Ligo.skymap

===================

- In ``bayestar-mcmc``, correct a mistake in setting fixed parameters that
undergo sampling transformations.

- By default, ``bayestar-realize-coincs`` will rewrite ``simulation_id`` values
so that their integer values match the corresponding events'
``coinc_event_id`` values. The option ``--preserve-ids`` switches back to the
old behavior of preserving the original ``simulation_id`` values.

- Track rename of ``ligo.gracedb.rest.GraceDb.service_url`` to
``ligo.gracedb.rest.GraceDb._service_url`` in ligo-gracedb >= 2.0.1.

- Update common files and submodules from the Astropy package template.

- Work around a change (possibly a regression?) in Numpy 1.15.3 that broke
Astropy by requiring numpy <= 1.15.2. See
<https://github.com/astropy/astropy/issues/7943>.

- Work around a bug introduced in ligo-segments 1.1.0 by requiring an earlier
version of that package: its dependency on ligo-common, which does not
correctly implement the namespace package ``ligo``, broke the continuous
integration build.

- Depend on astropy-healpix >= 0.3 to pick up a bug fix related to HEALPix
bilinear interpolation that affected ``ligo-skymap-plot``. See
<https://github.com/astropy/astropy-healpix/pull/106>.

===================

- Drop support for Python 3.5.

- The ``--condor-submit`` option of the ``bayestar-localize-coincs`` and
``bayestar-mcmc`` tools now passes the submit file directives to
``condor_submit`` via stdin rather than on the command line, so that the
number of jobs is not limited by the operating system's maximum number of
command line arguments.

- Print warnings from ``ligo.skymap.io.events.ligolw.open()`` only once per
file to avoid excessive terminal output when reading large files.

- ``bayestar-realize-coincs`` now copies the process table from the injection
file and fills in the SimInspiral table and associates coincidences with
found injections. As a result, it is no longer necessary to run
``lalapps_inspinjfind`` on the output to find injections.

- ``bayestar-realize-coincs`` now prints a running count of the number of
injections that have been found and saved.

===================

- Parallelize ``bayestar-realize-coincs``.

- Add ``--min-distance`` and ``--max-distance`` options to
``bayestar-realize-coincs``.

- Add unit tests and binary wheels for Python 3.7.

===================

- Increase lifetime of continuous integration artifacts. The unit tests take
longer now because they are more complete.

===================

- Add ``bayestar-mcmc`` tool for pure Markov Chain Monte Carlo parameter
estimation, without sky map postprocessing but with options for holding
parameters at fixed values.

- Fix a corner case in the initialization of the ``distance.marginal_ppf``
solver that could cause NaN return values.

- Silence ``numpy.genfromtxt`` Unicode deprecation warning in
``ligo-skymap-plot-stats`` and update the minimum version of Numpy to 1.14.
See the related `Numpy changelog entry
<https://docs.scipy.org/doc/numpy/release.html#encoding-argument-for-text-io-functions>`_.

- Silence deprecation warning in ``ligo-skymap-plot-stats`` due to Matplotlib
renaming the ``hist`` method's keyword argument from ``normed`` to
``density``.

- The ``bayestar-realize-coincs`` tool now copies over spins from the input
``sim_inspiral`` table to the output ``sngl_inspiral`` table.

- Switch the FFT implementation from LAL (which calls `FFTW
<http://www.fftw.org>`_) to `scipy.fftpack
<https://docs.scipy.org/doc/scipy/reference/tutorial/fftpack.html>`_, which
is faster for small transform sizes (e.g. <= 1024).

- Add ``--seed`` option to ``bayestar-localize-coincs``,
``bayestar-localize-lvalert``, ``bayestar-mcmc``, and
``bayestar-realize-coincs``.

- Some reasonable sub-sample trigger interpolation schemes can return peak
times that are almost a full sample away from the maximum sample if the SNR
time series has a pronounced skew in one direction in the vicinity of the
maximum. Such an example occurs for the ``catmull-rom`` interpolation method
for the new unit tests in ``ligo.skymap.bayestar.tests.test_interpolation``.
Because of this, relax the tolerance of BAYESTAR's sanity check on
single-detector trigger times and SNR series timestamps to a full sample.

- Rewrite ``ligo-skymap-plot-stats`` to reduce code duplication.

- Add ``--measurement-error gaussian-noise`` option to
``bayestar-realize-coincs`` to simulate a matched filter in Gaussian noise.

- Remove deprecated module ``ligo.skymap.postprocess.detector_frame``.

===================

- ``bayestar_localize_lvalert`` will now write the correct GraceDb URL
to FITS file headers in the case that it is run with a non-default GraceDb
server.

- BAYESTAR's SNR series time stamp assertions now include a bit more detail.

- Add phase convention for gstlal-spiir, which needs to be confirmed upstream.

- Fix datatype of simulated SNR time series produced by
``bayestar-realize-coincs``.