Merge branch 'develop' into t/14801/public/piecewise-2

Makefile

@@ -13,6 +13,7 @@ build: all-build
 
 # Defer unknown targets to build/make/Makefile
 %::
+	@if [ -x relocate-once.py ]; then ./relocate-once.py; fi
 	$(MAKE) build/make/Makefile
 	+build/bin/sage-logger \
 		"cd build/make && ./install '$@'" logs/install.log

VERSION.txt

@@ -1 +1 @@
-Sage version 7.1.rc1, released 2016-03-17
+SageMath version 7.2.beta4, Release Date: 2016-04-12

build/bin/sage-uncompress-spkg

@@ -18,28 +18,29 @@ if __name__ == '__main__':
     filename = sys.argv[1]
     if tarfile.is_tarfile(filename):
         # tar file, possibly compressed:
-        with tarfile.open(filename, 'r:*') as archive:
-            if len(sys.argv) == 2:
-                archive.extractall()
-            else:
-                member = sys.argv[2]
-                if member in archive.getnames():
-                    SPKG_TXT = archive.extractfile(member)
-                    sys.stdout.write(SPKG_TXT.read())
-                else:
-                    exit(1)
+        archive = tarfile.open(filename, 'r:*')
+        if len(sys.argv) == 2:
+            archive.extractall()
+        else:
+            member = sys.argv[2]
+            if member in archive.getnames():
+                SPKG_TXT = archive.extractfile(member)
+                sys.stdout.write(SPKG_TXT.read())
+                exit(1)
+        archive.close()
         exit(0)
     if zipfile.is_zipfile(filename):
         # zip file:
-        with zipfile.ZipFile(filename, 'r') as archive:
-            if len(sys.argv) == 1:
-                archive.extractall()
+        archive = zipfile.ZipFile(filename, 'r')
+        if len(sys.argv) == 2:
+            archive.extractall()
+        else:
+            member = sys.argv[2]
+            if member in archive.namelist():
+                sys.stdout.write(archive.read(member))
             else:
-                member = sys.argv[2]
-                if member in archive.namelist():
-                    sys.stdout.write(archive.read(member))
-                else:
-                    exit(1)
+                exit(1)
+        archive.close()
         exit(0)
     else:
         print ('Error: Unknown file type: {}'.format(filename))

build/make/deps

@@ -149,7 +149,7 @@ sagelib: \
 		$(EXTCODE)
 	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
 		cd $(SAGE_SRC) && source bin/sage-env && \
-		sage-logger 'time $(MAKE) sage' '$(SAGE_LOGS)/sage-$(SAGE_VERSION).log'; \
+		sage-logger 'time $(MAKE) sage' '$(SAGE_LOGS)/sagelib-$(SAGE_VERSION).log'; \
 	fi
 
 

build/pkgs/cddlib/spkg-install

@@ -28,7 +28,7 @@ cd src
 cp ../patches/random.{c,h} lib-src/
 cp ../patches/random.{c,h} lib-src-gmp/
 
-# Required by sage.geometry.polyhedra 
+# Required by sage.geometry.polyhedron
 cp ../patches/cdd_both_reps.c src/
 cp ../patches/cdd_both_reps.c src-gmp/cdd_both_reps.c
 

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=cbc97440ac6c28ba5bb14cbc9257657aeab2b094
-md5=70c593564f8311ce050b593ae2e38755
-cksum=2867718865
+sha1=a688b4151ebffbd892199e47edf21f0e295ae06f
+md5=1da510585db296e3930eaa33cbb40a87
+cksum=3334341322

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-151
+158

build/pkgs/csdp/type

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

build/pkgs/cysignals/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cysignals-VERSION.tar.bz2
-sha1=392505d05d3cd849a94da614bd6d52aadf5a0db5
-md5=a2538b783d654f35d0c40d8a465470b0
-cksum=3111713488
+sha1=26b5fa9ac855af6ab33157fe7c8f095ca086063b
+md5=31e95c68349b33b7781969e0d1ecab91
+cksum=939390582

build/pkgs/cysignals/package-version.txt

@@ -1 +1 @@
-1.0.1
+1.1.0

build/pkgs/cython/checksums.ini

@@ -1,4 +1,4 @@
 tarball=Cython-VERSION.tar.gz
-sha1=fc574c5050cd5a8e34435432e2a4a693353ed807
-md5=157df1f69bcec6b56fd97e0f2e057f6e
-cksum=346066359
+sha1=32f12b8dd976111668ef8ba7e716a850869a0bf6
+md5=14fbc970f4a856845e633cbc09e61048
+cksum=2292891014

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.23.4.p0
+0.24.p0

build/pkgs/database_gap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=database_gap-VERSION.tar.bz2
-sha1=46760a6a606eb1eea55b86f12d429a86c97740d7
-md5=87273df691a15bcf6b4b75b372cb6d0c
-cksum=1428556919
+sha1=30f30b05f83eda0e092002e509b47768862a743f
+md5=b443d7e7852471f83d19dd409b19a221
+cksum=4104886394

build/pkgs/database_gap/package-version.txt

@@ -1 +1 @@
-4.7.9
+4.8.3

build/pkgs/database_gap/spkg-src

@@ -13,11 +13,11 @@ shopt -s extglob
 # Remove old sources and download new
 rm -rf src
 if [ -z "$UPSTREAM_SOURCE_TARBALL" ]; then
-    tar xjf <( curl http://www.gap-system.org/pub/gap/gap47/tar.bz2/gap4r7p8_2015_06_09-20_27.tar.bz2)
+    tar xf <( curl http://www.gap-system.org/pub/gap/gap47/tar.bz2/gap4r7p8_2015_06_09-20_27.tar.bz2)
 else
-    tar xjf "$UPSTREAM_SOURCE_TARBALL"
+    tar xf "$UPSTREAM_SOURCE_TARBALL"
 fi
-GAP=`pwd`/gap4r7
+GAP=`pwd`/gap4r8
 
 # Make everything writable
 chmod -R u+w "$GAP"

build/pkgs/database_mutation_class/SPKG.txt

@@ -0,0 +1,23 @@
+= Mutation class database =
+
+== Description ==
+
+ Contains a database of all exceptional mutation classes of quivers.
+
+ Every file in the database is of the form ``mutation_classes_n.dig6`` for some ``n`` and
+ - contains a ``cPickle.dump`` of a dictionary where
+   - the keys are tuples representing irreducible exceptional quiver mutation types of rank ``n``, and
+   - the values are all quivers in the given mutation class stored in canonical form as ``(dig6,edges)`` where
+     - ``dig6`` is the dig6 data of the given ``DiGraph``, and
+     - ``edges`` are the non-simply-laced edges thereof.
+ - is obtained by running the function
+ ``sage.combinat.cluster_algebra_quiver.quiver_mutation_type._save_data_dig6(n, types='Exceptional', verbose=False)``
+
+== SPKG Maintainers ==
+
+ * C. Stump <christian.stump@gmail.com>
+
+== Dependencies ==
+
+ * None
+

build/pkgs/database_mutation_class/checksums.ini

@@ -0,0 +1,4 @@
+tarball=database_mutation_class-VERSION.tar.gz
+sha1=0e7eb2e89e1d4a612cb60e3d6be14d42f3e55678
+md5=8186b8f75eae76825399f3a9e6378c7b
+cksum=364985299

build/pkgs/database_mutation_class/dependencies

@@ -0,0 +1 @@
+# no dependencies

build/pkgs/database_mutation_class/package-version.txt

@@ -0,0 +1 @@
+1.0

build/pkgs/database_mutation_class/spkg-install

@@ -0,0 +1,17 @@
+#!/usr/bin/env bash
+
+cd src
+
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "SAGE_LOCAL undefined database_mutation_class-1.0 exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+mkdir -p $SAGE_SHARE/cluster_algebra_quiver && cp src/* $SAGE_SHARE/cluster_algebra_quiver
+
+if [ $? -ne 0 ]; then
+    echo >&2 "Error: Failed to copy the data to $SAGE_SHARE/cluster_algebra_quiver. database_mutation_class-1.0 exiting"
+    exit 1
+fi
+

build/pkgs/database_mutation_class/type

@@ -0,0 +1 @@
+optional

build/pkgs/ecl/checksums.ini

@@ -1,4 +1,4 @@
 tarball=ecl-VERSION.tar.bz2
-sha1=d5b9f2f19847697f3cbe54e69daf609d1ea1b9ca
-md5=ba1d8acd05b2921c556a488191ff4b6b
-cksum=1247067343
+sha1=a2ba6f17df11e77149869d7d71c2175c284778ce
+md5=fdca3688a9171518f301e4200f82532a
+cksum=3217462385

build/pkgs/ecl/package-version.txt

@@ -1 +1 @@
-15.3.7p0
+15.3.7.p1

build/pkgs/ecl/patches/fix-cc.patch

@@ -0,0 +1,29 @@
+From d23d974654fbef889aa1c110d6e2968e07b58930 Mon Sep 17 00:00:00 2001
+From: "Erik M. Bray" <erik.bray@lri.fr>
+Date: Thu, 17 Mar 2016 15:57:16 +0100
+Subject: [PATCH] Allow CC and other environment variables passed to
+ safe-run-program to be a command with arguments
+
+---
+ src/cmp/cmpos-run.lsp | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/src/cmp/cmpos-run.lsp b/src/cmp/cmpos-run.lsp
+index 49f6605..b824409 100755
+--- a/src/cmp/cmpos-run.lsp
++++ b/src/cmp/cmpos-run.lsp
+@@ -54,7 +54,10 @@
+   (cmpnote "Invoking external command:~%  ~A ~{~A ~}" program args)
+   (multiple-value-bind (stream result process)
+       (let* ((*standard-output* ext:+process-standard-output+)
+-             (*error-output* ext:+process-error-output+))
++             (*error-output* ext:+process-error-output+)
++             (program (split-program-options program))
++             (args `(,@(cdr program) ,@args))
++             (program (car program)))
+         (with-current-directory
+             #-(and cygwin (not ecl-min))
+             (ext:run-program program args :input nil :output t :error t :wait t)
+-- 
+1.9.1
+

build/pkgs/ecl/spkg-install

@@ -8,6 +8,17 @@ fi
 
 cd src
 
+# Patch sources. Note that some patches (in the patches/src directory)
+# have been applied to the source tarball.
+for patch in ../patches/*.patch; do
+    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
+    patch -p1 <"$patch"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error applying '$patch'"
+        exit 1
+    fi
+done
+
 if [ -z "$CFLAG64" ] ; then
     CFLAG64=-m64
 fi
@@ -16,10 +27,6 @@ if [ -z "$CXXFLAG64" ] ; then
     CXXFLAG64=-m64
 fi
 
-# Do NOT quote SAGE_LOCAL here, as has caused problems.
-# See: http://trac.sagemath.org/sage_trac/ticket/10187#comment:117
-
-CPPFLAGS="$CPPFLAGS -I$SAGE_LOCAL/include"
 
 # Compile for 64-bit if SAGE64 is set to 'yes'
 if [ "x$SAGE64" = "xyes" ]  ; then
@@ -37,6 +44,11 @@ else
     CXXFLAGS="-g -O2 $CXXFLAGS"
 fi
 
+export CFLAGS
+export CXXFLAGS
+export LDFLAGS
+
+
 # These are all used by GNU to specify compilers.
 echo "Using CC=$CC"
 echo "Using CXX=$CXX"
@@ -49,17 +61,7 @@ echo "Using CPPFLAGS=$CPPFLAGS"
 echo "Using LDFLAGS=$LDFLAGS"
 echo "configure scripts and/or makefiles might override these later"
 echo ""
-echo "Note that the patches were applied by spkg-src"
-echo ""
-
-# export everything. Probably not necessary in most cases.
-export CFLAGS
-export CXXFLAGS
-export CPPFLAGS
-export LDFLAGS
 
-# Building ECL in parallel doesn't work, so use only 1 thread
-MAKE="$MAKE -j1"
 
 if [ "`uname -sm`" = "SunOS i86pc" ] && [ "x$SAGE64" = xyes ]; then
     # Need to add --with-dffi=no to disable assembly code on OpenSolaris x64.
@@ -85,6 +87,10 @@ fi
 # Before running make we touch build/TAGS so its building process is never triggered
 touch build/TAGS
 
+# Ensure that ECL will not ask interactive questions (for example, when
+# pressing CTRL-C during the build)
+exec </dev/null
+
 $MAKE
 if [ $? -ne 0 ]; then
     echo >&2 "Error - Failed to build ECL ... exiting"