migrate lalinference_burst_dev branch

.gitignore

-*.dSYM
 *.egg-info
 *.swp
 *.trs
@@ -11,7 +10,6 @@
 /_inst/
 /index.html
 /lalsuite-*/
-/lalsuiterc
 TAGS
 aclocal.m4
 auto/
@@ -20,10 +18,5 @@ config.cache
 config.log
 config.status
 configure
-cscope.*
-lalsuite-*.tar.xz
-lalsuite-user-env.csh
-lalsuite-user-env.fish
-lalsuite-user-env.sh
-lalsuite-user-env.shell
+lalsuite-*.tar.gz
 tags

.mailmap-update

-#!/usr/bin/perl
-
-use strict;
-
-my %name2mails;
-my %cmail2cname;
-
-open IN, ".mailmap" or die $!;
-while (<IN>) {
-  chomp;
-
-  my ($pname, $pmail, $cname, $cmail) = /^([^<]*?)\s*<([^>]*)>(?:\s*([^<]*?)\s*<([^>]*)>)?$/ or die;
-
-  $cmail = $pmail if $cmail eq "";
-
-  $name2mails{$pname}->{$pmail} = -1;
-  $name2mails{$pname}->{$cmail} = 0 if !defined($name2mails{$pname}->{$cmail});
-  $cmail2cname{$cmail} = $cname;
-
-}
-close IN;
-
-open IN, "git shortlog -s -e -n |" or die $!;
-while (<IN>) {
-  chomp;
-
-  my ($n, $cname, $cmail) = m/^\s*(\d+)\s+([^<>]+)\s+<([^>]+)>\s*$/ or die;
-
-  $name2mails{$cname}->{$cmail} = $n if !defined($name2mails{$cname}->{$cmail});
-
-}
-close IN;
-
-foreach my $pname (sort { $a cmp $b } keys(%name2mails)) {
-
-  my $pname2mail = lc($pname);
-  $pname2mail =~ s/\s+/./g;
-
-  my @pmails;
-  push @pmails, grep { /^${pname2mail}[@]ligo[.]org$/ } keys(%{$name2mails{$pname}});
-  push @pmails, grep { /^[a-z.-]+[@]ligo[.]org$/ } keys(%{$name2mails{$pname}});
-  push @pmails, grep { /[@]ligo[.]org$/ } keys(%{$name2mails{$pname}});
-  push @pmails, grep { $name2mails{$pname}->{$_} < 0 } keys(%{$name2mails{$pname}});
-  push @pmails, sort { $name2mails{$pname}->{$b} <=> $name2mails{$pname}->{$a} } keys(%{$name2mails{$pname}});
-  shift @pmails if $pmails[0] =~ /^albert[.]einstein@/i;
-
-  my $pmail = shift @pmails;
-  die "Could not determine email address for $pname" unless defined($pmail);
-
-  next unless keys(%{$name2mails{$pname}}) > 1 || $name2mails{$pname}->{$pmail} <= 0;
-
-  print "$pname <$pmail>\n";
-  foreach my $mail (sort { $a cmp $b } keys(%{$name2mails{$pname}})) {
-    next if $mail eq $pmail;
-    if ($cmail2cname{$mail} ne "") {
-      print "$pname <$pmail> $cmail2cname{$mail} <$mail>\n";
-    } else {
-      print "$pname <$pmail> <$mail>\n";
-    }
-  }
-
-}

Dockerfile

-FROM ligo/lalsuite-runtime:jessie
-COPY /opt/lalsuite /opt/lalsuite
-ENV LD_LIBRARY_PATH="/opt/lalsuite/lib" \
-    OCTAVE_PATH="/opt/lalsuite/lib/x86_64-linux-gnu/octave/3.8.2/site/oct/x86_64-pc-linux-gnu" \
-    PATH="/opt/lalsuite/bin:${PATH}" \
-    PKG_CONFIG_PATH="/opt/lalsuite/lib/pkgconfig" \
-    PYTHONPATH="/opt/lalsuite/lib/python2.7/site-packages" \

Makefile.am

-BUILT_SOURCES =
-sysconf_DATA =
-MOSTLYCLEANFILES =
-EXTRA_DIST =
-include $(top_srcdir)/gnuscripts/lalsuite_top.am
-
 ACLOCAL_AMFLAGS = -I gnuscripts
 
 SUBDIRS = @subdirs@
@@ -20,41 +14,21 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps)
 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
 	$(SHELL) $(top_srcdir)/configure $(ac_configure_args)
 
-.PHONY: cscopelist-subdirs
-cscopelist-am: cscopelist-subdirs
-cscopelist-subdirs:
-	for subdir in $(SUBDIRS); do \
-		sed "s|^|$${subdir}/|" $${subdir}/cscope.files >> $(top_builddir)/cscope.files; \
-	done
-
-user_environment = \
-	`for dir in $(SUBDIRS); do printf 'source %s; ' "$(sysconfdir)/$${dir}-user-env"; done` \
-	$(END_OF_LIST)
-
-BUILT_SOURCES += $(PACKAGE)rc
-sysconf_DATA += $(PACKAGE)rc
-MOSTLYCLEANFILES += $(PACKAGE)rc
-$(PACKAGE)rc: Makefile
-	$(AM_V_GEN)echo "# source this file to access $(PACKAGE_NAME) from Bourne or C shells" >$@; \
-	echo "expr \"X\$$0\" : '^X.*csh' >/dev/null && source $(sysconfdir)/$(PACKAGE)-user-env.csh || . $(sysconfdir)/$(PACKAGE)-user-env.sh" >>$@
-
 if DOXYGEN
 
 html-local: Makefile $(CONFIG_CLEAN_FILES)
-	$(AM_V_at)set -e; \
-	echo "$(subdir)/Makefile: Doxygen documentation was built successfully!"; \
-	echo "$(subdir)/Makefile: $(PACKAGE_NAME) main page is at file://$(abs_builddir)/index.html"
+	$(AM_V_at)echo "=== Doxygen documentation was built successfully!"; \
+	echo "=== $(PACKAGE_NAME) main page is at file://$(abs_builddir)/index.html"
 
 install-html-local: html-local
-	$(AM_V_at)set -e; \
-	echo " $(MKDIR_P) '$(DESTDIR)$(htmldir)'"; \
-	$(MKDIR_P) "$(DESTDIR)$(htmldir)"; \
+	$(AM_V_at)echo " $(MKDIR_P) '$(DESTDIR)$(htmldir)'"; \
+	$(MKDIR_P) "$(DESTDIR)$(htmldir)" || exit 1; \
 	echo " $(INSTALL_DATA) index.html '$(DESTDIR)$(htmldir)/index.html'"; \
-	$(SED) -e 's|\(lal[a-z]*\)/doxygen/out|../\1|g' index.html > $@.tmp; \
-	$(INSTALL_DATA) $@.tmp "$(DESTDIR)$(htmldir)/index.html"; \
+	$(SED) -e 's|\(lal[a-z]*\)/doxygen/out|../\1|g' index.html > $@.tmp || exit 1; \
+	$(INSTALL_DATA) $@.tmp "$(DESTDIR)$(htmldir)/index.html" || exit 1; \
 	rm -f $@.tmp; \
-	echo "$(subdir)/Makefile: Doxygen documentation was installed successfully!"; \
-	echo "$(subdir)/Makefile: installed $(PACKAGE_NAME) main page is at file://$(DESTDIR)$(htmldir)/index.html"
+	echo "=== Doxygen documentation was installed successfully!"; \
+	echo "=== Installed $(PACKAGE_NAME) main page is at file://$(DESTDIR)$(htmldir)/index.html"
 
 uninstall-local:
 	-rm -rf "$(DESTDIR)$(htmldir)/"

README.md

-# LALSuite
-
-This is the main LALSuite development repository, past development is
-captured in the repository below:
-
-https://git.ligo.org/lscsoft/lalsuite-archive
-
-This new repository utilizes [git-lfs](https://wiki.ligo.org/DASWG/GitLFS#Install_the_git_LFS_client) for the managament of large files and as such `git-lfs` needs to be installed and configured to correctly clone this repository. After installing `git-lfs` it can be configured using:
-
-```
-$ git lfs install
-```
-
-This only needs to be done once for each machine you access the repository. It can then be cloned using:
-
-```
-$ git clone git@git.ligo.org:lscsoft/lalsuite.git
-```

configure.ac

 AC_PREREQ([2.63])
-AC_INIT([LALSuite],[6.48.1],[lal-discuss@ligo.org])
+AC_INIT([LALSuite],[6.28.1],[lal-discuss@ligo.org])
 AC_CONFIG_SRCDIR([configure.ac])
 AC_CONFIG_AUX_DIR([gnuscripts])
 AC_CONFIG_MACRO_DIR([gnuscripts])
 AC_PREFIX_DEFAULT(["`pwd`/_inst"])
 AC_CONFIG_FILES([Makefile])
-AM_INIT_AUTOMAKE([ \
-  1.11 \
-  foreign \
-  subdir-objects \
-  color-tests \
-  parallel-tests \
-  tar-ustar \
-  dist-xz \
-  no-dist-gzip \
-])
+AM_INIT_AUTOMAKE([1.11 foreign subdir-objects color-tests parallel-tests])
 
 LALSUITE_DISTCHECK_CONFIGURE_FLAGS
 
 # use silent build rules
 AM_SILENT_RULES([yes])
 
-# check for programs
-AC_PROG_AWK
-AC_PROG_SED
-
 # provide LAL library enable/disable options
 LALSUITE_ENABLE_ALL_LAL
 lal=true
@@ -44,6 +31,7 @@ LALSUITE_ENABLE_LALAPPS
 LALSUITE_ENABLE_DOXYGEN
 LALSUITE_ENABLE_MODULE([DOXYGEN])
 AS_IF([test "x${doxygen}" = xtrue],[
+  AC_PROG_SED
   AC_CONFIG_FILES([index.html:gnuscripts/lalsuite_index.html.in])
   AC_SUBST([DOXYGEN_PACKAGE_LINKS],[])
   AM_SUBST_NOTMAKE([DOXYGEN_PACKAGE_LINKS])
@@ -61,7 +49,8 @@ AC_DEFUN([lalsuite_config_doxygen],[
 
 # directories of top-level build and source
 lalsuite_abs_top_builddir="`pwd`"
-lalsuite_abs_top_srcdir='$(abs_top_srcdir)/..'
+#lalsuite_top_builddir='$(top_builddir)/..'
+lalsuite_top_srcdir='$(top_srcdir)/..'
 
 # configure a lalsuite package
 AC_DEFUN([lalsuite_config_subdir],[
@@ -74,7 +63,7 @@ AC_DEFUN([lalsuite_config_subdir],[
     # export precious environment variables
     uppercase[]_LIBS="${lalsuite_abs_top_builddir}/lowercase/src/lib[]lowercase.la"
     uppercase[]_CFLAGS="-I${lalsuite_abs_top_builddir}/lowercase/include"
-    uppercase[]_DATA_PATH="${lalsuite_abs_top_srcdir}/lowercase/test"
+    uppercase[]_DATA_PATH="${lalsuite_top_srcdir}/lowercase/test"
     uppercase[]_OCTAVE_PATH="${lalsuite_abs_top_builddir}/lowercase/octave"
     uppercase[]_PYTHON_PATH="${lalsuite_abs_top_builddir}/lowercase/python"
     uppercase[]_HTMLDIR="${htmldir}/../lowercase"
@@ -101,13 +90,13 @@ AC_DEFUN([lalsuite_config_subdir],[
 # lal and lalsupport are always configured
 lalsuite_config_doxygen([LAL])
 AC_CONFIG_SUBDIRS(lal)
-LAL_LIBS="${lalsuite_abs_top_builddir}/lal/src/liblal.la"
+LAL_LIBS="${lalsuite_abs_top_builddir}/lal/lib/lal/liblal.la"
 LAL_CFLAGS="-I${lalsuite_abs_top_builddir}/lal/include"
-LAL_DATA_PATH="${lalsuite_abs_top_srcdir}/lal/test"
+LAL_DATA_PATH="${lalsuite_top_srcdir}/lal/test"
 LAL_OCTAVE_PATH="${lalsuite_abs_top_builddir}/lal/octave"
 LAL_PYTHON_PATH="${lalsuite_abs_top_builddir}/lal/python"
 LAL_HTMLDIR="${htmldir}/../lal"
-LALSUPPORT_LIBS="${lalsuite_abs_top_builddir}/lal/src/support/liblalsupport.la"
+LALSUPPORT_LIBS="${lalsuite_abs_top_builddir}/lal/lib/lalsupport/src/liblalsupport.la"
 LALSUPPORT_CFLAGS="-I${lalsuite_abs_top_builddir}/lal/include"
 LALSUPPORT_DATA_PATH="${LAL_DATA_PATH}"
 LALSUPPORT_OCTAVE_PATH="${LAL_OCTAVE_PATH}"

gnuscripts/ax_check_compile_flag.m4

+# ===========================================================================
+#   http://www.gnu.org/software/autoconf-archive/ax_check_compile_flag.html
+# ===========================================================================