Merge branch 'develop' into t/9424/9424

* develop: (374 commits)
  Updated Sage version to 6.8.beta3
  Add HughesPlane to the catalog
  Added Element attribute to FreeAbelianMonoid_class
  Changed the return value of gen() in FreeAbelianMonoid_class
  Small formating fixes (adding outputs, fixing doc indent)
  Trac 18086: fixed a small Dirichlet character bug
  Trac 18086: reviewer comments
  Trac 18086: implement twisting of newforms by Dirichlet characters
  Trac #18527: (review) cleaning
  Trac #18257: (review) remove trailing whitespaces
  Add authors, cleaned description
  Trac #18527: (review) small cleanup
  Trac #18527: (review) fix the case of non prime q
  Trac #18257: (review) better q3_minus_one_matrix
  Trac #18527: (review) rename random_q3_xxx -> q3_xxx
  Trac #18527: (review) remove trailing whitespaces
  Corrected HughesPlane description
  Changed HughesPlane description according to the review
  Add type file
  Trac #18527 (review): improve the documentation
  ...

VERSION.txt

@@ -1 +1 @@
-Sage version 6.8.beta0, released 2015-05-23
+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
@@ -109,34 +108,23 @@ $(INST)/sage: \
 		 $(INST)/$(NTL) \
 		 $(INST)/$(NUMPY) \
 		 $(INST)/$(PARI) \
+		 $(INST)/$(PLANARITY) \
 		 $(INST)/$(POLYBORI) \
 		 $(INST)/$(PPL) \
 		 $(INST)/$(PYNAC) \
 		 $(INST)/$(PYTHON) \
 		 $(INST)/$(RATPOINTS) \
 		 $(INST)/$(READLINE) \
 		 $(INST)/$(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

@@ -311,9 +311,12 @@ filtered_packages_list() {
     for DIR in $SAGE_ROOT/build/pkgs/*; do
 
         PKG_TYPE_FILE="$DIR/type"
-        PKG_TYPE=`cat $PKG_TYPE_FILE`
-        if [ $? -ne 0 ]; then
-            continue
+        if [ -f "$PKG_TYPE_FILE" ]; then
+            PKG_TYPE=`cat $PKG_TYPE_FILE`
+        else
+            echo >&2 "\"$PKG_TYPE_FILE\" is missing. Create it, and set its content"
+            echo >&2 "to 'base', 'standard', 'optional' or 'experimental'."
+            return 1
         fi
 
         # Check consistency of 'DIR/type' file
@@ -332,6 +335,9 @@ filtered_packages_list() {
     done
 }
 
+# Check that all packages define a (valid) 'type' file, or exit
+filtered_packages_list none || exit $?
+
 echo >&5 "# All Sage packages"
 
 filtered_packages_list all | while read PKG_NAME PKG_VERSION PKG_VAR; do
@@ -344,8 +350,17 @@ cat >&5 <<EOF
 # Directory to keep track of which packages are installed
 INST=`echo "$SAGE_SPKG_INST" | sed 's/ /\\\\ /g'`
 
+# Aliases for optional packages selected at build time
 EOF
 
+
+# Python version
+if [ "$SAGE_PYTHON3" = yes ]; then
+    echo >&5 'PYTHON = $(PYTHON3)'
+else
+    echo >&5 'PYTHON = $(PYTHON2)'
+fi
+
 # Sage MP library
 echo >&5 "SAGE_MP_LIBRARY = \$($SAGE_MP_LIBRARY)"
 
@@ -372,11 +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=8a7caccab5eeda4632ef48746ca0765731a25694
-md5=b3831378287897b2b91cbc54b97f4fe4
-cksum=3325770959
+sha1=ba70d13aace4a7894ceec5d6e56f29b39756ab30
+md5=b2e6ae57f6f348b3f5bf9baaa2b7049f
+cksum=2993700783

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-94
+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/checksums.ini

@@ -1,4 +1,4 @@
 tarball=latte_int-VERSION.tar.gz
-sha1=165c9173b13f4bc9cb825ef63c06d6fb20dc41b5
-md5=57b151f7bb49fe5154a5697b70d359f9
-cksum=1072837189
+sha1=3bdf739efe12f5e910668afa17341db21204d38c
+md5=2ec40606c6755ba1770c8ac31155ecd9
+cksum=1498070052

build/pkgs/latte_int/package-version.txt

@@ -1 +1 @@
-1.7.2
+1.7.3

build/pkgs/latte_int/spkg-check

@@ -16,7 +16,8 @@ fi
 
 export CFLAGS
 
-dirsr="$CUR"/src
+LATTE_VERSION="$(cat ${SAGE_ROOT}/build/pkgs/latte_int/package-version.txt)"
+dirsr="$CUR"/latte-int-${LATTE_VERSION}
 echo "Testing in $dirsr"
 cd "$dirsr"
 $MAKE check

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