Merge tag '7.3' into t/20278/ticket/20278

SageMath version 7.3

Makefile

@@ -15,7 +15,7 @@ build: all-build
 %::
 	@if [ -x relocate-once.py ]; then ./relocate-once.py; fi
 	$(MAKE) build/make/Makefile
-	+build/bin/sage-logger -p \
+	+build/bin/sage-logger \
 		"cd build/make && ./install '$@'" logs/install.log
 
 # If configure was run before, rerun it with the old arguments.

README.md

@@ -3,7 +3,7 @@
 >   "Creating a Viable Open Source Alternative to
 >    Magma, Maple, Mathematica, and MATLAB"
 
->   Copyright (C) 2005-2014 The Sage Development Team
+>   Copyright (C) 2005-2016 The Sage Development Team
 
    http://www.sagemath.org
 
@@ -67,7 +67,7 @@ source. More detailed instructions, including how to build faster on
 multicore machines, are contained later in this README and in the  
 Installation Guide:  
 
-   http://www.sagemath.org/doc/installation
+   http://doc.sagemath.org/html/en/installation
 
 __1. Make sure you have the dependencies and 5 GB of free disk space.__
 
@@ -110,14 +110,19 @@ __3. cd into the Sage directory and type make:__
    should work fine on all fully supported platforms. If it does not, we  
    want to know!  
 
+   If you'd like to contribute to Sage, be sure to read the
+   Developer's Guide:
+
+   http://doc.sagemath.org/html/en/developer/index.html
+
 
 Environment Variables
 ---------------------
 
 There are a lot of environment variables which control the install  
 process of Sage, see:  
 
-   http://sagemath.org/doc/installation/source.html#environment-variables
+   http://doc.sagemath.org/html/en/installation/source.html#environment-variables
 
 
 Implementation
@@ -325,7 +330,7 @@ SAGE_ROOT                 Root directory (sage-x.y.z in Sage tarball)
 ```
 For more details, see:
 
-    http://sagemath.org/doc/developer/coding_basics.html#files-and-directory-structure
+    http://doc.sagemath.org/html/en/developer/coding_basics.html#files-and-directory-structure
 
 
 Relocation
@@ -343,7 +348,7 @@ Sage as root at least once prior to using the system-wide Sage as a
 normal user. See the Installation Guide for further information on  
 performing a system-wide installation:
 
-   http://www.sagemath.org/doc/installation/source.html#installation-in-a-multiuser-environment
+   http://doc.sagemath.org/html/en/installation/source.html#installation-in-a-multiuser-environment
 
 If you find anything that doesn't work correctly after you moved the  
 directory, please email the sage-support mailing list.  

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.3.beta2, Release Date: 2016-05-28
+SageMath version 7.3, Release Date: 2016-08-04

build/bin/sage-download-file

@@ -24,5 +24,5 @@ except ImportError:
     sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
     import sage_bootstrap
 
-from sage_bootstrap.cmdline import SageDownloadFileApplication
-SageDownloadFileApplication().run()
+from sage_bootstrap.download.cmdline import run_safe
+run_safe()

build/bin/sage-logger

@@ -41,13 +41,24 @@ else
     prefix=""
 fi
 
+# Use sed option to reduce buffering, to make the output appear more
+# smoothly. For GNU sed, this is the --unbuffered option.
+# For BSD sed (which is also on OS X), this is the -l option.
+if sed </dev/null 2>/dev/null --unbuffered ""; then
+    SED="sed --unbuffered"
+elif sed </dev/null 2>/dev/null -l ""; then
+    SED="sed -l"
+else
+    SED="sed"
+fi
+
 mkdir -p "$logdir"
 
 # Redirect stdout and stderr to a subprocess running tee.
 # We trap SIGINT such that SIGINT interrupts the main process being
 # run, not the logging.
-( exec 2>&1; eval "$cmd" ) | ( trap '' SIGINT; tee -a "$logfile" ) | \
-    (while read line; do echo "${prefix}${line}"; done)
+( exec 2>&1; eval "$cmd" ) | \
+    ( trap '' SIGINT; tee -a "$logfile" | $SED "s/^/$prefix/" )
 
 pipestatus=(${PIPESTATUS[*]})
 

build/bin/sage-package

@@ -38,5 +38,5 @@ except ImportError:
     sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
     import sage_bootstrap
 
-from sage_bootstrap.cmdline import SagePkgApplication
-SagePkgApplication().run()
+from sage_bootstrap.cmdline import run
+run()

build/bin/sage-spkg

@@ -272,7 +272,8 @@ elif [ -z "$PKG_HAS_PATH" ]; then
             echo "that it will build correctly, or behave as expected."
             echo "Use at your own risk!"
             echo "==============================================================="
-            read -p "Are you sure you want to continue [Y/n]? " answer
+            echo "Are you sure you want to continue [Y/n]?"
+            read -p "Answer: " answer
             case "$answer" in
                 n*|N*) exit 0;;
             esac
@@ -365,7 +366,8 @@ if [ ! -f "$PKG_SRC" ]; then
                             echo "For more information about making Sage packages, see"
                             echo "http://doc.sagemath.org/html/en/developer/packaging.html"
                             echo "=========================================================================="
-                            read -p "Are you sure you want to continue [Y/n]? " answer
+                            echo "Are you sure you want to continue [Y/n]?"
+                            read -p "Answer: " answer
                             case "$answer" in
                                 n*|N*) exit 0;;
                             esac
@@ -381,7 +383,8 @@ if [ ! -f "$PKG_SRC" ]; then
                             echo "http://doc.sagemath.org/html/en/developer/packaging.html"
                             echo "=========================================================================="
                             echo
-                            read -t 30 -p "Are you sure (automatically continuing in 30 seconds) [Y/n]? " answer
+                            echo "Are you sure (automatically continuing in 30 seconds) [Y/n]?"
+                            read -t 30 -p "Answer: " answer
                             case "$answer" in
                                 n*|N*) exit 0;;
                             esac
@@ -520,44 +523,36 @@ fi
 ##################################################################
 
 if [ "$USE_LOCAL_SCRIPTS" = yes ]; then
+    # New-style package
     echo "Setting up build directory for $PKG_NAME"
     cp -Rp "$PKG_SCRIPTS" "$PKG_NAME"
     cd "$PKG_NAME" || exit $?
+
+    sage-uncompress-spkg -d src "$PKG_SRC"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error: failed to extract $PKG_SRC"
+        exit 1
+    fi
 else
+    # Old-style package (deprecated)
     echo "Extracting package $PKG_SRC"
     ls -l "$PKG_SRC"
-fi
 
-sage-uncompress-spkg "$PKG_SRC"
-if [ $? -ne 0 ]; then
-    echo >&2 "Error: failed to extract $PKG_SRC"
-    exit 1
-fi
-
-if [ "$USE_LOCAL_SCRIPTS" = yes ]; then
-    shopt -s nocaseglob      # see trac:16415
-    # Strip file extension from the archive file and hope (as per
-    # automake standards) that this is the same as the directory name
-    # inside; move the directory to "src".  (This goes wrong for
-    # upstream package archives that have been renamed to appease some
-    # other Sage script, such as "latte-int", whose archive is renamed
-    # to "latte_int".)
-    mv "$(echo "$PKG_NAME_UPSTREAM" | sed 's/\.zip$//g;s/\.tgz$//g;s/\.tar\.gz$//g;s/\.tar\.xz$//g;s/\.tar\.lz$//g;s/\.tar\.bz2$//g;s/\.tar$//g')"* src
-    # Do not check for errors here; the "mv" fails in the situation
-    # mentioned above, and the package-specific script needs to do
-    # this work itself.
-    shopt -u nocaseglob
-    echo "Finished set up"
-else
-    echo "Finished extraction"
+    sage-uncompress-spkg "$PKG_SRC"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error: failed to extract $PKG_SRC"
+        exit 1
+    fi
 
     cd "$PKG_NAME"
     if [ $? -ne 0 ]; then
-        echo >&2 "Error: after extracting, the directory $PKG_NAME does not exist"
+        echo >&2 "Error: after extracting, the directory '$PKG_NAME' does not exist"
         exit 1
     fi
 fi
 
+echo "Finished extraction"
+
 ##################################################################
 # The package has been extracted, prepare for installation
 ##################################################################

build/bin/sage-uncompress-spkg

@@ -1,74 +1,23 @@
 #!/usr/bin/env python
 
-# USAGE:
-#
-#   sage-uncompress-spkg PKG [FILE]
-#
-# With a single argument, unpack the file PKG to the current directory.
-#
-# If FILE is specified, extract FILE from PKG and send it to
-# stdout. (This option is present only for backwards compatibility:
-# printing the SPKG.txt file from an old-style spkg.)
-
-import copy
-import os
-import sys
-import tarfile
-import zipfile
-
-
-class UmaskExtractTarFile(tarfile.TarFile):
-    """
-    Sage as tarfile.TarFile, but applies the user's current umask to the
-    permissions of al extracted files and directories.
-
-    This mimics the default behavior of the ``tar`` utility.
-
-    See http://trac.sagemath.org/ticket/20218#comment:16 for more background.
-    """
-
-    def __init__(self, *args, **kwargs):
-        super(UmaskExtractTarFile, self).__init__(*args, **kwargs)
-
-        # Unfortunately the only way to get the current umask is to set it
-        # and then restore it
-        self.umask = os.umask(0777)
-        os.umask(self.umask)
-
-    def chmod(self, tarinfo, target):
-        tarinfo = copy.copy(tarinfo)
-        tarinfo.mode &= ~self.umask
-        return super(UmaskExtractTarFile, self).chmod(tarinfo, target)
-
-
-if __name__ == '__main__':
-    filename = sys.argv[1]
-    if tarfile.is_tarfile(filename):
-        # tar file, possibly compressed:
-        archive = UmaskExtractTarFile.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:
-        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:
-                exit(1)
-        archive.close()
-        exit(0)
-    else:
-        print ('Error: Unknown file type: {}'.format(filename))
-        exit(1)
+# usage: sage-uncompress-spkg [-h] [-d DIR] PKG [FILE]
+# 
+# positional arguments:
+#   PKG         the archive to extract
+#   FILE        (deprecated) print the contents of the given archive member to
+#               stdout
+# 
+# optional arguments:
+#   -h, --help  show this help message and exit
+#   -d DIR      directory to extract archive contents into
+
+
+try:
+    import sage_bootstrap
+except ImportError:
+    import os, sys
+    sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
+    import sage_bootstrap
+
+from sage_bootstrap.uncompress.cmdline import run
+run()

build/make/deps

@@ -192,7 +192,7 @@ DOC_DEPENDENCIES = sagelib $(inst_sphinx) $(inst_sagenb) \
 	| $(SAGERUNTIME) $(inst_maxima) $(inst_networkx) $(inst_scipy) \
 	$(inst_matplotlib) $(inst_pillow) $(inst_mathjax) $(inst_mpmath) \
 	$(inst_ipykernel) $(inst_jupyter_client) $(inst_conway_polynomials) \
-	$(inst_tachyon)
+	$(inst_tachyon) $(inst_jmol)
 
 doc: doc-html
 

build/pkgs/4ti2/dependencies

@@ -0,0 +1,5 @@
+zlib $(MP_LIBRARY) glpk
+
+----------
+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/atlas/patches/Makefile.patch

@@ -1,5 +1,5 @@
---- src/CONFIG/src/Makefile	2012-06-23 17:27:27.000000000 +0100
-+++ new/CONFIG/src/Makefile	2012-06-24 03:05:52.043151077 +0100
+--- src/ATLAS/CONFIG/src/Makefile	2012-06-23 17:27:27.000000000 +0100
++++ new/ATLAS/CONFIG/src/Makefile	2012-06-24 03:05:52.043151077 +0100
 @@ -580,6 +580,6 @@
  confclean: $(CLEANdep)
  	rm -f *core* *.o config?.out

build/pkgs/atlas/patches/arm_hard_floats.patch

@@ -1,6 +1,6 @@
-diff -druN ATLAS.detect/CONFIG/src/atlcomp.txt ATLAS/CONFIG/src/atlcomp.txt
---- ATLAS.detect/CONFIG/src/atlcomp.txt	2013-01-08 10:15:42.000000000 -0800
-+++ ATLAS/CONFIG/src/atlcomp.txt	2014-02-10 04:36:26.113011794 -0800
+diff -druN ATLAS.detect/ATLAS/CONFIG/src/atlcomp.txt ATLAS/ATLAS/CONFIG/src/atlcomp.txt
+--- ATLAS.detect/ATLAS/CONFIG/src/atlcomp.txt	2013-01-08 10:15:42.000000000 -0800
++++ ATLAS/ATLAS/CONFIG/src/atlcomp.txt	2014-02-10 04:36:26.113011794 -0800
 @@ -255,13 +255,13 @@
  # ARM defaults
  #

build/pkgs/atlas/patches/cygwin_threads.patch

@@ -1,7 +1,7 @@
 Let ATLAS use Cygwin thread functions on Cygwin64.
-diff -druN ATLAS.orig/src/threads/ATL_thread_start.c ATLAS.new/src/threads/ATL_thread_start.c
---- ATLAS.orig/src/threads/ATL_thread_start.c	2014-07-10 09:22:06.000000000 -0700
-+++ ATLAS.new/src/threads/ATL_thread_start.c	2014-11-18 07:17:39.207997205 -0800
+diff -druN ATLAS.orig/ATLAS/src/threads/ATL_thread_start.c ATLAS.new/ATLAS/src/threads/ATL_thread_start.c
+--- ATLAS.orig/ATLAS/src/threads/ATL_thread_start.c	2014-07-10 09:22:06.000000000 -0700
++++ ATLAS.new/ATLAS/src/threads/ATL_thread_start.c	2014-11-18 07:17:39.207997205 -0800
 @@ -14,14 +14,14 @@
   */
  {

build/pkgs/atlas/patches/detect.patch

@@ -1,6 +1,6 @@
-diff -druN ATLAS.orig/CONFIG/include/atlconf.h ATLAS/CONFIG/include/atlconf.h
---- ATLAS.orig/CONFIG/include/atlconf.h	2013-01-08 10:15:42.000000000 -0800
-+++ ATLAS/CONFIG/include/atlconf.h	2014-02-10 04:31:19.992981182 -0800
+diff -druN ATLAS.orig/ATLAS/CONFIG/include/atlconf.h ATLAS/ATLAS/CONFIG/include/atlconf.h
+--- ATLAS.orig/ATLAS/CONFIG/include/atlconf.h	2013-01-08 10:15:42.000000000 -0800
++++ ATLAS/ATLAS/CONFIG/include/atlconf.h	2014-02-10 04:31:19.992981182 -0800
 @@ -18,7 +18,7 @@
  enum ARCHFAM {AFOther=0, AFPPC, AFSPARC, AFALPHA, AFX86, AFIA64, AFMIPS,
                AFARM, AFS390};

build/pkgs/atlas/patches/do_not_force_mutex.patch

@@ -1,10 +1,10 @@
 Always use assembly over mutex since the mutex version fails to build
 a shared library. See #15045 for details.
 
-diff --git a/tune/threads/tune_count.c b/tune/threads/tune_count.c
+diff --git a/ATLAS/tune/threads/tune_count.c b/ATLAS/tune/threads/tune_count.c
 index f09717f..4dc3fde 100644
---- a/tune/threads/tune_count.c
-+++ b/tune/threads/tune_count.c
+--- a/ATLAS/tune/threads/tune_count.c
++++ b/ATLAS/tune/threads/tune_count.c
 @@ -241,8 +241,8 @@ int main(int nargs, char **args)
   */
        if (tmut < tldec*1.02)

build/pkgs/atlas/patches/glibc_scanf_workaround.patch

@@ -1,8 +1,8 @@
 Bug in glibc-2.18: https://sourceware.org/bugzilla/show_bug.cgi?id=15917
 
 
---- a/tune/sysinfo/masrch.c
-+++ b/tune/sysinfo/masrch.c
+--- a/ATLAS/tune/sysinfo/masrch.c
++++ b/ATLAS/tune/sysinfo/masrch.c
 @@ -1,6 +1,7 @@
  #include <stdio.h>
  #include <stdlib.h>