_ROOT="$PWD" \
+         SAGE_SRC="$PWD" \
+         SAGE_NUM_THREADS=10
   python2 setup.py build
 }
 
@@ -124,14 +110,14 @@
 
   cd sage-$pkgver/src
 
-  export SAGE_ROOT="$PWD"
-  export SAGE_LOCAL="/usr"
-  export SAGE_EXTCODE="$PWD"/ext
+  export SAGE_ROOT="$PWD" \
+         SAGE_LOCAL="/usr" \
+         SAGE_EXTCODE="$PWD"/ext
   python2 setup.py install --root="$pkgdir" --optimize=1
 
   mkdir -p "$pkgdir"/usr/bin
   cp bin/{sage,math-readline} "$pkgdir"/usr/bin
-  for _i in cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran ipynb2rst \
+  for _i in cachegrind callgrind cleaner coverage coverageall cython env eval fixdoctests grep grepdoc inline-fortran ipynb2rst \
     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
@@ -143,6 +129,9 @@
   
 # Remove sage_setup
   rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
+# Install tests
+  cp -r sage/doctest/tests "$pkgdir"/usr/lib/python2.7/site-packages/sage/doctest
+  cp -r sage/tests/books "$pkgdir"/usr/lib/python2.7/site-packages/sage/tests
 
 # Split jupyter kernel
   rm -r "$pkgdir"/usr/share/jupyter
@@ -155,9 +144,8 @@
 
   cd sage-$pkgver/src
 
-  export SAGE_ROOT="$PWD"
-  export SAGE_LOCAL="/usr"
-
+  export SAGE_ROOT="$PWD" \
+         SAGE_LOCAL="/usr"
   python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update(prefix='$pkgdir/usr')"
 # fix symlinks to assets
   for _i in $(ls ext/notebook-ipython); do

Modified: latte-count.patch
===================================================================
--- latte-count.patch	2019-06-27 03:36:32 UTC (rev 484663)
+++ latte-count.patch	2019-06-27 05:59:51 UTC (rev 484664)
@@ -2,7 +2,7 @@
 index 268af9db0d..70d41dfa30 100644
 --- a/src/sage/geometry/polyhedron/base_ZZ.py
 +++ b/src/sage/geometry/polyhedron/base_ZZ.py
-@@ -171,7 +171,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+@@ -170,7 +170,7 @@ class Polyhedron_ZZ(Polyhedron_base):
              sage: p = P.ehrhart_polynomial(maxdet=5, verbose=True)  # optional - latte_int
              This is LattE integrale ...
              ...
@@ -11,7 +11,7 @@
              ...
              sage: p    # optional - latte_int
              1/2*t^2 + 3/2*t + 1
-@@ -179,7 +179,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+@@ -178,7 +178,7 @@ class Polyhedron_ZZ(Polyhedron_base):
              sage: p = P.ehrhart_polynomial(dual=True, verbose=True)  # optional - latte_int
              This is LattE integrale ...
              ...
@@ -20,7 +20,7 @@
              ...
              sage: p   # optional - latte_int
              1/2*t^2 + 3/2*t + 1
-@@ -187,7 +187,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+@@ -186,7 +186,7 @@ class Polyhedron_ZZ(Polyhedron_base):
              sage: p = P.ehrhart_polynomial(irrational_primal=True, verbose=True)   # optional - latte_int
              This is LattE integrale ...
              ...
@@ -29,7 +29,7 @@
              ...
              sage: p   # optional - latte_int
              1/2*t^2 + 3/2*t + 1
-@@ -195,7 +195,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+@@ -194,7 +194,7 @@ class Polyhedron_ZZ(Polyhedron_base):
              sage: p = P.ehrhart_polynomial(irrational_all_primal=True, verbose=True)  # optional - latte_int
              This is LattE integrale ...
              ...
@@ -38,7 +38,7 @@
              ...
              sage: p   # optional - latte_int
              1/2*t^2 + 3/2*t + 1
-@@ -207,7 +207,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+@@ -206,7 +206,7 @@ class Polyhedron_ZZ(Polyhedron_base):
              ...
              RuntimeError: LattE integrale program failed (exit code 1):
              ...
@@ -73,7 +73,7 @@
 index 63d227fd35..040a5cf1f9 100644
 --- a/src/sage/features/latte.py
 +++ b/src/sage/features/latte.py
-@@ -10,10 +10,10 @@ from . import Executable, Feature, FeatureTestResult
+@@ -9,10 +9,10 @@ from . import Executable, Feature, FeatureTestResult
  
  class Latte_count(Executable):
      r"""
@@ -81,9 +81,9 @@
 +    Feature for the executable ``latte-count`` from the LattE suite.
      """
      def __init__(self):
--        Executable.__init__(self, "count", executable="count", spkg="latte_int", url="https://www.math.ucdavis.edu/~latte/software.php")
-+        Executable.__init__(self, "latte-count", executable="latte-count", spkg="latte_int", url="https://www.math.ucdavis.edu/~latte/software.php")
+-        Executable.__init__(self, "count", executable="count",
++        Executable.__init__(self, "latte-count", executable="count",
+                             spkg="latte_int",
+                             url=LATTE_URL)
  
- class Latte_integrate(Executable):
-     r"""
 

Modified: package.patch
===================================================================
--- package.patch	2019-06-27 03:36:32 UTC (rev 484663)
+++ package.patch	2019-06-27 05:59:51 UTC (rev 484664)
@@ -1,6 +1,6 @@
 --- 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
-@@ -335,7 +335,7 @@
+@@ -336,7 +336,7 @@
          Use the framework provided by :mod:`sage.features` to check
          whether a library is installed and functional.
      """

Modified: sagemath-env.patch
===================================================================
--- sagemath-env.patch	2019-06-27 03:36:32 UTC (rev 484663)
+++ sagemath-env.patch	2019-06-27 05:59:51 UTC (rev 484664)
@@ -42,7 +42,7 @@
  
  
  # Don't execute the commands more than once for the same version of
-@@ -174,33 +174,9 @@
+@@ -174,35 +174,9 @@
  export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION
  
  export SAGE_ROOT="$NEW_SAGE_ROOT"
@@ -54,10 +54,12 @@
 -# Note that SAGE_SCRIPTS_DIR is only used here, so it does not need to
 -# be exported.
 -if [ -z "$SAGE_SCRIPTS_DIR" ]; then
--    if [ -n "$SAGE_LOCAL" ] && [ -f "$SAGE_LOCAL/bin/sage-env-config" ]; then
+-    if [ -f "$SAGE_ROOT/src/bin/sage-env-config" ]; then
+-        # Prefer src/bin/sage-env-config because that's directly
+-        # generated by configure (see Trac #27422)
+-        SAGE_SCRIPTS_DIR="$SAGE_ROOT/src/bin"
+-    elif [ -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
@@ -78,7 +80,7 @@
  
  # The compilers are set in order of priority by
  # 1) environment variables
-@@ -296,8 +296,8 @@
+@@ -298,8 +298,8 @@
  export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
  export SAGE_SPKG_SCRIPTS="$SAGE_LOCAL/var/lib/sage/scripts"
  export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
@@ -89,7 +91,7 @@
  export SAGE_DOC="$SAGE_SHARE/doc/sage"
  
  if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
-@@ -409,28 +409,8 @@
+@@ -411,28 +411,8 @@
      export SAGE_STARTUP_FILE
  fi
  
@@ -120,7 +122,7 @@
  
  LDFLAGS="-L$SAGE_LOCAL/lib -Wl,-rpath,$SAGE_LOCAL/lib $LDFLAGS"
  export LDFLAGS
-@@ -495,8 +495,6 @@
+@@ -497,8 +497,6 @@
      fi
  fi
 
@@ -129,7 +131,7 @@
  
  PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
  
-@@ -607,9 +607,6 @@
+@@ -609,9 +609,6 @@
      LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
  fi
  

Deleted: sagemath-gap-4.10.1.patch
===================================================================
--- sagemath-gap-4.10.1.patch	2019-06-27 03:36:32 UTC (rev 484663)
+++ sagemath-gap-4.10.1.patch	2019-06-27 05:59:51 UTC (rev 484664)
@@ -1,381 +0,0 @@
-diff --git a/src/sage/interfaces/tests.py b/src/sage/interfaces/tests.py
-index 6bcbfef..fc77f12 100644
---- a/src/sage/interfaces/tests.py
-+++ b/src/sage/interfaces/tests.py
-@@ -33,8 +33,8 @@ Test that write errors to stderr are handled gracefully by GAP
-     sage: kwds = dict(shell=True, stdout=f, stderr=f)
-     sage: subprocess.call("echo syntax error | ecl", **kwds)
-     0
--    sage: subprocess.call("echo syntax error | gap", **kwds)
--    0
-+    sage: subprocess.call("echo syntax error | gap", **kwds) in (0, 1)
-+    True
-     sage: subprocess.call("echo syntax error | gp", **kwds)
-     0
-     sage: subprocess.call("echo syntax error | ipython", **kwds) in (0, 1, 120)
-diff --git a/src/sage/libs/gap/gap_includes.pxd b/src/sage/libs/gap/gap_includes.pxd
-index 864a13b..f624ccd 100644
---- a/src/sage/libs/gap/gap_includes.pxd
-+++ b/src/sage/libs/gap/gap_includes.pxd
-@@ -10,14 +10,14 @@
- ###############################################################################
- 
- 
--cdef extern from "<gap/system.h>":
-+cdef extern from "gap/system.h" nogil:
-     ctypedef char Char
-     ctypedef int Int
-     ctypedef unsigned int UInt
-     ctypedef void* Obj
- 
- 
--cdef extern from "<gap/ariths.h>":
-+cdef extern from "gap/ariths.h" nogil:
-     Obj SUM(Obj, Obj)
-     Obj DIFF(Obj, Obj)
-     Obj PROD(Obj, Obj)
-@@ -28,12 +28,12 @@ cdef extern from "<gap/ariths.h>":
-     bint LT(Obj opL, Obj opR)
- 
- 
--cdef extern from "<gap/bool.h>":
-+cdef extern from "gap/bool.h" nogil:
-     cdef Obj GAP_True "True"
-     cdef Obj GAP_False "False"
- 
- 
--cdef extern from "<gap/calls.h>":
-+cdef extern from "gap/calls.h" nogil:
-     bint IS_FUNC(Obj)
-     Obj CALL_0ARGS(Obj f)              # 0 arguments
-     Obj CALL_1ARGS(Obj f, Obj a1)      # 1 argument
-@@ -45,49 +45,47 @@ cdef extern from "<gap/calls.h>":
-     Obj CALL_XARGS(Obj f, Obj args)   # more than 6 arguments
- 
- 
--cdef extern from "<gap/gasman.h>":
-+cdef extern from "gap/gasman.h" nogil:
-     Obj NewBag "NewBag"(UInt type, UInt size)
-     void MarkBag(Obj bag)
-     UInt CollectBags(UInt size, UInt full)
- 
- 
--cdef extern from "<gap/gasman_intern.h>":
-+cdef extern from "gap/gasman_intern.h" nogil:
-     void CallbackForAllBags(void (*func)(Obj))
- 
- 
--cdef extern from "<gap/gvars.h>":
-+cdef extern from "gap/gvars.h" nogil:
-     UInt GVarName "GVarName"(char* name)
-     void AssGVar "AssGVar"(UInt gvar, Obj val)
- 
- 
--cdef extern from "<gap/integer.h>":
-+cdef extern from "gap/integer.h" nogil:
-     Int IS_INT(Obj)
- 
- 
--cdef extern from "<gap/intobj.h>":
-+cdef extern from "gap/intobj.h" nogil:
-     bint IS_INTOBJ(Obj obj)
-     Obj INTOBJ_INT(Int)
-     Int INT_INTOBJ(Obj)
- 
- 
--cdef extern from "<gap/io.h>":
-+cdef extern from "gap/io.h" nogil:
-     UInt OpenOutputStream(Obj stream)
-     UInt CloseOutput()
- 
- 
--cdef extern from "<gap/libgap-api.h>":
--    ctypedef void (*CallbackFunc)()
--    void GAP_Initialize(int argc, char ** argv, char ** env,
--        CallbackFunc, CallbackFunc)
--    Obj GAP_EvalString(const char *) except *
--    Obj GAP_EvalStringNoExcept "GAP_EvalString"(const char *)
--    Obj GAP_ValueGlobalVariable(const char *)
--
--
--cdef extern from "<gap/libgap-api.h>" nogil:
-+cdef extern from "gap/libgap-api.h" nogil:
-     """
-     #define sig_GAP_Enter()  {int t = GAP_Enter(); if (!t) sig_error();}
-     """
-+    ctypedef void (*GAP_CallbackFunc)()
-+    void GAP_Initialize(int argc, char ** argv,
-+            GAP_CallbackFunc markBagsCallback, GAP_CallbackFunc errorCallback,
-+            int handleSignals)
-+    Obj GAP_EvalString(const char *) except *
-+    Obj GAP_EvalStringNoExcept "GAP_EvalString"(const char *)
-+    Obj GAP_ValueGlobalVariable(const char *)
-     cdef void GAP_EnterStack()
-     cdef void GAP_LeaveStack()
-     cdef int GAP_Enter() except 0
-@@ -96,7 +94,7 @@ cdef extern from "<gap/libgap-api.h>" nogil:
-     cdef int GAP_Error_Setjmp() except 0
- 
- 
--cdef extern from "<gap/lists.h>":
-+cdef extern from "gap/lists.h" nogil:
-     bint IS_LIST(Obj lst)
-     int LEN_LIST(Obj lst)
-     Obj ELM_LIST(Obj lst, int pos)
-@@ -104,15 +102,15 @@ cdef extern from "<gap/lists.h>":
-     void ASS_LIST(Obj lst, int pos, Obj elt)
- 
- 
--cdef extern from "<gap/listfunc.h>":
-+cdef extern from "gap/listfunc.h" nogil:
-     void AddList(Obj list, Obj obj)
- 
- 
--cdef extern from "<gap/macfloat.h>":
-+cdef extern from "gap/macfloat.h" nogil:
-     double VAL_MACFLOAT(Obj obj)
- 
- 
--cdef extern from "<gap/objects.h>":
-+cdef extern from "gap/objects.h" nogil:
-     bint IS_MUTABLE_OBJ(Obj obj)
-     Obj SHALLOW_COPY_OBJ(Obj obj)
-     Obj CopyObj(Obj obj, int mut)
-@@ -121,28 +119,34 @@ cdef extern from "<gap/objects.h>":
-     UInt TNUM_OBJ(Obj obj)
-     char* TNAM_OBJ(Obj obj)
- 
--    cdef int T_INTPOS
--    cdef int T_INTNEG
--    cdef int T_RAT
--    cdef int T_CYC
--    cdef int T_FFE
--    cdef int T_PERM2
--    cdef int T_PERM4
--    cdef int T_BOOL
--    cdef int T_CHAR
--    cdef int T_FUNCTION
--    cdef int T_MACFLOAT
--    cdef int T_PLIST
--    cdef int T_PLIST_CYC
--    cdef int T_BLIST
--    cdef int T_STRING
--    cdef int T_COMOBJ
--    cdef int T_POSOBJ
--    cdef int T_DATOBJ
--    cdef int T_WPOBJ
--
--
--cdef extern from "<gap/precord.h>":
-+    cdef enum TNUM:
-+        T_INT
-+        T_INTPOS
-+        T_INTNEG
-+        T_RAT
-+        T_CYC
-+        T_FFE
-+        T_MACFLOAT
-+        T_PERM2
-+        T_PERM4
-+        T_TRANS2
-+        T_TRANS4
-+        T_PPERM2
-+        T_PPERM4
-+        T_BOOL
-+        T_CHAR
-+        T_FUNCTION
-+        T_PLIST
-+        T_PLIST_CYC
-+        T_BLIST
-+        T_STRING
-+        T_COMOBJ
-+        T_POSOBJ
-+        T_DATOBJ
-+        T_WPOBJ
-+
-+
-+cdef extern from "gap/precord.h" nogil:
-     Obj NEW_PREC(int len)
-     int LEN_PREC(Obj rec)
-     int GET_RNAM_PREC(Obj rec, int i)
-@@ -150,14 +154,14 @@ cdef extern from "<gap/precord.h>":
-     void AssPRec(Obj rec, UInt rnam, Obj val)
- 
- 
--cdef extern from "<gap/records.h>":
-+cdef extern from "gap/records.h" nogil:
-     char* NAME_RNAM(UInt rnam)
-     bint IS_REC(Obj obj)
-     Obj ELM_REC(Obj rec, UInt rnam)
-     UInt RNamName(Char* name)
- 
- 
--cdef extern from "<gap/stringobj.h>":
-+cdef extern from "gap/stringobj.h" nogil:
-     char* CSTR_STRING(Obj list)
-     bint IS_STRING(Obj obj)
-     bint IsStringConv(Obj obj)
-diff --git a/src/sage/libs/gap/libgap.pyx b/src/sage/libs/gap/libgap.pyx
-index e78b88a..e66be59 100644
---- a/src/sage/libs/gap/libgap.pyx
-+++ b/src/sage/libs/gap/libgap.pyx
-@@ -232,15 +232,6 @@ from sage.misc.superseded import deprecated_function_alias, deprecation
- ### Debugging ##############################################################
- ############################################################################
- 
--
--cdef void report(Obj bag):
--    print(TNAM_OBJ(bag),  <int>SIZE_OBJ(bag))
--
--
--cdef void print_gasman_objects():
--    CallbackForAllBags(report)
--
--
- from sage.misc.lazy_import import is_during_startup
- if is_during_startup():
-     import sys, traceback
-diff --git a/src/sage/libs/gap/util.pyx b/src/sage/libs/gap/util.pyx
-index 7f6a924..27609f8 100644
---- a/src/sage/libs/gap/util.pyx
-+++ b/src/sage/libs/gap/util.pyx
-@@ -14,19 +14,16 @@ Utility functions for GAP
- 
- from __future__ import print_function, absolute_import
- 
--import os
--import signal
--import warnings
-+from libc.signal cimport signal, SIGCHLD, SIG_DFL
- from posix.dlfcn cimport dlopen, dlclose, RTLD_NOW, RTLD_GLOBAL
--from libc.string cimport strcpy, strlen
- 
- from cpython.exc cimport PyErr_Fetch, PyErr_Restore
- from cpython.object cimport Py_LT, Py_LE, Py_EQ, Py_NE, Py_GT, Py_GE
- from cpython.ref cimport PyObject, Py_XINCREF, Py_XDECREF
--from cysignals.memory cimport sig_malloc
--from cysignals.pysignals import containsignals
--from cysignals.signals cimport sig_on, sig_off, sig_error
-+from cysignals.signals cimport sig_on, sig_off
- 
-+import os
-+import warnings
- import sage.env
- 
- from .gap_includes cimport *
-@@ -105,7 +102,7 @@ cdef class ObjWrapper(object):
-             sage: hash(x)
-             0
-         """
--        return <int>(self.value)
-+        return <Py_hash_t>(self.value)
- 
- 
- cdef ObjWrapper wrap_obj(Obj obj):
-@@ -197,7 +194,6 @@ def gap_root():
- 
- # To ensure that we call initialize_libgap only once.
- cdef bint _gap_is_initialized = False
--cdef extern char **environ
- 
- 
- cdef char* _reset_error_output_cmd = """\
-@@ -216,33 +212,6 @@ MakeImmutable(libgap_errout);
- """
- 
- 
--cdef char** copy_environ(char** env):
--    """
--    Make a copy of the environment block given by ``env``.
--
--    Returns a pointer to the copy, which is the caller's responsibility to
--    free.
--    """
--
--    cdef char** env_copy
--    cdef int envc = 0;
--    cdef int idx
--    cdef size_t size
--
--    while env[envc]:
--        envc += 1
--
--    env_copy = <char**>sig_malloc((envc + 1) * sizeof(char*))
--
--    for idx in range(envc):
--        size = strlen(env[idx]) + 1
--        env_copy[idx] = <char*>sig_malloc(size)
--        strcpy(env_copy[idx], env[idx])
--
--    env_copy[envc] = NULL
--    return env_copy
--
--
- cdef initialize():
-     """
-     Initialize the GAP library, if it hasn't already been
-@@ -253,7 +222,7 @@ cdef initialize():
-         sage: libgap(123)   # indirect doctest
-         123
-     """
--    global _gap_is_initialized, environ
-+    global _gap_is_initialized
-     if _gap_is_initialized: return
-     # Hack to ensure that all symbols provided by libgap are loaded into the
-     # global symbol table
-@@ -268,10 +237,9 @@ cdef initialize():
-                 "be loaded!")
-     dlclose(handle)
- 
--    # Define argv and environ variables, which we will pass in to
-+    # Define argv variable, which we will pass in to
-     # initialize GAP. Note that we must pass define the memory pool
-     # size!
--    cdef char** env
-     cdef char* argv[18]
-     argv[0] = "sage"
-     argv[1] = "-l"
-@@ -318,21 +286,15 @@ cdef initialize():
- 
-     argv[argc] = NULL
- 
--    env = copy_environ(environ)
--
--    # Need to save/restore current SIGINT handling since GAP_Initialize
--    # currently clobbers it; it doesn't matter what we set SIGINT to
--    # temporarily.
--    with containsignals():
--        sig_on()
--        try:
--            # Initialize GAP and capture any error messages. The
--            # initialization just prints any errors and does not
--            # use the error handler.
--            GAP_Initialize(argc, argv, env, &gasman_callback,
--                           &error_handler)
--        finally:
--            sig_off()
-+    sig_on()
-+    # Initialize GAP but disable their SIGINT handler
-+    GAP_Initialize(argc, argv, gasman_callback, error_handler,
-+                   handleSignals=False)
-+    sig_off()
-+
-+    # Disable GAP's SIGCHLD handler ChildStatusChanged(), which calls
-+    # waitpid() on random child processes.
-+    signal(SIGCHLD, SIG_DFL)
- 
-     # Set the ERROR_OUTPUT global in GAP to an output stream in which to
-     # receive error output
-diff --git a/src/sage/tests/books/judson-abstract-algebra/sylow-sage.py b/src/sage/tests/books/judson-abstract-algebra/sylow-sage.py
-index b3312b8..6d81f0a 100644
---- a/src/sage/tests/books/judson-abstract-algebra/sylow-sage.py
-+++ b/src/sage/tests/books/judson-abstract-algebra/sylow-sage.py
-@@ -225,7 +225,7 @@ r"""
- 
- ~~~~~~~~~~~~~~~~~~~~~~ ::
- 
--    sage: gap.version()
-+    sage: gap.version()  # random
-     '4.10.0'
- 
- ~~~~~~~~~~~~~~~~~~~~~~ ::

Modified: sagemath-python3-notebook.patch
===================================================================
--- sagemath-python3-notebook.patch	2019-06-27 03:36:32 UTC (rev 484663)
+++ sagemath-python3-notebook.patch	2019-06-27 05:59:51 UTC (rev 484664)
@@ -16,7 +16,7 @@
 index 3912b8cdf5..bd40cdadda 100644
 --- a/src/sage/repl/ipython_kernel/install.py
 +++ b/src/sage/repl/ipython_kernel/install.py
-@@ -303,7 +303,6 @@ def have_prerequisites(debug=True):
+@@ -304,7 +304,6 @@ def have_prerequisites(debug=True):
          True
      """
      try:

Deleted: sagemath-sphinx-1.8.patch
===================================================================
--- sagemath-sphinx-1.8.patch	2019-06-27 03:36:32 UTC (rev 484663)
+++ sagemath-sphinx-1.8.patch	2019-06-27 05:59:51 UTC (rev 484664)
@@ -1,28 +0,0 @@
---- a/src/sage/misc/sphinxify.py	2018-09-14 20:13:32.788831484 +0200
-+++ b/src/sage/misc/sphinxify.py	2018-09-14 20:14:07.142478667 +0200
-@@ -68,6 +68,7 @@
-         sage: assert n == len(sys.path)
-     """
-     srcdir = mkdtemp()
-+    outdir = mkdtemp()
-     base_name = os.path.join(srcdir, 'docstring')
-     rst_name = base_name + '.rst'
- 
-@@ -75,7 +76,7 @@
-         suffix = '.html'
-     else:
-         suffix = '.txt'
--    output_name = base_name + suffix
-+    output_name = os.path.join(outdir, 'docstring') + suffix
- 
-     with open(rst_name, 'w') as filed:
-         filed.write(docstring)
-@@ -93,7 +94,7 @@
- 
-     import sys
-     old_sys_path = list(sys.path)  # Sphinx modifies sys.path
--    sphinx_app = Sphinx(srcdir, confdir, srcdir, doctreedir, format,
-+    sphinx_app = Sphinx(srcdir, confdir, outdir, doctreedir, format,
-                         confoverrides, None, None, True)
-     sphinx_app.build(None, [rst_name])
-     sys.path = old_sys_path

Deleted: sagemath-threejs-100.patch
===================================================================
--- sagemath-threejs-100.patch	2019-06-27 03:36:32 UTC (rev 484663)
+++ sagemath-threejs-100.patch	2019-06-27 05:59:51 UTC (rev 484664)
@@ -1,52 +0,0 @@
-diff --git a/src/ext/threejs/threejs_template.html b/src/ext/threejs/threejs_template.html
-index 0243bc1..48e8268 100644
---- a/src/ext/threejs/threejs_template.html
-+++ b/src/ext/threejs/threejs_template.html
-@@ -114,7 +114,7 @@ SAGE_SCRIPTS
-         scene.add( sprite );
-     }
- 
--    if ( options.axes ) scene.add( new THREE.AxisHelper( Math.min( a[0]*b[1].x, a[1]*b[1].y, a[2]*b[1].z ) ) );
-+    if ( options.axes ) scene.add( new THREE.AxesHelper( Math.min( a[0]*b[1].x, a[1]*b[1].y, a[2]*b[1].z ) ) );
- 
-     var camera = new THREE.PerspectiveCamera( 45, window.innerWidth / window.innerHeight, 0.1, 1000 );
-     camera.up.set( 0, 0, 1 );
-@@ -177,7 +177,11 @@ SAGE_SCRIPTS
-                                                    transparent: transparent, opacity: json.opacity,
-                                                    alphaTest: .1 } );
- 
--        var c = geometry.center().multiplyScalar( -1 );
-+        var c = new THREE.Vector3();
-+        geometry.computeBoundingBox();
-+        geometry.boundingBox.getCenter( c );
-+        geometry.translate( -c.x, -c.y, -c.z );
-+
-         var mesh = new THREE.Points( geometry, material );
-         mesh.position.set( c.x, c.y, c.z );
-         scene.add( mesh );
-@@ -199,7 +203,11 @@ SAGE_SCRIPTS
-         var material = new THREE.LineBasicMaterial( { color: json.color, linewidth: json.linewidth,
-                                                       transparent: transparent, opacity: json.opacity } );
- 
--        var c = geometry.center().multiplyScalar( -1 );
-+        var c = new THREE.Vector3();
-+        geometry.computeBoundingBox();
-+        geometry.boundingBox.getCenter( c );
-+        geometry.translate( -c.x, -c.y, -c.z );
-+
-         var mesh = new THREE.LineSegments( geometry, material );
-         mesh.position.set( c.x, c.y, c.z );
-         scene.add( mesh );
-@@ -235,7 +243,11 @@ SAGE_SCRIPTS
-                                      transparent: transparent, opacity: json.opacity,
-                                      shininess: 20 } );
- 
--        var c = geometry.center().multiplyScalar( -1 );
-+        var c = new THREE.Vector3();
-+        geometry.computeBoundingBox();
-+        geometry.boundingBox.getCenter( c );
-+        geometry.translate( -c.x, -c.y, -c.z );
-+
-         var mesh = new THREE.Mesh( geometry, material );
-         mesh.position.set( c.x, c.y, c.z );
-         scene.add( mesh );

Modified: sagemath-threejs.patch
===================================================================
--- sagemath-threejs.patch	2019-06-27 03:36:32 UTC (rev 484663)
+++ sagemath-threejs.patch	2019-06-27 05:59:51 UTC (rev 484664)
@@ -7,5 +7,5 @@
 -            version = installed_packages()['threejs'].split('.')[0]
 +            version = 'r100'
              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>
+ <script src="https://cdn.jsdelivr.net/gh/mrdoob/three.js@{0}/build/three.min.js"></script>
+ <script src="https://cdn.jsdelivr.net/gh/mrdoob/three.js@{0}/examples/js/controls/OrbitControls.js"></script>

Modified: test-optional.patch
===================================================================
--- test-optional.patch	2019-06-27 03:36:32 UTC (rev 484663)
+++ test-optional.patch	2019-06-27 05:59:51 UTC (rev 484664)
@@ -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
-@@ -347,22 +347,6 @@
+@@ -347,17 +347,6 @@
                  # Special case to run all optional tests
                  options.optional = True
              else:
@@ -15,11 +15,6 @@
 -                        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))
--
-                 options.optional |= auto_optional_tags
-
-         self.options = options
+                 # Check that all tags are valid
+                 for o in options.optional:
+                     if not optionaltag_regex.search(o):


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