Merge tag '6.8.beta3' into t/18558/18558

Sage version 6.8.beta3

VERSION.txt

@@ -1 +1 @@
-Sage version 6.8.beta2, released 2015-05-29
+Sage version 6.8.beta3, released 2015-06-04

build/deps

@@ -27,7 +27,6 @@ all-sage: \
      $(STANDARD_PACKAGES) \
      $(INST)/$(SAGE_MP_LIBRARY) \
      $(INST)/sage \
-     $(INST)/csage \
      $(EXTCODE) \
      $(SCRIPTS)
 
@@ -50,7 +49,7 @@ toolchain-deps:
 
 # Everything needed to start up Sage using "./sage".  Of course, not
 # every part of Sage will work.  It does not include Maxima for example.
-SAGERUNTIME = $(SCRIPTS) $(INST)/sage $(INST)/$(SAGENB) $(INST)/$(IPYTHON)
+SAGERUNTIME = $(SCRIPTS) $(INST)/sage $(INST)/$(IPYTHON)
 
 ###############################################################################
 # Building the base system
@@ -109,6 +108,7 @@ $(INST)/sage: \
 		 $(INST)/$(NTL) \
 		 $(INST)/$(NUMPY) \
 		 $(INST)/$(PARI) \
+		 $(INST)/$(PLANARITY) \
 		 $(INST)/$(POLYBORI) \
 		 $(INST)/$(PPL) \
 		 $(INST)/$(PYNAC) \
@@ -118,26 +118,13 @@ $(INST)/sage: \
 		 $(INST)/$(SINGULAR) \
 		 $(INST)/$(SIX) \
 		 $(INST)/$(SYMMETRICA) \
-		 $(INST)/$(ZN_POLY) \
-		 $(INST)/csage
+		 $(INST)/$(ZN_POLY)
 	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
 		cd $(SAGE_SRC) && source bin/sage-env && \
 		$(PIPE) 'time $(MAKE) sage 2>&1' 'tee -a $(SAGE_LOGS)/sage-$(SAGE_VERSION).log' && \
 		touch $@; \
 	fi
 
-$(INST)/csage: $(INST)/$(SCONS) \
-       $(INST)/$(SAGE_MP_LIBRARY) \
-       $(INST)/$(NTL) \
-       $(INST)/$(PARI) \
-       $(INST)/$(PYTHON) \
-       $(CSAGE_SOURCES)
-	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
-		cd $(SAGE_SRC) && source bin/sage-env && \
-		$(PIPE) 'time $(MAKE) csage 2>&1' 'tee -a $(SAGE_LOGS)/csage-$(SAGE_VERSION).log' && \
-		touch $@; \
-	fi
-
 # TODO: remove this once ccache is a new-style package
 CCACHE = ccache
 $(INST)/ccache: base $(INST)/$(ZLIB)

build/install

@@ -387,11 +387,6 @@ echo >&5
 echo >&5
 
 
-echo >&5 'CSAGE_SOURCES = \'
-for file in "$SAGE_SRC/c_lib/src/"*.cpp "$SAGE_SRC/c_lib/include"/*.h; do
-    echo >&5 "                \$(SAGE_SRC)${file#$SAGE_SRC} \\"
-done
-echo >&5
 echo >&5 'SCRIPT_SOURCES = \'
 for file in "$SAGE_SRC/bin/"*; do
     echo >&5 "                 \$(SAGE_SRC)${file#$SAGE_SRC} \\"

build/pkgs/4ti2/type

@@ -1 +1 @@
-optional
+experimental

build/pkgs/atlas/enums.py

@@ -198,5 +198,5 @@ def make_check_enums():
     from subprocess import check_output
     output = check_output('make xprint_enums ; ./xprint_enums', shell=True)
     print(output)
-    check_enums(output)
+    check_enums(output.decode('ascii'))
 

build/pkgs/autotools/type

@@ -1 +1 @@
-optional
+experimental

build/pkgs/compilerwrapper/type

@@ -1 +1 @@
-optional
+experimental

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=91e932368075d8b87417cf6329200821979cf2e3
-md5=f6a3b167b025abc45ba826b8b76e0c69
-cksum=1942390217
+sha1=ba70d13aace4a7894ceec5d6e56f29b39756ab30
+md5=b2e6ae57f6f348b3f5bf9baaa2b7049f
+cksum=2993700783

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-96
+97

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.22.p3
+0.22.p4

build/pkgs/cython/patches/show_progress.patch

@@ -0,0 +1,72 @@
+commit ce5250b8d893e17b18add232ba1e9263c73b5909
+Author: Jeroen Demeyer <jdemeyer@cage.ugent.be>
+Date:   Sat Apr 25 22:24:40 2015 +0200
+
+    Progress indicator for cythonize()
+
+diff --git a/Cython/Build/Dependencies.py b/Cython/Build/Dependencies.py
+index 4514493..853c591 100644
+--- a/Cython/Build/Dependencies.py
++++ b/Cython/Build/Dependencies.py
+@@ -832,7 +832,15 @@ def cythonize(module_list, exclude=[], nthreads=0, aliases=None, quiet=False, fo
+         if not os.path.exists(options.cache):
+             os.makedirs(options.cache)
+     to_compile.sort()
+-    if len(to_compile) <= 1:
++    # Drop "priority" component of "to_compile" entries and add a
++    # simple-minded progress indicator.
++    N = len(to_compile)
++    progress_fmt = "[{:%i}/{}] " % len(str(N))
++    for i in range(N):
++        progress = progress_fmt.format(i+1, N)
++        to_compile[i] = to_compile[i][1:] + (progress,)
++
++    if N <= 1:
+         nthreads = 0
+     if nthreads:
+         # Requires multiprocessing (or Python >= 2.6)
+@@ -862,7 +870,7 @@ def cythonize(module_list, exclude=[], nthreads=0, aliases=None, quiet=False, fo
+             pool.join()
+     if not nthreads:
+         for args in to_compile:
+-            cythonize_one(*args[1:])
++            cythonize_one(*args)
+
+     if exclude_failures:
+         failed_modules = set()
+@@ -927,7 +935,7 @@ else:
+
+ # TODO: Share context? Issue: pyx processing leaks into pxd module
+ @record_results
+-def cythonize_one(pyx_file, c_file, fingerprint, quiet, options=None, raise_on_failure=True, embedded_metadata=None):
++def cythonize_one(pyx_file, c_file, fingerprint, quiet, options=None, raise_on_failure=True, embedded_metadata=None, progress=""):
+     from ..Compiler.Main import compile, default_options
+     from ..Compiler.Errors import CompileError, PyrexError
+
+@@ -944,7 +952,7 @@ def cythonize_one(pyx_file, c_file, fingerprint, quiet, options=None, raise_on_f
+             options.cache, "%s-%s%s" % (os.path.basename(c_file), fingerprint, gzip_ext))
+         if os.path.exists(fingerprint_file):
+             if not quiet:
+-                print("Found compiled %s in cache" % pyx_file)
++                print("%sFound compiled %s in cache" % (progress, pyx_file))
+             os.utime(fingerprint_file, None)
+             g = gzip_open(fingerprint_file, 'rb')
+             try:
+@@ -957,7 +965,7 @@ def cythonize_one(pyx_file, c_file, fingerprint, quiet, options=None, raise_on_f
+                 g.close()
+             return
+     if not quiet:
+-        print("Cythonizing %s" % pyx_file)
++        print("%sCythonizing %s" % (progress, pyx_file))
+     if options is None:
+         options = CompilationOptions(default_options)
+     options.output_file = c_file
+@@ -1000,7 +1008,7 @@ def cythonize_one(pyx_file, c_file, fingerprint, quiet, options=None, raise_on_f
+ def cythonize_one_helper(m):
+     import traceback
+     try:
+-        return cythonize_one(*m[1:])
++        return cythonize_one(*m)
+     except Exception:
+         traceback.print_exc()
+         raise

build/pkgs/cython/patches/transitive_dependencies.patch

@@ -0,0 +1,78 @@
+commit 2285a087a3976ef301a8ea740fb5568f91930c8e
+Author: Jeroen Demeyer <jdemeyer@cage.ugent.be>
+Date:   Tue Apr 21 14:40:12 2015 +0200
+
+    When merging a transitive_list, copy the list
+
+diff --git a/Cython/Build/Dependencies.py b/Cython/Build/Dependencies.py
+index 3fe6885..ae47c62 100644
+--- a/Cython/Build/Dependencies.py
++++ b/Cython/Build/Dependencies.py
+@@ -216,12 +216,13 @@ class DistutilsInfo(object):
+                 self.values[key] = value
+             elif type is transitive_list:
+                 if key in self.values:
+-                    all = self.values[key]
++                    # Change a *copy* of the list (Trac #845)
++                    all = self.values[key][:]
+                     for v in value:
+                         if v not in all:
+                             all.append(v)
+-                else:
+-                    self.values[key] = value
++                    value = all
++                self.values[key] = value
+         return self
+
+     def subs(self, aliases):
+@@ -250,9 +251,8 @@ class DistutilsInfo(object):
+         for key, value in self.values.items():
+             type = distutils_settings[key]
+             if type in [list, transitive_list]:
+-                getattr(extension, key).extend(value)
+-            else:
+-                setattr(extension, key, value)
++                value = getattr(extension, key) + list(value)
++            setattr(extension, key, value)
+
+ @cython.locals(start=long, q=long, single_q=long, double_q=long, hash_mark=long,
+                end=long, k=long, counter=long, quote_len=long)
+diff --git a/tests/compile/distutils_libraries_T845.srctree b/tests/compile/distutils_libraries_T845.srctree
+new file mode 100644
+index 0000000..69c8549
+--- /dev/null
++++ b/tests/compile/distutils_libraries_T845.srctree
+@@ -0,0 +1,33 @@
++PYTHON setup.py build_ext --inplace
++
++######## setup.py ########
++
++from Cython.Build import cythonize
++from Cython.Distutils.extension import Extension
++
++ext_modules = [
++    Extension("a", ["a.pyx"]),
++    Extension("x", ["x.pyx"]),
++    Extension("y", ["y.pyx"]),
++]
++
++ext_modules = cythonize(ext_modules)
++
++assert ext_modules[1].libraries == ["lib_x"]
++assert ext_modules[2].libraries == ["lib_y"]
++
++######## libx.pxd ########
++# distutils: libraries = lib_x
++
++######## liby.pxd ########
++# distutils: libraries = lib_y
++
++######## a.pyx ########
++cimport libx
++cimport liby
++
++######## x.pyx ########
++cimport libx
++
++######## y.pyx ########
++cimport liby

build/pkgs/fricas/type

@@ -1 +1 @@
-optional
+experimental

build/pkgs/gap_packages/type

@@ -1 +1 @@
-optional
+experimental

build/pkgs/git_trac/checksums.ini

@@ -1,4 +1,4 @@
 tarball=git_trac-VERSION.tar.bz2
-sha1=624d927bc0d6cb315f7158df97293adac46e14b0
-md5=87d6eeb330abbba494e5bb898f73c0fd
-cksum=1266226813
+sha1=90c1e2c279fcac22b050c62253cfb53c8fe9c9c1
+md5=1f6e913132aa16b19cb5c99ee921f3f5
+cksum=774035580

build/pkgs/git_trac/package-version.txt

@@ -1 +1 @@
-1.0
+20150522

build/pkgs/jmol/dependencies

@@ -1,4 +1,4 @@
-| $(INST)/$(SAGENB)
+
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/latte_int/type

@@ -1 +1 @@
-optional
+experimental

build/pkgs/planarity/SPKG.txt

@@ -0,0 +1,32 @@
+= planarity =
+
+== Description ==
+
+This code project provides a library for implementing graph algorithms as well
+as implementations of several planarity-related graph algorithms. The origin of
+this project is the reference implementation for the Edge Addition Planarity
+Algorithm [1], which is now the fastest and simplest linear-time method for
+planar graph embedding and planarity obstruction isolation (i.e. Kuratowski
+subgraph isolation).
+
+[1] http://dx.doi.org/10.7155/jgaa.00091
+
+== License ==
+
+New BSD License
+
+== SPKG Maintainers ==
+
+Nathann Cohen  (nathann.cohen@gmail.com)
+
+== Upstream Contact ==
+
+John Boyer <John.Boyer.PhD@gmail.com>
+
+== Dependencies ==
+
+None
+
+== Patches ==
+
+None

build/pkgs/planarity/checksums.ini

@@ -0,0 +1,4 @@
+tarball=planarity-VERSION.tar.bz2
+sha1=3ef0985a2b8476123969cef5c1273d11286605f2
+md5=3e05f05ad8bf777e6a7ad48958a18c06
+cksum=679137721

build/pkgs/planarity/package-version.txt

@@ -0,0 +1 @@
+2.2.0

build/pkgs/planarity/patches/extern.patch

@@ -0,0 +1,23 @@
+Variables must be declared "extern" in header file
+
+diff -ru planarity-2.2.0/c/planarity.h b/c/planarity.h
+--- planarity-2.2.0/c/planarity.h	2015-05-05 14:20:57.000000000 +0200
++++ b/c/planarity.h	2015-05-12 12:10:49.780865449 +0200
+@@ -77,7 +77,7 @@
+ int legacyCommandLine(int argc, char *argv[]);
+ int menu();
+
+-char Mode,
++extern char Mode,
+      OrigOut,
+      EmbeddableOut,
+      ObstructedOut,
+@@ -88,7 +88,7 @@
+
+ /* Low-level Utilities */
+ #define MAXLINE 1024
+-char Line[MAXLINE];
++extern char Line[MAXLINE];
+
+ void Message(char *message);
+ void ErrorMessage(char *message);

build/pkgs/planarity/patches/malloc.patch

@@ -0,0 +1,26 @@
+Change <malloc.h> to <stdlib.h>
+
+diff -ru src/c/graphColorVertices.c b/c/graphColorVertices.c
+--- src/c/graphColorVertices.c	2015-05-05 14:20:57.000000000 +0200
++++ b/c/graphColorVertices.c	2015-05-07 11:18:43.927221207 +0200
+@@ -50,7 +50,7 @@
+ #include "graph.h"
+
+ #include <string.h>
+-#include <malloc.h>
++#include <stdlib.h>
+ #include <stdio.h>
+
+ extern void _FillVisitedFlags(graphP theGraph, int FillValue);
+diff -ru src/c/graphDrawPlanar.c b/c/graphDrawPlanar.c
+--- src/c/graphDrawPlanar.c	2015-05-05 14:20:57.000000000 +0200
++++ b/c/graphDrawPlanar.c	2015-05-07 11:18:30.608065652 +0200
+@@ -50,7 +50,7 @@
+ #include "graph.h"
+
+ #include <string.h>
+-#include <malloc.h>
++#include <stdlib.h>
+ #include <stdio.h>
+
+ extern void _FillVisitedFlags(graphP theGraph, int FillValue);

build/pkgs/planarity/patches/without_nauty.patch

@@ -0,0 +1,27 @@
+Minimal patch to compile planarity without Nauty
+
+--- a/c/planarityCommandLine.c	2015-05-05 14:20:57.000000000 +0200
++++ b/c/planarityCommandLine.c	2015-05-07 11:05:24.053668256 +0200
+@@ -157,6 +157,7 @@
+ extern unsigned long numErrors;
+ extern unsigned long numOKs;
+
++#ifdef HAVE_NAUTY
+ int callNauty(int argc, char *argv[])
+ {
+ 	char command;
+@@ -294,6 +295,14 @@
+ 		return 0;
+ 	}
+ }
++#else
++unsigned long numGraphs, numErrors, numOKs;
++int callNauty(int argc, char *argv[])
++{
++	fprintf(stderr, "Nauty is not installed, aborting\n");
++	exit(1);
++}
++#endif
+
+ /****************************************************************************
+  Quick regression test