Merge branch 't/21318/sequences/rec-basic-arith' into t/21319/sequenc…

…es/rec-hash

* t/21318/sequences/rec-basic-arith: (1894 commits)
  fix building of docs (no idea why it failed)
  fix doctests (experimental warning)
  factor out subsequence to separat ticket
  extend to negative shifts in subsequence
  doctesting all parameters in coefficient_of_word
  Updated SageMath version to 7.4.beta1
  Dots removed.
  Minor changes.
  More cleanup
  Add sphinx plots and cleanup
  Fix doctests and minor cleanup
  Corrections, changes etc.
  Trac #21181: Yet a few more formatting fixes in docstrings of sage/combinat/words/finite_word.py
  Trac #21181 (previously #21178): Change to imperative form in docstrings of sage/combinat/words/finite_word.py, part II
  Trac #21181 (previously #21178): Change to imperative form in docstrings of sage/combinat/words/finite_word.py
  Trac #21178: A few more markup/formatting fixes in docstrings of sage/combinat/words/finite_word.py
  Trac #21178: Fix typos and a lot of markup/formatting in docstrings of sage/combinat/words/finite_word.py
  py3: no longer use file(name, kind)
  21137: minor doc change
  sqome more typos
  ...

Makefile

@@ -130,22 +130,12 @@ configure: configure.ac src/bin/sage-version.sh m4/*.m4
 	./bootstrap -d
 
 install:
-	echo "Experimental use only!"
-	if [ "$(DESTDIR)" = "" ]; then \
-		echo >&2 "Set the environment variable DESTDIR to the install path."; \
-		exit 1; \
-	fi
-	# Make sure we remove only an existing directory. If $(DESTDIR)/sage is
-	# a file instead of a directory then the mkdir statement later will fail
-	if [ -d "$(DESTDIR)"/sage ]; then \
-		rm -rf "$(DESTDIR)"/sage; \
-	fi
-	mkdir -p "$(DESTDIR)"/sage
-	mkdir -p "$(DESTDIR)"/bin
-	cp -Rp * "$(DESTDIR)"/sage
-	rm -f "$(DESTDIR)"/bin/sage
-	ln -s ../sage/sage "$(DESTDIR)"/bin/sage
-	"$(DESTDIR)"/bin/sage -c # Run sage-location
+	@echo "******************************************************************"
+	@echo "The '$@' target is no longer supported:"
+	@echo "either build SageMath in-place or use the binary packaging scripts"
+	@echo "from https://github.com/sagemath/binary-pkg"
+	@echo "******************************************************************"
+	@exit 1
 
 
 .PHONY: default build install micro_release \

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 7.2, Release Date: 2016-05-15
+SageMath version 7.4.beta1, Release Date: 2016-08-17

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

@@ -1,11 +1,14 @@
 #!/usr/bin/env bash
 #
-# sage-logger COMMAND LOGFILE
+# sage-logger [-p] COMMAND LOGFILE
 #
 # Evaluate shell command COMMAND while logging stdout and stderr to
 # LOGFILE. If either the command or the logging failed, return a
 # non-zero exit status.
 #
+# If the -p argument is given, each line printed to stdout is prefixed
+# with the name of the log file.
+#
 # AUTHOR:
 #
 # - Jeroen Demeyer (2015-07-26): initial version based on old pipestatus
@@ -20,16 +23,42 @@
 #                  http://www.gnu.org/licenses/
 #*****************************************************************************
 
+use_prefix=false
+
+if [[ "$1" = -p ]]; then
+    use_prefix=true
+    shift
+fi
+
 cmd="$1"
 logfile="$2"
+logname="$(basename $logfile .log)"
 logdir=`dirname "$logfile"`
 
+if [[ $use_prefix = true ]]; then
+    prefix="[${logname}] "
+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" )
+( 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

@@ -1,47 +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.)
+# 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
 
-import sys
-import tarfile
-import zipfile
 
-if __name__ == '__main__':
-    filename = sys.argv[1]
-    if tarfile.is_tarfile(filename):
-        # tar file, possibly compressed:
-        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:
-        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)
+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

@@ -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)/sagelib-$(SAGE_VERSION).log'; \
+		sage-logger -p 'time $(MAKE) sage' '$(SAGE_LOGS)/sagelib-$(SAGE_VERSION).log'; \
 	fi
 
 
@@ -192,28 +192,28 @@ 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
 
 doc-html: $(DOC_DEPENDENCIES)
-	cd ../.. && sage-logger './sage --docbuild --no-pdf-links all html $(SAGE_DOCBUILD_OPTS)' logs/dochtml.log
+	cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html $(SAGE_DOCBUILD_OPTS)' logs/dochtml.log
 
 # 'doc-html-no-plot': build docs without building the graphics coming
 # from the '.. plot' directive, in case you want to save a few
 # megabytes of disk space. 'doc-clean' is a prerequisite because the
 # presence of graphics is cached in src/doc/output.
 doc-html-no-plot: doc-clean $(DOC_DEPENDENCIES)
-	cd ../.. && sage-logger './sage --docbuild --no-pdf-links --no-plot all html $(SAGE_DOCBUILD_OPTS)' logs/dochtml.log
+	cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links --no-plot all html $(SAGE_DOCBUILD_OPTS)' logs/dochtml.log
 
 doc-html-mathjax: $(DOC_DEPENDENCIES)
-	cd ../.. && sage-logger './sage --docbuild --no-pdf-links all html -j $(SAGE_DOCBUILD_OPTS)' logs/dochtml.log
+	cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html -j $(SAGE_DOCBUILD_OPTS)' logs/dochtml.log
 
 # Keep target 'doc-html-jsmath' for backwards compatibility.
 doc-html-jsmath: doc-html-mathjax
 
 doc-pdf: $(DOC_DEPENDENCIES)
-	cd ../.. && sage-logger './sage --docbuild all pdf $(SAGE_DOCBUILD_OPTS)' logs/docpdf.log
+	cd ../.. && sage-logger -p './sage --docbuild all pdf $(SAGE_DOCBUILD_OPTS)' logs/docpdf.log
 
 doc-clean: doc-src-clean doc-output-clean
 

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/alabaster/checksums.ini

@@ -1,4 +1,4 @@
 tarball=alabaster-VERSION.tar.gz
-sha1=ff3e575ee7eb4ba1721f17d91ec5a54b16283603
-md5=957c665d7126dea8121f98038debcba7
-cksum=738605178
+sha1=c80dedaf4a1906410e53b653de059fe9d8b17c68
+md5=346a71e8a6d51dff2e02086fdd9c5ffe
+cksum=2849350596

build/pkgs/alabaster/package-version.txt

@@ -1 +1 @@
-0.7.7
+0.7.8

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