migrate tgr_o2 branch

e47bb086 · Adam Mercer · 837952ed · e47bb086 · 837952ed · e47bb086
Commit e47bb086 authored Dec 06, 2017 by Adam Mercer
--- a/.gitignore
+++ b/.gitignore
@@ -22,8 +22,4 @@ config.status
 configure
 cscope.*
 lalsuite-*.tar.xz
-lalsuite-user-env.csh
-lalsuite-user-env.fish
-lalsuite-user-env.sh
-lalsuite-user-env.shell
 tags
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
-image: docker:latest
-
-variables:
-  DOCKER_DRIVER: overlay
-#  GIT_DEPTH: 1
-  COMMIT: $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA
-  BRANCH: $CI_REGISTRY_IMAGE:$CI_COMMIT_REF_NAME
-  TAG: $CI_REGISTRY_IMAGE:$CI_COMMIT_TAG
-  LAL_DIR: $CI_PROJECT_DIR/opt/lalsuite
-
-stages:
-  - level0
-  - level1
-  - level2
-  - level3
-  - level4
-  - nightly
-  - container
-  - tag
-
-before_script:
-  - ulimit -S -c 0
-  - export VERBOSE="true"
-  - export PATH=/usr/lib/ccache:$PATH
-  - export CCACHE_DIR=${PWD}/ccache
-  - export PKG_CONFIG_PATH=${LAL_DIR}/lib/pkgconfig
-  - mkdir -p opt/lalsuite
-
-cache:
-  key: $CI_JOB_NAME
-  paths:
-    - ccache
-
-level0:lal:
-  image: ligo/lalsuite-dev:jessie
-  stage: level0
-  script:
-    - cd lal
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf lal-*.tar.xz
-    - cd lal-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  only:
-    - pushes
-
-level1:lalframe:
-  image: ligo/lalsuite-dev:jessie
-  stage: level1
-  script:
-    - cd lalframe
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf lalframe-*.tar.xz
-    - cd lalframe-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  dependencies:
-    - level0:lal
-  only:
-    - pushes
-
-level1:lalmetaio:
-  image: ligo/lalsuite-dev:jessie
-  stage: level1
-  script:
-    - cd lalmetaio
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf lalmetaio-*.tar.xz
-    - cd lalmetaio-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  dependencies:
-    - level0:lal
-  only:
-    - pushes
-
-level1:lalsimulation:
-  image: ligo/lalsuite-dev:jessie
-  stage: level1
-  script:
-    - cd lalsimulation
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf lalsimulation-*.tar.xz
-    - cd lalsimulation-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  dependencies:
-    - level0:lal
-  only:
-    - pushes
-
-level1:lalxml:
-  image: ligo/lalsuite-dev:jessie
-  stage: level1
-  script:
-    - cd lalxml
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf lalxml-*.tar.xz
-    - cd lalxml-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  dependencies:
-    - level0:lal
-  only:
-    - pushes
-
-level2:lalburst:
-  image: ligo/lalsuite-dev:jessie
-  stage: level2
-  script:
-    - cd lalburst
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf lalburst-*.tar.xz
-    - cd lalburst-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  dependencies:
-    - level1:lalmetaio
-    - level1:lalsimulation
-  only:
-    - pushes
-
-level2:lalinspiral:
-  image: ligo/lalsuite-dev:jessie
-  stage: level2
-  script:
-    - cd lalinspiral
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf lalinspiral-*.tar.xz
-    - cd lalinspiral-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  dependencies:
-    - level1:lalframe
-    - level1:lalmetaio
-    - level1:lalsimulation
-  only:
-    - pushes
-
-level2:lalpulsar:
-  image: ligo/lalsuite-dev:jessie
-  stage: level2
-  script:
-    - cd lalpulsar
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf lalpulsar-*.tar.xz
-    - cd lalpulsar-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  dependencies:
-    - level1:lalxml
-  only:
-    - pushes
-
-level2:lalstochastic:
-  image: ligo/lalsuite-dev:jessie
-  stage: level2
-  script:
-    - cd lalstochastic
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf lalstochastic-*.tar.xz
-    - cd lalstochastic-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  dependencies:
-    - level1:lalmetaio
-  only:
-    - pushes
-
-level3:laldetchar:
-  image: ligo/lalsuite-dev:jessie
-  stage: level3
-  script:
-    - cd laldetchar
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf laldetchar-*.tar.xz
-    - cd laldetchar-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  dependencies:
-    - level2:lalburst
-  only:
-    - pushes
-
-level3:lalinference:
-  image: ligo/lalsuite-dev:jessie
-  stage: level3
-  script:
-    - cd lalinference
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf lalinference-*.tar.xz
-    - cd lalinference-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  dependencies:
-    - level2:lalburst
-    - level2:lalinspiral
-    - level2:lalpulsar
-  only:
-    - pushes
-
-level4:lalapps:
-  image: ligo/lalsuite-dev:jessie
-  stage: level4
-  script:
-    - cd lalapps
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make dist
-    - tar xf lalapps-*.tar.xz
-    - cd lalapps-*
-    - ./configure --enable-swig --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 V=1
-    - make -j4 V=1 check
-    - make -j4 install
-    - make -j4 install-html
-  artifacts:
-    expire_in: 3h
-    paths:
-      - opt/lalsuite
-  dependencies:
-    - level2:lalstochastic
-    - level3:laldetchar
-    - level3:lalinference
-  only:
-    - pushes
-
-nightly:top-level:el7:
-  image: ligo/lalsuite-dev:el7
-  stage: nightly
-  script:
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen
-    - make -j4 distcheck
-  only:
-    - schedules
-    - web
-
-nightly:top-level:jessie:
-  image: ligo/lalsuite-dev:jessie
-  stage: nightly
-  script:
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen
-    - make -j4 distcheck
-  only:
-    - schedules
-    - web
-
-nightly:top-level:stretch:
-  image: ligo/lalsuite-dev:stretch
-  stage: nightly
-  script:
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen
-    - make -j4 distcheck
-  only:
-    - schedules
-    - web
-
-nightly:top-level:trusty:
-  image: skymoo/ligo-lalsuite-dev:trusty
-  stage: nightly
-  script:
-    - ./00boot
-    - ./configure --disable-swig --enable-doxygen
-    - make -j4 distcheck
-  only:
-    - schedules
-    - web
-
-nightly:top-level:xenial:
-  image: skymoo/ligo-lalsuite-dev:xenial
-  stage: nightly
-  script:
-    - ./00boot
-    - ./configure --disable-swig --enable-doxygen
-    - make -j4 distcheck
-  only:
-    - schedules
-    - web
-
-nightly:top-level:buster:
-  image: skymoo/ligo-lalsuite-dev:buster
-  stage: nightly
-  script:
-    - ./00boot
-    - ./configure --enable-swig-python --enable-doxygen
-    - make -j4 distcheck
-  only:
-    - schedules
-    - web
-  allow_failure: true
-
-nightly:mpi:jessie:
-  image: ligo/lalsuite-dev:jessie
-  stage: nightly
-  script:
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --enable-mpi
-    - make -j4 distcheck
-  only:
-    - schedules
-    - web
-
-nightly:openmp:jessie:
-  image: ligo/lalsuite-dev:jessie
-  stage: nightly
-  script:
-    - ./00boot
-    - ./configure --enable-swig --enable-doxygen --enable-openmp
-    - make -j4 distcheck
-  only:
-    - schedules
-    - web
-
-nightly:python3:stretch:
-  image: ligo/lalsuite-dev:stretch
-  stage: nightly
-  script:
-    - ./00boot
-    - PYTHON=python3 ./configure --enable-swig --enable-doxygen
-    - make -j4 distcheck
-  only:
-    - schedules
-    - web
-
-pages:
-  image: ligo/lalsuite-dev:stretch
-  stage: nightly
-  script:
-    - ./00boot
-    - ./configure --enable-doxygen --prefix=${LAL_DIR}
-    - make -j4 install-html
-    - cp -r ${LAL_DIR}/share/doc public/
-  artifacts:
-    paths:
-      - public
-  only:
-    - master@adam-mercer/lalsuite-git-lfs
-    - schedules
-    - web
-  except:
-    - pushes
-
-dockerize:
-  stage: container
-  before_script: []
-  script:
-    - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY
-    - docker build --pull -t $COMMIT -t $BRANCH .
-    - docker push $COMMIT
-  dependencies:
-    - level4:lalapps
-  only:
-    - pushes
-
-tagged:
-  stage: tag
-  only:
-    - tags
-  before_script: []
-  script:
-    - docker tag $COMMIT $TAG
-    - docker push $TAG
--- a/.mailmap
+++ b/.mailmap
--- a/.mailmap-update
+++ b/.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 $!;
+my %authors;
+my %emails;
 while (<IN>) {
-  chomp;
-
-  my ($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";
+    chomp;
+    $_ =~ m/^\s*\d+\s+([^<>]+)\s+<([^>]+)>\s*$/ or die;
+    my $author = $1;
+    my $email = $2;
+    next if $author =~ /^UNKNOWN/;
+    if (defined($authors{$author})) {
+        print "$authors{$author} <$email>\n";
+    } elsif (defined($emails{$email})) {
+        print "$emails{$email} <$email>\n";
    } else {
-      print "$pname <$pmail> <$mail>\n";
+        $authors{$author} = $emails{$email} = "$author <$email>";
    }
-  }
-
 }
--- a/Dockerfile
+++ b/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" \
--- a/Makefile.am
+++ b/Makefile.am
-BUILT_SOURCES =
-sysconf_DATA =
-MOSTLYCLEANFILES =
-EXTRA_DIST =
-include $(top_srcdir)/gnuscripts/lalsuite_top.am
-
 ACLOCAL_AMFLAGS = -I gnuscripts

 SUBDIRS = @subdirs@
@@ -27,16 +21,14 @@ cscopelist-subdirs:
 		sed "s|^|$${subdir}/|" $${subdir}/cscope.files >> $(top_builddir)/cscope.files; \
 	done

-user_environment = \
-	`for dir in $(SUBDIRS); do printf 'source %s; ' "$(sysconfdir)/$${dir}-user-env"; done` \
-	$(END_OF_LIST)
-
-BUILT_SOURCES += $(PACKAGE)rc
-sysconf_DATA += $(PACKAGE)rc
-MOSTLYCLEANFILES += $(PACKAGE)rc
+BUILT_SOURCES = $(PACKAGE)rc
+sysconf_DATA = $(PACKAGE)rc
+MOSTLYCLEANFILES = $(PACKAGE)rc
 $(PACKAGE)rc: Makefile
-	$(AM_V_GEN)echo "# source this file to access $(PACKAGE_NAME) from Bourne or C shells" >$@; \
-	echo "expr \"X\$$0\" : '^X.*csh' >/dev/null && source $(sysconfdir)/$(PACKAGE)-user-env.csh || . $(sysconfdir)/$(PACKAGE)-user-env.sh" >>$@
+	$(AM_V_GEN)echo "# source this file to access $(PACKAGE_NAME)" >$@; \
+	for dir in $(SUBDIRS); do \
+		echo "eval \`sh -c \"case \$$0 in *csh) echo source $(sysconfdir)/$${dir}-user-env.csh;; *) echo . $(sysconfdir)/$${dir}-user-env.sh;; esac\"\`" >>$@; \
+	done

 if DOXYGEN

@@ -60,3 +52,26 @@ uninstall-local:
 	-rm -rf "$(DESTDIR)$(htmldir)/"

 endif
+
+.PHONY: print-build-success
+all-local: print-build-success
+print-build-success:
+	@echo "";\
+	echo "==================================================";\
+	echo "$(PACKAGE_NAME) has now been successfully built.";\
+	echo "Now run 'make install' to install $(PACKAGE_NAME).";\
+	echo "==================================================";\
+	echo ""
+.PHONY: print-install-success
+install-exec-local: print-install-success
+print-install-success:
+	@echo "";\
+	echo "==================================================";\
+	echo "$(PACKAGE_NAME) has now been successfully installed.";\
+	echo "To set up your environment, please add the line";\
+	echo "  . $(sysconfdir)/$(PACKAGE)rc";\
+	echo "to ~/.profile for Bourne shells (e.g. bash), or";\
+	echo "  source $(sysconfdir)/$(PACKAGE)rc";\
+	echo "to ~/.login for C shells (e.g. tcsh).";\
+	echo "==================================================";\
+	echo ""
--- a/README.md
+++ b/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:
-
-```