From fbc0e8d0555505c45e510ad0450b6760c7a0bc24 Mon Sep 17 00:00:00 2001 From: pcpa Date: Thu, 9 May 2013 11:45:42 -0300 Subject: [PATCH] Update to sagemath 5.9 --- sagemath-4ti2.patch | 17 +- sagemath-buildroot.patch | 6 +- sagemath-cbc.patch | 42 ++--- sagemath-cremona.patch | 6 +- sagemath-cryptominisat.patch | 19 +-- sagemath-ecl-unicode.patch | 12 +- sagemath-extensions.patch | 8 +- sagemath-fes.patch | 6 +- sagemath-fplll.patch | 18 +-- sagemath-gap-hap.patch | 6 +- sagemath-gmp.patch | 4 +- sagemath-jmol.patch | 6 +- sagemath-libgap.patch | 26 ++- sagemath-libmpc.patch | 12 +- sagemath-lrcalc.patch | 8 +- sagemath-lrslib.patch | 12 +- sagemath-m4rie.patch | 8 +- sagemath-maxima.patch | 12 +- sagemath-maxima.system.patch | 6 +- sagemath-nauty.patch | 8 +- sagemath-nolibgap.patch | 21 ++- sagemath-nopari2.6.patch | 12 +- sagemath-ntl6.patch | 12 +- sagemath-pari.patch | 32 ++-- sagemath-png.patch | 26 +-- sagemath-readonly.patch | 11 +- sagemath-rpmbuild.patch | 164 ++++++++----------- sagemath-sagedoc.patch | 113 +++++++------ sagemath-sagenb.patch | 32 ++-- sagemath-scons.patch | 6 +- sagemath-scripts.patch | 301 +++++++++++++++-------------------- sagemath-unpatched_ntl.patch | 60 +++++++ sagemath.spec | 143 ++++++++++------- 33 files changed, 597 insertions(+), 578 deletions(-) create mode 100644 sagemath-unpatched_ntl.patch diff --git a/sagemath-4ti2.patch b/sagemath-4ti2.patch index 23f660a..b3e95ab 100644 --- a/sagemath-4ti2.patch +++ b/sagemath-4ti2.patch @@ -1,21 +1,20 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/sandpiles/sandpile.py.orig sage-5.8/spkg/build/sage-5.8/sage/sandpiles/sandpile.py ---- sage-5.8/spkg/build/sage-5.8/sage/sandpiles/sandpile.py.orig 2012-07-11 14:39:38.474386100 -0400 -+++ sage-5.8/spkg/build/sage-5.8/sage/sandpiles/sandpile.py 2012-07-11 14:40:33.870388225 -0400 -@@ -22,9 +22,6 @@ http://sagemath.org/download-packages.ht - packages. An alternative is to install 4ti2 separately, then point the +diff -up sage-5.9/spkg/build/sage-5.9/sage/sandpiles/sandpile.py.orig sage-5.9/spkg/build/sage-5.9/sage/sandpiles/sandpile.py +--- sage-5.9/spkg/build/sage-5.9/sage/sandpiles/sandpile.py.orig 2013-05-06 13:50:14.882749079 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/sandpiles/sandpile.py 2013-05-06 13:50:34.526749831 -0300 +@@ -24,8 +24,6 @@ packages. An alternative is to install following variable to the correct path. """ --SAGE_ROOT = os.environ['SAGE_ROOT'] --path_to_zsolve = SAGE_ROOT+'/local/bin/' + +-path_to_zsolve = os.path.join(SAGE_LOCAL,'bin','zsolve') - r""" Sage Sandpiles -@@ -4097,7 +4094,7 @@ class SandpileDivisor(dict): +@@ -4098,7 +4096,7 @@ class SandpileDivisor(dict): sign_file.close() # compute try: -- os.system(path_to_zsolve+'zsolve -q ' + lin_sys + ' > ' + lin_sys_log) +- os.system(path_to_zsolve+' -q ' + lin_sys + ' > ' + lin_sys_log) + os.system('zsolve -q ' + lin_sys + ' > ' + lin_sys_log) # process the results zhom_file = open(lin_sys_zhom,'r') diff --git a/sagemath-buildroot.patch b/sagemath-buildroot.patch index 379e2c9..83b3240 100644 --- a/sagemath-buildroot.patch +++ b/sagemath-buildroot.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sage-5.8/module_list.py ---- sage-5.8/spkg/build/sage-5.8/module_list.py.orig 2013-03-19 16:03:38.039687555 -0300 -+++ sage-5.8/spkg/build/sage-5.8/module_list.py 2013-03-19 16:03:47.215687907 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/module_list.py.orig sage-5.9/spkg/build/sage-5.9/module_list.py +--- sage-5.9/spkg/build/sage-5.9/module_list.py.orig 2013-03-19 16:03:38.039687555 -0300 ++++ sage-5.9/spkg/build/sage-5.9/module_list.py 2013-03-19 16:03:47.215687907 -0300 @@ -16,7 +16,7 @@ else: SAGE_ROOT = os.environ['SAGE_ROOT'] SAGE_LOCAL = SAGE_ROOT + '/local' diff --git a/sagemath-cbc.patch b/sagemath-cbc.patch index 2421382..27b6357 100644 --- a/sagemath-cbc.patch +++ b/sagemath-cbc.patch @@ -1,7 +1,7 @@ -diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sage-5.8/module_list.py ---- sage-5.8/spkg/build/sage-5.8/module_list.py.orig 2013-03-19 18:12:56.762984664 -0300 -+++ sage-5.8/spkg/build/sage-5.8/module_list.py 2013-03-19 18:13:07.073985059 -0300 -@@ -2029,7 +2029,7 @@ if (os.path.isfile(SAGE_INC + "cplex.h") +diff -up sage-5.9/spkg/build/sage-5.9/module_list.py.orig sage-5.9/spkg/build/sage-5.9/module_list.py +--- sage-5.9/spkg/build/sage-5.9/module_list.py.orig 2013-05-06 14:18:02.386812933 -0300 ++++ sage-5.9/spkg/build/sage-5.9/module_list.py 2013-05-06 14:18:07.352813123 -0300 +@@ -2021,7 +2021,7 @@ if (os.path.isfile(SAGE_INC + "/cplex.h" libraries = ["csage", "stdc++", "cplex"]) ) @@ -10,9 +10,9 @@ diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sa ext_modules.append( Extension("sage.numerical.backends.coin_backend", ["sage/numerical/backends/coin_backend.pyx"], -diff -up sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/coin_backend.pxd.orig sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/coin_backend.pxd ---- sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/coin_backend.pxd.orig 2013-03-19 18:12:59.568984771 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/coin_backend.pxd 2013-03-19 18:13:07.074985059 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/sage/numerical/backends/coin_backend.pxd.orig sage-5.9/spkg/build/sage-5.9/sage/numerical/backends/coin_backend.pxd +--- sage-5.9/spkg/build/sage-5.9/sage/numerical/backends/coin_backend.pxd.orig 2013-05-06 14:18:23.609813746 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/numerical/backends/coin_backend.pxd 2013-05-06 14:19:37.702816583 -0300 @@ -22,23 +22,23 @@ from libcpp cimport bool cdef extern from *: ctypedef double* const_double_ptr "const double*" @@ -22,8 +22,7 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/coin_backend.pxd.o cdef cppclass CbcStrategy: pass cdef cppclass CbcStrategyDefault(CbcStrategy): -- CbcStrategyDefault(int cutsOnlyAtRoot=?, int numberStrong = ?, int numberBeforeTrust = ?, int printLevel = ?) -+ CbcStrategyDefault(int cutsOnlyAtRoot=1, int numberStrong = 5, int numberBeforeTrust = 0, int printLevel = 0) + CbcStrategyDefault() -cdef extern from "../../local/include/coin/CoinPackedVectorBase.hpp": +cdef extern from "coin/CoinPackedVectorBase.hpp": @@ -74,7 +73,7 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/coin_backend.pxd.o cdef cppclass OsiSolverInterface: -@@ -130,19 +130,19 @@ cdef extern from "../../local/include/co +@@ -130,7 +130,7 @@ cdef extern from "../../local/include/co # miscellaneous double getInfinity() @@ -83,29 +82,6 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/coin_backend.pxd.o cdef cppclass CbcModel: # default constructor CbcModel() - # constructor from solver - CbcModel(OsiSolverInterface & si) - # assigning, owning solver -- void assignSolver(OsiSolverInterface * & solver, bool deleteSolver=?) -+ void assignSolver(OsiSolverInterface * & solver, bool deleteSolver=true) - void setModelOwnsSolver(bool ourSolver) - # get solver - OsiSolverInterface * solver() - # copy constructor -- CbcModel(CbcModel & rhs, int cloneHandler = ?) -+ CbcModel(CbcModel & rhs, int cloneHandler = false) - # shut up - void setLogLevel(int value) - int logLevel() -@@ -152,7 +152,7 @@ cdef extern from "../../local/include/co - void setNumberThreads (int) - int getSolutionCount() - # solve -- void branchAndBound(int doStatistics = ?) -+ void branchAndBound(int doStatistics = 0) - # not sure we need this but it can't hurt - CoinMessageHandler * messageHandler () - void CbcMain0(CbcModel m) @@ -160,11 +160,11 @@ cdef extern from "../../local/include/co CbcModel *new_CbcModel "new CbcModel" () void del_CbcModel "delete" (CbcModel *) diff --git a/sagemath-cremona.patch b/sagemath-cremona.patch index d591723..3b8f19d 100644 --- a/sagemath-cremona.patch +++ b/sagemath-cremona.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/databases/cremona.py.orig sage-5.8/spkg/build/sage-5.8/sage/databases/cremona.py ---- sage-5.8/spkg/build/sage-5.8/sage/databases/cremona.py.orig 2013-02-22 17:33:50.579875129 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/databases/cremona.py 2013-02-22 17:34:05.051875683 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/sage/databases/cremona.py.orig sage-5.9/spkg/build/sage-5.9/sage/databases/cremona.py +--- sage-5.9/spkg/build/sage-5.9/sage/databases/cremona.py.orig 2013-02-22 17:33:50.579875129 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/databases/cremona.py 2013-02-22 17:34:05.051875683 -0300 @@ -889,14 +889,9 @@ class MiniCremonaDatabase(SQLDatabase): if N < self.largest_conductor(): message = "There is no elliptic curve with label " + label \ diff --git a/sagemath-cryptominisat.patch b/sagemath-cryptominisat.patch index 17ddec0..78f5c61 100644 --- a/sagemath-cryptominisat.patch +++ b/sagemath-cryptominisat.patch @@ -1,7 +1,7 @@ -diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sage-5.8/module_list.py ---- sage-5.8/spkg/build/sage-5.8/module_list.py.orig 2013-03-20 12:35:59.851109864 -0300 -+++ sage-5.8/spkg/build/sage-5.8/module_list.py 2013-03-20 12:36:15.993110482 -0300 -@@ -2039,16 +2039,16 @@ if is_package_installed('cbc'): +diff -up sage-5.9/spkg/build/sage-5.9/module_list.py.orig sage-5.9/spkg/build/sage-5.9/module_list.py +--- sage-5.9/spkg/build/sage-5.9/module_list.py.orig 2013-05-06 16:47:00.734155214 -0300 ++++ sage-5.9/spkg/build/sage-5.9/module_list.py 2013-05-06 16:47:19.820155945 -0300 +@@ -2031,7 +2031,7 @@ if is_package_installed('cbc'): ) @@ -10,14 +10,3 @@ diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sa ext_modules.extend([ Extension("sage.sat.solvers.cryptominisat.cryptominisat", ["sage/sat/solvers/cryptominisat/cryptominisat.pyx"], -- include_dirs = [SAGE_INC, SAGE_INC+"/cmsat"], -+ include_dirs = [SAGE_INC, SAGE_INC+"cmsat"], - language = "c++", - libraries = ['cryptominisat', 'z']), - Extension("sage.sat.solvers.cryptominisat.solverconf", - ["sage/sat/solvers/cryptominisat/solverconf.pyx", "sage/sat/solvers/cryptominisat/solverconf_helper.cpp"], -- include_dirs = [SAGE_INC, SAGE_INC+"/cmsat"], -+ include_dirs = [SAGE_INC, SAGE_INC+"cmsat"], - language = "c++", - libraries = ['cryptominisat', 'z']) - ]) diff --git a/sagemath-ecl-unicode.patch b/sagemath-ecl-unicode.patch index 060b8d6..0d7d6b8 100644 --- a/sagemath-ecl-unicode.patch +++ b/sagemath-ecl-unicode.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/libs/ecl.pxd.orig sage-5.8/spkg/build/sage-5.8/sage/libs/ecl.pxd ---- sage-5.8/spkg/build/sage-5.8/sage/libs/ecl.pxd.orig 2013-03-19 16:11:17.358705144 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/libs/ecl.pxd 2013-03-19 16:11:27.719705541 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/sage/libs/ecl.pxd.orig sage-5.9/spkg/build/sage-5.9/sage/libs/ecl.pxd +--- sage-5.9/spkg/build/sage-5.9/sage/libs/ecl.pxd.orig 2013-03-19 16:11:17.358705144 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/libs/ecl.pxd 2013-03-19 16:11:27.719705541 -0300 @@ -133,6 +133,7 @@ cdef extern from "ecl/ecl.h": cl_object ecl_read_from_cstring_safe(char *s, cl_object err) cl_object cl_write_to_string(cl_narg narg, cl_object o) @@ -9,9 +9,9 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/libs/ecl.pxd.orig sage-5.8/spkg/build # S-expr evaluation and function calls -diff -up sage-5.8/spkg/build/sage-5.8/sage/libs/ecl.pyx.orig sage-5.8/spkg/build/sage-5.8/sage/libs/ecl.pyx ---- sage-5.8/spkg/build/sage-5.8/sage/libs/ecl.pyx.orig 2013-03-19 16:11:07.489704766 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/libs/ecl.pyx 2013-03-19 16:11:27.719705541 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/sage/libs/ecl.pyx.orig sage-5.9/spkg/build/sage-5.9/sage/libs/ecl.pyx +--- sage-5.9/spkg/build/sage-5.9/sage/libs/ecl.pyx.orig 2013-03-19 16:11:07.489704766 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/libs/ecl.pyx 2013-03-19 16:11:27.719705541 -0300 @@ -238,17 +238,19 @@ cdef cl_object ecl_safe_eval(cl_object f ... RuntimeError: ECL says: Console interrupt. diff --git a/sagemath-extensions.patch b/sagemath-extensions.patch index 299ce7d..13d446f 100644 --- a/sagemath-extensions.patch +++ b/sagemath-extensions.patch @@ -1,7 +1,7 @@ -diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sage-5.8/module_list.py ---- sage-5.8/spkg/build/sage-5.8/module_list.py.orig 2013-03-19 15:53:00.047663124 -0300 -+++ sage-5.8/spkg/build/sage-5.8/module_list.py 2013-03-19 15:53:10.095663509 -0300 -@@ -1983,7 +1983,8 @@ ext_modules = [ +diff -up sage-5.9/spkg/build/sage-5.9/module_list.py.orig sage-5.9/spkg/build/sage-5.9/module_list.py +--- sage-5.9/spkg/build/sage-5.9/module_list.py.orig 2013-05-06 12:26:26.802556536 -0300 ++++ sage-5.9/spkg/build/sage-5.9/module_list.py 2013-05-06 12:26:39.837557035 -0300 +@@ -1975,7 +1975,8 @@ ext_modules = [ # These extensions are to be compiled only if the # corresponding packages have been installed diff --git a/sagemath-fes.patch b/sagemath-fes.patch index d554256..e13644b 100644 --- a/sagemath-fes.patch +++ b/sagemath-fes.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sage-5.8/module_list.py ---- sage-5.8/spkg/build/sage-5.8/module_list.py.orig 2013-03-19 18:13:55.457986912 -0300 -+++ sage-5.8/spkg/build/sage-5.8/module_list.py 2013-03-19 18:14:03.785987230 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/module_list.py.orig sage-5.9/spkg/build/sage-5.9/module_list.py +--- sage-5.9/spkg/build/sage-5.9/module_list.py.orig 2013-03-19 18:13:55.457986912 -0300 ++++ sage-5.9/spkg/build/sage-5.9/module_list.py 2013-03-19 18:14:03.785987230 -0300 @@ -1988,7 +1988,7 @@ ext_modules = [ def is_package_installed(name): return False diff --git a/sagemath-fplll.patch b/sagemath-fplll.patch index c543dfe..c67be9b 100644 --- a/sagemath-fplll.patch +++ b/sagemath-fplll.patch @@ -1,17 +1,17 @@ -diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sage-5.8/module_list.py ---- sage-5.8/spkg/build/sage-5.8/module_list.py.orig 2013-03-19 18:10:02.994978010 -0300 -+++ sage-5.8/spkg/build/sage-5.8/module_list.py 2013-03-19 18:10:19.754978651 -0300 -@@ -660,6 +660,7 @@ ext_modules = [ +diff -up sage-5.9/spkg/build/sage-5.9/module_list.py.orig sage-5.9/spkg/build/sage-5.9/module_list.py +--- sage-5.9/spkg/build/sage-5.9/module_list.py.orig 2013-05-06 13:59:12.394769662 -0300 ++++ sage-5.9/spkg/build/sage-5.9/module_list.py 2013-05-06 13:59:23.359770082 -0300 +@@ -647,6 +647,7 @@ ext_modules = [ libraries = ['gmp', 'mpfr', 'stdc++', 'fplll'], language="c++", - include_dirs = [SAGE_INC + 'fplll'], + include_dirs = [SAGE_INC + '/fplll'], + extra_compile_args=["-DFPLLL_V3_COMPAT"], - depends = [SAGE_INC + "fplll/fplll.h"]), + depends = [SAGE_INC + "/fplll/fplll.h"]), Extension('sage.libs.linbox.linbox', -diff -up sage-5.8/spkg/build/sage-5.8/sage/libs/fplll/fplll.pxi.orig sage-5.8/spkg/build/sage-5.8/sage/libs/fplll/fplll.pxi ---- sage-5.8/spkg/build/sage-5.8/sage/libs/fplll/fplll.pxi.orig 2013-03-19 18:10:17.008978546 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/libs/fplll/fplll.pxi 2013-03-19 18:10:19.755978652 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/sage/libs/fplll/fplll.pxi.orig sage-5.9/spkg/build/sage-5.9/sage/libs/fplll/fplll.pxi +--- sage-5.9/spkg/build/sage-5.9/sage/libs/fplll/fplll.pxi.orig 2013-05-06 13:59:47.144770993 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/libs/fplll/fplll.pxi 2013-05-06 14:06:27.254786314 -0300 @@ -10,22 +10,22 @@ cdef extern from "fplll/fplll.h": # diff --git a/sagemath-gap-hap.patch b/sagemath-gap-hap.patch index 0f13901..e19864f 100644 --- a/sagemath-gap-hap.patch +++ b/sagemath-gap-hap.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/groups/perm_gps/permgroup.py.orig sage-5.8/spkg/build/sage-5.8/sage/groups/perm_gps/permgroup.py ---- sage-5.8/spkg/build/sage-5.8/sage/groups/perm_gps/permgroup.py.orig 2013-03-19 16:22:36.592731155 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/groups/perm_gps/permgroup.py 2013-03-19 16:22:58.320731987 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/sage/groups/perm_gps/permgroup.py.orig sage-5.9/spkg/build/sage-5.9/sage/groups/perm_gps/permgroup.py +--- sage-5.9/spkg/build/sage-5.9/sage/groups/perm_gps/permgroup.py.orig 2013-03-19 16:22:36.592731155 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/groups/perm_gps/permgroup.py 2013-03-19 16:22:58.320731987 -0300 @@ -180,8 +180,7 @@ def hap_decorator(f): """ @wraps(f) diff --git a/sagemath-gmp.patch b/sagemath-gmp.patch index 7b02eb2..b50983b 100644 --- a/sagemath-gmp.patch +++ b/sagemath-gmp.patch @@ -1,5 +1,5 @@ ---- sage-5.8/spkg/build/sage-5.8/c_lib/src/memory.c.orig 2012-07-10 11:46:54.516595967 -0400 -+++ sage-5.8/spkg/build/sage-5.8/c_lib/src/memory.c 2012-07-10 11:47:12.688596755 -0400 +--- sage-5.9/spkg/build/sage-5.9/c_lib/src/memory.c.orig 2012-07-10 11:46:54.516595967 -0400 ++++ sage-5.9/spkg/build/sage-5.9/c_lib/src/memory.c 2012-07-10 11:47:12.688596755 -0400 @@ -17,7 +17,7 @@ AUTHORS: * http://www.gnu.org/licenses/ ****************************************************************************/ diff --git a/sagemath-jmol.patch b/sagemath-jmol.patch index d5eb232..ff8b31d 100644 --- a/sagemath-jmol.patch +++ b/sagemath-jmol.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/interfaces/jmoldata.py.orig sage-5.8/spkg/build/sage-5.8/sage/interfaces/jmoldata.py ---- sage-5.8/spkg/build/sage-5.8/sage/interfaces/jmoldata.py.orig 2012-11-10 12:03:07.742817945 -0200 -+++ sage-5.8/spkg/build/sage-5.8/sage/interfaces/jmoldata.py 2012-11-10 12:03:34.499818970 -0200 +diff -up sage-5.9/spkg/build/sage-5.9/sage/interfaces/jmoldata.py.orig sage-5.9/spkg/build/sage-5.9/sage/interfaces/jmoldata.py +--- sage-5.9/spkg/build/sage-5.9/sage/interfaces/jmoldata.py.orig 2012-11-10 12:03:07.742817945 -0200 ++++ sage-5.9/spkg/build/sage-5.9/sage/interfaces/jmoldata.py 2012-11-10 12:03:34.499818970 -0200 @@ -86,7 +86,7 @@ class JmolData(SageObject): sage_makedirs(jmolscratch) scratchout = os.path.join(jmolscratch,"jmolout.txt") diff --git a/sagemath-libgap.patch b/sagemath-libgap.patch index 3558c2c..f62685d 100644 --- a/sagemath-libgap.patch +++ b/sagemath-libgap.patch @@ -1,2 +1,24 @@ -diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sage-5.8/module_list.py -diff -up sage-5.8/spkg/build/sage-5.8/sage/libs/gap/util.pyx.orig sage-5.8/spkg/build/sage-5.8/sage/libs/gap/util.pyx +diff -up sage-5.9/spkg/build/sage-5.9/sage/libs/gap/util.pyx.orig sage-5.9/spkg/build/sage-5.9/sage/libs/gap/util.pyx +--- sage-5.9/spkg/build/sage-5.9/sage/libs/gap/util.pyx.orig 2013-05-06 14:24:03.160826749 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/libs/gap/util.pyx 2013-05-06 14:25:25.806829913 -0300 +@@ -155,18 +155,9 @@ def gap_root(): + + sage: from sage.libs.gap.util import gap_root + sage: gap_root() # random output +- '/home/vbraun/opt/sage-5.3.rc0/local/gap/latest' ++ '/usr/lib/gap' + """ +- import os.path +- gapdir = os.path.join(SAGE_LOCAL, 'gap', 'latest') +- if os.path.exists(gapdir): +- return gapdir +- print 'The gap-4.5.5.spkg (or later) seems to be not installed!' +- gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap')).read().splitlines() +- gapdir = filter(lambda dir:dir.strip().startswith('GAP_DIR'), gap_sh)[0] +- gapdir = gapdir.split('"')[1] +- gapdir = gapdir.replace('$SAGE_LOCAL', SAGE_LOCAL) +- return gapdir ++ return '/usr/lib/gap' + + + cdef initialize(): diff --git a/sagemath-libmpc.patch b/sagemath-libmpc.patch index f35382b..9c1548d 100644 --- a/sagemath-libmpc.patch +++ b/sagemath-libmpc.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sage-5.8/c_lib/SConstruct.orig sage-5.8/spkg/build/sage-5.8/c_lib/SConstruct ---- sage-5.8/spkg/build/sage-5.8/c_lib/SConstruct.orig 2013-02-23 12:42:08.694809731 -0300 -+++ sage-5.8/spkg/build/sage-5.8/c_lib/SConstruct 2013-02-23 12:43:00.412811711 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/c_lib/SConstruct.orig sage-5.9/spkg/build/sage-5.9/c_lib/SConstruct +--- sage-5.9/spkg/build/sage-5.9/c_lib/SConstruct.orig 2013-02-23 12:42:08.694809731 -0300 ++++ sage-5.9/spkg/build/sage-5.9/c_lib/SConstruct 2013-02-23 12:43:00.412811711 -0300 @@ -145,7 +145,7 @@ soname = libname + "." + major shlink_flags += [ '-Wl,-Bsymbolic', '-Wl,-soname=%s' % soname ] @@ -10,9 +10,9 @@ diff -up sage-5.8/spkg/build/sage-5.8/c_lib/SConstruct.orig sage-5.8/spkg/build/ LIBPATH=['@@libdir@@','@@libdir@@/python$PYV/config/'], SHLIBSUFFIX=shlib_suffix, SHLINKFLAGS=shlink_flags, -diff -up sage-5.8/spkg/build/sage-5.8/c_lib/src/stdsage.c.orig sage-5.8/spkg/build/sage-5.8/c_lib/src/stdsage.c ---- sage-5.8/spkg/build/sage-5.8/c_lib/src/stdsage.c.orig 2013-02-23 12:42:18.286810098 -0300 -+++ sage-5.8/spkg/build/sage-5.8/c_lib/src/stdsage.c 2013-02-23 12:43:15.062812272 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/c_lib/src/stdsage.c.orig sage-5.9/spkg/build/sage-5.9/c_lib/src/stdsage.c +--- sage-5.9/spkg/build/sage-5.9/c_lib/src/stdsage.c.orig 2013-02-23 12:42:18.286810098 -0300 ++++ sage-5.9/spkg/build/sage-5.9/c_lib/src/stdsage.c 2013-02-23 12:43:15.062812272 -0300 @@ -58,3 +58,49 @@ void init_csage_module() { init_csage(); #endif diff --git a/sagemath-lrcalc.patch b/sagemath-lrcalc.patch index 41d04cd..0cd2a01 100644 --- a/sagemath-lrcalc.patch +++ b/sagemath-lrcalc.patch @@ -1,7 +1,7 @@ -diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sage-5.8/module_list.py ---- sage-5.8/spkg/build/sage-5.8/module_list.py.orig 2013-03-19 18:11:46.450981971 -0300 -+++ sage-5.8/spkg/build/sage-5.8/module_list.py 2013-03-19 18:11:55.761982328 -0300 -@@ -2064,7 +2064,7 @@ if UNAME[0] == "Darwin" and not UNAME[2] +diff -up sage-5.9/spkg/build/sage-5.9/module_list.py.orig sage-5.9/spkg/build/sage-5.9/module_list.py +--- sage-5.9/spkg/build/sage-5.9/module_list.py.orig 2013-05-06 14:14:11.852804105 -0300 ++++ sage-5.9/spkg/build/sage-5.9/module_list.py 2013-05-06 14:14:20.940804453 -0300 +@@ -2056,7 +2056,7 @@ if UNAME[0] == "Darwin" and not UNAME[2] ) diff --git a/sagemath-lrslib.patch b/sagemath-lrslib.patch index 8840ff0..1321c07 100644 --- a/sagemath-lrslib.patch +++ b/sagemath-lrslib.patch @@ -1,7 +1,7 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/geometry/polyhedron/base.py.orig sage-5.8/spkg/build/sage-5.8/sage/geometry/polyhedron/base.py ---- sage-5.8/spkg/build/sage-5.8/sage/geometry/polyhedron/base.py.orig 2013-03-19 16:20:52.760727178 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/geometry/polyhedron/base.py 2013-03-19 16:21:00.096727459 -0300 -@@ -3129,11 +3129,6 @@ class Polyhedron_base(Element): +diff -up sage-5.9/spkg/build/sage-5.9/sage/geometry/polyhedron/base.py.orig sage-5.9/spkg/build/sage-5.9/sage/geometry/polyhedron/base.py +--- sage-5.9/spkg/build/sage-5.9/sage/geometry/polyhedron/base.py.orig 2013-05-06 14:12:21.664799886 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/geometry/polyhedron/base.py 2013-05-06 14:12:28.625800152 -0300 +@@ -3281,11 +3281,6 @@ class Polyhedron_base(Element): David Avis's lrs program. """ @@ -10,6 +10,6 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/geometry/polyhedron/base.py.orig sage - 'for this function to work' - raise NotImplementedError - + from sage.misc.temporary_file import tmp_filename + from subprocess import Popen, PIPE in_str = self.cdd_Vrepresentation() - in_str += 'volume' - in_filename = tmp_filename() diff --git a/sagemath-m4rie.patch b/sagemath-m4rie.patch index 1272341..e2ca4de 100644 --- a/sagemath-m4rie.patch +++ b/sagemath-m4rie.patch @@ -1,5 +1,5 @@ ---- sage-5.8/spkg/build/sage-5.8/sage/libs/m4rie.pxd.orig 2013-05-07 08:12:27.137652862 -0600 -+++ sage-5.8/spkg/build/sage-5.8/sage/libs/m4rie.pxd 2013-05-07 11:45:12.067923724 -0600 +--- sage-5.9/spkg/build/sage-5.9/sage/libs/m4rie.pxd.orig 2013-05-07 08:12:27.137652862 -0600 ++++ sage-5.9/spkg/build/sage-5.9/sage/libs/m4rie.pxd 2013-05-07 11:45:12.067923724 -0600 @@ -52,9 +52,9 @@ cdef extern from "m4rie/m4rie.h": void mzed_add_elem(mzed_t *a, const_size_t row, const_size_t col, const_int elem) @@ -28,8 +28,8 @@ mzd_slice_t *mzd_slice_init(gf2e *ff, size_t m, size_t n) ---- sage-5.8/spkg/build/sage-5.8/sage/matrix/matrix_mod2e_dense.pyx.orig 2013-05-07 08:12:27.139652859 -0600 -+++ sage-5.8/spkg/build/sage-5.8/sage/matrix/matrix_mod2e_dense.pyx 2013-05-07 11:21:05.095668016 -0600 +--- sage-5.9/spkg/build/sage-5.9/sage/matrix/matrix_mod2e_dense.pyx.orig 2013-05-07 08:12:27.139652859 -0600 ++++ sage-5.9/spkg/build/sage-5.9/sage/matrix/matrix_mod2e_dense.pyx 2013-05-07 11:21:05.095668016 -0600 @@ -561,9 +561,6 @@ cdef class Matrix_mod2e_dense(matrix_den if self._ncols != right._nrows: raise ArithmeticError("left ncols must match right nrows") diff --git a/sagemath-maxima.patch b/sagemath-maxima.patch index 4aac0e9..95149d1 100644 --- a/sagemath-maxima.patch +++ b/sagemath-maxima.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/interfaces/maxima.py.orig sage-5.8/spkg/build/sage-5.8/sage/interfaces/maxima.py ---- sage-5.8/spkg/build/sage-5.8/sage/interfaces/maxima.py.orig 2012-08-04 13:21:54.100575138 -0400 -+++ sage-5.8/spkg/build/sage-5.8/sage/interfaces/maxima.py 2012-08-04 13:22:15.580575956 -0400 +diff -up sage-5.9/spkg/build/sage-5.9/sage/interfaces/maxima.py.orig sage-5.9/spkg/build/sage-5.9/sage/interfaces/maxima.py +--- sage-5.9/spkg/build/sage-5.9/sage/interfaces/maxima.py.orig 2012-08-04 13:21:54.100575138 -0400 ++++ sage-5.9/spkg/build/sage-5.9/sage/interfaces/maxima.py 2012-08-04 13:22:15.580575956 -0400 @@ -544,7 +544,7 @@ class Maxima(MaximaAbstract, Expect): Expect.__init__(self, name = 'maxima', @@ -20,9 +20,9 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/interfaces/maxima.py.orig sage-5.8/sp self._eval_line('0;') def __reduce__(self): -diff -up sage-5.8/spkg/build/sage_scripts-5.7/sage-maxima.lisp.orig sage-5.8/spkg/build/sage_scripts-5.7/sage-maxima.lisp ---- sage-5.8/spkg/build/sage_scripts-5.8/sage-maxima.lisp.orig 2012-08-04 13:22:07.842575668 -0400 -+++ sage-5.8/spkg/build/sage_scripts-5.8/sage-maxima.lisp 2012-08-04 13:22:15.580575956 -0400 +diff -up sage-5.9/spkg/build/sage_scripts-5.7/sage-maxima.lisp.orig sage-5.9/spkg/build/sage_scripts-5.7/sage-maxima.lisp +--- sage-5.9/spkg/build/sage_scripts-5.9/sage-maxima.lisp.orig 2012-08-04 13:22:07.842575668 -0400 ++++ sage-5.9/spkg/build/sage_scripts-5.9/sage-maxima.lisp 2012-08-04 13:22:15.580575956 -0400 @@ -3,4 +3,8 @@ ;(setf *general-display-prefix* "") diff --git a/sagemath-maxima.system.patch b/sagemath-maxima.system.patch index acbf36d..d804bea 100644 --- a/sagemath-maxima.system.patch +++ b/sagemath-maxima.system.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/interfaces/maxima_lib.py.orig sage-5.8/spkg/build/sage-5.8/sage/interfaces/maxima_lib.py ---- sage-5.8/spkg/build/sage-5.8/sage/interfaces/maxima_lib.py.orig 2012-12-29 15:42:54.811218546 -0200 -+++ sage-5.8/spkg/build/sage-5.8/sage/interfaces/maxima_lib.py 2012-12-29 15:43:06.739219003 -0200 +diff -up sage-5.9/spkg/build/sage-5.9/sage/interfaces/maxima_lib.py.orig sage-5.9/spkg/build/sage-5.9/sage/interfaces/maxima_lib.py +--- sage-5.9/spkg/build/sage-5.9/sage/interfaces/maxima_lib.py.orig 2012-12-29 15:42:54.811218546 -0200 ++++ sage-5.9/spkg/build/sage-5.9/sage/interfaces/maxima_lib.py 2012-12-29 15:43:06.739219003 -0200 @@ -77,7 +77,7 @@ from maxima_abstract import (MaximaAbstr ## We begin here by initializing Maxima in library mode ## i.e. loading it into ECL diff --git a/sagemath-nauty.patch b/sagemath-nauty.patch index 63d6c29..e9db3d5 100644 --- a/sagemath-nauty.patch +++ b/sagemath-nauty.patch @@ -1,7 +1,7 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/graphs/graph_generators.py.orig sage-5.8/spkg/build/sage-5.8/sage/graphs/graph_generators.py ---- sage-5.8/spkg/build/sage-5.8/sage/graphs/graph_generators.py.orig 2013-02-22 17:34:47.243877299 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/graphs/graph_generators.py 2013-02-22 17:34:56.066877637 -0300 -@@ -769,8 +769,7 @@ class GraphGenerators(): +diff -up sage-5.9/spkg/build/sage-5.9/sage/graphs/graph_generators.py.orig sage-5.9/spkg/build/sage-5.9/sage/graphs/graph_generators.py +--- sage-5.9/spkg/build/sage-5.9/sage/graphs/graph_generators.py.orig 2013-05-06 14:13:14.875801924 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/graphs/graph_generators.py 2013-05-06 14:13:24.820802304 -0300 +@@ -772,8 +772,7 @@ class GraphGenerators(): """ import subprocess from sage.misc.package import is_package_installed diff --git a/sagemath-nolibgap.patch b/sagemath-nolibgap.patch index b8c2864..d6b87b2 100644 --- a/sagemath-nolibgap.patch +++ b/sagemath-nolibgap.patch @@ -1,7 +1,7 @@ -diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sage-5.8/module_list.py ---- sage-5.8/spkg/build/sage-5.8/module_list.py.orig 2013-03-19 16:34:20.048758092 -0300 -+++ sage-5.8/spkg/build/sage-5.8/module_list.py 2013-03-19 16:34:33.078758591 -0300 -@@ -498,8 +498,8 @@ ext_modules = [ +diff -up sage-5.9/spkg/build/sage-5.9/module_list.py.orig sage-5.9/spkg/build/sage-5.9/module_list.py +--- sage-5.9/spkg/build/sage-5.9/module_list.py.orig 2013-05-06 14:26:48.178833068 -0300 ++++ sage-5.9/spkg/build/sage-5.9/module_list.py 2013-05-06 14:28:09.378836177 -0300 +@@ -485,8 +485,8 @@ ext_modules = [ Extension('sage.groups.old', sources = ['sage/groups/old.pyx']), @@ -12,20 +12,19 @@ diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sa Extension('sage.groups.perm_gps.permgroup_element', sources = ['sage/groups/perm_gps/permgroup_element.pyx']), -@@ -793,25 +793,25 @@ ext_modules = [ +@@ -780,25 +780,25 @@ ext_modules = [ ## ################################ - Extension('sage.libs.gap.util', - sources = ["sage/libs/gap/util.pyx"], - libraries = ['csage', 'gmp', 'gap', 'm'], -- include_dirs = [SAGE_LOCAL + '/include/']), +- include_dirs = [SAGE_INC]), - - Extension('sage.libs.gap.element', - sources = ["sage/libs/gap/element.pyx"], - libraries = ['csage', 'gmp', 'gap', 'm'], -- include_dirs = [SAGE_LOCAL + '/include/']), -- +- include_dirs = [SAGE_INC]), +# Extension('sage.libs.gap.util', +# sources = ["sage/libs/gap/util.pyx"], +# libraries = ['csage', 'gmp', 'gap', 'm'], @@ -35,16 +34,16 @@ diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sa +# sources = ["sage/libs/gap/element.pyx"], +# libraries = ['csage', 'gmp', 'gap', 'm'], +# include_dirs = [SAGE_INC]), -+# + # Extension('sage.libs.gap.type', # sources = ["sage/libs/gap/type.pyx"], # libraries = ['csage', 'gmp', 'gap', 'm'], - # include_dirs = [SAGE_LOCAL + '/include/']), + # include_dirs = [SAGE_INC]), - - Extension('sage.libs.gap.libgap', - sources = ["sage/libs/gap/libgap.pyx"], - libraries = ['csage', 'gmp', 'gap', 'm'], -- include_dirs = [SAGE_LOCAL + '/include/']), +- include_dirs = [SAGE_INC]), +# +# Extension('sage.libs.gap.libgap', +# sources = ["sage/libs/gap/libgap.pyx"], diff --git a/sagemath-nopari2.6.patch b/sagemath-nopari2.6.patch index fd30e93..3001eec 100644 --- a/sagemath-nopari2.6.patch +++ b/sagemath-nopari2.6.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/libs/pari/decl.pxi.orig sage-5.8/spkg/build/sage-5.8/sage/libs/pari/decl.pxi ---- sage-5.8/spkg/build/sage-5.8/sage/libs/pari/decl.pxi.orig 2013-03-19 17:20:25.960864009 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/libs/pari/decl.pxi 2013-03-19 17:20:33.246864288 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/sage/libs/pari/decl.pxi.orig sage-5.9/spkg/build/sage-5.9/sage/libs/pari/decl.pxi +--- sage-5.9/spkg/build/sage-5.9/sage/libs/pari/decl.pxi.orig 2013-03-19 17:20:25.960864009 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/libs/pari/decl.pxi 2013-03-19 17:20:33.246864288 -0300 @@ -595,7 +595,6 @@ cdef extern from 'pari/pari.h': GEN polredabs0(GEN x, long flag) GEN polredabs2(GEN x) @@ -9,9 +9,9 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/libs/pari/decl.pxi.orig sage-5.8/spkg GEN qflll0(GEN x, long flag) GEN qflllgram0(GEN x, long flag) GEN smallpolred(GEN x) -diff -up sage-5.8/spkg/build/sage-5.8/sage/libs/pari/gen.pyx.orig sage-5.8/spkg/build/sage-5.8/sage/libs/pari/gen.pyx ---- sage-5.8/spkg/build/sage-5.8/sage/libs/pari/gen.pyx.orig 2013-03-19 17:20:55.992865159 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/libs/pari/gen.pyx 2013-03-19 17:21:02.118865393 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/sage/libs/pari/gen.pyx.orig sage-5.9/spkg/build/sage-5.9/sage/libs/pari/gen.pyx +--- sage-5.9/spkg/build/sage-5.9/sage/libs/pari/gen.pyx.orig 2013-03-19 17:20:55.992865159 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/libs/pari/gen.pyx 2013-03-19 17:21:02.118865393 -0300 @@ -8011,10 +8011,6 @@ cdef class gen(sage.structure.element.Ri sig_on() return self.new_gen(polredabs0(self.g, flag)) diff --git a/sagemath-ntl6.patch b/sagemath-ntl6.patch index 6b87ade..1f3344e 100644 --- a/sagemath-ntl6.patch +++ b/sagemath-ntl6.patch @@ -1,5 +1,5 @@ ---- sage-5.8/spkg/build/sage-5.8/c_lib/include/ntl_wrap.h.orig 2010-06-28 10:37:05.000000000 -0600 -+++ sage-5.8/spkg/build/sage-5.8/c_lib/include/ntl_wrap.h 2013-05-03 15:42:32.931073654 -0600 +--- sage-5.9/spkg/build/sage-5.9/c_lib/include/ntl_wrap.h.orig 2010-06-28 10:37:05.000000000 -0600 ++++ sage-5.9/spkg/build/sage-5.9/c_lib/include/ntl_wrap.h 2013-05-03 15:42:32.931073654 -0600 @@ -40,91 +40,92 @@ EXTERN void setup_NTL_error_callback(voi //////// ZZ ////////// @@ -450,8 +450,8 @@ -EXTERN void mat_GF2_setitem(struct mat_GF2* x, int i, int j, const struct GF2* z); +EXTERN void mat_GF2_setitem(mat_GF2* x, int i, int j, const GF2* z); ---- sage-5.8/spkg/build/sage-5.8/c_lib/src/ntl_wrap.cpp.orig 2013-01-21 14:18:15.000000000 -0700 -+++ sage-5.8/spkg/build/sage-5.8/c_lib/src/ntl_wrap.cpp 2013-05-03 16:05:09.640847922 -0600 +--- sage-5.9/spkg/build/sage-5.9/c_lib/src/ntl_wrap.cpp.orig 2013-01-21 14:18:15.000000000 -0700 ++++ sage-5.9/spkg/build/sage-5.9/c_lib/src/ntl_wrap.cpp 2013-05-03 16:05:09.640847922 -0600 @@ -29,7 +29,7 @@ int ZZ_to_int(const ZZ* x) /* Returns a *new* ZZ object. @@ -1348,8 +1348,8 @@ { //int j; cpn.restore(); ---- sage-5.8/spkg/build/sage-5.8/sage/libs/ntl/decl.pxi.orig 2010-06-28 10:37:01.000000000 -0600 -+++ sage-5.8/spkg/build/sage-5.8/sage/libs/ntl/decl.pxi 2013-05-07 09:38:36.134950663 -0600 +--- sage-5.9/spkg/build/sage-5.9/sage/libs/ntl/decl.pxi.orig 2010-06-28 10:37:01.000000000 -0600 ++++ sage-5.9/spkg/build/sage-5.9/sage/libs/ntl/decl.pxi 2013-05-07 09:38:36.134950663 -0600 @@ -23,7 +23,7 @@ from sage.libs.ntl.ntl_ZZ_pEX_decl cimpo cdef extern from "ntl_wrap.h": diff --git a/sagemath-pari.patch b/sagemath-pari.patch index a2c91ad..3d9d54b 100644 --- a/sagemath-pari.patch +++ b/sagemath-pari.patch @@ -1,20 +1,24 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/interfaces/gp.py.orig sage-5.8/spkg/build/sage-5.8/sage/interfaces/gp.py ---- sage-5.8/spkg/build/sage-5.8/sage/interfaces/gp.py.orig 2013-03-19 16:16:17.815716650 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/interfaces/gp.py 2013-03-19 16:16:27.031717003 -0300 -@@ -980,8 +980,8 @@ def is_GpElement(x): - from sage.misc.all import DOT_SAGE, SAGE_ROOT +diff -up sage-5.9/spkg/build/sage-5.9/sage/interfaces/gp.py.orig sage-5.9/spkg/build/sage-5.9/sage/interfaces/gp.py +--- sage-5.9/spkg/build/sage-5.9/sage/interfaces/gp.py.orig 2013-03-28 16:19:35.000000000 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/interfaces/gp.py 2013-05-06 17:34:56.021265319 -0300 +@@ -977,11 +977,11 @@ def is_GpElement(x): + """ + return isinstance(x, GpElement) + +-from sage.env import DOT_SAGE, SAGE_LOCAL ++from sage.env import DOT_SAGE, SAGE_EXTCODE import os --# Set GPRC environment variable to $SAGE_ROOT/local/etc/gprc.expect --os.environ["GPRC"] = '%s/local/etc/gprc.expect'%SAGE_ROOT -+# Set GPRC environment variable to $SAGE_ROOT/data/extcode/pari/gprc.expect -+os.environ["GPRC"] = '%s/data/extcode/pari/gprc.expect'%SAGE_ROOT +-# Set GPRC environment variable to $SAGE_LOCAL/etc/gprc.expect +-os.environ["GPRC"] = os.path.join(SAGE_LOCAL, 'etc', 'gprc.expect') ++# Set GPRC environment variable to $SAGE_EXTCODE/pari/gprc.expect ++os.environ["GPRC"] = '%s/pari/gprc.expect'%SAGE_EXTCODE # An instance - gp = Gp(logfile=DOT_SAGE+'/gp-expect.log') # useful for debugging! -diff -up sage-5.8/spkg/build/sage-5.8/sage/libs/pari/gen.pyx.orig sage-5.8/spkg/build/sage-5.8/sage/libs/pari/gen.pyx ---- sage-5.8/spkg/build/sage-5.8/sage/libs/pari/gen.pyx.orig 2013-03-19 16:16:10.607716374 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/libs/pari/gen.pyx 2013-03-19 16:16:27.035717003 -0300 + gp = Gp(logfile=os.path.join(DOT_SAGE,'gp-expect.log')) # useful for debugging! +diff -up sage-5.9/spkg/build/sage-5.9/sage/libs/pari/gen.pyx.orig sage-5.9/spkg/build/sage-5.9/sage/libs/pari/gen.pyx +--- sage-5.9/spkg/build/sage-5.9/sage/libs/pari/gen.pyx.orig 2013-05-06 17:34:09.952263554 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/libs/pari/gen.pyx 2013-05-06 17:34:24.826264124 -0300 @@ -182,6 +182,10 @@ include '../../ext/stdsage.pxi' cdef extern from "mpz_pylong.h": cdef int mpz_set_pylong(mpz_t dst, src) except -1 @@ -26,7 +30,7 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/libs/pari/gen.pyx.orig sage-5.8/spkg/ # Make sure we don't use mpz_t_offset before initializing it by # putting in a value that's likely to provoke a segmentation fault, # rather than silently corrupting memory. -@@ -9175,7 +9179,12 @@ cdef class PariInstance(sage.structure.p +@@ -9218,7 +9222,12 @@ cdef class PariInstance(sage.structure.p # The size here doesn't really matter, because we will allocate # our own stack anyway. We ask PARI not to set up signal handlers. diff --git a/sagemath-png.patch b/sagemath-png.patch index 9445d38..df45518 100644 --- a/sagemath-png.patch +++ b/sagemath-png.patch @@ -1,30 +1,30 @@ -diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sage-5.8/module_list.py ---- sage-5.8/spkg/build/sage-5.8/module_list.py.orig 2013-03-19 16:11:57.438706679 -0300 -+++ sage-5.8/spkg/build/sage-5.8/module_list.py 2013-03-19 16:12:05.927707004 -0300 -@@ -1036,7 +1036,7 @@ ext_modules = [ +diff -up sage-5.9/spkg/build/sage-5.9/module_list.py.orig sage-5.9/spkg/build/sage-5.9/module_list.py +--- sage-5.9/spkg/build/sage-5.9/module_list.py.orig 2013-05-06 13:47:27.554742671 -0300 ++++ sage-5.9/spkg/build/sage-5.9/module_list.py 2013-05-06 13:47:44.223743310 -0300 +@@ -1023,7 +1023,7 @@ ext_modules = [ Extension('sage.matrix.matrix_mod2_dense', sources = ['sage/matrix/matrix_mod2_dense.pyx'], - libraries = ['gmp','m4ri', 'gd', 'png12', 'z'], + libraries = ['gmp','m4ri', 'gd', 'png', 'z'], extra_compile_args = ['-std=c99'] + m4ri_extra_compile_args, - depends = [SAGE_INC + "png.h", SAGE_INC + "m4ri/m4ri.h"]), + depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]), -@@ -1298,7 +1298,7 @@ ext_modules = [ +@@ -1285,7 +1285,7 @@ ext_modules = [ Extension('sage.modules.vector_mod2_dense', sources = ['sage/modules/vector_mod2_dense.pyx'], - libraries = ['gmp','m4ri', 'png12', 'gd'], + libraries = ['gmp','m4ri', 'png', 'gd'], extra_compile_args = ['-std=c99'] + m4ri_extra_compile_args, - depends = [SAGE_INC + "png.h", SAGE_INC + "m4ri/m4ri.h"]), + depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]), -@@ -1772,7 +1772,7 @@ ext_modules = [ - +@@ -1760,7 +1760,7 @@ ext_modules = [ Extension('sage.rings.polynomial.pbori', sources = ['sage/rings/polynomial/pbori.pyx'], -- libraries=['polybori', 'polybori_groebner', 'cudd', 'gd', 'png12', 'm4ri'], -+ libraries=['polybori', 'polybori_groebner', 'cudd', 'gd', 'png', 'm4ri'], + libraries=['polybori-' + polybori_major_version, +- 'polybori_groebner-' + polybori_major_version, 'm4ri', 'png12'], ++ 'polybori_groebner-' + polybori_major_version, 'm4ri', 'png'], include_dirs = [SAGE_INC, "sage/libs/polybori"], - depends = [SAGE_INC + "polybori/" + hd + ".h" for hd in ["polybori", "config"] ] + \ - [SAGE_INC + 'm4ri/m4ri.h'], + depends = [SAGE_INC + "/polybori/" + hd + ".h" for hd in ["polybori", "config"] ] + \ + [SAGE_INC + '/m4ri/m4ri.h'], diff --git a/sagemath-readonly.patch b/sagemath-readonly.patch index 1bf31b6..0a6b3e3 100644 --- a/sagemath-readonly.patch +++ b/sagemath-readonly.patch @@ -1,7 +1,7 @@ -diff -up sage-5.8/spkg/build/sage-5.8/sage/all.py.orig sage-5.8/spkg/build/sage-5.8/sage/all.py ---- sage-5.8/spkg/build/sage-5.8/sage/all.py.orig 2013-02-22 17:28:29.394862830 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/all.py 2013-02-22 17:28:54.808863803 -0300 -@@ -288,13 +288,13 @@ def _write_started_file(): +diff -up sage-5.9/spkg/build/sage-5.9/sage/all.py.orig sage-5.9/spkg/build/sage-5.9/sage/all.py +--- sage-5.9/spkg/build/sage-5.9/sage/all.py.orig 2013-05-06 13:45:07.053737291 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/all.py 2013-05-06 13:45:35.317738373 -0300 +@@ -307,11 +307,11 @@ def _write_started_file(): Check that the file exists when Sage is running:: @@ -10,9 +10,6 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/all.py.orig sage-5.8/spkg/build/sage- sage: os.path.isfile(started_file) True """ -- from sage.misc.all import SAGE_LOCAL -+ from sage.misc.all import DOT_SAGE - - started_file = os.path.join(SAGE_LOCAL, 'etc', 'sage-started.txt') + started_file = os.path.join(DOT_SAGE, 'sage-started.txt') # Do nothing if the file already exists diff --git a/sagemath-rpmbuild.patch b/sagemath-rpmbuild.patch index 3c9928f..245790d 100644 --- a/sagemath-rpmbuild.patch +++ b/sagemath-rpmbuild.patch @@ -1,7 +1,16 @@ -diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sage-5.8/module_list.py ---- sage-5.8/spkg/build/sage-5.8/module_list.py.orig 2013-03-19 18:08:36.523974698 -0300 -+++ sage-5.8/spkg/build/sage-5.8/module_list.py 2013-03-19 18:08:39.383974808 -0300 -@@ -48,10 +48,11 @@ else: +diff -up sage-5.9/spkg/build/sage-5.9/module_list.py.orig sage-5.9/spkg/build/sage-5.9/module_list.py +--- sage-5.9/spkg/build/sage-5.9/module_list.py.orig 2013-05-06 16:21:08.750095783 -0300 ++++ sage-5.9/spkg/build/sage-5.9/module_list.py 2013-05-06 16:22:01.411097799 -0300 +@@ -5,7 +5,7 @@ from distutils.core import setup + from distutils.extension import Extension + from sage.env import * + +-SAGE_INC = os.path.join(SAGE_LOCAL, 'include') ++SAGE_INC = '/usr/include' + + ######################################################### + ### BLAS setup +@@ -36,10 +36,11 @@ else: ### Commonly used definitions ######################################################### @@ -13,20 +22,29 @@ diff -up sage-5.8/spkg/build/sage-5.8/module_list.py.orig sage-5.8/spkg/build/sa -numpy_depends = [SAGE_LOCAL + '/lib/python/site-packages/numpy/core/include/numpy/_numpyconfig.h'] +numpy_depends = [get_python_lib(1) + '/numpy/core/include/numpy/_numpyconfig.h'] - flint_depends = [SAGE_INC + 'FLINT/flint.h'] - singular_depends = [SAGE_INC + 'libsingular.h', SAGE_INC + 'givaro/givconfig.h'] -@@ -1771,7 +1772,7 @@ ext_modules = [ + flint_depends = [SAGE_INC + '/FLINT/flint.h'] + singular_depends = [SAGE_INC + '/libsingular.h', SAGE_INC + '/givaro/givconfig.h'] +@@ -71,7 +72,7 @@ givaro_extra_compile_args =['-D__STDC_LI + ### PolyBoRi settings + ######################################################### - Extension('sage.rings.polynomial.pbori', - sources = ['sage/rings/polynomial/pbori.pyx'], -- libraries=['polybori', 'polybori_groebner', 'gd', 'png12', 'm4ri'], -+ libraries=['polybori', 'polybori_groebner', 'cudd', 'gd', 'png12', 'm4ri'], - include_dirs = [SAGE_INC, "sage/libs/polybori"], - depends = [SAGE_INC + "polybori/" + hd + ".h" for hd in ["polybori", "config"] ] + \ - [SAGE_INC + 'm4ri/m4ri.h'], -diff -up sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/glpk_backend.pxd.orig sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/glpk_backend.pxd ---- sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/glpk_backend.pxd.orig 2013-03-19 18:08:36.526974699 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/glpk_backend.pxd 2013-03-19 18:08:39.383974808 -0300 +-polybori_extra_compile_args = [] ++polybori_extra_compile_args = ['-DPBORI_USE_ORIGINAL_CUDD'] + polybori_major_version = '0.8' + + +@@ -662,7 +663,7 @@ ext_modules = [ + sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'], + libraries = ['m', 'ntl', 'mpfr', 'gmp', 'gmpxx', + 'Lfunction', 'stdc++'], +- include_dirs = [SAGE_INC + "/libLfunction"], ++ include_dirs = [SAGE_INC + "/Lfunction"], + extra_compile_args=["-O3", "-ffast-math"], + language = 'c++'), + +diff -up sage-5.9/spkg/build/sage-5.9/sage/numerical/backends/glpk_backend.pxd.orig sage-5.9/spkg/build/sage-5.9/sage/numerical/backends/glpk_backend.pxd +--- sage-5.9/spkg/build/sage-5.9/sage/numerical/backends/glpk_backend.pxd.orig 2013-05-06 16:21:08.763095783 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/numerical/backends/glpk_backend.pxd 2013-05-06 16:21:12.815095939 -0300 @@ -16,7 +16,7 @@ cdef extern from *: cdef extern from "float.h": cdef double DBL_MAX @@ -36,30 +54,17 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/numerical/backends/glpk_backend.pxd.o ctypedef struct c_glp_prob "glp_prob": pass ctypedef struct c_glp_iocp "glp_iocp": -diff -up sage-5.8/spkg/build/sage-5.8/setup.py.orig sage-5.8/spkg/build/sage-5.8/setup.py ---- sage-5.8/spkg/build/sage-5.8/setup.py.orig 2013-03-20 03:54:28.401811272 -0300 -+++ sage-5.8/spkg/build/sage-5.8/setup.py 2013-03-20 03:54:53.892811608 -0300 -@@ -37,6 +37,11 @@ else: - SAGE_DEVEL = SAGE_ROOT + '/devel' - SAGE_INC = SAGE_LOCAL + '/include/' +diff -up sage-5.9/spkg/build/sage-5.9/setup.py.orig sage-5.9/spkg/build/sage-5.9/setup.py +--- sage-5.9/spkg/build/sage-5.9/setup.py.orig 2013-05-06 16:21:08.770095784 -0300 ++++ sage-5.9/spkg/build/sage-5.9/setup.py 2013-05-06 16:21:12.817095939 -0300 +@@ -38,21 +38,11 @@ except KeyError: -+if os.environ.has_key('DESTDIR'): -+ DESTDIR = os.environ['DESTDIR'] -+else: -+ DESTDIR = '' -+ - if not os.environ.has_key('SAGE_VERSION'): - SAGE_VERSION=0 - else: -@@ -49,21 +54,13 @@ except KeyError: - compile_result_dir = None - keep_going = False + SAGE_INC = os.path.join(SAGE_LOCAL,'include') -SITE_PACKAGES = '%s/lib/python%s/site-packages/'%(SAGE_LOCAL,platform.python_version().rsplit('.', 1)[0]) -+SITE_PACKAGES = '%s/lib/python%s/site-packages'%(SAGE_LOCAL,platform.python_version().rsplit('.', 1)[0]) - if not os.path.exists(SITE_PACKAGES): - raise RuntimeError, "Unable to find site-packages directory (see setup.py file in sage python code)." - +-if not os.path.exists(SITE_PACKAGES): +- raise RuntimeError, "Unable to find site-packages directory (see setup.py file in sage python code)." +- -if not os.path.exists('build/sage'): - os.makedirs('build/sage') - @@ -67,15 +72,16 @@ diff -up sage-5.8/spkg/build/sage-5.8/setup.py.orig sage-5.8/spkg/build/sage-5.8 -if not os.path.islink(sage_link) or not os.path.exists(sage_link): - os.system('rm -rf "%s"'%sage_link) - os.system('cd %s; ln -sf ../../../../devel/sage/build/sage .'%SITE_PACKAGES) -- ++SITE_PACKAGES = '%s/lib/python%s/site-packages'%(SAGE_LOCAL,platform.python_version().rsplit('.', 1)[0]) + # search for dependencies and add to gcc -I - include_dirs = ['%s/include'%SAGE_LOCAL, -- '%s/include/csage'%SAGE_LOCAL, + include_dirs = [SAGE_INC, +- os.path.join(SAGE_INC, 'csage'), + 'c_lib/include', - '%s/sage/sage/ext'%SAGE_DEVEL] + os.path.join(SAGE_SRC, 'sage', 'ext')] # search for dependencies only -@@ -173,11 +170,11 @@ for m in ext_modules: +@@ -170,11 +160,11 @@ for m in ext_modules: # FIMXE: Do NOT link the following libraries to each and # every module (regardless of the language btw.): @@ -89,66 +95,20 @@ diff -up sage-5.8/spkg/build/sage-5.8/setup.py.orig sage-5.8/spkg/build/sage-5.8 -@@ -507,8 +504,8 @@ class sage_build_ext(build_ext): - ############################################# +diff -up sage-5.9/spkg/build/conway_polynomials-0.4.p0/spkg-install.orig sage-5.9/spkg/build/conway_polynomials-0.4.p0/spkg-install +--- sage-5.9/spkg/build/conway_polynomials-0.4.p0/spkg-install.orig 2013-05-06 17:47:06.493293291 -0300 ++++ sage-5.9/spkg/build/conway_polynomials-0.4.p0/spkg-install 2013-05-06 17:48:27.883296408 -0300 +@@ -2,9 +2,11 @@ - CYTHON_INCLUDE_DIRS=[ -- SAGE_LOCAL + '/lib/python/site-packages/Cython/Includes/', -- SAGE_LOCAL + '/lib/python/site-packages/Cython/Includes/Deprecated/', -+ SAGE_LOCAL + '/lib/python2.7/site-packages/Cython/Includes/', -+ SAGE_LOCAL + '/lib/python2.7/site-packages/Cython/Includes/Deprecated/', - ] + import os + from sage.all import save +-from sage.misc.misc import SAGE_SHARE - # matches any dependency -@@ -534,7 +531,7 @@ class DependencyTree: - self._timestamps = {} - self._deps = {} - self._deps_all = {} -- self.root = "%s/devel/sage/" % SAGE_ROOT -+ self.root = "%s/devel/sage" % SAGE_ROOT - - def __getstate__(self): - """ -@@ -555,7 +552,7 @@ class DependencyTree: - self.__dict__.update(state) - self._timestamps = {} - self._deps_all = {} -- self.root = "%s/devel/sage/" % SAGE_ROOT -+ self.root = "%s/devel/sage" % SAGE_ROOT - - def timestamp(self, filename): - """ -@@ -642,11 +639,8 @@ class DependencyTree: - # so we really couldn't find the dependency -- raise - # an exception. - if not found_include: -- msg = 'could not find dependency %s included in %s.'%(path, filename) -- if is_cython_file(path): -- raise IOError, msg -- else: -- warnings.warn(msg+' I will assume it is a system C/C++ header.') -+ if path[-2:] != '.h' and path[-4:] != '.hpp' and path[-4:] != '.pxd': # there are implicit headers from distutils, etc -+ raise IOError, "could not find dependency %s included in %s."%(path, filename) - f.close() - return list(deps) - -@@ -738,6 +732,10 @@ def compile_command0(p): - outfile += ".c" - cplus = '' - -+ # speed up if doing an incremental builds -+ if os.path.exists(outfile) and os.path.getmtime(outfile) > os.path.getmtime(f): -+ return 0 +-install_root = os.path.join(SAGE_SHARE, 'conway_polynomials') ++if 'SAGE_SHARE' not in os.environ: ++ raise RuntimeError("SAGE_SHARE undefined, maybe run `sage -sh`?") + - if os.environ.get('SAGE_DEBUG', None)=='no': - debug = '' - else: -@@ -750,7 +748,7 @@ def compile_command0(p): - return r ++install_root = os.path.join(os.environ['SAGE_SHARE'], 'conway_polynomials') - # if cython worked, copy the file to the build directory -- pyx_inst_file = '%s/%s'%(SITE_PACKAGES, f) -+ pyx_inst_file = '%s%s/%s'%(DESTDIR, SITE_PACKAGES, f) - retval = os.system('cp %s %s 2>/dev/null'%(f, pyx_inst_file)) - # we could do this more elegantly -- load the files, use - # os.path.exists to check that they exist, etc. ... but the + def create_db(): + db = {} diff --git a/sagemath-sagedoc.patch b/sagemath-sagedoc.patch index cad6ade..da8b615 100644 --- a/sagemath-sagedoc.patch +++ b/sagemath-sagedoc.patch @@ -1,42 +1,86 @@ -diff -up sage-5.8/spkg/build/sage-5.8/doc/common/builder.py.orig sage-5.8/spkg/build/sage-5.8/doc/common/builder.py ---- sage-5.8/spkg/build/sage-5.8/doc/common/builder.py.orig 2013-03-19 16:06:49.142694873 -0300 -+++ sage-5.8/spkg/build/sage-5.8/doc/common/builder.py 2013-03-19 16:07:08.156695601 -0300 -@@ -31,7 +31,7 @@ from sage.misc.misc import sage_makedirs +diff -up sage-5.9/spkg/build/sage-5.9/doc/common/builder.py.orig sage-5.9/spkg/build/sage-5.9/doc/common/builder.py +--- sage-5.9/spkg/build/sage-5.9/doc/common/builder.py.orig 2013-05-07 18:11:12.277264082 -0300 ++++ sage-5.9/spkg/build/sage-5.9/doc/common/builder.py 2013-05-07 18:11:15.785264216 -0300 +@@ -32,7 +32,7 @@ from sage.env import SAGE_DOC, SAGE_SRC # SAGE_DOC, LANGUAGES, SPHINXOPTS, PAPER, OMIT, # PAPEROPTS, ALLSPHINXOPTS, NUM_THREADS, WEBSITESPHINXOPTS # from build_options.py. --execfile(os.path.join(os.getenv('SAGE_ROOT'), 'devel', 'sage', 'doc', 'common' , 'build_options.py')) -+execfile(os.path.join(os.getenv('SAGE_ROOT'), 'devel', 'doc', 'common' , 'build_options.py')) +-execfile(os.path.join(SAGE_DOC, 'common' , 'build_options.py')) ++execfile(os.path.join(os.getenv('SAGE_ROOT'), 'src', 'doc', 'common' , 'build_options.py')) ########################################## -diff -up sage-5.8/spkg/build/sage-5.8/doc/common/conf.py.orig sage-5.8/spkg/build/sage-5.8/doc/common/conf.py ---- sage-5.8/spkg/build/sage-5.8/doc/common/conf.py.orig 2013-03-19 16:07:24.854696241 -0300 -+++ sage-5.8/spkg/build/sage-5.8/doc/common/conf.py 2013-03-19 16:08:21.261698401 -0300 -@@ -1,7 +1,7 @@ +diff -up sage-5.9/spkg/build/sage-5.9/doc/common/conf.py.orig sage-5.9/spkg/build/sage-5.9/doc/common/conf.py +--- sage-5.9/spkg/build/sage-5.9/doc/common/conf.py.orig 2013-05-07 18:11:12.286264082 -0300 ++++ sage-5.9/spkg/build/sage-5.9/doc/common/conf.py 2013-05-07 18:11:15.788264216 -0300 +@@ -1,5 +1,5 @@ import sys, os, sphinx - --SAGE_ROOT = os.environ['SAGE_ROOT'] --SAGE_DOC = os.path.join(SAGE_ROOT, 'devel/sage/doc') -+SAGE_DEVEL = os.environ['SAGE_DEVEL'] -+SAGE_DOC = os.environ['SAGE_DOC'] +-from sage.env import SAGE_DOC ++from sage.env import SAGE_DOC, SAGE_SRC def get_doc_abspath(path): """ -@@ -204,8 +204,7 @@ if (os.environ.get('SAGE_DOC_MATHJAX', ' +@@ -202,8 +202,7 @@ if (os.environ.get('SAGE_DOC_MATHJAX', ' from sage.misc.latex_macros import sage_mathjax_macros html_theme_options['mathjax_macros'] = sage_mathjax_macros() - from pkg_resources import Requirement, working_set - sagenb_path = working_set.find(Requirement.parse('sagenb')).location -+ sagenb_path = SAGE_DEVEL ++ sagenb_path = SAGE_SRC mathjax_relative = os.path.join('sagenb','data','mathjax') # It would be really nice if sphinx would copy the entire mathjax directory, -diff -up sage-5.8/spkg/build/sage-5.8/sage/interfaces/singular.py.orig sage-5.8/spkg/build/sage-5.8/sage/interfaces/singular.py ---- sage-5.8/spkg/build/sage-5.8/sage/interfaces/singular.py.orig 2013-03-19 16:08:38.847699074 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/interfaces/singular.py 2013-03-19 16:08:52.885699612 -0300 -@@ -2144,7 +2144,7 @@ def generate_docstring_dictionary(): +diff -up sage-5.9/spkg/build/sage-5.9/sage/doctest/control.py.orig sage-5.9/spkg/build/sage-5.9/sage/doctest/control.py +--- sage-5.9/spkg/build/sage-5.9/sage/doctest/control.py.orig 2013-05-07 18:11:29.325264735 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/doctest/control.py 2013-05-07 18:12:09.794266284 -0300 +@@ -88,7 +88,6 @@ class DocTestDefaults(SageObject): + self.valgrind = False + self.massif = False + self.cachegrind = False +- self.omega = False + self.failed = False + self.new = False + self.show_skipped = False +@@ -161,7 +160,7 @@ class DocTestController(SageObject): + if options.gdb or options.debug: + # Interactive debuggers: "infinite" timeout + options.timeout = 0 +- elif options.valgrind or options.massif or options.cachegrind or options.omega: ++ elif options.valgrind or options.massif or options.cachegrind: + # Non-interactive debuggers: 48 hours + options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60)) + elif options.long: +@@ -766,13 +765,8 @@ class DocTestController(SageObject): + elif opt.cachegrind: + toolname = "cachegrind" + flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "") +- elif opt.omega: +- toolname = "exp-omega" +- flags = os.getenv("SAGE_OMEGA_FLAGS", "") + cmd = "exec valgrind --tool=%s "%(toolname) + flags += ''' --log-file="%s" ''' % logfile +- if opt.omega: +- toolname = "omega" + if "%s" in flags: + flags %= toolname + ".%p" # replace %s with toolname + cmd += flags + sage_cmd +@@ -832,10 +826,10 @@ class DocTestController(SageObject): + 0 + """ + opt = self.options +- L = (opt.gdb, opt.valgrind, opt.massif, opt.cachegrind, opt.omega) ++ L = (opt.gdb, opt.valgrind, opt.massif, opt.cachegrind) + if any(L): + if L.count(True) > 1: +- self.log("You may only specify one of gdb, valgrind/memcheck, massif, cachegrind, omega") ++ self.log("You may only specify one of gdb, valgrind/memcheck, massif, cachegrind") + return 2 + return self.run_val_gdb() + else: +diff -up sage-5.9/spkg/build/sage-5.9/sage/interfaces/singular.py.orig sage-5.9/spkg/build/sage-5.9/sage/interfaces/singular.py +--- sage-5.9/spkg/build/sage-5.9/sage/interfaces/singular.py.orig 2013-05-07 18:11:12.296264082 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/interfaces/singular.py 2013-05-07 18:11:15.792264216 -0300 +@@ -2149,7 +2149,7 @@ def generate_docstring_dictionary(): nodes.clear() node_names.clear() @@ -45,9 +89,9 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/interfaces/singular.py.orig sage-5.8/ new_node = re.compile("File: singular\.hlp, Node: ([^,]*),.*") new_lookup = re.compile("\* ([^:]*):*([^.]*)\..*") -diff -up sage-5.8/spkg/build/sage-5.8/sage/misc/latex_macros.py.orig sage-5.8/spkg/build/sage-5.8/sage/misc/latex_macros.py ---- sage-5.8/spkg/build/sage-5.8/sage/misc/latex_macros.py.orig 2013-03-19 16:09:05.806700107 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/misc/latex_macros.py 2013-03-19 16:09:20.564700672 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/sage/misc/latex_macros.py.orig sage-5.9/spkg/build/sage-5.9/sage/misc/latex_macros.py +--- sage-5.9/spkg/build/sage-5.9/sage/misc/latex_macros.py.orig 2013-05-07 18:11:12.303264083 -0300 ++++ sage-5.9/spkg/build/sage-5.9/sage/misc/latex_macros.py 2013-05-07 18:11:15.793264216 -0300 @@ -142,7 +142,7 @@ def convert_latex_macro_to_mathjax(macro return name + ': ["' + defn + '",' + str(num_args) + ']' @@ -57,24 +101,3 @@ diff -up sage-5.8/spkg/build/sage-5.8/sage/misc/latex_macros.py.orig sage-5.8/sp # To add a new macro for use in the Sage documentation, add a list or # tuple to the following list. Each list (or tuple) should have the -diff -up sage-5.8/spkg/build/sage-5.8/sage/misc/sagedoc.py.orig sage-5.8/spkg/build/sage-5.8/sage/misc/sagedoc.py ---- sage-5.8/spkg/build/sage-5.8/sage/misc/sagedoc.py.orig 2013-03-19 16:09:31.254701081 -0300 -+++ sage-5.8/spkg/build/sage-5.8/sage/misc/sagedoc.py 2013-03-19 16:10:05.277702384 -0300 -@@ -704,13 +704,13 @@ def _search_src_or_doc(what, string, ext - module = '' - exts = ['html'] - title = 'Documentation' -- base_path = os.path.join('devel', 'sage', 'doc', 'output') -- doc_path = os.path.join(ROOT, 'devel', 'sage', 'doc') -+ base_path = os.path.join('devel', 'output') -+ doc_path = os.path.join(ROOT, 'devel', 'doc') - -- # We need to import stuff from SAGE_ROOT/devel/sage/doc/common -+ # We need to import stuff from SAGE_ROOT/devel/doc/common - # To do this, we temporarily change sys.path - oldpath = sys.path -- sys.path = oldpath + [os.path.join(ROOT, 'devel', 'sage', 'doc', 'common')] -+ sys.path = oldpath + [os.path.join(ROOT, 'devel', 'doc', 'common')] - import build_options as builder - # List of languages - lang = builder.LANGUAGES diff --git a/sagemath-sagenb.patch b/sagemath-sagenb.patch index 045f821..d9eec3f 100644 --- a/sagemath-sagenb.patch +++ b/sagemath-sagenb.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py.orig sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py ---- sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py.orig 2012-10-20 11:29:36.315150735 -0300 -+++ sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py 2012-10-20 11:29:56.569151510 -0300 +diff -up sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py.orig sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py +--- sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py.orig 2012-10-20 11:29:36.315150735 -0300 ++++ sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py 2012-10-20 11:29:56.569151510 -0300 @@ -27,7 +27,7 @@ class SageNBFlask(Flask): self.add_static_path('/javascript', DATA) self.add_static_path('/static', DATA) @@ -10,9 +10,9 @@ diff -up sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py.orig import mimetypes mimetypes.add_type('text/plain','.jmol') -diff -up sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html.orig sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html ---- sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html.orig 2012-10-20 11:31:17.315154602 -0300 -+++ sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html 2012-10-20 11:31:41.764155539 -0300 +diff -up sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html.orig sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html +--- sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html.orig 2012-10-20 11:31:17.315154602 -0300 ++++ sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html 2012-10-20 11:31:41.764155539 -0300 @@ -69,7 +69,7 @@ INPUT: @@ -22,9 +22,9 @@ diff -up sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/note {% if JEDITABLE_TINYMCE and not worksheet.docbrowser() and not worksheet.is_published() %} -diff -up sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py.orig sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py ---- sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py.orig 2012-10-20 11:33:00.483158553 -0300 -+++ sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py 2012-10-20 11:33:17.700159212 -0300 +diff -up sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py.orig sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py +--- sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py.orig 2012-10-20 11:33:00.483158553 -0300 ++++ sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py 2012-10-20 11:33:17.700159212 -0300 @@ -2367,7 +2367,7 @@ class Cell(Cell_generic): jmol_script = jmol_file.read() jmol_file.close() @@ -34,9 +34,9 @@ diff -up sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py.or jmol_file = open(jmol_name, 'w') jmol_file.write(jmol_script) -diff -up sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py.orig sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py ---- sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py.orig 2012-10-20 11:31:55.106156049 -0300 -+++ sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py 2012-10-20 11:32:51.460158207 -0300 +diff -up sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py.orig sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py +--- sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py.orig 2012-10-20 11:31:55.106156049 -0300 ++++ sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py 2012-10-20 11:32:51.460158207 -0300 @@ -46,15 +46,14 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s # Flask # ######### @@ -44,7 +44,7 @@ diff -up sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebo -flask_dir = os.path.join(os.environ['SAGE_ROOT'], 'devel', 'sagenb', 'flask_version') -sys.path.append(flask_dir) -import base as flask_base -+sagenb_dir = os.path.join(os.environ['SAGE_ROOT'], 'devel', 'sagenb') ++sagenb_dir = os.path.join(os.environ['SAGE_ROOT'], 'src', 'sagenb') +sys.path.append(sagenb_dir) +import flask_version.base as flask_base opts={} @@ -57,9 +57,9 @@ diff -up sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebo def save_notebook(notebook): print "Quitting all running worksheets..." -diff -up sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js.orig sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js ---- sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js.orig 2012-11-14 22:46:56.488853512 -0200 -+++ sage-5.8/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js 2012-11-14 22:49:02.772858348 -0200 +diff -up sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js.orig sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js +--- sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js.orig 2012-11-14 22:46:56.488853512 -0200 ++++ sage-5.9/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js 2012-11-14 22:49:02.772858348 -0200 @@ -256,9 +256,6 @@ function makeCntrlPanels(url, n, functio panelHTML +=' arbitrarily resizable.
'; //static image to save diff --git a/sagemath-scons.patch b/sagemath-scons.patch index 45a11e0..05efd17 100644 --- a/sagemath-scons.patch +++ b/sagemath-scons.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/build/sage-5.8/c_lib/SConstruct.orig sage-5.8/spkg/build/sage-5.8/c_lib/SConstruct ---- sage-5.8/spkg/build/sage-5.8/c_lib/SConstruct.orig 2013-02-23 12:55:48.382841120 -0300 -+++ sage-5.8/spkg/build/sage-5.8/c_lib/SConstruct 2013-02-23 12:56:25.037842523 -0300 +diff -up sage-5.9/spkg/build/sage-5.9/c_lib/SConstruct.orig sage-5.9/spkg/build/sage-5.9/c_lib/SConstruct +--- sage-5.9/spkg/build/sage-5.9/c_lib/SConstruct.orig 2013-02-23 12:55:48.382841120 -0300 ++++ sage-5.9/spkg/build/sage-5.9/c_lib/SConstruct 2013-02-23 12:56:25.037842523 -0300 @@ -126,18 +126,31 @@ env['PYV']=platform.python_version().rsp # The SCons convenience function Split is the only strange thing # to python programmers. It just makes a list by splitting on diff --git a/sagemath-scripts.patch b/sagemath-scripts.patch index bb9b6ca..b3ba932 100644 --- a/sagemath-scripts.patch +++ b/sagemath-scripts.patch @@ -1,6 +1,6 @@ -diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage ---- sage-5.8/spkg/bin/sage.orig 2013-02-22 17:09:59.465820327 -0300 -+++ sage-5.8/spkg/bin/sage 2013-02-22 17:17:23.824837343 -0300 +diff -up sage-5.9/spkg/bin/sage.orig sage-5.9/spkg/bin/sage +--- sage-5.9/spkg/bin/sage.orig 2013-05-06 12:05:34.567508584 -0300 ++++ sage-5.9/spkg/bin/sage 2013-05-06 12:21:04.123544180 -0300 @@ -11,17 +11,14 @@ usage() { echo " file. -- run given .sage, .py or .spyx files" echo " -advanced -- list all command line options" @@ -19,20 +19,26 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage echo " -python [...] -- run the Python interpreter" echo " -R [...] -- run Sage's R with given arguments" echo " -singular [...] -- run Sage's singular with given arguments" -@@ -38,10 +35,8 @@ usage() { - echo " -only-optional -- only run tests" - echo " including one of the #optional tags" - echo " -randorder[=seed] -- randomize order of tests" +@@ -36,10 +33,6 @@ usage() { + echo " --verbose - print debugging output during the test" + echo " --optional - controls which optional tests are run" + echo " --help - show all testing options" - echo " -upgrade [url] -- download, build and install standard packages from" - echo " given url. If url not given, automatically selects a" - echo " suitable mirror. If url='ask', it lets you select" - echo " the mirror (uses SAGE_SERVER as default)." -+ echo " -testall [options] -- test all source files, docs, and examples. options" -+ echo " like -t" echo " -v, -version -- print the Sage version" exit 0 } -@@ -71,8 +66,6 @@ usage_advanced() { +@@ -63,14 +56,14 @@ usage_advanced() { + echo " -root -- print the Sage root directory" + echo " -gthread, -qthread, -q4thread, -wthread, -pylab" + echo " -- pass the option through to ipython" ++ echo " -testall [options] -- test all source files, docs, and examples. options" ++ echo " like -t" + echo " -v, -version -- print the Sage version" + + echo #### 1.......................26..................................................78 #### |.....................--.|...................................................| echo "Running the notebook:" @@ -41,13 +47,16 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage echo " -inotebook [...] -- start the *insecure* Sage notebook" echo " -n, -notebook [...] -- start the Sage notebook (options are the same" echo " as for the notebook command in Sage)" -@@ -90,13 +83,8 @@ usage_advanced() { - echo " -hg [...] -- run Sage's Mercurial with given arguments" +@@ -85,16 +78,11 @@ usage_advanced() { + echo " -gap [...] -- run Sage's Gap with given arguments" + echo " -gdb -- run Sage under the control of gdb" + echo " -gp [...] -- run Sage's PARI/GP calculator with given arguments" +- echo " -hg [...] -- run Sage's Mercurial with given arguments" echo " -ipython [...] -- run Sage's IPython using the default environment (not" echo " Sage), passing additional options to IPython" - echo " -kash [...] -- run Sage's Kash with given arguments" - test -x "$SAGE_LOCAL/bin/kash" || \ -- echo " (not installed currently, run sage -i kash)" + echo " (not installed currently, run sage -i kash)" echo " -lisp [...] -- run Lisp interpreter included with Sage" echo " -M2 [...] -- run Sage's Macaulay2 with given arguments" - test -x "$SAGE_LOCAL/bin/M2" || \ @@ -55,7 +64,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage echo " -maxima [...] -- run Sage's Maxima with given arguments" echo " -mwrank [...] -- run Sage's mwrank with given arguments" echo " -python [...] -- run the Python interpreter" -@@ -110,77 +98,10 @@ usage_advanced() { +@@ -108,73 +96,6 @@ usage_advanced() { echo #### 1.......................26..................................................78 #### |.....................--.|...................................................| @@ -106,17 +115,18 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage - echo " -startuptime [module] -- display how long each component of Sage takes to" - echo " start up; optionally specify a module to get more" - echo " details about that particular module" -- echo " -t [options] " -- echo " -- test examples in .py, .pyx, .sage or .tex files" -- echo " options:" -- echo " -long -- include lines with the phrase 'long time'" -- echo " -verbose -- print debugging output during the test" -- echo " -optional -- also test all #optional examples" -- echo " -only-optional -- only run tests" -- echo " including one of the #optional tags" -- echo " -randorder[=seed] -- randomize order of tests" -- echo " -tnew [...] -- like -t above, but only tests files modified since" -- echo " last commit" +- echo " -t [options] <--all|files|dir>" +- echo " -- test examples in .py, .pyx, .sage, .tex or .rst files" +- echo " selected options:" +- echo " --long - include lines with the phrase 'long time'" +- echo " --verbose - print debugging output during the test" +- echo " --optional - controls which optional tests are run" +- echo " --randorder[=seed] - randomize order of tests" +- echo " --new - only test files modified since last commit" +- echo " --initial - only show the first failure per block" +- echo " --debug - drop into PDB after an unexpected error" +- echo " --failed - only test files that failed last test" +- echo " --help - show all testing options" - echo " -tp [...] -- like -t above, but tests in parallel using N threads" - echo " with 0 interpreted as a sensible default" - echo " -testall [options] -- test all source files, docs, and examples. options" @@ -128,12 +138,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage echo "Documentation:" echo " -coverage -- give info about doctest coverage of files" echo " -coverageall -- give summary info about doctest coverage of all" - echo " files in the Sage library" -- echo " -docbuild [lang/] -- Build the Sage documentation" - echo " -search_src -- search through all the Sage library code for string" - echo " -search_doc -- search through the Sage documentation for string" - echo " -grep -- same as -search_src" -@@ -198,20 +119,6 @@ usage_advanced() { +@@ -197,20 +118,6 @@ usage_advanced() { echo #### 1.......................26..................................................78 #### |.....................--.|...................................................| @@ -154,7 +159,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage echo "Valgrind memory debugging:" echo " -cachegrind -- run Sage using Valgrind's cachegrind tool. The log" echo " files are named sage-cachegrind.PID can be found in" -@@ -225,9 +132,6 @@ usage_advanced() { +@@ -224,9 +131,6 @@ usage_advanced() { echo " -memcheck -- run Sage using Valgrind's memcheck tool. The log" echo " files are named sage-memcheck.PID can be found in" echo " $DOT_SAGE" @@ -164,7 +169,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage echo " -valgrind -- this is an alias for -memcheck" echo echo "You can also use -- before a long option, e.g., 'sage --optional'." -@@ -247,15 +151,6 @@ if [ "$1" = '--nodotsage' ]; then +@@ -246,15 +150,6 @@ if [ "$1" = '--nodotsage' ]; then exit $status fi @@ -180,8 +185,11 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage if [ $# -gt 0 ]; then if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then usage -@@ -268,30 +163,11 @@ fi +@@ -264,28 +159,13 @@ if [ $# -gt 0 ]; then + fi + fi +- # Prepare for running Sage, either interactively or non-interactively. sage_setup() { - # Check that we're not in a source tarball which hasn't been built yet (#13561). @@ -201,17 +209,34 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage cat "$SAGE_LOCAL/bin/sage-banner" fi -- # Check to see if the whole Sage install tree has moved. If so, -- # change various hardcoded paths. Skip this if we don't have write -- # access to $SAGE_LOCAL (e.g. when running as a different user). -- if [ -w "$SAGE_LOCAL" ]; then -- sage-location || exit $? -- fi +- maybe_sage_location - if [ ! -d "$IPYTHONDIR" ]; then # make sure that $DOT_SAGE exists so that ipython will happily # create its config directories there. If DOT_SAGE doesn't -@@ -340,12 +216,6 @@ if [ "$1" = '-root' -o "$1" = '--root' +@@ -295,21 +175,6 @@ sage_setup() { + sage-cleaner &>/dev/null & + } + +- +-# Check to see if the whole Sage install tree has moved. If so, +-# change various hardcoded paths. Skip this if we don't have write +-# access to $SAGE_LOCAL (e.g. when running as a different user) or +-# if Python and sage-location haven't been installed yet. +-maybe_sage_location() +-{ +- if [ -w "$SAGE_LOCAL" ]; then +- if [ -x "$SAGE_LOCAL/bin/python" ] && [ -x "$SAGE_LOCAL/bin/sage-location" ]; then +- sage-location || exit $? +- fi +- fi +-} +- +- + # Start an interactive Sage session, this function never returns. + interactive_sage() { + sage_setup +@@ -348,12 +213,6 @@ if [ "$1" = '-root' -o "$1" = '--root' exit 0 fi @@ -224,7 +249,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage ##################################################################### # Run Sage's versions of the standard Algebra/Geometry etc. software ##################################################################### -@@ -355,74 +225,59 @@ if [ "$1" = '-axiom' -o "$1" = '--axiom' +@@ -363,74 +222,59 @@ if [ "$1" = '-axiom' -o "$1" = '--axiom' exec axiom "$@" fi @@ -248,7 +273,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage if [ "$1" = '-singular' -o "$1" = '--singular' ]; then shift - exec "$SAGE_LOCAL/bin/singular" "$@" -+ exec singular "$@" ++ exec Singular "$@" fi if [ "$1" = '-sqlite3' -o "$1" = '--sqlite3' ]; then @@ -310,7 +335,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage fi if [ "$1" = '-python' -o "$1" = '--python' ]; then -@@ -432,12 +287,12 @@ fi +@@ -440,7 +284,7 @@ fi if [ "$1" = '-R' -o "$1" = '--R' ]; then shift @@ -319,13 +344,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage fi if [ "$1" = '-ipython' -o "$1" = '--ipython' ]; then - shift -- exec "$SAGE_LOCAL/bin/ipython" "$@" -+ exec ipython "$@" - fi - - if [ "$1" = '-sh' -o "$1" = '--sh' ]; then -@@ -558,33 +413,6 @@ EOF +@@ -566,33 +410,6 @@ EOF exit $status fi @@ -359,7 +378,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage ##################################################################### # File conversion ##################################################################### -@@ -600,35 +428,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2 +@@ -608,36 +425,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2 fi ##################################################################### @@ -376,6 +395,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage ##################################################################### -build_sage() { +- maybe_sage_location - sage-build "$@" || exit $? -} - @@ -395,7 +415,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then shift sage-cleaner &>/dev/null & -@@ -651,79 +459,7 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep +@@ -656,86 +452,14 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep exit 0 fi @@ -468,40 +488,41 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage - exit $? -fi - --if [ "$1" = '-t' -o "$1" = '-bt' ]; then -- if [ "$1" = '-bt' ]; then -- build_sage -- fi -+if [ "$1" = '-t' ]; then - if ! [ -f "$DOT_SAGE"/init.sage ]; then - echo >&2 "init.sage does not exist ... creating" - touch "$DOT_SAGE"/init.sage -@@ -735,10 +471,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' ]; then - exit $? - fi - --if [ "$1" = '-tp' -o "$1" = '-btp' ]; then -- if [ "$1" = '-btp' ]; then -- build_sage -- fi -+if [ "$1" = '-tp' ]; then - if ! [ -f "$DOT_SAGE"/init.sage ]; then - echo >&2 "init.sage does not exist ... creating" - touch "$DOT_SAGE"/init.sage -@@ -750,10 +483,7 @@ if [ "$1" = '-tp' -o "$1" = '-btp' ]; th - exit $? +-if [ "$1" = '-t' -o "$1" = '-bt' -o "$1" = '-tp' -o "$1" = '-btp' ]; then +- if [ "$1" = '-bt' -o "$1" = '-btp' ]; then +- build_sage +- fi ++if [ "$1" = '-t' -o "$1" = '-tp' ]; then + if [ ! -f "$DOT_SAGE"/init.sage ]; then + echo >&2 "init.sage does not exist ... creating" + touch "$DOT_SAGE"/init.sage + fi + SAGE_BANNER="no" + sage_setup +- if [ "$1" = '-tp' -o "$1" = '-btp' ]; then ++ if [ "$1" = '-tp' ]; then + shift + exec sage-runtests -p "$@" + else +@@ -744,16 +468,6 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1" + fi fi -if [ "$1" = '-tnew' -o "$1" = '-btnew' ]; then -- if [ "$1" = '-btnew' ]; then -- build_sage -- fi -+if [ "$1" = '-tnew' ]; then - shift - SAGE_BANNER="no" - sage_setup -@@ -769,12 +499,6 @@ if [ "$1" = '-testall' -o "$1" = "--test - exit $? +- if [ "$1" = '-btnew' ]; then +- build_sage +- fi +- shift +- SAGE_BANNER="no" +- sage_setup +- exec sage-runtests --new "$@" +-fi +- + if [ "$1" = '-testall' -o "$1" = "--testall" ]; then + shift + SAGE_BANNER="no" +@@ -761,12 +475,6 @@ if [ "$1" = '-testall' -o "$1" = "--test + exec sage-runtests -a "$@" fi -if [ "$1" = '-patchbot' -o "$1" = "--patchbot" ]; then @@ -513,11 +534,13 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage if [ "$1" = '-c' ]; then shift SAGE_BANNER="no" -@@ -783,164 +507,6 @@ if [ "$1" = '-c' ]; then +@@ -775,166 +483,6 @@ if [ "$1" = '-c' ]; then exec sage-eval "$@" fi -install() { +- maybe_sage_location +- - mkdir -p "$SAGE_LOGS" - for PKG in "$@" - do @@ -547,16 +570,13 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage - - "$SAGE_ROOT"/spkg/pipestatus \ - "sage-spkg $OPTINFO $OPTF $OPTS $OPTC '$PKG' 2>&1" \ -- "(trap '' SIGINT; tee -a '$SAGE_ROOT/install.log' '$SAGE_LOGS/$PKG_NAME.log')" +- "(trap '' SIGINT; tee -a '$SAGE_ROOT/logs/install.log' '$SAGE_LOGS/$PKG_NAME.log')" - # Do not try to install further packages if one failed - if [ $? -ne 0 ]; then - exit 1 - fi - done -- -- # Run sage-location to update paths of the package(s) we just -- # installed. -- exec sage-location +- exit 0 -} - -if [ "$1" = '-optional' -o "$1" = "--optional" ]; then @@ -615,6 +635,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage - echo >&2 "** MISSING VERSION NUMBER! **" - exit 2 - fi +- maybe_sage_location - exec sage-sdist $2 "$SAGE_ROOT" -fi - @@ -623,6 +644,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage - echo >&2 "** MISSING VERSION NUMBER! **" - exit 2 - fi +- maybe_sage_location - exec sage-rsyncdist $2 -fi - @@ -631,6 +653,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage - echo >&2 "** MISSING VERSION NUMBER! **" - exit 2 - fi +- maybe_sage_location - cd "$SAGE_ROOT" - exec sage-bdist $2 "$SAGE_ROOT" -fi @@ -678,7 +701,7 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then shift sage_setup -@@ -989,12 +555,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca +@@ -983,12 +531,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca exec sage-callgrind "$@" fi @@ -691,87 +714,23 @@ diff -up sage-5.8/spkg/bin/sage.orig sage-5.8/spkg/bin/sage if [ "$1" = '-startuptime' -o "$1" = '--startuptime' ]; then exec sage-startuptime.py "$@" fi -diff -up sage-5.8/spkg/build/sage_scripts-5.8/sage-doctest.orig sage-5.8/spkg/build/sage_scripts-5.8/sage-doctest ---- sage-5.8/spkg/build/sage_scripts-5.8/sage-doctest.orig 2013-02-22 17:19:08.426841348 -0300 -+++ sage-5.8/spkg/build/sage_scripts-5.8/sage-doctest 2013-02-22 17:20:08.600843653 -0300 -@@ -90,11 +90,6 @@ def delete_tmpfiles(): - # Set environment variables - ###################################################### - SAGE_ROOT = os.environ["SAGE_ROOT"] --LD = os.environ["LD_LIBRARY_PATH"] --os.environ["LD_LIBRARY_PATH"] = os.path.join(SAGE_ROOT, 'local', -- 'lib') + ":" + LD --os.environ["PYTHONPATH"] = os.path.join(SAGE_ROOT, 'local', 'lib', 'python', -- 'site-packages') - if os.environ.has_key('SAGE_PATH'): - os.environ["PYTHONPATH"] = os.environ["PYTHONPATH"] + ':' + os.environ['SAGE_PATH'] +diff -up sage-5.9/spkg/build/sage_scripts-5.9/sage-runtests.orig sage-5.9/spkg/build/sage_scripts-5.9/sage-runtests +--- sage-5.9/spkg/build/sage_scripts-5.9/sage-runtests.orig 2013-05-06 12:10:00.030518749 -0300 ++++ sage-5.9/spkg/build/sage_scripts-5.9/sage-runtests 2013-05-06 12:22:51.300548284 -0300 +@@ -54,10 +54,6 @@ if __name__ == "__main__": + help="run doctests using Valgrind's cachegrind tool. The log " + "files are named sage-cachegrind.PID and can be found in " + + os.path.join(os.environ["DOT_SAGE"], "valgrind")) +- parser.add_option("--omega", action="store_true", default=False, +- help="run doctests using Valgrind's omega tool. The log " +- "files are named sage-omega.PID and can be found in " + +- os.path.join(os.environ["DOT_SAGE"], "valgrind")) -@@ -125,11 +120,6 @@ try: - except: - SAGE_CALLGRIND_FLAGS = logfile % 'cachegrind.%p' - --try: -- SAGE_OMEGA_FLAGS = os.environ['SAGE_OMEGA_FLAGS'] --except: -- SAGE_OMEGA_FLAGS = logfile % 'omega.%p' -- - ###################################################### - # The Python binary - ###################################################### -@@ -790,8 +780,6 @@ def test_file(file, library_code): - cmd = "valgrind --tool=massif " + SAGE_MASSIF_FLAGS + cmd - if cachegrind: - cmd = "valgrind --tool=cachegrind " + SAGE_CACHEGRIND_FLAGS + cmd -- if omega: -- cmd = "valgrind --tool=exp-omega " + SAGE_OMEGA_FLAGS + cmd - - VALGRIND = os.path.join(DOT_SAGE, 'valgrind') - try: -@@ -945,13 +933,12 @@ if __name__ == '__main__': - memcheck = has_opt('memcheck') or has_opt('valgrind') - massif = has_opt('massif') - cachegrind = has_opt('cachegrind') -- omega = has_opt('omega') - force_lib = has_opt('force_lib') - random_order = parse_rand() - only_optional, only_optional_tags = parse_only_opt() - if long_time: - TIMEOUT = TIMEOUT_LONG -- if gdb or memcheck or massif or cachegrind or omega: -+ if gdb or memcheck or massif or cachegrind: - TIMEOUT = TIMEOUT_VALGRIND - if argv[1][0] == '-': - usage() -@@ -959,7 +946,7 @@ if __name__ == '__main__': - ext = os.path.splitext(argv[1])[1] - - library_code = True -- dev_path = os.path.realpath(os.path.join(SAGE_ROOT, 'devel')) -+ dev_path = os.path.realpath(os.environ['SAGE_DEVEL'] + '/sage') - our_path = os.path.realpath(argv[1]) - - if not force_lib and (ext in ['.spyx', '.sage'] or -diff -up sage-5.8/spkg/build/sage_scripts-5.8/sage-maketest.orig sage-5.8/spkg/build/sage_scripts-5.8/sage-maketest ---- sage-5.8/spkg/build/sage_scripts-5.8/sage-maketest.orig 2013-02-22 17:20:29.074844437 -0300 -+++ sage-5.8/spkg/build/sage_scripts-5.8/sage-maketest 2013-02-22 17:20:51.800845307 -0300 -@@ -16,10 +16,10 @@ echo `date` >> "$SAGE_TEST_LOG" - # whose names consist of two lowercase letters: those should match the - # various languages. - --"$SAGE_ROOT"/sage -t --sagenb "$@" \ -- "$SAGE_ROOT"/devel/sage/doc/common \ -- "$SAGE_ROOT"/devel/sage/doc/[a-z][a-z] \ -- "$SAGE_ROOT"/devel/sage/sage 2>&1 | tee -a "$SAGE_TEST_LOG" -+sage -t --sagenb "$@" \ -+ devel/sage/doc/common \ -+ devel/sage/doc/[a-z][a-z] \ -+ devel/sage/sage 2>&1 | tee -a "$SAGE_TEST_LOG" - - if [ "$SAGE_TESTDIR" = "$SAGE_ROOT/tmp" ]; then - cat "$SAGE_TEST_LOG" >> "$SAGE_ROOT"/test.log -diff -up sage-5.8/spkg/build/sage_scripts-5.8/sage-valgrind.orig sage-5.8/spkg/build/sage_scripts-5.8/sage-valgrind ---- sage-5.8/spkg/build/sage_scripts-5.8/sage-valgrind.orig 2013-02-22 17:21:05.994845850 -0300 -+++ sage-5.8/spkg/build/sage_scripts-5.8/sage-valgrind 2013-02-22 17:21:14.960846194 -0300 + parser.add_option("-f", "--failed", action="store_true", default=False, + help="doctest only those files that failed in the previous run") +diff -up sage-5.9/spkg/build/sage_scripts-5.9/sage-valgrind.orig sage-5.9/spkg/build/sage_scripts-5.9/sage-valgrind +--- sage-5.9/spkg/build/sage_scripts-5.9/sage-valgrind.orig 2013-05-06 12:05:34.644508587 -0300 ++++ sage-5.9/spkg/build/sage_scripts-5.9/sage-valgrind 2013-05-06 12:22:03.076546437 -0300 @@ -11,7 +11,7 @@ fi LOG="$DOT_SAGE"/valgrind/sage-memcheck.%p echo "Log file is $LOG" diff --git a/sagemath-unpatched_ntl.patch b/sagemath-unpatched_ntl.patch new file mode 100644 index 0000000..54c39de --- /dev/null +++ b/sagemath-unpatched_ntl.patch @@ -0,0 +1,60 @@ +diff -up sage-5.9/spkg/build/sage-5.9/c_lib/include/ntl_wrap.h.orig sage-5.9/spkg/build/sage-5.9/c_lib/include/ntl_wrap.h +--- sage-5.9/spkg/build/sage-5.9/c_lib/include/ntl_wrap.h.orig 2013-01-25 21:54:01.313110341 -0200 ++++ sage-5.9/spkg/build/sage-5.9/c_lib/include/ntl_wrap.h 2013-01-25 21:54:13.153110794 -0200 +@@ -35,8 +35,6 @@ using namespace NTL; + + EXTERN void del_charstar(char*); + +-EXTERN void setup_NTL_error_callback(void (*function)(const char*, void*), void* context); +- + //////// ZZ ////////// + + #ifndef __cplusplus +diff -up sage-5.9/spkg/build/sage-5.9/c_lib/src/ntl_wrap.cpp.orig sage-5.9/spkg/build/sage-5.9/c_lib/src/ntl_wrap.cpp +--- sage-5.9/spkg/build/sage-5.9/c_lib/src/ntl_wrap.cpp.orig 2013-01-25 21:53:32.800109249 -0200 ++++ sage-5.9/spkg/build/sage-5.9/c_lib/src/ntl_wrap.cpp 2013-01-25 21:53:49.625109893 -0200 +@@ -11,13 +11,6 @@ void del_charstar(char* a) { + delete[] a; + } + +- +-void setup_NTL_error_callback(void (*function)(const char*, void*), void* context) +-{ +- NTL::SetErrorCallbackFunction(function, context); +-} +- +- + //////// ZZ ////////// + + /* Return value is only valid if the result should fit into an int. +diff -up sage-5.9/spkg/build/sage-5.9/c_lib/src/stdsage.c.orig sage-5.9/spkg/build/sage-5.9/c_lib/src/stdsage.c +--- sage-5.9/spkg/build/sage-5.9/c_lib/src/stdsage.c.orig 2013-01-25 21:54:34.072111596 -0200 ++++ sage-5.9/spkg/build/sage-5.9/c_lib/src/stdsage.c 2013-01-25 21:54:49.832112199 -0200 +@@ -29,27 +29,12 @@ void init_global_empty_tuple(void) { + global_empty_tuple = PyTuple_New(0); + } + +- +-/* +- This function gets called whenever NTL calls Error(). +- s is the error message generated by NTL. +- We just copy the error message into a global buffer, and then abort() to run +- the usual interrupt machinery. +- */ +-void global_NTL_error_callback(const char* s, void* context) +-{ +- set_sage_signal_handler_message(s); +- abort(); +-} +- +- + /* This is called once during Sage startup. On some platforms like + * Cygwin, this is also called from init_csage_module(). */ + void init_csage() { + init_global_empty_tuple(); + init_memory_functions(); + setup_sage_signal_handler(); +- setup_NTL_error_callback(global_NTL_error_callback, NULL); + } + + /* This is called once for every single module that links in stdsage */ diff --git a/sagemath.spec b/sagemath.spec index fc6e89b..98c9f8b 100644 --- a/sagemath.spec +++ b/sagemath.spec @@ -58,23 +58,23 @@ %global polytopes_db_pkg polytopes_db-20100210.p2 %global rubiks_pkg rubiks-20070912.p18 %global sagenb_pkg sagenb-0.10.4 -%global sagetex_pkg sagetex-2.3.3.p2 +%global sagetex_pkg sagetex-2.3.4 %global sagemath_share %{_datadir}/%{name} %global SAGE_ROOT %{_libdir}/sagemath %global SAGE_LOCAL %{SAGE_ROOT}/local -%global SAGE_DEVEL %{SAGE_ROOT}/devel +%global SAGE_SRC %{SAGE_ROOT}/src %global SAGE_DOC %{_docdir}/%{name}-%{version} %global SAGE_SHARE %{_datadir}/sagemath -%global SAGE_EXTCODE %{SAGE_SHARE}/extcode +%global SAGE_EXTCODE %{SAGE_SHARE}/ext %global SAGE_PYTHONPATH %{SAGE_ROOT}/site-packages Name: sagemath Group: Applications/Engineering Summary: A free open-source mathematics software system -Version: 5.8 -Release: 9%{?dist} +Version: 5.9 +Release: 1%{?dist} # The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file # Additionally, every $files section has a comment with the license name # before files with that license @@ -108,13 +108,20 @@ Patch1: %{name}-gmp.patch # Set of patches to work with system wide packages Patch2: %{name}-scripts.patch +# *** Apply patch3, not patch4, this patch for fedora <= 19 +# Do not mandate a patched ntl. It was requested to ntl upstream to +# provide an api to match what sagemath expects. +# http://shoup.net/pipermail/ntl_shoup.net/2012-April/000033.html +Patch3: %{name}-unpatched_ntl.patch + +# *** Apply patch4, not patch3, this patch for fedora > 19 # Adapt to ntl 6.0.0. -Patch3: %{name}-ntl6.patch +Patch4: %{name}-ntl6.patch # remove call to not implemented sagemath "is_package_installed" interfaces # need to package coin-or solver in fedora # remove check for non free solvers -Patch4: %{name}-extensions.patch +Patch5: %{name}-extensions.patch # helper to: # o respect a DESTDIR environment variable @@ -122,10 +129,7 @@ Patch4: %{name}-extensions.patch # o minor change to help in incremental builds by avoiding rebuilding # files # o do not assume there is an installed sagemath -Patch5: %{name}-rpmbuild.patch - -# avoid buildroot in some binaries due to not expanding symlinks -Patch6: %{name}-buildroot.patch +Patch6: %{name}-rpmbuild.patch # build documentation in buildroot environment Patch7: %{name}-sagedoc.patch @@ -210,12 +214,8 @@ Patch31: %{name}-nopari2.6.patch # and does not work with cryptominisat 2.9.5 (in f18) Patch32: %{name}-cryptominisat.patch -# Upgrade to Cython 0.19 -# http://trac.sagemath.org/sage_trac/ticket/14452 -Patch33: 14452_cython_0.19.patch - # Adapt to m4rie 20130416 -Patch34: %{name}-m4rie.patch +Patch33: %{name}-m4rie.patch BuildRequires: 4ti2 BuildRequires: atlas-devel @@ -632,8 +632,11 @@ popd %patch0 -p1 %patch1 -p1 %patch2 -p1 +%if 0%{?fedora} <= 19 %patch3 -p1 +%else %patch4 -p1 +%endif %patch5 -p1 %patch6 -p1 %patch7 -p1 @@ -695,16 +698,7 @@ popd %if 0%{?fedora} >= 19 %patch32 -p1 -%endif - -%if 0%{?fedora} >= 20 -pushd spkg/build/sage-%{version} %patch33 -p1 -popd -%endif - -%if 0%{?fedora} >= 19 -%patch34 -p1 %endif #------------------------------------------------------------------------ @@ -728,7 +722,7 @@ export CFLAGS="%{optflags}" export CXXFLAGS="%{optflags}" export SAGE_ROOT=%{buildroot}%{SAGE_ROOT} export SAGE_LOCAL=%{buildroot}%{SAGE_LOCAL} -export SAGE_DEVEL=%{buildroot}%{SAGE_DEVEL} +export SAGE_SRC=%{buildroot}%{SAGE_SRC} export SAGE_FORTRAN=%{_bindir}/gfortran export SAGE_FORTRAN_LIB=`gfortran --print-file-name=libgfortran.so` export DESTDIR=%{buildroot} @@ -739,9 +733,9 @@ mkdir -p $DOT_SAGE/tmp # match system packages as sagemath packages export SAGE_ROOT=%{buildroot}%{SAGE_ROOT} export SAGE_LOCAL=%{buildroot}%{SAGE_LOCAL} -export SAGE_DEVEL=%{buildroot}%{SAGE_DEVEL} -mkdir -p $SAGE_ROOT $SAGE_LOCAL $SAGE_DEVEL/sage -ln -sf $PWD/spkg/build/sage-%{version}/sage $SAGE_DEVEL/sage/sage +export SAGE_SRC=%{buildroot}%{SAGE_SRC} +mkdir -p $SAGE_ROOT $SAGE_LOCAL $SAGE_SRC +ln -sf $PWD/spkg/build/sage-%{version}/sage $SAGE_SRC/sage ln -sf %{_libdir} $SAGE_LOCAL/lib ln -sf %{_includedir} $SAGE_LOCAL/include ln -sf %{_datadir} $SAGE_LOCAL/share @@ -789,7 +783,7 @@ rm -fr $DOT_SAGE %install export SAGE_ROOT=%{buildroot}%{SAGE_ROOT} export SAGE_LOCAL=%{buildroot}%{SAGE_LOCAL} -export SAGE_DEVEL=%{buildroot}%{SAGE_DEVEL} +export SAGE_SRC=%{buildroot}%{SAGE_SRC} export SAGE_SHARE=%{buildroot}%{SAGE_SHARE} export SAGE_EXTCODE=%{buildroot}%{SAGE_EXTCODE} export SAGE_DOC=%{buildroot}%{SAGE_DOC} @@ -806,9 +800,9 @@ export PYTHONPATH=%{buildroot}%{python_sitearch}:$PYTHONPATH mkdir -p %{buildroot}%{_bindir} mkdir -p %{buildroot}%{_libdir} mkdir -p $SAGE_PYTHONPATH -rm -fr $SAGE_DEVEL/sage $SAGE_LOCAL/{include,lib,share,notebook} -mkdir -p $SAGE_SHARE $SAGE_DOC $SAGE_LOCAL/bin $SAGE_DEVEL/sage -ln -sf $PWD/spkg/build/sage-%{version}/sage $SAGE_DEVEL/sage/sage +rm -fr $SAGE_LOCAL/{include,lib,share,notebook} +mkdir -p $SAGE_SHARE $SAGE_DOC $SAGE_LOCAL/bin $SAGE_SRC +ln -sf $PWD/spkg/build/sage-%{version}/sage $SAGE_SRC/sage ln -sf %{_libdir} $SAGE_LOCAL/lib ln -sf %{_includedir} $SAGE_LOCAL/include ln -sf %{_datadir} $SAGE_LOCAL/share @@ -845,7 +839,7 @@ pushd spkg/build/%{sagenb_pkg}/src/sagenb %endif # flask stuff not installed cp -ar flask_version %{buildroot}%{python_sitearch}/sagenb - ln -sf %{python_sitearch}/sagenb %{buildroot}%{SAGE_DEVEL}/sagenb + ln -sf %{python_sitearch}/sagenb %{buildroot}%{SAGE_SRC}/sagenb popd #------------------------------------------------------------------------ @@ -859,7 +853,7 @@ popd cp -fa COPYING.txt $SAGE_ROOT pushd spkg/build/sage_scripts-%{version} mkdir -p $SAGE_LOCAL/bin - cp -fa sage-* *doctest.py $SAGE_LOCAL/bin + cp -fa sage-* $SAGE_LOCAL/bin pushd $SAGE_LOCAL/bin ln -sf %{_bindir}/python sage.bin ln -sf %{_bindir}/gp sage_pari @@ -886,15 +880,42 @@ pushd spkg/build/%{rubiks_pkg}/src popd #------------------------------------------------------------------------ -rm -f %{buildroot}%{_bindir}/spkg-debian-maybe pushd $SAGE_LOCAL/bin/ - rm -f sage-{bdist,build,build-debian,clone,crap,debsource,download_package,env,libdist,location,make_devel_packages,omega,pkg,pkg-nocompress,pull,push,sdist,sbuildhack,upgrade} - rm -f sage-list-* sage-mirror* SbuildHack.pm sage-test-* - rm -f sage-{verify-pyc,hardcode_sage_root,check-64,spkg*,update*,starts} - rm -f *~ - rm -f sage-{check-libraries.py,ldwrap,open,osx-open,README-osx.txt} - rm -f sage-rebase_sage.sh - rm -f sage-{combinat,massif} + for file in \ + sage-apply-ticket \ + sage-bdist \ + sage-build \ + sage-clone \ + sage-combinat \ + sage-crap \ + sage-list-experimental \ + sage-list-optional \ + sage-list-packages \ + sage-list-standard \ + sage-location \ + sage-make_devel_packages \ + sage-omega \ + sage-pkg \ + sage-pull \ + sage-push \ + sage-pypkg-location \ + sage-README-osx.txt \ + sage-rebaseall.bat \ + sage-rebaseall.sh \ + sage-rebase.bat \ + sage-rebase.sh \ + sage-rsyncdist \ + sage-sdist \ + sage-spkg-install \ + sage-startuptime.py \ + sage-sync-build.py \ + sage-test-import \ + sage-update \ + sage-update-build \ + sage-upgrade \ + spkg-install; do + rm -f $file + done popd #------------------------------------------------------------------------ @@ -976,7 +997,7 @@ export SAGE_ROOT="$SAGE_ROOT" export SAGE_LOCAL="$SAGE_LOCAL" export SAGE_SHARE="$SAGE_SHARE" export SAGE_EXTCODE="$SAGE_EXTCODE" -export SAGE_DEVEL="$SAGE_DEVEL" +export SAGE_SRC="$SAGE_SRC" ##export SAGE_DOC="$SAGE_DOC" module load 4ti2-%{_arch} %if %{have_lrcalc} @@ -1004,7 +1025,7 @@ chmod +x %{buildroot}%{_bindir}/sage cat > %{buildroot}%{SAGE_LOCAL}/bin/sage3d << EOF #!/bin/sh -java -classpath %{SAGE_DEVEL}/sage/sagenb/data/sage3d/lib/sage3d.jar:%{_javadir}/j3dcore.jar:%{_javadir}/vecmath.jar:%{_javadir}/j3dutils.jar org.sagemath.sage3d.ObjectViewerApp "\$1" +java -classpath %{SAGE_SRC}/sage/sagenb/data/sage3d/lib/sage3d.jar:%{_javadir}/j3dcore.jar:%{_javadir}/vecmath.jar:%{_javadir}/j3dutils.jar org.sagemath.sage3d.ObjectViewerApp "\$1" EOF chmod +x %{buildroot}%{SAGE_LOCAL}/bin/sage3d %endif @@ -1051,7 +1072,7 @@ pushd spkg/build/sage-%{version}/doc %endif # there we go - ln -sf %{buildroot}%{SAGE_DOC} $SAGE_ROOT/devel/doc + ln -sf %{buildroot}%{SAGE_DOC} $SAGE_SRC/doc python common/builder.py all html export SAGE_DOC=%{buildroot}%{SAGE_DOC} cp -far output $SAGE_DOC @@ -1089,13 +1110,14 @@ perl -pi -e 's|%{buildroot}||g;' \ #------------------------------------------------------------------------ # Fix links -rm -fr $SAGE_DEVEL/sage $SAGE_EXTCODE/sage $SAGE_ROOT/doc $SAGE_ROOT/devel/doc -ln -sf %{python_sitearch} $SAGE_DEVEL/sage +rm -fr $SAGE_EXTCODE/sage $SAGE_ROOT/doc $SAGE_ROOT/src/doc +ln -sf %{python_sitearch} $SAGE_SRC/sage ln -sf %{python_sitearch} $SAGE_EXTCODE/sage ln -sf %{SAGE_DOC} $SAGE_ROOT/doc -ln -sf %{SAGE_DOC} $SAGE_ROOT/devel/doc +ln -sf %{SAGE_DOC} $SAGE_SRC/doc ln -sf %{SAGE_SHARE} $SAGE_ROOT/share -rm -fr %{buildroot}%{python_sitearch}/site-packages +# compat devel symlink +ln -sf src $SAGE_ROOT/devel # Install menu and icons pushd spkg/build/extcode-%{version} @@ -1182,7 +1204,9 @@ exit 0 exit 0 %postun sagetex -%{_bindir}/mktexlsr +if [ $1 -eq 0 ] ; then + %{_bindir}/mktexlsr +fi exit 0 ######################################################################## @@ -1192,7 +1216,6 @@ exit 0 %doc %{SAGE_ROOT}/COPYING.txt %dir %{SAGE_LOCAL} %dir %{SAGE_LOCAL}/bin -%{SAGE_LOCAL}/bin/ncadoctest.py %{SAGE_LOCAL}/bin/QuadraticSieve %{SAGE_LOCAL}/bin/ecm %{SAGE_LOCAL}/bin/gap_stamp @@ -1202,10 +1225,11 @@ exit 0 %{SAGE_LOCAL}/lib %{SAGE_LOCAL}/share %{SAGE_ROOT}/doc +%{SAGE_ROOT}/devel %{SAGE_ROOT}/share -%dir %{SAGE_DEVEL} -%{SAGE_DEVEL}/doc -%{SAGE_DEVEL}/sage +%dir %{SAGE_SRC} +%{SAGE_SRC}/doc +%{SAGE_SRC}/sage %dir %{SAGE_PYTHONPATH} %if %{with_sage_pexpect} # MIT @@ -1314,7 +1338,7 @@ exit 0 #------------------------------------------------------------------------ %files notebook # GPLv2+ -%{SAGE_DEVEL}/sagenb +%{SAGE_SRC}/sagenb %dir %{python_sitearch}/sagenb %{python_sitearch}/sagenb/*.py* %{python_sitearch}/sagenb-*.egg-info @@ -1393,6 +1417,13 @@ exit 0 ######################################################################## %changelog +* Mon May 6 2013 pcpa - 5.9-1 +- Update to sagemath 5.9. +- Match upstream rename of SAGE_DEVEL to SAGE_SRC. +- Merged -buildroot in -rpmbuild patch. +- Drop cython 0.19 patch already applied to sagemath 5.9. +- Add macro conditionals to use same spec and patches in f18, f19 and f20. + * Mon May 6 2013 Jerry James - 5.8-9 - Rebuild for libfplll 4.0.3, m4ri and m4rie 20130416, and ntl 6.0.0 - Drop sagemath-unpatched_ntl.patch now that Fedora's NTL is patched