Astrobase

New stuff

- `periodbase.kbls`: now returns BLS stats along with the period finder results.

- `varbase.trends`: added External Parameter Decorrelation with arbitrary
external parameters, optimizer function, and objective function.

- `periodbase`: added a wrapper for the Transit Least Squares period-finder
(Hippke & Heller 2019; added by lgbouma)

- `periodbase.zgls`: added calculation of the analytic false-alarm probability.

- `services.gaia`, `services.mast`: added single-object search-by-name
functions.

- `lcfit.utils`: added an `iterative_fit` function.


Changes

- `lcproc.tfa`: now removes template objects from consideration if they're too
close to the target object.

- `periodbase`: broke out all of the functions in `periodbase/__init__.py` to
`periodbase/utils.py` and `periodbase/falsealarm.py` as appropriate.


Fixes

- `periodbase`: fixed epsilon checking against values of previous best periods
when iterating through periodogram peaks (by joshuawallace).

- `periodbase.zgls`: now correctly uses `tau` in the calculation of the
periodogram value.

- `varclass.starfeatures`: fixed missing `and` in an if-statement (by
joshuawallace).

- `lcproc.tfa`: various bug-fixes.

This is a new major release. Several modules have been moved around. Most public
facing modules and functions now have full docstrings that auto-generate Sphinx
documentation (https://astrobase.readthedocs.io).

Work for the v0.4 series of releases will be tracked at:

https://github.com/waqasbhatti/astrobase/projects/1

New stuff

- New top-level `lcproc`, `checkplot`, and `lcfit` subpackages.
- `services.mast`: now has a `tic_xmatch` function.
- `lcfit.transits`: added new `mandelagol_and_line_fit_magseries` function (by
lgbouma).
- `timeutils`: added new `get_epochs_given_midtimes_and_period` function (by
lgbouma).
- New `periodbase.abls` module to use Astropy 3.1's BoxLeastSquares as the BLS
runner instead of the wrapped eebls.f used by
`periodbase.kbls`. `periodbase.kbls` remains the default implementation when
you do `from astrobase import periodbase`. You can call
`periodbase.use_astropy_bls()` immediately after importing `periodbase` to
switch the default BLS implementation to `periodbase.abls`.

Changes

- `varbase.lcfit` has been moved to a new top-level subpackage called `lcfit`,
and is broken up into `lcfit.sinusoidal`, `lcfit.eclipses`,
`lcfit.nonphysical` and `lcfit.transits` submodules. The `varbase/lcfit.py`
module will be removed in Astrobase 0.4.5.
- `lcproc.py` has been moved to a new top-level subpackage called `lcproc`, and
is broken up by specific functionality.
- `checkplot.py` has been moved to a new top-level subpackage called
`checkplot`, and is broken up into `checkplot.pkl` for making checkplot
pickles, and `checkplot.png` for making checkplot PNGs.
- `periodbase.kbls.bls_stats_singleperiod` and `periodbase.kbls.bls_snr` now do
a trapezoidal transit model fit to the prospective transit found by an initial
run of BLS and calculate the transit depth, duration, ingress duration, refit
period, and refit epoch that way.
- `plotbase`: the function `plot_phased_mag_series` is now called
`plot_phased_magseries`.
- `plotbase`: the function `plot_mag_series` is now called
`plot_magseries`.
- `lcproc_aws.py` has been moved to `lcproc.awsrun`.
- `lcproc` now uses JSON files stored in either `[astrobase install
path]/data/lcformats` or `~/.astrobase/lcformat-jsons` to register custom LC
formats. This is more flexible than the older approach of adding these to a
top-level dict in `lcproc.py`.
- `lcfit.sinusoidal`: the `fourier_fit_magseries` function now returns
times.min() as the `epoch` value in its `fitinfo` dict (by
joshuawallace). The actual time of minimum light is returned as
`actual_fitepoch` in the `fitinfo` dict.
- `periodbase/oldpf.py` has been moved to `periodbase/_oldpf.py`. It will be
removed in Astrobase 0.4.2.
- The `services.tic` module has been deprecated and will be removed in Astrobase
0.4.2.
- The `astrotess.get_time_flux_errs_from_Ames_lightcurve` function has been
deprecated and will be removed in Astrobase 0.4.2. Use the
`astrotess.read_tess_fitslc` and `astrotess.filter_tess_lcdict` functions
instead.
- We no longer run the Astrobase test suite on Python 2.7. Most things should
continue to function, but there are no guarantees. Python 2.7 support will end
in December 2019.

Fixes

- Lots of bug fixes everywhere. See the commit history for details.

New stuff

- `plotbase.plot_phased_magseries` can now overplot a light curve model. Added
by lgbouma.
- new `varbase/transits.py` module for planet transit specific tools. Added by
lgbouma.
- new `awsutils.py` module for interfacing with various AWS services for
`lcproc_aws.py`.
- new `lcproc_aws.py` module for lcproc functions ported to AWS workflows.
- `astrotess` now has `read_tess_fitslc`, `consolidate_tess_fitslc`, and
`filter_tess_fitslc` functions like `astrokep`.
- new `services/mast.py` module for querying the STScI MAST API. Added a
`tic_conesearch` function to help with future checkplot making that will
include TIC IDs and TESS mags.
- `lcproc.register_custom_lcformat` can now provide arbitrary kwargs to the
LC reader and normalization functions.


Changes

- `services`: service clients that talk to single mirrors now use a random sleep
before launching the request to avoid overload when running in many parallel
processes.
- `checkplot, starfeatures`: include all GAIA neighbor proper motions instead of
just the target object proper motions.
- `starfeatures` functions now recognize TESS and Kepler mags for checkplot
making.
- `services/lccs.py`: updated for v0.2 of the LCC-Server's API.
- `lcproc.make_lclist` now accepts an input list of actual filenames to turn
into a lclist catalog pickle.
- `hatsurveys.hatlc.normalize_lcdict_byinst` now also uses the LC's CCD column
to generate the normalization key.


Fixes

- added checks in various places for both lists and tuples where lists only were
expected.
- `lcfit.mandelagol_fit_magseries`: various bugfixes.
- `lcproc.make_lclist` now handles duplicate object IDs with different light
curve files correctly.
- `lcproc, checkplot`: remove spaces in object IDs for output filenames.
- `astrokep.py`: fix LC normalization.

New stuff

- `varbase.lcfit`: now includes a `mandelagol_fit_magseries` function to fit a
Mandel-Agol transit model. Implemented by lgbouma. Requires `emcee`, `h5py`,
`corner` and `BATMAN`.
- Added `astrotess.py` by lgbouma containing basic TESS TOI light curve reader
functions.
- Added `services/tic.py` by lgbouma containing a basic TESS Input Catalog at
MAST API client.
- `lcproc.parallel_cp`: can now slice task lists using start and end indices.


Changes

- `services/skyview`: added configurable retry behavior if the downloaded FITS
file is corrupted.
- `checkplot`: the `fast_mode` kwarg now disables SIMBAD lookup because the
service is unreliable.
- `hatsurveys/hatlc`: added a quiet kwarg for the normalization functions.


Fixes

- `lcproc.add_cpinfo_to_lclist`: fix typo `abs_gaiamag` -> `gaia_absmag`; these
values will now be extracted correctly from checkplots.
- `periodbase.kbls.bls_serial/parallel_pfind`: also returns the `magsarefluxes`
kwarg from the input.
- `periodbase.kbls.bls_stats_singleperiod` and `bls_snr`: fix transit depth sign
if `magsarefluxes = True`.

New stuff

- checkplot: added a `fast_mode` kwarg for `checkplot_pickle` so external
service queries time out faster when the services are not responsive.

Changes

- `lcmath.sigclip_magseries`: `sigclip` can now be either int or float.

Fixes

- lcfit: in the `*_fit_magseries` functions, `fitmagminind` can be a
multiple-item array instead of a single item for flat light curves. This will
break the time-of-minimum finding routine for an LC fit. Now uses the first
item in the array for `magseriesepoch` if this is the case. Added by
joshuawallace.

New stuff

- kbls: added a dedicated `bls_stats_singleperiod` function to get time of
center-transit, refit period, and transit duration
- hatlc: added console script to directly read/dump HAT LCs and metadata from the
command-line
- hatlc: added support for LCC server produced CSV light curves
- services: removed hatds.py, added new lccs.py for common LCC server API
- checkplotserver: added a standalone mode for serving checkplot pickles
- `checkplot.checkplot_pickle_to_png`: add support for LCC server produced JSON


Changes

- k2hat: fixes to column names in lcdict to bring into line with other LC
readers in the `hatsurveys` subpackage
- `hatlc.read_and_filter_sqlitecurve`: make less verbose in case of errors
- `kbls.bls_snr`: get time of center-transit using a better method
- `kbls.bls_snr`: return refit periods and epochs
- cpserver.js: added parsing of `observatory` and `telescope` keys in
checkplots if present

Fixes

- `cp.checkplot_pickle_update`: fix unicode filename handling for py2 (52)
- coordutils: fix sign parsing bug in `dms_str_to_tuple`
- `lcproc.add_cpinfo_to_lclist`: fix incorrect cpdict keys for varfeatures