Merge branch 'public/11111-more_support_for_finite_dimensional_modules_and_algebras_with_basis' of git://trac.sagemath.org/sage into t/11111

Author: saliola

COPYING.txt

@@ -80,6 +80,7 @@ markupsafe                  Simplified BSD
 mathjax                     Apache License 2.0
 matplotlib                  Matplotlib License (BSD compatible, see below)
 maxima                      See below
+mistune                     Modified BSD
 mpc                         LGPLv3+
 mpfi                        COPYING is GPLv2, source files state LGPLv2.1+
 mpfr                        LGPLv3+

Makefile

@@ -20,7 +20,7 @@ build: logs configure
 	"../$(PIPE)" \
 		"env SAGE_PARALLEL_SPKG_BUILD='$(SAGE_PARALLEL_SPKG_BUILD)' ./install all 2>&1" \
 		"tee -a ../logs/install.log"
-	./sage -b
+	+./sage -b
 
 # Preemptively download all standard upstream source tarballs.
 download:

VERSION.txt

@@ -1 +1 @@
-Sage version 6.6.rc3, released 2015-04-12
+Sage version 6.7.beta0, released 2015-04-15

build/deps

@@ -72,6 +72,7 @@ all-sage: \
      $(INST)/$(MATHJAX) \
      $(INST)/$(MATPLOTLIB) \
      $(INST)/$(MAXIMA) \
+     $(INST)/$(MISTUNE) \
      $(INST)/$(MPC) \
      $(INST)/$(MPFI) \
      $(INST)/$(MPFR) \
@@ -316,6 +317,9 @@ $(INST)/$(LIBGAP): $(INST)/$(GAP)
 $(INST)/$(JSONSCHEMA): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(JSONSCHEMA) 2>&1" "tee -a $(SAGE_LOGS)/$(JSONSCHEMA).log"
 
+$(INST)/$(MISTUNE): $(INST)/$(PIP) $(INST)/$(CYTHON)
+	+$(PIPE) "$(SAGE_SPKG) $(MISTUNE) 2>&1" "tee -a $(SAGE_LOGS)/$(MISTUNE).log"
+
 $(INST)/$(IPYTHON): $(INST)/$(PYTHON) $(INST)/$(JINJA2) $(INST)/$(TORNADO) $(INST)/$(PYZMQ)
 	+$(PIPE) "$(SAGE_SPKG) $(IPYTHON) 2>&1" "tee -a $(SAGE_LOGS)/$(IPYTHON).log"
 
@@ -523,7 +527,7 @@ $(INST)/sage: \
 		 $(INST)/csage
 	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
 		cd $(SAGE_SRC) && source bin/sage-env && \
-		$(PIPE) 'time python setup.py install 2>&1' 'tee -a $(SAGE_LOGS)/sage-$(SAGE_VERSION).log' && \
+		$(PIPE) 'time $(MAKE) sage 2>&1' 'tee -a $(SAGE_LOGS)/sage-$(SAGE_VERSION).log' && \
 		touch $@; \
 	fi
 
@@ -534,8 +538,8 @@ $(INST)/csage: $(INST)/$(SCONS) \
        $(INST)/$(PYTHON) \
        $(CSAGE_SOURCES)
 	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
-		cd $(SAGE_SRC) && source bin/sage-env && cd c_lib && \
-		$(PIPE) 'time scons -Q install 2>&1' 'tee -a $(SAGE_LOGS)/csage-$(SAGE_VERSION).log' && \
+		cd $(SAGE_SRC) && source bin/sage-env && \
+		$(PIPE) 'time $(MAKE) csage 2>&1' 'tee -a $(SAGE_LOGS)/csage-$(SAGE_VERSION).log' && \
 		touch $@; \
 	fi
 

build/install

@@ -347,6 +347,7 @@ MARKUPSAFE=`newest_version markupsafe`
 MATHJAX=`newest_version mathjax`
 MATPLOTLIB=`newest_version matplotlib`
 MAXIMA=`newest_version maxima`
+MISTUNE=`newest_version mistune`
 MPC=`newest_version mpc`
 MPFI=`newest_version mpfi`
 MPFR=`newest_version mpfr`

build/pkgs/cbc/SPKG.txt

@@ -0,0 +1,28 @@
+= COIN-OR / CBC =
+
+== Description ==
+
+The Computational Infrastructure for Operations Research (COIN-OR**,
+or simply COIN)  project is an initiative to spur the development of
+open-source software for the operations research community.
+
+The COIN Branch and Cut solver (CBC) is an open-source
+mixed-integer program (MIP) solver written in C++. CBC is intended to
+be used primarily as a callable library to create customized
+branch-and-cut solvers. A basic, stand-alone executable version is
+also available. CBC is an active open-source project led by John
+Forrest at www.coin-or.org.
+
+== License ==
+
+Eclipse Public License, Version 1.0 (EPL-1.0)
+(http://opensource.org/licenses/eclipse-1.0)
+
+== Upstream Contact ==
+
+ * John Forrest <[email protected]>
+ * Robin Lougee-Heimer
+
+== Project Home Page ==
+
+ * https://projects.coin-or.org/Cbc

build/pkgs/cbc/checksums.ini

@@ -0,0 +1,4 @@
+tarball=cbc-VERSION.tar.gz
+sha1=d937d6af1ee8838d44659ebd4cf7bbb1b20372ce
+md5=2134576233cc95cdfedc63991a4944ec
+cksum=1215468781

build/pkgs/cbc/package-version.txt

@@ -0,0 +1 @@
+2.9.4

build/pkgs/cbc/spkg-install

@@ -0,0 +1,22 @@
+if [ "$SAGE_LOCAL" = "" ]; then
+   echo >&2 "SAGE_LOCAL undefined ... exiting";
+   echo >&2 "Maybe run 'sage -sh'?"
+   exit 1
+fi
+
+export LDFLAGS="$LDFLAGS -lz -lbz2"
+#export CPPFLAGS="-DHAVE_CLOCK_GETTIME=0"
+
+# See discussion on #12220
+#
+#-> Mac and Linux behave differently according to the presence of librt, and a
+#   good way around if to make the computer believe that it does not exist
+#   locally, or more precisely that it does not contain the clock_gettime
+#   function. Cbc uses an alternative method to do the job, and it looks like
+#   all this is required when Cbc solves LP with several threads.
+#
+cd src &&
+sed -i -e "s/clock\_gettime ()/Grrrrrrrrrrrr\ ()/g" Cbc/configure &&
+./configure --prefix="$SAGE_LOCAL" "${args[@]}" --enable-cbc-parallel --enable-parallel --enable-gnu-packages --enable-static &&
+make &&
+make install

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=beac54655b8d0fbff44d578bcb2b4f676d40b3c9
-md5=ac8c8051aebfe3d45bf36bdf498c9b59
-cksum=3023873269
+sha1=470ca91bf3a1628a646d1ce53572ce8c1228e7e3
+md5=46f06fc9a5374cdc595e9e853beb0c18
+cksum=1589755960

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-81
+86

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.22
+0.22.p1

build/pkgs/cython/patches/embedsignatures.patch

@@ -0,0 +1,44 @@
+commit 9139a7f836151fb5bdb1624a05dce13b1bb17164
+Author: Stefan Behnel <[email protected]>
+Date:   Mon Apr 6 10:45:48 2015 +0200
+
+    support NULL as default argument in auto doc transform
+
+diff --git a/Cython/Compiler/AutoDocTransforms.py b/Cython/Compiler/AutoDocTransforms.py
+index 775f635..88b0cd8 100644
+--- a/Cython/Compiler/AutoDocTransforms.py
++++ b/Cython/Compiler/AutoDocTransforms.py
+@@ -51,6 +51,8 @@ class EmbedSignature(CythonTransform):
+         default_val = arg.default
+         if not default_val:
+             return None
++        if isinstance(default_val, ExprNodes.NullNode):
++            return 'NULL'
+         try:
+             denv = self.denv  # XXX
+             ctval = default_val.compile_time_value(self.denv)
+diff --git a/tests/run/embedsignatures.pyx b/tests/run/embedsignatures.pyx
+index 0bfebfe..781cd21 100644
+--- a/tests/run/embedsignatures.pyx
++++ b/tests/run/embedsignatures.pyx
+@@ -199,6 +199,9 @@ __doc__ = ur"""
+ 
+     >>> print(funcdoc(f_defexpr5))
+     f_defexpr5(int x=4)
++
++    >>> print(funcdoc(f_charptr_null))
++    f_charptr_null(char *s=NULL) -> char *
+ """
+ 
+ cdef class Ext:
+@@ -403,6 +406,10 @@ cpdef f_defexpr4(int x = (Ext.CONST1 + FLAG1) * Ext.CONST2):
+ cpdef f_defexpr5(int x = 2+2):
+     pass
+ 
++cpdef (char*) f_charptr_null(char* s=NULL):
++    return s or b'abc'
++
++
+ # no signatures for lambda functions
+ lambda_foo = lambda x: 10
+ lambda_bar = lambda x: 20

build/pkgs/mistune/SPKG.txt

@@ -0,0 +1,19 @@
+= mistune =
+
+== Description ==
+
+The fastest markdown parser in pure Python
+
+== License ==
+
+BSD License
+
+== Upstream Contact ==
+
+Home Page: https://github.com/lepture/mistune
+
+== Dependencies ==
+
+Python, Cython, Pip
+
+

build/pkgs/mistune/checksums.ini

@@ -0,0 +1,4 @@
+tarball=mistune-VERSION.tar.gz
+sha1=21f0c7bf9bad7fac2e34355ed2c50e48557e2c8d
+md5=10a42265bfc7e9ad817fe777a4857821
+cksum=492791270

build/pkgs/mistune/package-version.txt

@@ -0,0 +1 @@
+0.5.1

build/pkgs/mistune/spkg-install

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "SAGE_LOCAL undefined ... exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+pip install --upgrade --no-dependencies --force-reinstall src/
+if [ $? -ne 0 ]; then
+    echo "Error installing mistune ... exiting"
+    exit 1
+fi

build/pkgs/numpy/package-version.txt

@@ -1 +1 @@
-1.8.1
+1.8.1.p0

build/pkgs/numpy/spkg-install

@@ -37,6 +37,8 @@ for patch in $patches; do
     fi
 done
 
+set -e
+
 echo "[DEFAULT]" > site.cfg
 echo "library_dirs = $SAGE_LOCAL/lib" >> site.cfg
 echo "include_dirs = $SAGE_LOCAL/include" >> site.cfg
@@ -58,15 +60,20 @@ export NUMPY_FCONFIG="config_fc --noopt --noarch"
 
 ################################################
 
-rm -rf "$SAGE_LOCAL"/lib/python/site-packages/numpy
+rm -rf "$SAGE_LOCAL/lib/python/site-packages/numpy"
 
 # Program around a bug in SciPY's distutils.
 unset CFLAGS
 
 python setup.py install ${NUMPY_FCONFIG}
 
-if [ $? -ne 0 ]; then
-    echo "Error building numpy."
-    exit 1
-fi
-
+# Touch all includes such that dependency checking works properly:
+# the timestamp of the includes should be *now*, not the time when
+# the numpy package was created.
+python <<EOF
+import os
+os.chdir(os.environ["SAGE_ROOT"])  # Import numpy from safe location
+import numpy
+os.chdir(numpy.get_include())
+os.system("touch numpy/*")
+EOF

build/pkgs/pari/package-version.txt

@@ -1 +1 @@
-2.8-1369-g0e48e9b
+2.8-1369-g0e48e9b.p0

src/Makefile

@@ -1,3 +1,16 @@
+.PHONY: all sage csage clean
+
+# By default, build csage and sage (in this order)
+all:
+	$(MAKE) csage
+	$(MAKE) sage
+
+sage: sage/libs/pari/auto_gen.pxi sage/ext/interpreters/__init__.py
+	python setup.py install
+
+csage:
+	cd c_lib && scons -Q install
+
 clean:
 	@echo "Deleting Sage library build artifacts..."
 	rm -f c_lib/.sconsign.dblite
@@ -6,3 +19,13 @@ clean:
 	find c_lib -name '*.dylib' | xargs rm -f
 	rm -rf build
 	find . -name '*.pyc' | xargs rm -f
+	rm -f sage/libs/pari/auto_*
+	rm -rf sage/ext/interpreters
+
+
+# Auto-generated files
+sage/libs/pari/auto_gen.pxi: $(SAGE_LOCAL)/share/pari/pari.desc sage_setup/autogen/pari/*.py
+	python -c "from sage_setup.autogen.pari import rebuild; rebuild()"
+
+sage/ext/interpreters/__init__.py: sage_setup/autogen/interpreters.py
+	python -c "from sage_setup.autogen.interpreters import rebuild; rebuild('sage/ext/interpreters')"

src/bin/sage

@@ -635,7 +635,7 @@ fi
 
 build_sage() {
     maybe_sage_location
-    sage-build "$@" || exit $?
+    ( cd "$SAGE_SRC" && $MAKE ) || exit $?
 }
 
 if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
@@ -674,14 +674,12 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grepdoc" -o "$1" = "-search_doc" -o "$1" = "
 fi
 
 if [ "$1" = '-b' ]; then
-    shift
-    time build_sage "$@"
+    time build_sage
     exit $?
 fi
 
 if [ "$1" = '-br' -o "$1" = "--br" ]; then
-    shift
-    build_sage "$@"
+    build_sage
     interactive_sage
 fi
 
@@ -691,9 +689,8 @@ if [ "$1" = '-r' ]; then
 fi
 
 if [ "$1" = '-ba' -o "$1" = '-ba-force' -o "$1" = '--ba-force' ]; then
-    shift
     ( cd "$SAGE_SRC" && make clean )
-    build_sage "$@"
+    build_sage
     exit $?
 fi
 
@@ -707,6 +704,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1" = '-tp' -o "$1" = '-btp' ]; then
     fi
     SAGE_BANNER="no"
     sage_setup
+    export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
     if [ "$1" = '-tp' -o "$1" = '-btp' ]; then
         shift
         exec sage-runtests -p "$@"
@@ -723,13 +721,15 @@ if [ "$1" = '-tnew' -o "$1" = '-btnew' ]; then
     shift
     SAGE_BANNER="no"
     sage_setup
+    export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
     exec sage-runtests --new "$@"
 fi
 
 if [ "$1" = '-testall' -o "$1" = "--testall" ]; then
     shift
     SAGE_BANNER="no"
     sage_setup
+    export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
     exec sage-runtests -a "$@"
 fi
 

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ SageMath Version 6.6.rc3, Release Date: 2015-04-12                 │
+│ SageMath Version 6.7.beta0, Release Date: 2015-04-15               │
 │ Type "notebook()" for the browser-based notebook interface.        │
 │ Type "help()" for help.                                            │
 └────────────────────────────────────────────────────────────────────┘