Merge 7.2.beta3 into t/20311/ISM_enchancements

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 7.2.beta0, released 2016-03-24
+SageMath version 7.2.beta3, Release Date: 2016-04-07

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) == 2:
-                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=195df1ea1be9cb31ff40e367a2f059f2d94da443
-md5=e9f6023b1d841bef10836f5046398e45
-cksum=1859203132
+sha1=00d7bd6cb4d1cb6ef378cf2ecc0bfe733abf845e
+md5=36b19a7d55b3a105f7971b3380a22baf
+cksum=1610953959

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-153
+157

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/flint/package-version.txt

@@ -1 +1 @@
-2.5.2
+2.5.2.p0

build/pkgs/flint/patches/flintxx-include.patch

@@ -0,0 +1,19 @@
+Fix include errors with flintxx
+
+https://github.com/wbhart/flint2/commit/c0768dc54b5ece38252857f8e7423d5ce81a43f7
+
+
+
+diff --git a/flintxx/flint_classes.h b/flintxx/flint_classes.h
+index eac2d1a..6baa392 100644
+--- a/flintxx/flint_classes.h
++++ b/flintxx/flint_classes.h
+@@ -27,7 +27,7 @@
+ // Contrary to other parts of this library, they are tailored very
+ // specifically towards FLINT.
+
+-#include "flint.h"
++#include "../flint.h"
+ #include "mp.h"
+ #include "expression.h"
+ #include "expression_traits.h"

build/pkgs/gap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gap-VERSION.tar.bz2
-sha1=a200b6c5188e5c3464b14cbf37b32dabb78d8687
-md5=0e2a80bc711601d7f3320fe563fff86a
-cksum=2560320934
+sha1=2d7ca54d7c38dbfdc5bad6d5fe3304119f71cbc9
+md5=61fe8c83b7ca80a5212a79bbe5803467
+cksum=2414776374

build/pkgs/gap/package-version.txt

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

build/pkgs/gap/spkg-install

@@ -112,3 +112,8 @@ if [[ "$SAGE_SPKG_INSTALL_DOCS" = yes ]]; then
         exit 1
     fi
 fi
+
+# Delete tests that rely on the non-GPL small group library
+rm "$INSTALL_DIR"/tst/testinstall/ctblsolv.tst
+rm "$INSTALL_DIR"/tst/testinstall/grppc.tst
+rm "$INSTALL_DIR"/tst/testinstall/morpheus.tst 

build/pkgs/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
-mv gap4r7 src
+mv gap4r8 src
 
 
 # Make everything writable

build/pkgs/gap3/SPKG.txt

@@ -0,0 +1,73 @@
+= Jean Michel's GAP 3 distribution =
+
+== Description ==
+
+This package installs Jean Michel's pre-packaged GAP3, which is a minimal GAP3
+distribution containing packages that have no equivalent in GAP4.
+
+Below is the full description from Jean Michel's webpage
+(accessed 23 July 2015).
+
+    A pre-packaged GAP3 with everything you need
+
+    To help people who are just interested in GAP3 because they need a package
+    which has not been ported to GAP4, I have prepared an easy-to install
+    minimal GAP3 distribution containing an up-to-date versions of the
+    packages:
+
+        anusq, arep, autag, chevie, cryst, dce, grim, matrix, meataxe, monoid,
+        nq, pcqa, sisyphos, specht, ve, vkcurve.
+
+    These packages have been chosen since most have no equivalent in GAP4. They
+    are autoloaded when starting gap.
+
+    This distribution includes only partial lists of small groups, 2-groups,
+    3-groups, character tables from the Atlas and tables of marks. It does not
+    include either the packages:
+
+        anupq, grape, kbmag, xgap, cohomolo, gliss, guava, xmod
+
+    which have some equivalent in GAP4. You can get these extra features at
+
+        http://www.math.rwth-aachen.de/~Frank.Luebeck/gap/GAP3
+
+    In this distribution:
+
+    - The on-line help includes the documentation of the included packages.
+    - The html documentation (htm/index.html) also does.
+    - The manual (manual.pdf) also does.
+
+== License ==
+
+Most parts of the GAP distribution, including the core part of the GAP system,
+are distributed under the terms of the GNU General Public License (see
+http://www.gnu.org/licenses/gpl.html or the file GPL in the etc directory of
+the GAP installation).
+
+== SPKG Maintainers ==
+
+* Christian Stump <christian.stump@gmail.com>
+
+== Upstream Contact ==
+
+Jean Michel <jmichel@math.jussieu.fr>
+http://webusers.imj-prg.fr/~jean.michel/
+
+== Special Update/Build Instructions ==
+
+The difference between the distributed tarball and Jean Michel's
+original tarball is that all binary files have been deleted one by one
+from the listing obtained by
+
+    grep -r -m 1 "^"  . | grep "^Binary file"
+
+=== Patches ===
+
+ * gap3_makefile.patch: modifies src/src/Makefile such that if autodetects
+   the system
+
+ * gap3_startup.patch: modifies src/bin/gap.sh to set GAP_DIR and GAP_PRG
+
+== Dependencies ===
+
+None

build/pkgs/gap3/checksums.ini

@@ -0,0 +1,4 @@
+tarball=gap3-VERSION.tar.gz
+sha1=0d64737250f3e028716881c9d7e82338c80244d0
+md5=569bf72d516c1da183d43f09851fa1bb
+cksum=3760972699

build/pkgs/gap3/dependencies

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

build/pkgs/gap3/package-version.txt

@@ -0,0 +1 @@
+jm5-2015-02-01

build/pkgs/gap3/patches/gap3_init.patch

@@ -0,0 +1,33 @@
+Commenting out the optional packages
+RequirePackage("arep");
+RequirePackage("meataxe");
+RequirePackage("nq");
+RequirePackage("sisyphos");
+RequirePackage("ve");
+
+diff -ur src/gap3/lib/init.g.orig src/gap3/lib/init.g
+--- src/gap3/lib/init.g.orig	2016-03-30 17:58:09.557517250 +0200
++++ src/gap3/lib/init.g	2016-03-30 17:58:23.265517363 +0200
+@@ -1142,17 +1142,17 @@
+ Print(" gap3-jm5 final 21Mar2016 -- see webusers.imj-prg.fr/~jmichel/gap3\n");
+ Print(" Minimal distribution -- loading the following packages:\n");
+ fi;
+-RequirePackage("anusq");
++#RequirePackage("anusq");
+ RequirePackage("arep");
+ RequirePackage("autag");
+ RequirePackage("cryst");
+ RequirePackage("dce");
+ RequirePackage("grim");
+ RequirePackage("matrix");
+-RequirePackage("meataxe");
++#RequirePackage("meataxe");
+ RequirePackage("monoid");
+-RequirePackage("nq");
++#RequirePackage("nq");
+ RequirePackage("pcqa");
+-RequirePackage("sisyphos");
+-RequirePackage("ve");
++#RequirePackage("sisyphos");
++#RequirePackage("ve");
+ RequirePackage("chevie"); # requires vkcurve, specht, algebra