Merge branch 'develop' into u/tscrim/kac_polynomial

* develop: (95 commits)
  Trac #14858: more robust type checks for arith.py
  Updated Sage version to 6.1.beta3
  Trac #11271: making the curve inaccessible + documentation
  Trac #11271: Corrections to is_surjective in Galois representations over Q.
  sage-sdist: copy upstream tarballs using sage-spkg
  Fixed docbuild.
  Removed removed file from doc.
  Fix wrong NOTE block.
  Where possible, remove optional - database_stein_watkins
  Stein-Watkins database: reviewer patch
  buid/deps : added a dependency of freetype on libpng in order to work around a build-time race condition.
  Replace bytes_to_long/long_to_bytes by ord/chr.
  Revert "Filter pycrypto warning about insecure modular exponentiaiton."
  first version of the git-trac package
  Filter pycrypto warning about insecure modular exponentiaiton.
  Update PyCrypto to version 2.6.1.
  Let PyCrypto build on FreeBSD.
  trac #15435: WeylGroup and CoxeterGroup to groups.<tab>
  trac #15369: Alias groups.misc.AdditiveCyclic to IntegerModRing
  Fix for comparison of padics.
  ...

VERSION.txt

@@ -1 +1 @@
-Sage version 6.1.beta2, released 2013-12-23
+Sage version 6.1.beta3, released 2014-01-04

build/deps

@@ -80,7 +80,7 @@ all-sage: \
      $(INST)/$(PALP) \
      $(INST)/$(PARI) \
      $(INST)/$(PEXPECT) \
-     $(INST)/$(PIL) \
+     $(INST)/$(PILLOW) \
      $(INST)/$(POLYBORI) \
      $(INST)/$(POLYTOPES_DB) \
      $(INST)/$(PPL) \
@@ -311,7 +311,7 @@ $(INST)/$(SQLITE): $(INST)/$(READLINE)
 # SageTeX, you actually need to run Sage, produce plots,...
 $(INST)/$(SAGETEX): $(INST)/$(PYTHON) \
                     $(SAGERUNTIME) $(INST)/$(MAXIMA) $(INST)/$(SCIPY) \
-                    $(INST)/$(MATPLOTLIB) $(INST)/$(PIL) $(INST)/$(TACHYON)
+                    $(INST)/$(MATPLOTLIB) $(INST)/$(PILLOW) $(INST)/$(TACHYON)
 	+$(PIPE) "$(SAGE_SPKG) $(SAGETEX) 2>&1" "tee -a $(SAGE_LOGS)/$(SAGETEX).log"
 
 $(INST)/$(SETUPTOOLS): $(INST)/$(PYTHON)
@@ -336,7 +336,7 @@ $(INST)/$(ZLIB):
 $(INST)/$(JMOL): $(INST)/$(SAGENB)
 	+$(PIPE) "$(SAGE_SPKG) $(JMOL) 2>&1" "tee -a $(SAGE_LOGS)/$(JMOL).log"
 
-$(INST)/$(FREETYPE):
+$(INST)/$(FREETYPE): $(INST)/$(LIBPNG)
 	+$(PIPE) "$(SAGE_SPKG) $(FREETYPE) 2>&1" "tee -a $(SAGE_LOGS)/$(FREETYPE).log"
 
 $(INST)/$(LIBPNG): $(INST)/$(ZLIB)
@@ -484,8 +484,8 @@ $(INST)/$(GCC): $(INST)/$(MPIR) $(INST)/$(MPFR) $(INST)/$(MPC) \
                 $(INST)/$(ZLIB)
 	+$(PIPE) "$(SAGE_SPKG) $(GCC) 2>&1" "tee -a $(SAGE_LOGS)/$(GCC).log"
 
-$(INST)/$(PIL): $(INST)/$(PYTHON)
-	+$(PIPE) "$(SAGE_SPKG) $(PIL) 2>&1" "tee -a $(SAGE_LOGS)/$(PIL).log"
+$(INST)/$(PILLOW): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
+	+$(PIPE) "$(SAGE_SPKG) $(PILLOW) 2>&1" "tee -a $(SAGE_LOGS)/$(PILLOW).log"
 
 $(INST)/$(NUMPY): $(INST)/$(PYTHON) $(INST)/$(ATLAS)
 	+$(PIPE) "$(SAGE_SPKG) $(NUMPY) 2>&1" "tee -a $(SAGE_LOGS)/$(NUMPY).log"
@@ -507,6 +507,7 @@ $(INST)/$(CEPHES):
 # setuptools forgets to update easy-install.pth during parallel
 # builds, so we build the relevant packages serially.
 
+$(INST)/$(SQLALCHEMY): $(INST)/$(PILLOW)
 $(INST)/$(PYGMENTS): $(INST)/$(SQLALCHEMY)
 $(INST)/$(JINJA2): $(INST)/$(PYGMENTS)
 $(INST)/$(SPHINX): $(INST)/$(JINJA2)

build/install

@@ -442,7 +442,7 @@ PALP=`newest_version palp`
 PARI=`newest_version pari`
 PATCH=`newest_version patch`
 PEXPECT=`newest_version pexpect`
-PIL=`newest_version pil`
+PILLOW=`newest_version pillow`
 POLYBORI=`newest_version polybori`
 POLYTOPES_DB=`newest_version polytopes_db`
 PPL=`newest_version ppl`

build/pkgs/atlas/configuration.py

@@ -3,6 +3,8 @@
 #                  http://www.gnu.org/licenses/
 ######################################################################
 
+from __future__ import print_function
+
 import platform, os, sys, time, shutil, glob, subprocess
 
 
@@ -37,9 +39,9 @@
 ### Sanity check
 ######################################################################
 
-if not os.environ.has_key('SAGE_LOCAL'):
-    print "SAGE_LOCAL undefined ... exiting"
-    print "Maybe run 'sage -sh'?"
+if 'SAGE_LOCAL' not in os.environ:
+    print("SAGE_LOCAL undefined ... exiting")
+    print("Maybe run 'sage -sh'?")
     sys.exit(1)
 
 
@@ -63,15 +65,15 @@ def try_run(command, ignore=False):
     if (not ignore) and (rc!=0):
         return None
     # concatenate stdout and stderr
-    return result[0].strip() + result[1].strip()
+    return (result[0].strip() + result[1].strip()).decode('utf8')
 
 
 def cp(source_pattern, destination):
     """
     Portable implementation of "cp -p"
     """
     for filename in glob.iglob(source_pattern):
-        print 'Copying', filename, 'to', destination
+        print('Copying', filename, 'to', destination)
         shutil.copy2(filename, destination)
 
 
@@ -81,7 +83,7 @@ def ln(source, destination):
     """
     if os.path.exists(destination):
         os.remove(destination)
-    print 'Linking', source, 'to', destination
+    print('Linking', source, 'to', destination)
     os.symlink(source, destination)
 
 
@@ -134,7 +136,7 @@ def close(self):
     conf['system'] = platform.system()
 
 try:
-    conf['release'] = subprocess.check_output(['uname', '-r']).strip()
+    conf['release'] = subprocess.check_output(['uname', '-r']).decode('utf8').strip()
 except subprocess.CalledProcessError:
     conf['release'] = ""
 
@@ -179,14 +181,14 @@ def close(self):
 
 fortran_version = try_run('$FC --version')
 if fortran_version is None:
-    print 'Cannot execute fortran compiler ($FC)!'
+    print('Cannot execute fortran compiler ($FC)!')
     sys.exit(3)
 if 'G95' in fortran_version:
     conf['fortran'] = 'g95'
 elif 'GNU Fortran' in fortran_version:
     conf['fortran'] = 'gfortran'
 else:
-    print 'Unknown fortran compiler version: '+fortran_version
+    print('Unknown fortran compiler version: '+fortran_version)
     conf['fortran'] = None
 
 
@@ -211,7 +213,7 @@ def close(self):
     ld_version = try_run('ld  -v')
 
 if ld_version is None:
-    print 'Cannot execute ld!'
+    print('Cannot execute ld!')
     sys.exit(3)
 if 'GNU' in ld_version:
     conf['ld'] = 'GNU'
@@ -220,7 +222,7 @@ def close(self):
 elif 'Apple' in ld_version:
     conf['ld'] = 'Darwin'
 else:
-    print 'Unknown linker: '+ld_version
+    print('Unknown linker: '+ld_version)
     conf['ld'] = None
 
 conf['linker_GNU?'] = (conf['ld'] == 'GNU')
@@ -229,11 +231,11 @@ def close(self):
 
 
 if conf['Solaris?'] and conf['linker_GNU?']:
-    print "WARNING: You are using the GNU linker from 'binutils'"
-    print "Generally it is considered better to use the Sun linker"
-    print "but Sage has been built on Solaris using the GNU linker"
-    print "although that was a very old version of Sage, which"
-    print "never passes all the Sage test-suite."
+    print("WARNING: You are using the GNU linker from 'binutils'")
+    print("Generally it is considered better to use the Sun linker")
+    print("but Sage has been built on Solaris using the GNU linker")
+    print("although that was a very old version of Sage, which")
+    print("never passes all the Sage test-suite.")
 
 
 
@@ -249,9 +251,9 @@ def close(self):
 ### The end: print configuration
 ######################################################################
 
-print "Configuration:"
+print("Configuration:")
 for key, value in conf.items():
-    print '    '+str(key)+': '+str(value)
+    print('    '+str(key)+': '+str(value))
 
 
 

build/pkgs/atlas/enums.py

@@ -6,6 +6,8 @@
     sage: check_enums(sample_print_enums_output)
 """
 
+from __future__ import print_function
+
 # constants from src/ATLAS/CONFIG/include/atlconf.h
 # Note: must be lists, not tuples, for Python-2.4 support
 
@@ -189,6 +191,6 @@ def make_check_enums():
     """
     from subprocess import check_output
     output = check_output('make xprint_enums ; ./xprint_enums', shell=True)
-    print output
+    print(output)
     check_enums(output)