migrate SEOBNRv4p branch

5474aab2 · Adam Mercer · 837952ed · 837952ed · 837952ed · 837952ed
Commit 5474aab2 authored Dec 06, 2017 by Adam Mercer
60 changed files
--- 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 $TAG
--- a/Dockerfile
+++ b/Dockerfile
-FROM ligo/lalsuite-runtime:jessie
-COPY /opt/lalsuite /opt/lalsuite
-ENV LD_LIBRARY_PATH="/opt/lalsuite/lib" \
-    OCTAVE_PATH="/opt/lalsuite/lib/x86_64-linux-gnu/octave/3.8.2/site/oct/x86_64-pc-linux-gnu" \
-    PATH="/opt/lalsuite/bin:${PATH}" \
-    PKG_CONFIG_PATH="/opt/lalsuite/lib/pkgconfig" \
-    PYTHONPATH="/opt/lalsuite/lib/python2.7/site-packages" \
--- a/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:
-```
-$ git clone git@git.ligo.org:lscsoft/lalsuite.git
-```
--- a/lalframe/src/fmt.c
+++ b/lalframe/src/fmt.c
@@ -113,7 +113,7 @@ int main(int argc, char *argv[])
            fp = stdin;
        else
            fp = fopen(fname, "r");
-        if (!fp)
+        if (!output)
            FAILURE("could not open file %s\n", fname);
        readdata(&ndim, &dimlen, &data, &channames, &chanunits, fp);

--- a/lalinference/python/bayestar_samples_ppplot.py
+++ b/lalinference/python/bayestar_samples_ppplot.py
@@ -22,6 +22,7 @@ Create a P-P plot to compare a posterior sample chain with a sky map.
 # Command line interface.
 from argparse import FileType
 from lalinference.bayestar import command
+parser = command.ArgumentParser()
 parser = command.ArgumentParser(parents=[command.figure_parser])
 parser.add_argument(
    'skymap', metavar='SKYMAP.fits[.gz]', type=FileType('rb'),

--- a/lalinference/python/lalinference/bayestar/command.py
+++ b/lalinference/python/lalinference/bayestar/command.py
@@ -54,11 +54,6 @@ import distutils.version
 mpl_version = distutils.version.LooseVersion(matplotlib.__version__)
-def get_version():
-    from .. import InferenceVCSInfo as vcs_info
-    return vcs_info.name + ' ' + vcs_info.version
 @contextlib.contextmanager
 def TemporaryDirectory(suffix='', prefix='tmp', dir=None, delete=True):
    try:
@@ -174,16 +169,7 @@ class MatplotlibFigureType(argparse.FileType):
    def __save(self):
        from matplotlib import pyplot as plt
-        _, ext = os.path.splitext(self.string)
+        return plt.savefig(self.string)
-        ext = ext.lower()
-        program, _ = os.path.splitext(os.path.basename(sys.argv[0]))
-        cmdline = ' '.join([program] + sys.argv[1:])
-        metadata = {'Title': cmdline}
-        if ext == '.png':
-            metadata['Software'] = get_version()
-        elif ext in {'.pdf', '.ps', '.eps'}:
-            metadata['Creator'] = get_version()
-        return plt.savefig(self.string, metadata=metadata)
    def __call__(self, string):
        from matplotlib import pyplot as plt
@@ -298,7 +284,8 @@ del group
 # Defer loading SWIG bindings until version string is needed.
 class VersionAction(argparse._VersionAction):
    def __call__(self, parser, namespace, values, option_string=None):
-        self.version = get_version()
+        from .. import InferenceVCSInfo
+        self.version = 'LALInference ' + InferenceVCSInfo.version
        super(VersionAction, self).__call__(
            parser, namespace, values, option_string)

--- a/lalinference/python/lalinference/rapid_pe/lalsimutils.py
+++ b/lalinference/python/lalinference/rapid_pe/lalsimutils.py
@@ -109,9 +109,6 @@ class ChooseWaveformParams:
        for k, p in ChooseWaveformParams._LAL_DICT_PARAMS.iteritems():
            typfunc = ChooseWaveformParams._LAL_DICT_PTYPE[k]
            typfunc(extra_params, k, getattr(self, p))
-        # Properly add tidal parammeters
-        lalsim.SimInspiralWaveformParamsInsertTidalLambda1(extra_params, self.lambda1)
-        lalsim.SimInspiralWaveformParamsInsertTidalLambda2(extra_params, self.lambda2)
        return extra_params
    def copy(self):

--- a/lalinference/python/rapidpe_compute_intrinsic_grid.py
+++ b/lalinference/python/rapidpe_compute_intrinsic_grid.py
@@ -42,9 +42,9 @@ from glue.ligolw.utils import process
 import lalsimulation
 from lalinference.rapid_pe import amrlib, lalsimutils, common_cl
-def get_cr_from_grid(cells, weight, cr_thr=0.9, min_n=None, max_n=None):
+def get_cr_from_grid(cells, weight, cr_thr=0.9):
    """
-    Given a set of cells and the weight of that cell, calculate a N% CR including cells which contribute to that probability mass. If n is set, cr_thr is ignored and instead this many points are taken.
+    Given a set of cells and the weight of that cell, calculate a N% CR including cells which contribute to that probability mass.
    """
    if cr_thr == 0.0:
        return numpy.empty((0,))
@@ -57,13 +57,8 @@ def get_cr_from_grid(cells, weight, cr_thr=0.9, min_n=None, max_n=None):
    cell_sort[:,0] = cell_sort[:,0].cumsum()
    cell_sort[:,0] /= cell_sort[-1,0]
+    # find the CR probability
    idx = cell_sort[:,0].searchsorted(1-cr_thr)
-    n_select = cell_sort.shape[0] - idx
-    if min_n is not None:
-        n_select = max(n_select, min_n)
-    if max_n is not None:
-        n_select = min(n_select, max_n)
-    idx = cell_sort.shape[0] - n_select
    return cell_sort[idx:,1:]
@@ -90,7 +85,7 @@ def find_olap_index(tree, intr_prms, exact=True, **kwargs):
    pt = numpy.array([kwargs[k] for k in intr_prms])
    # FIXME: Replace with standard function
-    dist, m_idx = tree.query(numpy.atleast_2d(pt), k=1)
+    dist, m_idx = tree.query(pt, k=1)