Merge branch 'master' into ticket/15229

* master: (216 commits)
  also remove untracked directories after an aborted import patch
  trac_interface: encode fields with utf-8 as well
  sage.dev: don't textwrap during doctesting
  patch.py: deal with hg's silly copy commands
  SageDev: fix pull doctest
  SageDev: remove branch keyword from pull
  fix doctest errors in SageDev.push
  remove (now) bad uses of SageDev.pull
  remove unused garbage
  dumb down pull to fix it
  don't abort ticket editing on nop push
  remove last reference to download command
  fix dev scripts in emacs shell
  remove , from my name
  fixed missleading error message for trac authentication error
  [FIXUP] 5.13.beta2: update git specific files
  5.13.beta2
  5.13.beta2
  fixed import statement for the commandline interface
  fix doctest failure from bad merge conflict resolution
  ...

Author: simon-king-jena

.gitignore

@@ -4,3 +4,52 @@
 /local
 /logs
 /upstream
+
+###################
+# Temporary Files #
+###################
+
+# Various editors
+*~
+
+# Emacs
+\#*\#
+.\#*
+
+# Vim
+*.s[a-w][a-z]
+*.un~
+.netrwhist
+
+# PyCharm
+.idea
+.iml
+
+# Eclipse
+*.pydevproject
+.project
+.metadata
+*.tmp
+*.bak
+*.swp
+*~.nib
+.classpath
+.settings/
+.loadpath
+.externalToolBuilders/
+.cproject
+.buildpath
+
+# OSX specific temporary files
+.DS_Store
+._*
+.AppleDouble
+.LSOverride
+.Spotlight-V100
+.Trashes
+
+# Windows
+$RECYCLE.BIN/
+
+# SublimeText
+*.sublime-workspace

Makefile

@@ -21,6 +21,12 @@ build: logs
 		"tee -a ../logs/install.log"
 	./sage -b
 
+# Preemptively download all standard upstream source tarballs.
+download:
+	export SAGE_ROOT=$$(pwd) && \
+	export PATH=$$SAGE_ROOT/src/bin:$$PATH && \
+	./src/bin/sage-download-upstream
+
 # ssl: build Sage, and also install pyOpenSSL. This is necessary for
 # running the secure notebook. This make target requires internet
 # access. Note that this requires that your system have OpenSSL

VERSION.txt

@@ -1 +1 @@
-Sage version 5.12.beta5, released 2013-09-06
+Sage version 5.13.beta2, released 2013-10-31

build/pkgs/atlas/SPKG.txt

@@ -95,6 +95,11 @@ The package can be configured via three environment variables:
 
 == ChangeLog ==
 
+=== atlas-3.10.1.p6, lapack-3.4.2 (Volker Braun, 11 October 2013) ===
+ * Trac #15270: Do not give up if the upstream shared library build
+   fails
+ * Solaris / ZFS fixes
+
 === atlas-3.10.1.p5, lapack-3.4.2 (Volker Braun, 30 August 2013) ===
  * Trac #15045: Another workaround for shared library bug that does
    not involve static libraries

build/pkgs/atlas/package-version.txt

@@ -1 +1 @@
-3.10.1.p5
+3.10.1.p6

build/pkgs/atlas/spkg-install

@@ -268,6 +268,7 @@ def configure(arch=None, isa_ext=None):
     print 'Running configure with arch = '+str(arch)+ \
         ', isa extensions '+str(isa_ext), ' thread limit '+str(thread_limit)
     if os.path.isdir(BUILD_DIR):
+        os.chdir(conf['SPKG_DIR'])   # Solaris/ZFS can't delete cwd
         shutil.rmtree(BUILD_DIR)
     os.mkdir(BUILD_DIR)
     os.chdir(BUILD_DIR)
@@ -529,38 +530,39 @@ build_and_save_archdef()
 ######################################################################
 
 rc = make_atlas_library('shared')
-assert_success(rc, bad='Failed to install ATLAS single-threaded shared library',
-               good='Installed ATLAS single-threaded shared library')
+if rc!=0:
+    print 'Failed to build shared library (using the ATLAS build system)'
+else:
+    print 'Installed ATLAS shared library (ATLAS build system)'
 
 rc = make_atlas_library('ptshared')
 if rc!=0:
-    print 'Failed to build threaded library, possibly because your'
-    print 'system does not support it.'
+    print 'Failed to build threaded library (using the ATLAS build system)'
 else:
-    print 'Installed ATLAS multi-threaded shared library'
+    print 'Installed ATLAS multi-threaded shared library (ATLAS build system)'
 
 
 ######################################################################
 ### configure and build atlas and lapack shared library hack
 ######################################################################
 
 rc = configure_shared_library()
-assert_success(rc, bad='Configuring shared ATLAS library failed.',
-               good='Finished configuring shared ATLAS library.')
+assert_success(rc, bad='Configuring shared ATLAS library failed (libtool).',
+               good='Finished configuring shared ATLAS library (libtool).')
 
 have_serial_libs = False
 have_parallel_libs = False
 
 rc = make_shared_library()
 if rc!=0:
     print 'Failed to build serial+parallel shared libraries, possibly because your'
-    print 'system does not support both. Trying to build serial libraries only.'
+    print 'system does not support both. Trying to build serial libraries only (libtool).'
     rc = make_shared_library('all_serial')
     if rc!=0:
-        print 'Failed to build any shared library, installing static library as last resort.'
+        print 'Failed to build any shared library, installing static library as last resort (libtool).'
         INSTALL_STATIC_LIBRARIES = True
     else:
-        print 'Finished building serial shared ATLAS library.'
+        print 'Finished building serial shared ATLAS library (libtool).'
     have_serial_libs = True
 else:
     have_parallel_libs = True
@@ -572,13 +574,13 @@ else:
 
 if have_parallel_libs:
     rc = make_shared_library('install')
-    assert_success(rc, bad='Installing the parallel+serial shared ATLAS library failed.',
-                   good='Finished installing parallel+serial shared ATLAS library.')
+    assert_success(rc, bad='Installing the parallel+serial shared ATLAS library failed (libtool).',
+                   good='Finished installing parallel+serial shared ATLAS library (libtool).')
 
 if have_serial_libs:
     rc = make_shared_library('install_serial')
-    assert_success(rc, bad='Installing the serial shared ATLAS library failed.',
-                   good='Finished installing serial shared ATLAS library.')
+    assert_success(rc, bad='Installing the serial shared ATLAS library failed (libtool).',
+                   good='Finished installing serial shared ATLAS library (libtool).')
 
 
 ######################################################################

build/pkgs/boehm_gc/SPKG.txt

@@ -6,11 +6,7 @@ The Boehm-Demers-Weiser conservative garbage collector.
 
 == License ==
 
-Permissive BSD + GPL 2.0+
-
-== SPKG Maintainers ==
-
-  * William Stein
+* Permissive BSD + GPL 2.0+
 
 == Upstream Contact ==
 
@@ -23,10 +19,17 @@ None.
 
 == Special Update/Build Instructions ==
 
-None. Sources in src are vanilla.
+=== Patches ===
+ * cygwin64.patch: let libgc build on Cygwin64.
 
 == Changelog ==
 
+=== boehm_gc-7.2d.p0 (Jean-Pierre Flori, 11 June 2013) ===
+ * #14710: Update to version 7.2d.
+ * Remove patches integrated upstream.
+ * Add cygwin64.patch from Cygwin64 libgc package to let it build
+   on Cygwin64.
+
 === boehm_gc-7.2.alpha6.p2 (Simon King, Dec 10 2011) ===
  * #12131: Use --libdir, to make the package work on openSUSE
 
@@ -78,4 +81,3 @@ None. Sources in src are vanilla.
 
 === boehm_gc-7.1 (Gary Furnish) ===
  * Initial version
-

build/pkgs/boehm_gc/checksums.ini

@@ -1,3 +1,3 @@
-sha1=d2b73db75ea173ebd07a3ee04b4cd91e1af81eaf
-md5=1eee767e11296fb1b7d11d273fe072c7
-cksum=2375122679
+sha1=4013e5d6b685e1a3c7ff9b5447405a2b452731be
+md5=48232de5b36573da6415ece66a9b9084
+cksum=2689595432

build/pkgs/boehm_gc/package-version.txt

@@ -1 +1 @@
-7.2.alpha6.p2
+7.2d.p0

build/pkgs/boehm_gc/patches/cygwin64.patch

@@ -0,0 +1,104 @@
+--- a/include/gc.h	2012-08-09 16:25:13.000000000 -0400
++++ b/include/gc.h	2013-04-22 13:10:01.101686000 -0400
+@@ -1385,7 +1385,14 @@
+ /* THREAD_LOCAL_ALLOC defined and the initial allocation call is not    */
+ /* to GC_malloc() or GC_malloc_atomic().                                */
+ 
+-#ifdef __CYGWIN32__
++#ifdef __CYGWIN__
++#ifdef __x86_64__
++  extern int __data_start__[], __data_end__[], __bss_start__[], __bss_end__[];
++#define GC_DATASTART (__data_start__ < __bss_start__ ?\
++                      (void *)__data_start__ : (void *)__bss_start__)
++#define GC_DATAEND (__data_end__ < __bss_end__ ?\
++                      (void *)__data_end__ : (void *)__bss_end__)
++#else
+   /* Similarly gnu-win32 DLLs need explicit initialization from the     */
+   /* main program, as does AIX.                                         */
+   extern int _data_start__[], _data_end__[], _bss_start__[], _bss_end__[];
+@@ -1393,6 +1400,7 @@
+                        (void *)_data_start__ : (void *)_bss_start__)
+ # define GC_DATAEND (_data_end__ > _bss_end__ ? \
+                      (void *)_data_end__ : (void *)_bss_end__)
++#endif
+ # define GC_INIT_CONF_ROOTS GC_add_roots(GC_DATASTART, GC_DATAEND); \
+                                  GC_gcollect() /* For blacklisting. */
+         /* Required at least if GC is in a DLL.  And doesn't hurt. */
+--- a/include/private/gcconfig.h	2012-08-09 16:25:13.000000000 -0400
++++ b/include/private/gcconfig.h	2013-04-21 12:52:28.024399600 -0400
+@@ -432,10 +432,20 @@
+ #   endif
+ #   define mach_type_known
+ # endif
+-# if defined(__CYGWIN32__) || defined(__CYGWIN__)
++# if defined(__CYGWIN32__)
+ #   define I386
+ #   define CYGWIN32
+ #   define mach_type_known
++#if defined(__CYGWIN__)
++#  if defined(__LP64__)
++#    define X86_64
++#    define mach_type_known
++#  else
++#    define I386
++#  endif
++#  define CYGWIN32
++#  define mach_type_known
++#endif
+ # endif
+ # if defined(__MINGW32__) && !defined(mach_type_known)
+ #   define I386
+@@ -502,6 +512,16 @@
+ #    define mach_type_known
+ # endif
+ 
++#if defined(__CYGWIN__)
++#  if defined(__LP64__)
++#    define X86_64
++#    define mach_type_known
++#  else
++#    define I386
++#  endif
++#  define CYGWIN32
++#  define mach_type_known
++#endif
+ /* Feel free to add more clauses here */
+ 
+ /* Or manually define the machine type here.  A machine type is         */
+@@ -2259,6 +2279,19 @@
+ #       define GWW_VDB
+ #       define DATAEND  /* not needed */
+ #   endif
++
++#   ifdef CYGWIN32
++#       define OS_TYPE "CYGWIN32"
++#       define DATASTART ((ptr_t)GC_DATASTART)  /* From gc.h */
++#       define DATAEND   ((ptr_t)GC_DATAEND)
++#       define ALIGNMENT 8
++#       undef STACK_GRAN
++#       define STACK_GRAN 0x10000
++#       ifdef USE_MMAP
++#         define NEED_FIND_LIMIT
++#         define USE_MMAP_ANON
++#       endif
++#   endif
+ # endif /* X86_64 */
+ 
+ # ifdef HEXAGON
+--- a/os_dep.c	2012-08-09 16:25:13.000000000 -0400
++++ b/os_dep.c	2013-04-22 12:43:32.202498600 -0400
+@@ -770,7 +770,14 @@
+     /* gcc version of boehm-gc).                                        */
+     GC_API int GC_CALL GC_get_stack_base(struct GC_stack_base *sb)
+     {
++# ifdef __x86_64__
++      PNT_TIB pTib = NtCurrentTeb();
++      void * _tlsbase = pTib->StackBase;
++      /*void * _tlsbase = NtCurrentTeb()->pTib.StackBase;*/
++      /*extern void * _tlsbase __asm__ ("%gs:8");*/
++# else
+       extern void * _tlsbase __asm__ ("%fs:4");
++# endif
+       sb -> mem_base = _tlsbase;
+       return GC_SUCCESS;
+     }