Merge branch 'develop' into t/16086/ignore_write_output

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.0.beta2, Release Date: 2017-04-12
+SageMath version 8.0.beta3, Release Date: 2017-04-23

build/bin/sage-logger

@@ -60,14 +60,17 @@ else
     SED=cat
 fi
 
-# Store the current value of V, but do all logging of child processes
-# with V=1 to ensure that no information is lost.
-currentV=$V
-export V=1
-
 mkdir -p "$logdir"
 
-if [[ "$currentV" = 0 && $use_prefix = true ]]; then
+# Do all logging of child processes with V=1 to ensure that no
+# information is lost.
+export MAKEFLAGS="$MAKEFLAGS V=1"
+
+if [ "$V" = 0 ]; then
+    export SAGE_SILENT_BUILD=yes
+fi
+
+if [ -n "$SAGE_SILENT_BUILD" -a ${use_prefix} = true ]; then
     # Silent build.
     # Similar to https://www.gnu.org/software/automake/manual/html_node/Automake-Silent-Rules.html#Automake-Silent-Rules
     echo "[$logname] installing. Log file: $logfile"

build/pkgs/brial/spkg-install

@@ -7,7 +7,7 @@ if [ "$SAGE_LOCAL" = "" ]; then
 fi
 
 echo "Cleaning out old PolyBoRi and BRiAl installations"
-rm -rf "$SAGE_LOCAL"/lib/python/site-packages/{polybori,brial}
+rm -rf "$SAGE_LOCAL"/lib/python*/site-packages/{polybori,brial}
 rm -f "$SAGE_LOCAL"/lib/lib{polybori,brial}*
 rm -rf "$SAGE_LOCAL"/include/polybori*
 rm -rf "$SAGE_LOCAL"/share/polybori

build/pkgs/cmake/SPKG.txt

@@ -25,5 +25,8 @@ CMake is distributed under the OSI-approved BSD 3-clause License.
 
 == Dependencies ==
 
+* curl
 * zlib
 * bzip2
+* xz
+

build/pkgs/cmake/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cmake-VERSION.tar.gz
-sha1=fa176cc5b1ccf2e98196b50908432d0268323501
-md5=d51c92bf66b1e9d4fe2b7aaedd51377c
-cksum=3408528151
+sha1=660ec06a46b46dc5d675371a2256ec739f8bb8b7
+md5=f28cba717ba38ad82a488daed8f45b5b
+cksum=233346693

build/pkgs/cmake/dependencies

@@ -0,0 +1,5 @@
+curl zlib bzip2 xz
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/cmake/package-version.txt

@@ -1 +1 @@
-3.2.3
+3.8.0

build/pkgs/cmake/spkg-check

@@ -1,4 +1,6 @@
 #!/usr/bin/env bash
 
 cd src
-ctest -E CTestTestStopTime
+unset MACOSX_DEPLOYMENT_TARGET
+ctest --extra-verbose --output-on-failure -E "(CTestTestStopTime|TestUpload|ctest_submit)"
+

build/pkgs/cmake/spkg-install

@@ -2,17 +2,11 @@
 
 cd src
 
-system_curl=""
-
-if [ "$UNAME" = "Darwin" ]; then
-    system_curl="--system-curl"
-    unset MACOSX_DEPLOYMENT_TARGET
-fi
-
 ./bootstrap --prefix=$SAGE_LOCAL \
     --system-bzip2 \
     --system-zlib \
-    $system_curl \
+    --system-liblzma \
+    --system-curl \
     -- \
     -DCMAKE_PREFIX_PATH=$SAGE_LOCAL \
     -DCMAKE_TESTS_CDASH_SERVER=NOTFOUND

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=8bdfb4b87a803b90d6b9a937d961835955723a09
-md5=1f1aa69a7ac98e4443e82611a3bbea23
-cksum=4121821509
+sha1=1191f0229692e23f4544b68cf56c3443391c9c88
+md5=a37eab0bd6a75b55be567ea8fff5b09e
+cksum=1527621800

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-216
+217

build/pkgs/conway_polynomials/checksums.ini

@@ -1,4 +1,4 @@
 tarball=conway_polynomials-VERSION.tar.bz2
-sha1=25b7abe5c935d20c3ebcde943308652c412d14dc
-md5=17f061204b3a6133abb21e17b3abea19
-cksum=3204784255
+sha1=d4d89bda60ac54e73121f84635e774766e19a8b6
+md5=a2725ba21f44554196781424d957f68a
+cksum=1387933493

build/pkgs/conway_polynomials/package-version.txt

@@ -1 +1 @@
-0.4.p0
+0.5

build/pkgs/conway_polynomials/spkg-install

@@ -1,21 +1,22 @@
 #!/usr/bin/env python
-
 import os
-from sage.structure.sage_object import save
+from six.moves import cPickle as pickle
 from sage.env import SAGE_SHARE
 
 install_root = os.path.join(SAGE_SHARE, 'conway_polynomials')
 
+
 def create_db():
     db = {}
     from src import conway_polynomials
-    for p,n,v in conway_polynomials:
+    for p, n, v in conway_polynomials:
         if not p in db:
             db[p] = {}
         db[p][n] = v
     if not os.path.exists(install_root):
         os.makedirs(install_root)
-    save(db, os.path.join(install_root, 'conway_polynomials.sobj'))
+    with open(os.path.join(install_root, 'conway_polynomials.p'), 'wb') as f:
+        pickle.dump(db, f)
 
 if __name__ == '__main__':
     create_db()

build/pkgs/curl/spkg-check

@@ -1,4 +1,4 @@
 #!/usr/bin/env bash
 
 cd src
-$MAKE check V=1
+$MAKE check

build/pkgs/curl/spkg-install

@@ -29,13 +29,13 @@ if [ $? -ne 0 ]; then
     exit 1
 fi
 
-$MAKE V=1
+$MAKE
 if [ $? -ne 0 ]; then
     echo >&2 "Error building curl."
     exit 1
 fi
 
-$MAKE install V=1
+$MAKE install
 if [ $? -ne 0 ]; then
     echo >&2 "Error installing curl."
     exit 1

build/pkgs/cysignals/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cysignals-VERSION.tar.bz2
-sha1=4394b36d8b30a7afd81df45c6266048d49567af0
-md5=abc98cb7b07c3a40979ee24dead06a38
-cksum=1213194811
+sha1=34508e9ff71da18b66b1eec3464c1ff6a63608e9
+md5=f00b9a39a3e785ee822ca00de27da362
+cksum=722688943

build/pkgs/cysignals/package-version.txt

@@ -1 +1 @@
-1.3.2
+1.6.3

build/pkgs/cysignals/spkg-check

@@ -6,4 +6,4 @@ if [ -z "$SAGE_LOCAL" ]; then
     exit 1
 fi
 
-cd src && $MAKE check
+cd src && $MAKE check-install

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.25.2.p0
+0.25.2.p1

build/pkgs/cython/patches/include_dirs_from_externs.patch

@@ -0,0 +1,123 @@
+https://github.com/cython/cython/pull/1654
+
+commit 8f71406d1713f97979a602dbf4af92f0da8926ca
+Author: Jeroen Demeyer <jdemeyer@cage.ugent.be>
+Date:   Fri Mar 31 16:08:40 2017 +0200
+
+    Automatically add include_dirs for externs
+
+diff --git a/Cython/Build/Dependencies.py b/Cython/Build/Dependencies.py
+index 9817c30..658d850 100644
+--- a/Cython/Build/Dependencies.py
++++ b/Cython/Build/Dependencies.py
+@@ -375,14 +375,30 @@ def normalize_existing(base_path, rel_paths):
+
+ @cached_function
+ def normalize_existing0(base_dir, rel_paths):
++    """
++    Given some base directory ``base_dir`` and a list of path names
++    ``rel_paths``, normalize each relative path name ``rel`` by
++    replacing it by ``os.path.join(base, rel)`` if that file exists.
++
++    Return a couple ``(normalized, needed_base)`` where ``normalized``
++    if the list of normalized file names and ``needed_base`` is
++    ``base_dir`` if we actually needed ``base_dir``. If no paths were
++    changed (for example, if all paths were already absolute), then
++    ``needed_base`` is ``None``.
++    """
+     normalized = []
++    needed_base = None
+     for rel in rel_paths:
++        if os.path.isabs(rel):
++            normalized.append(rel)
++            continue
+         path = join_path(base_dir, rel)
+         if path_exists(path):
+             normalized.append(os.path.normpath(path))
++            needed_base = base_dir
+         else:
+             normalized.append(rel)
+-    return normalized
++    return (normalized, needed_base)
+
+
+ def resolve_depends(depends, include_dirs):
+@@ -483,20 +499,25 @@ class DependencyTree(object):
+         return all
+
+     @cached_method
+-    def cimports_and_externs(self, filename):
++    def cimports_externs_incdirs(self, filename):
+         # This is really ugly. Nested cimports are resolved with respect to the
+         # includer, but includes are resolved with respect to the includee.
+         cimports, includes, externs = self.parse_dependencies(filename)[:3]
+         cimports = set(cimports)
+         externs = set(externs)
++        incdirs = set()
+         for include in self.included_files(filename):
+-            included_cimports, included_externs = self.cimports_and_externs(include)
++            included_cimports, included_externs, included_incdirs = self.cimports_externs_incdirs(include)
+             cimports.update(included_cimports)
+             externs.update(included_externs)
+-        return tuple(cimports), normalize_existing(filename, externs)
++            incdirs.update(included_incdirs)
++        externs, incdir = normalize_existing(filename, externs)
++        if incdir:
++            incdirs.add(incdir)
++        return tuple(cimports), externs, incdirs
+
+     def cimports(self, filename):
+-        return self.cimports_and_externs(filename)[0]
++        return self.cimports_externs_incdirs(filename)[0]
+
+     def package(self, filename):
+         return package(filename)
+@@ -579,12 +600,22 @@ class DependencyTree(object):
+
+     def distutils_info0(self, filename):
+         info = self.parse_dependencies(filename)[3]
+-        externs = self.cimports_and_externs(filename)[1]
++        kwds = info.values
++        cimports, externs, incdirs = self.cimports_externs_incdirs(filename)
++        # Add dependencies on "cdef extern from ..." files
+         if externs:
+-            if 'depends' in info.values:
+-                info.values['depends'] = list(set(info.values['depends']).union(externs))
++            if 'depends' in kwds:
++                kwds['depends'] = list(set(kwds['depends']).union(externs))
+             else:
+-                info.values['depends'] = list(externs)
++                kwds['depends'] = list(externs)
++        # Add include_dirs to ensure that the C compiler will find the
++        # "cdef extern from ..." files
++        if incdirs:
++            include_dirs = kwds.get('include_dirs', [])
++            for inc in incdirs:
++                if inc not in include_dirs:
++                    include_dirs = include_dirs + [inc]
++            kwds['include_dirs'] = include_dirs
+         return info
+
+     def distutils_info(self, filename, aliases=None, base=None):
+diff --git a/tests/run/cimport_from_sys_path.srctree b/tests/run/cimport_from_sys_path.srctree
+index 1fc031e..e6f619d 100644
+--- a/tests/run/cimport_from_sys_path.srctree
++++ b/tests/run/cimport_from_sys_path.srctree
+@@ -19,8 +19,15 @@ setup(
+
+ ######## site-packages/b/other.pxd ########
+
+-cdef inline foo(int a):
+-     return a**2
++cdef extern from "foo.c":
++    int foo(int)
++
++######## site-packages/b/foo.c ########
++
++static int foo(int a)
++{
++    return a * a;
++}
+
+ ######## a.pyx ########
+

build/pkgs/ecl/package-version.txt

@@ -1 +1 @@
-16.1.2.p2
+16.1.2.p3

build/pkgs/ecl/patches/flisten-bug.patch

@@ -0,0 +1,16 @@
+Prevent busy loop during ECL interpreter shutdown on Cygwin.
+
+See https://trac.sagemath.org/ticket/22337
+diff --git a/src/c/file.d b/src/c/file.d
+index 2285a60..aeed899 100755
+--- a/src/c/file.d
++++ b/src/c/file.d
+@@ -5317,7 +5317,7 @@ static int
+ flisten(cl_object stream, FILE *fp)
+ {
+         int aux;
+-        if (feof(fp))
++        if (feof(fp) || ferror(fp))
+                 return ECL_LISTEN_EOF;
+ #ifdef FILE_CNT
+         if (FILE_CNT(fp) > 0)

build/pkgs/fpylll/package-version.txt

@@ -1 +1 @@
-0.2.4dev
+0.2.4dev.p0