Merge branch 't/21203/sequences/k-regular' into t/21318/sequences/rec…

…-basic-arith

* t/21203/sequences/k-regular: (1892 commits)
  fix building of docs (no idea why it failed)
  fix doctests (experimental warning)
  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
  trac 21241 details
  Fix formatting
  ...

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