Commit a8ff7299 authored by Shaon Ghosh's avatar Shaon Ghosh
Browse files

Merge remote-tracking branch 'upstream/master' into embright_branch

parents f620e057 8195b3aa
Pipeline #49075 failed with stages
in 59 minutes and 9 seconds
......@@ -378,98 +378,86 @@ docker:tags:stretch:
# nightly builds
#
nightly:top-level:jessie:
image: ligo/lalsuite-dev:jessie
stage: nightly
script:
- ./00boot
- ./configure --enable-swig --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
# compilers
nightly:top-level:el7-cr:
image: ligo/lalsuite-dev:el7-cr
nightly:clang:6:
image: skymoo/ligo-lalsuite-clang:6
stage: nightly
script:
- ./00boot
- ./configure --enable-swig --enable-doxygen
- CC=clang-6.0 CXX=clang++-6.0 ./configure --enable-swig --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
nightly:top-level:sl7:
image: ligo/lalsuite-dev:sl7
nightly:clang:7:
image: skymoo/ligo-lalsuite-clang:7
stage: nightly
script:
- ./00boot
- ./configure --enable-swig --enable-doxygen
- CC=clang-7 CXX=clang++-7 ./configure --enable-swig --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
nightly:top-level:trusty:
image: skymoo/ligo-lalsuite-dev:trusty
nightly:clang:8:
image: skymoo/ligo-lalsuite-clang:8
stage: nightly
script:
- ./00boot
- ./configure --disable-swig --enable-doxygen
- CC=clang-8 CXX=clang++-8 ./configure --enable-swig --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
allow_failure: true
nightly:top-level:xenial:
image: skymoo/ligo-lalsuite-dev:xenial
nightly:gcc:7:
image: skymoo/ligo-lalsuite-gcc:7
stage: nightly
script:
- ./00boot
- ./configure --disable-swig --enable-doxygen
- ./configure --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
allow_failure: true
nightly:top-level:bionic:
image: skymoo/ligo-lalsuite-dev:bionic
nightly:gcc:8:
image: skymoo/ligo-lalsuite-gcc:8
stage: nightly
script:
- ./00boot
- ./configure --enable-doxygen
- :./configure --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
allow_failure: true
nightly:top-level:cosmic:
image: skymoo/ligo-lalsuite-dev:cosmic
# debian
nightly:debian:jessie:
image: ligo/lalsuite-dev:jessie
stage: nightly
script:
- ./00boot
- ./configure --enable-doxygen
- ./configure --enable-swig --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
allow_failure: true
# FIXME: It seems that Octave on buster currently has a few bugs which
# cause the Octave bindings to fail, disable building the Octave SWIG
# bindings for the time being.
nightly:top-level:buster:
# FIXME: Disable building of Octave SWIG bindings until SWIG-4.0.0 is
# available
# FIXME: allow failure due to #124
nightly:debian:buster:
image: skymoo/ligo-lalsuite-dev:buster
stage: nightly
dependencies: []
......@@ -482,30 +470,34 @@ nightly:top-level:buster:
- web
allow_failure: true
nightly:top-level:clang:
image: skymoo/ligo-lalsuite-clang:jessie
# el7
nightly:rhel:el7-cr:
image: ligo/lalsuite-dev:el7-cr
stage: nightly
script:
- ./00boot
- CC=clang CXX=clang++ ./configure --enable-swig --enable-doxygen
- ./configure --enable-swig --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
nightly:openmp:stretch:
image: ligo/lalsuite-dev:stretch
nightly:rhel:sl7:
image: ligo/lalsuite-dev:sl7
stage: nightly
dependencies: []
script:
- ./00boot
- ./configure --enable-swig --enable-doxygen --enable-openmp
- ./configure --enable-swig --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
# macOS
nightly:macos:highsierra:
tags:
- macos_highsierra
......@@ -522,9 +514,9 @@ nightly:macos:highsierra:
- schedules
- web
nightly:macos:elcapitan:
nightly:macos:sierra:
tags:
- macos_elcapitan
- macos_sierra
stage: nightly
script:
- ./00boot
......@@ -538,6 +530,62 @@ nightly:macos:elcapitan:
- schedules
- web
# ubuntu
# FIXME: allow failure due to #123
nightly:ubuntu:trusty:
image: skymoo/ligo-lalsuite-dev:trusty
stage: nightly
script:
- ./00boot
- ./configure --disable-swig --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
allow_failure: true
# FIXME: allow failure due to #123
nightly:ubuntu:xenial:
image: skymoo/ligo-lalsuite-dev:xenial
stage: nightly
script:
- ./00boot
- ./configure --disable-swig --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
allow_failure: true
nightly:ubuntu:bionic:
image: skymoo/ligo-lalsuite-dev:bionic
stage: nightly
script:
- ./00boot
- ./configure --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
# FIXME: allow failure due to #124
nightly:ubuntu:cosmic:
image: skymoo/ligo-lalsuite-dev:cosmic
stage: nightly
script:
- ./00boot
- ./configure --enable-doxygen
- make -j4 distcheck
dependencies: []
only:
- schedules
- web
allow_failure: true
#
# python wheels
#
......@@ -574,7 +622,7 @@ nightly:macos:elcapitan:
# Build receipe for standalone wheels on macOS
.nightly:wheel:macos: &nightly-wheel-macos
tags:
- macos_elcapitan
- macos_sierra
stage: wheels
script:
- PYVERS=$(echo ${CI_JOB_NAME} | sed 's/.*:cp\(.\)\(.\).*/\1.\2/')
......
# Contributing to LALSuite
This page outlines the recommended procedure for contributing changes to the LALSuite repository. Please read the introduction to [GitLab on git.ligo.org](https://wiki.ligo.org/DASWG/GitLigoOrg) before you start.
This page outlines the recommended procedure for contributing changes to the LALSuite repository. Please read the introduction to [GitLab on git.ligo.org](https://wiki.ligo.org/Computing/GitLigoOrg) before you start.
## Reporting Issues
......@@ -25,7 +25,7 @@ If you can't see the *Fork* button, make sure that you are logged in by checking
### Clone your fork
Make sure that you have installed and configured [git-lfs](https://wiki.ligo.org/DASWG/GitLFS#Install_the_git_LFS_client) for the management of large files. This is required to successfully build and install your development fork.
Make sure that you have installed and configured [git-lfs](https://wiki.ligo.org/Computing/GitLFS#Install_the_git_LFS_client) for the management of large files. This is required to successfully build and install your development fork.
Then, clone your fork with
......
......@@ -2,32 +2,78 @@
This is the main LALSuite development repository.
We now utilize [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:
## Acknowledgment
```
$ git lfs install
```
We request that any academic report, publication, or other academic
disclosure of results derived from the use of this software acknowledge
the use of the software by an appropriate acknowledgment or citation.
This only needs to be done once for each machine you access the repository. It can then be cloned using:
The whole LALSuite software suite can be cited with the DOI
[10.7935/GT1W-FZ16][doi]. An example BibTeX entry could look like this:
```
$ git clone git@git.ligo.org:lscsoft/lalsuite.git
```
@misc{lalsuite,
author = "{LIGO Scientific Collaboration}",
title = "{LIGO} {A}lgorithm {L}ibrary - {LALS}uite",
howpublished = "free software (GPL)",
doi = "10.7935/GT1W-FZ16",
year = "2018"
}
In addition, some codes contained in this package may be directly based
on one or several scientific papers, which should be cited when using
those specific codes; some of these can be discovered through the
documentation.
## Cloning the Repository
We now utilize [Git LFS][gitlfs] 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
## Contributing to LALSuite
The guide to [Contributing](https://git.ligo.org/lscsoft/lalsuite/blob/master/CONTRIBUTING.md) to LALSuite explains how to report issues and contribute fixes or new features using the fork and pull workflow. Please read and follow these directions.
The [guide to contributing to LALSuite][contributing] explains how to
report issues and contribute fixes or new features using the fork and
pull workflow. Please read and follow these directions.
## Nightly Documentation
The Doxygen Documentation is built under GitLab-CI every night and can be viewed at:
https://docs.ligo.org/lscsoft/lalsuite/
The [LALSuite Doxygen documentation][nightlydocs] is built under
GitLab-CI every night.
## Notes on Ancient History
LALSuite was transferred to git.ligo.org in December 2017. Older history has been imported, though commit hashes were rewritten during the GitLFS conversion. Please note:
LALSuite was transferred to `git.ligo.org` in December 2017. Older
history has been imported, though commit hashes were rewritten during
the [Git LFS][gitlfs] conversion. Please note:
1. The `Original:` commit IDs quoted in each commit message can be used
to compare with the [archived reference repo][oldlalsuite], old issue
discussions on the [Redmine tracker][oldredmine], review wiki pages
etc.
1. Commits before December 2017 may also include references to issues
(`#number`). These refer to the corresponding [Redmine
issue][oldredmine] (LVC-authorized access only), and any clickable
link the internal GitLab web interface produces for those old commits
will therefore be spurious.
## For More Information
1. The "Original: " commit IDs quoted in each commit message can be used to compare with the [archived reference repo](https://git.ligo.org/lscsoft/lalsuite-archive), old issue discussions on the [Redmine tracker](https://bugs.ligo.org/redmine/projects/lalsuite), review wiki pages etc.
Please visit the [LALSuite project page][project].
1. Commits before December 2017 may also include references to issues ("#number"). These refer to the corresponding [Redmine issue](https://bugs.ligo.org/redmine/projects/lalsuite) (LVC-authorized access only), and any clickable link the internal gitlab web interface produces for those old commits will be spurious.
[doi]: https://doi.org/10.7935/GT1W-FZ16
[gitlfs]: https://wiki.ligo.org/Computing/GitLFS#Install_the_git_LFS_client
[contributing]: https://git.ligo.org/lscsoft/lalsuite/blob/master/CONTRIBUTING.md
[nightlydocs]: https://lscsoft.docs.ligo.org/lalsuite
[oldlalsuite]: https://git.ligo.org/lscsoft/lalsuite-archive
[oldredmine]: https://bugs.ligo.org/redmine/projects/lalsuite
[project]: https://wiki.ligo.org/Computing/DASWG/LALSuite
AC_PREREQ([2.63])
AC_INIT([LALSuite],[6.49.1],[lal-discuss@ligo.org])
AC_INIT([LALSuite],[6.52.1],[lal-discuss@ligo.org])
AC_CONFIG_SRCDIR([configure.ac])
AC_CONFIG_AUX_DIR([gnuscripts])
AC_CONFIG_MACRO_DIR([gnuscripts])
......
include $(top_srcdir)/gnuscripts/lalsuite_top.am
EXTRA_DIST += README
if HAVE_GIT_REPO
# Override automake's default rule for rebuilding aclocal.m4, to ensure that
# ./configure is successfully recreated after certain build system changes which
......
......@@ -329,7 +329,12 @@ AC_DEFUN([LALSUITE_USE_SWIG_OCTAVE],[
# is installed in the same directory as Octave, .oct files will be found by
# Octave without having to add to OCTAVE_PATH
AC_MSG_CHECKING([${OCTAVE} .oct installation directory])
octave_prefix=[`${octave_cfg} -p PREFIX 2>/dev/null | ${SED} -e 's|/*$||'`]
# at least in Debian Buster, "HOME" has been dropped in favour of "OCTAVE_HOME"
octave_prefix=[`${octave_cfg} -p OCTAVE_HOME 2>/dev/null | ${SED} -e 's|/*$||'`]
# fallback if OCTAVE_HOME is yet unknown
AS_IF([test "x${octave_prefix}" = x],[
octave_prefix=[`${octave_cfg} -p PREFIX 2>/dev/null | ${SED} -e 's|/*$||'`]
])
octexecdir=[`${octave_cfg} -p LOCALVEROCTFILEDIR 2>/dev/null | ${SED} -e 's|/*$||'`]
octexecdir=[`echo ${octexecdir} | ${SED} -e "s|^${octave_prefix}/||"`]
AS_IF([test "x`echo ${octexecdir} | ${SED} -n -e '\|^/|p'`" != x],[
......
BUILT_SOURCES += $(PACKAGE)-user-env.csh $(PACKAGE)-user-env.sh $(PACKAGE)-user-env.fish
sysconf_DATA += $(PACKAGE)-user-env.csh $(PACKAGE)-user-env.sh $(PACKAGE)-user-env.fish
MOSTLYCLEANFILES += $(PACKAGE)-user-env.csh $(PACKAGE)-user-env.sh $(PACKAGE)-user-env.fish $(PACKAGE)-user-env.shell
EXTRA_DIST += gnuscripts/generate_user_env.awk
EXTRA_DIST += README.md gnuscripts/generate_user_env.awk
$(PACKAGE)-user-env.shell: Makefile $(srcdir)/gnuscripts/generate_user_env.awk
$(AM_V_GEN)if echo "$(user_environment)" | $(AWK) -f $(srcdir)/gnuscripts/generate_user_env.awk >$@; then \
......
LAL
================================
# LAL
Core gravitational wave analysis routines.
Acknowledgment
--------------------------------
## Acknowledgment
We request that any academic report, publication, or other academic
disclosure of results derived from the use of this software acknowledge
the use of the software by an appropriate acknowledgment or citation.
Basic Build Instructions
--------------------------------
The whole LALSuite software suite can be cited with the DOI
[10.7935/GT1W-FZ16][doi]. An example BibTeX entry could look like this:
@misc{lalsuite,
author = "{LIGO Scientific Collaboration}",
title = "{LIGO} {A}lgorithm {L}ibrary - {LALS}uite",
howpublished = "free software (GPL)",
doi = "10.7935/GT1W-FZ16",
year = "2018"
}
In addition, some codes contained in this package may be directly based
on one or several scientific papers, which should be cited when using
those specific codes; some of these can be discovered through the
documentation.
## Basic Build Instructions
./configure --prefix=...
make
......@@ -20,17 +33,18 @@ Basic Build Instructions
Please read the [LALSuite install how-to][install] for more detailed
build instructions.
Bug Reporting
--------------------------------
## Bug Reporting
Please visit the [LALSuite bug reporting system][bugs] (LIGO.org
authentication required).
authentication required to submit new issues), or use the [e-mail
helpdesk][helpdesk].
For More Information
--------------------------------
## For More Information
Please visit the [LALSuite project page][project].
[install]: https://wiki.ligo.org/DASWG/LALSuiteInstall
[bugs]: https://git.ligo.org/lscsoft/lalsuite/issues/
[project]: https://wiki.ligo.org/DASWG/LALSuite
[doi]: https://doi.org/10.7935/GT1W-FZ16
[helpdesk]: mailto:contact+lscsoft/lalsuite@support.ligo.org
[install]: https://wiki.ligo.org/Computing/DASWG/LALSuiteInstall
[bugs]: https://git.ligo.org/lscsoft/lalsuite/issues/
[project]: https://wiki.ligo.org/Computing/DASWG/LALSuite
AC_PREREQ([2.63])
AC_INIT([LAL],[6.19.0.1],[lal-discuss@ligo.org])
AC_INIT([LAL],[6.19.1.1],[lal-discuss@ligo.org])
AC_CONFIG_HEADERS([src/config.h src/LALConfig.h])
AC_CONFIG_SRCDIR([src/std/LALStdio.h])
AC_CONFIG_AUX_DIR([gnuscripts])
......@@ -89,7 +89,7 @@ LALSUITE_DISTCHECK_CONFIGURE_FLAGS
# 6. if any interfaces have been removed since the last public release,
# then set age to 0.
AC_SUBST([LIBCURRENT],[15])
AC_SUBST([LIBREVISION],[0])
AC_SUBST([LIBREVISION],[1])
AC_SUBST([LIBAGE],[1])
AC_SUBST([LIBVERSION],[${LIBCURRENT}:${LIBREVISION}:${LIBAGE}])
......
lal (6.19.1-1) unstable; urgency=low
* Intel FFT complilation fixes
-- Adam Mercer <adam.mercer@ligo.org> Mon, 07 Jan 2019 14:02:28 +0000
lal (6.19.0-1) unstable; urgency=low
* Pre O3 release
......
......@@ -46,7 +46,7 @@ html-local: Makefile $(CONFIG_CLEAN_FILES)
export doxygen_exclude; doxygen_exclude=`cat $(abs_srcdir)/exclude.list | tr '\n' ' '`; \
echo '/* Generated by $(subdir)/Makefile */' > autogen.dox; \
echo '/** \mainpage' >> autogen.dox; \
cat in/README >> autogen.dox; \
cat in/README.md >> autogen.dox; \
echo '*/' >> autogen.dox; \
echo '/** \page $(PACKAGE)_authors Author List' >> autogen.dox; \
$(SED) -e 's/^/- /' in/AUTHORS >> autogen.dox; \
......
......@@ -15,7 +15,7 @@ Summary: LSC Algorithm Library
License: GPLv2+
Group: LAL
Source: %{name}-%{version}%{?nightly:-%{nightly}}.tar.xz
URL: https://wiki.ligo.org/DASWG/LALSuite
URL: https://wiki.ligo.org/Computing/DASWG/LALSuite
Packager: Adam Mercer <adam.mercer@ligo.org>
BuildRequires: python2-rpm-macros
BuildRequires: bc
......@@ -136,6 +136,9 @@ rm -Rf ${RPM_BUILD_DIR}/%{name}-%{version}%{?nightly:-%{nightly}}
# dates should be formatted using: 'date +"%a %b %d %Y"'
%changelog
* Mon Jan 07 2019 Adam Mercer <adam.mercer@ligo.org> 6.19.1-1
- Intel FFT complilation fixes
* Thu Sep 13 2018 Adam Mercer <adam.mercer@ligo.org> 6.19.0-1
- Pre O3 release
......
......@@ -17,6 +17,7 @@ pymoduledir = $(pkgpythondir)
pymodule_PYTHON = \
__init__.py \
antenna.py \
git_version.py \
gpstime.py \
rate.py \
......
This diff is collapsed.
......@@ -1101,11 +1101,15 @@ class NDBins(tuple):
# instances cannot define a .__call__() attribute to make
# themselves callable, Python always looks up .__call__()
# on the class. so we define .__realcall__() here and then
# have .__call__() chain to it.
# have .__call__() chain to it. Python3 does not transfer
# the current variable scope into exec() so we have to do
# it for it ... whatever.
define__realcall__ = """def __realcall__(self, %s):
_getitems = self._getitems
return %s""" % (", ".join("x%d" % i for i in range(len(binnings))), ", ".join("_getitems[%d](x%d)" % (i, i) for i in range(len(binnings))))
exec(define__realcall__)
l = {}
exec(define__realcall__, globals(), l)
__realcall__ = l["__realcall__"]
self.__realcall__ = __realcall__.__get__(self)
def __getitem__(self, coords):
......@@ -1339,7 +1343,7 @@ class NDBins(tuple):
def bins_spanned(bins, seglist):
"""
Input is a Bins subclass instance and a glue.segments.segmentlist
Input is a Bins subclass instance and a ligo.segments.segmentlist
instance. The output is an array object the length of the binning,
which each element in the array set to the interval in the
corresponding bin spanned by the segment list.
......@@ -1774,7 +1778,7 @@ def InterpBinnedArray(binnedarray, fill_value = 0.0):
slices.append(slice(lo, hi + 1))
coords = tuple(c[s] for c, s in zip(coords, slices))
z = z[slices]
z = z[tuple(slices)]
# build the interpolator from the co-ordinates and array data.
# scipy/numpy interpolators return an array-like thing so we have
......@@ -2439,7 +2443,7 @@ def filter_array(a, window, cyclic = False, use_fft = True):
window_slices.append(slice(first, first + n))
else:
window_slices.append(slice(0, window.shape[d]))
window = window[window_slices]
window = window[tuple(window_slices)]
if use_fft:
# this loop works around dynamic range limits in the FFT
......
......@@ -142,7 +142,7 @@ class CacheEntry(object):
See also:
glue.segmentsUtils.fromlalcache()
ligo.segments.utils..fromlalcache()
"""
# How to parse a line in a LAL cache file. Five white-space
# delimited columns.
......@@ -307,7 +307,7 @@ class CacheEntry(object):
The \"observatory\" column of the cache entry, which is frequently
used to store instrument names, is parsed into instrument names for
the dictionary keys using the same rules as
glue.ligolw.lsctables.instrumentsproperty.get().
ligo.lw.lsctables.instrumentsproperty.get().
Example:
......@@ -317,7 +317,12 @@ class CacheEntry(object):
"""
# the import has to be done here to break the cyclic
# dependancy
from glue.ligolw.lsctables import instrumentsproperty
try:
from ligo.lw.lsctables import instrumentsproperty
except ImportError:
# FIXME: remove when we can rely on ligo.lw being installed
# (why isn't it!?)
from glue.ligolw.lsctables import instrumentsproperty
instruments = instrumentsproperty.get(self.observatory) or (None,)
return segments.segmentlistdict((instrument, segments.segmentlist(self.segment is not None and [self.segment] or [])) for instrument in instruments)
......
......@@ -33,7 +33,7 @@
if ( (fstat) != DFTI_NO_ERROR ) \