v0.5.3

New stuff

lcmath: The phase_bin_magseries_with_errs function can now accept per-measurement weights to allow different errors for each measurement. Added by @lgbouma.
services.tesslightcurves: The get_eleanor_lightcurves function now accepts an optional targetdata_kwargs dict to pass in custom target info parameters to the underlying eleanor.TargetData constructor. Added by @lgbouma.
services: A new alltesslightcurves module to get all available TESS light curves for an object was added by @mchris42.
checkplot.png: The _make_phased_magseries_plot function now accepts a trimylim kwarg to remove large outliers. Added by @lgbouma.
Gaia EDR3 support is now available in all functions in the services.gaia module and the dependent functions in the checkplot, identifiers, and varclass.starfeatures modules. Set the data_release kwarg to 'dr2' for using DR2, and 'edr3' to get data from EDR3.

The Vizier TAP service mirror for EDR3 (currently) uses column names that are different from the Gaia main EDR3 and Heidelberg EDR3 mirrors. The services.gaia.objectlist_conesearch, services.gaia.objectlist_radeclbox, and services.gaia.objectid_search functions will fall back to DR2 if the Vizier mirror is used. To avoid this, use another mirror, setting the gaia_mirror kwarg to either 'gaia' or 'heidelberg'.

Changes

The default timeout for the SkyView service clients in plotbase and services.skyview has been changed to 45 seconds.
Minor fixes for deprecated methods in matplotlib and numpy.

Fixes

services.gaia: The Heidelberg mirror URL now uses HTTPS and should no longer fail all the time.

v0.5.2

Fixes

periodbase: fix check for Astropy version tags so the import doesn't fail when the version contains letters.

v0.5.1

Fixes

lcproc.catalogs.add_cpinfo_to_lclist: make sure the catalog dict's 'columns' key's value is a list so it can be appended to.

v0.5.0

This is a new major release. Support for Python 2.7 has been dropped. Astrobase now requires Python 3.5+.

New stuff

New services.tesslightcurves module to retrieve TESS HLSP light curves from MAST. This requires the astroquery, eleanor, and lightkurve packages. By @lgbouma.
services.identifiers: new tic_to_gaiadr2 function. By @lgbouma.

Fixes

periodbase.kbls: now resorts the input times, mags, errs by time to avoid a segfault in the wrapped eebls Fortran code. Should fix #94.
services.lccs: now includes the logging bits to make it an actually standalone module.

Changes

periodbase: all period-finder functions now resort their input times, mags, errs arrays by time before operating on them.
cpserver: reorganized the Tornado handlers into their own modules.
various flake8 formatting fixes all over the package
removed Python 2 specific code all over the package

Removed

The deprecated astrobase.varbase.lcfit module has been removed. Use the top-level astrobase.lcfit subpackage instead.

v0.4.3

New stuff

New services.limbdarkening module to retrieve limb-darkening Claret+ 2017 coefficients from Vizier (just for the TESS band for now). Added by @lgbouma.
New services.identifiers module to convert between SIMBAD, GAIA DR2, and TIC identifiers for objects. Added by @lgbouma.
New imageutils module for some simple FITS operations.
Added the fivetransitparam_fit_magseries function to lcfit.transits for fitting a line plus a Mandel-Agol transit model with everything fixed leaving the t0, period, a/Rstar, Rp/Rstar, and inclination as free parameters. Added by @lgbouma.

Fixes

Minor fixes to the checkplot and services subpackages.

v0.4.2

Changes

All lcfit functions now use scipy.optimize.curve_fit instead of scipy.optimize.leastsq previously. This appears to produce much more reasonable fit parameter error estimates.
periodbase.kbls: The BLS stats functions now check for a sensible transit model when calculating stats (transit depth, duration, SNR, refit period and epoch).
checkplot.png: Added option to overplot circle on DSS finder-charts. checkplot.png.twolsp_checkplot_png can now return a matplotlib.Figure. Added by @lgbouma in #86.

Fixes

lcproc.tfa: Fixed caching of collected LC info when generating a TFA template.
checkplotserver: Fixed column errors in exported CSV from the interface (#85).

Removed

Removed deprecated function astrotess.get_time_flux_errs_from_Ames_lightcurve. Use astrotess.read_tess_fitslc instead.
Removed deprecated module services/tic.py. Use services/mast.py instead.

v0.4.1

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.

v0.4.0

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.

v0.3.20

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.

v0.3.19

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.

v0.3.18

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.

v0.3.17

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

v0.3.16

Fixes

services: fixed infinite mirror-hop loop when submitting queries for SIMBAD/GAIA, these should now bail out after maxtries number of submission tries are reached.
cpserver: fixed some issues with frontend JS breaking if GAIA xy positions are not available for some reason

v0.3.15

New stuff

cpserver: added a baseurl kwarg to checkplotserver so one can launch multiple instances of it and have them go to separate base URLs if reverse-proxying to external users.
plotbase.plot_phased_mag_series: allow output to an existing matplotlib.axes.Axes object

Changes

cpserver: checkplot filenames are now URI encoded in requests to checkplotserver

Fixes

cpserver: better handling of nans that may break JSON provided to the frontend's javascript handlers from the python backend.
coordutils.xmatch_kdtree: use correct order of query_ball_tree args
lcproc.collect_tfa_stats: better handling of all-nan magcol arrays

v0.3.14

New stuff

checkplot: add update_checkplot_objectinfo function to retroactively update checkplots with new information after they've been created
services: added a SIMBAD TAP query client
services.gaia: added complete_query_later kwarg to save still-running query info if a timeout is reached. the next invocation of the same query will check if it completed and will retrieve the results
varclass.starfeatures: get all possible external object IDs from SIMBAD
checkplot, lcproc, starfeatures: add gaia_max_timeout, gaia_mirror, and complete_query_later kwargs to query and checkplot related functions

Changes

services.gaia: now uses DR2
services.gaia: now figures out which GAIA mirrors to use automatically, uses CDS by default
services.gaia: can now skip to another GAIA mirror if the current one doesn't work. mirrors enabled are the GAIA main site, the Heidelberg mirror, and the CDS mirror
lcproc.add_cpinfo_to_lclist: add magcols to the output dict and run SIMBAD query again if necessary
checkplot._pkl_finder_objectinfo: allow direct use of dict as lclistpkl kwarg

Fixes

checkplot: actually retry finder chart with forcefetch=True
cpserver.js: handle errors correctly on checkplot load
cpserver.js: more failure handling
kbls: new chunk-size determination scheme, should fix Github #50
services.gaia: automatically figure out table names for mirrors
services.gaia: fix missing import, tests: use new expected GAIA ID for DR2
services.gaia: handle timeouts and 503s a bit better
services.gaia, skyview: add handling for corrupt cached results
services.simbad: enforce random wait time between retries
starfeatures: fix missing simbad_result var
tests: more fixes for GAIA DR2
varfeatures.nonperiodic_lightcurve_features: fix ndet inconsistency

v0.3.13

New stuff

checkplot, checkplotserver: handle cases of no PF results, also PF results w/ only 1 phased LC, allows making checkplots for objects with no period-finder results just to see their mags, colors, finder chart, and GAIA info
lcproc.runcp: allow empty pfpickle input for CPs w/o phased LCs
lcproc: new add_cpinfo_to_lclist function to add back checkplot info to the object catalog generated by lcproc.make_lclist
lcproc, plotbase: add overlay_zoomcontain kwarg for fits_finder_chart function to zoom finder charts automatically to the footprint of all annotated objects in the overlay
services.gaia: now randomly picks between GAIA archive mirrors and can skip dead ones automatically

Changes

checkplot: finder reticle now at radec -> xy of object instead of center of chart
services.gaia: return query params for info after an HTTPError

Fixes

services.gaia: standardize ra, dec etc strings to make cache hits more probable
lcproc.runcp: workaround for list of pfmethods if not provided in the period-finding result pickle
cps UI: fix overview LC tile widths if no PF methods
checkplot: handle 'objectid' not found in HAT LC objectinfo dicts

v0.3.12

New stuff

lcproc: added TFA (Kovacs et al. 2005; http://adsabs.harvard.edu/abs/2005MNRAS.356..557K) implementation and parallel drivers
lcproc: added EPD drivers for LC collections

Changes

lcproc, checkplotlist: make nworkers depend on actual number of CPUs
lcproc: add minobservations kwarg for runcp, parallel_cp, parallel_cpdir

Fixes

lcproc: fix addressing of magcols so stuff like epd.mags, tfa.mags works
lcproc.lcbin: write results to correct outdict keys based on magcols
lcfit: fix missing imports
lcfit.spline_fit_magseries: fix annoying 'x must be strictly increasing' thing
checkplot: fix axes -> ax typo

v0.3.11

New stuff

checkplot.checkplot_pickle_to_png: can now export to StringIO or BytesIO instance in addition to a PNG filename.
checkplot/lcproc: added a maxnumneighbors kwarg to control the number of neighbors the function retrieves around the target object (added by @joshuawallace).
cpserver UI: added object neighbor color and mag diffs to the UI if available
cpserver UI: zoom effects for phased LC tiles to make reviewing easier
lcproc.make_lclist/filter_lclist: can now make overlayed FITS finder charts if a FITS file for the object catalog is provided
plotbase: added a fits_finder_chart function to make an annotated finder chart from a given FITS file with WCS information

Changes

cpserver UI: finder chart reticle appearance changed slightly to obscure nearby stars less
cpserver UI: moved the 'Save to PNG' button to the overview tab so it's more obvious
checkplot:checkplot_pickle: can now fall back to GAIA proper motions if 'pmra' and 'pmdecl' are not provided in the input objectinfo dict kwarg
cpserver: now gzips the response (helps if the checkplotserver is running somewhere else other than localhost)
cpserver: PNG export for a checkplot is now done in memory

Fixes

checkplot.checkplot_pickle_to_png: fix py2 StringIO isinstance() issues
cpserver: fix broken handling of missing nbr mag and color diffs
cpserver UI: fix the CSV/JSON export to correctly include all previous reviewed objects instead of just the ones from the current session
cpserver: readonly mode now disables all input correctly
cpserver UI: fix checkplot list traverse breaking at ends of list
kbls.bls_snr: fixed transit duration calculation, pointed out in #45
lcproc: fix readerfunc apply if sequences are returned

v0.3.10

Fixes

lcproc: fixed various errors and typos
checkplotserver: fixed not being able to specify < 2 periodogram peaks in period search tab
checkplot: fixed handling of SNR keys from newgen checkplots

v0.3.9

New stuff

checkplot: can now provide epochs for folding phased light curves as input, overriding the default light curve time-of-minimum finding strategy
starfeatures and checkplot: can now use arbitrary mags and colors in input objectinfo dicts, can add custom bandpasses as well
checkplotserver UI: added highlight for each GAIA neighbor in the DSS finder chart as cursor mouses over its row in the GAIA neighbor list table to help with visualizing close neighbors
tests: added tests for new epoch and mag/color handling
added a CITE.md

Changes

checkplot: no longer warns if a pickle was written in Python 2 and latin1 encoding was needed to read it in Python 3
checkplot: a Savitsky-Golay fit is now tried before giving up on finding time-of-minimum of a light curve if the initial spline fit failed
checkplotserver: UI fixes to not squish phased LC tiles into too small an area; now they overflow off the page with scroll-bars, but should remain legible
lcmath.sigclip_magseries can now use either median/MAD or mean/stdev as the central and spread values in determining where to clip (added by @joshuawallace in #40)

Fixes

checkplotserver: handle more nan-JSON breakage
starfeatures: handle missing information correctly
fixed link at the top of hatlc.py to the astrobase-notebooks repository (added by @adrn in #37)
checkplotlist: fixed to not use non-existent str.isdecimal() in Python 2
various other Python 3 specific things were fixed to make them work on python 2.7 as well

v0.3.8

Fixes

astrokep: fix EPD application
checkplot.cp2png: guard against missing phased LCs for nbestperiods
checkplot: fix docstring
cp: multiple invocations of the same period-finder method allowed now
cpserver: handle previous-gen checkplot pickles correctly
cpserver.js: better handle missing checkplot info from GAIA, etc.
imageutils: some more tools added
lcmath: add sigclip_magseries_with_extparams
periodbase: periodepsilon now a fraction diff instead of actual diff
starfeatures.neighbor_gaia_features: handle missing K mag
test_lcfit: fix expected val for weird tiny diff in fit coeffs on test runner
tests: added test for #34
tests: various fixes
varbase/trends: added implementation of classic EPD and random-forest EPD

v0.3.7

Fixes

kbls: fixing nphasebins and messaging about autofreq
lcfit: add legendre fit coeffs to output dict
test_lcfit: rtol fix
tests: added lcfit, periodbase tests, test_endtoend -> test_checkplot

v0.3.6

Fixes

imageutils: some reorganization
kbls.bls_snr: fix for not using the same kwargs from the initial BLS run
lcproc.filter_lclist: get the whole matching row for xmatches
MANIFEST.in: ignore JPL ephemerides too
setup.py: use pip>=6 req format, fix conditional py2 dep on future pkg
timeutils: use HTTPS url for JPL ephem download

v0.3.5

Fixes

MANIFEST.in: removed pngs from examples to cut down on dist size

v0.3.4

Fixes

checkplot: added xmatch_external_catalogs fn
checkplot: add load_xmatch_external_catalog fn
checkplot: correctly handle xmatch pickles > 2 GB on OSX
checkplot, cpserver: various fixes to imports and nan-handling
checkplot: fix location for font
checkplot, lcproc: change default nbr radius to 60 arcsec
checkplot.load_xmatch_external_catalogs: fix col ordering issue
checkplot.load_xmatch_external_catalogs: handle gzipped files transparently
checkplot: some reorganization for xmatch functions
checkplot: starfeatures.neighbor_features -> neighbor_gaia_features
checkplot.xmatch_external_catalogs: return updated checkplotdict
coordutils: add general kdtree functions
cp JS: handle GAIA status
cp.load_xmatch...: add column names, units to import for later table making
cpserver: add display of GAIA CMD for object if available
cpserver: added xmatch results to frontend xmatch tab
cpserver: add new pfmethods, make phased LCs for best 10 pgram peaks
cpserver, cp: fix JSON encoder to handle more weird things
cpserver: default nav shortcut key now shift instead of ctrl
cpserver: handle case where neighbors don't have LCs
cpserver: handle nans better in arrays sent to frontend
cpserver: handle nans from xmatch results
cpserver.js: add abbr for xmatch catalog description
cpserver.js: add xypos to GAIA neighbor display, for TBD cutout overlay
cpserver: make ACF period search actually work from the frontend
cps handlers: fix unneeded sigclip kwarg
cps: LC filtering/sigclip for periodsearch tab, TODO: per-PF params
cps periodsearch tab: add not:t1:t2,... and not:y1:y2,... filters as well
cps: save UI filters back to the checkplot pickle
cps: slightly better notifications for no xmatches found
cps UI: add extra period-finder params to period-search tab
cps UI: better GAIA display, show parallaxes, abs mags
cps UI: better xmatch display
cps UI: clear periodsearch elems on checkplot load
cps UI: fancier GAIA nbr list, TBD controls for epoch, period aliases
cps UI: fix keyboard shortcuts a bit
cps UI: format float cols in xmatch tables
cps UI: link to neighbors' checkplots if they're in current collection
cps UI: load previously saved period/epoch for plotting in psearch-tab
cps UI: more small fixes
cps UI: reorganized for better workflow, disabled TBD elements for now
cps UI: show all available CMDs in the checkplot pickle
cps UI: some more fixes
cp UI: add some more var/obj tags available by default
lcmath: add missing imports
lcproc: add xmatch drivers
lcproc, checkplot: put in xmatch kwargs and calls
lcproc: fixed bugs with new neighbor processing
lcproc: fixing bugs with new neighbor processing...
lcproc: fix issue with missing LC renorm for runcp
lcproc: get color/mag diffs between object and LCC neighbors
lcproc: implemented functions to add CMDs to checkplots
magnitudes: add GAIA absolute mag calc
more reorg, TODO: fix import paths for everything, hoist stuff
periodbase.macf: fix filterwindow kwarg
README.md: update for new cps UI
README: update after moving lots of stuff around
services.gaia: also get parallaxes from the gaia_source table if available
setup.py: add cpserver subpackage
some TODO notes, macf: add kwargs for external consistency
starfeatures: attempt to handle no close GAIA matches
starfeatures: get BV from JHK if necessary
starfeatures: get GAIA xy positions on object Skyview cutout

v0.3.3

Fixes

checkplot: add back coordutils imports for checkplot_png, et al.
checkplot: added all new star features to cpd objectinfo
checkplot: add extra guards against measurements being nan
checkplot.checkplot_pickle_to_png: guard against missing nbr LCs
checkplot: fix checkplot_png download of finder charts
checkplotlist: add a default sortorder and sortkey
checkplotlist: fix horrendous bugs when no sorting/filtering specified
cpserver: added implementation for neighbors tab
cpserver: add GAIA nbrs, dered colors, color classes to web interface
cpserver js: fix long-broken arbitrary period, epoch, etc. input
cpserver: send neighbor info to the frontend
lcproc: check if neighbor LC actually exists before processing it
lcproc: guard against insufficient measurements for nbrs too
plotbase: fix long-broken stamp fetch that tests ignored
services.skyview: add sizepix param, gracefully handle older cache fnames
starfeatures.neighbor_features: correctly handle case where there are no GAIA neighbors

v0.3.2

Fixes

cpserver: correct imports for varfeatures
cpserver: enable specwindow LSP, AoVMH, ACF plots
cpserver: show time-sampling specwindow LSP if it exists
lcproc.get_periodicfeatures: handle insufficient # of finite LC pts
lcproc: makelclist -> make_lclist, getlclist -> filter_lclist
services.gaia: added GAIA cone-search function
varclass.periodicfeatures: lots of fixes for handling LC fit errors
varclass.starfeatures: fix dist_arcsec calculation from xyz_dist
varclass.starfeatures, lcproc: added GAIA nbr dist features, fixed more bugs

v0.3.0

Fixes

moved some modules around for better organization
- fakelcgen -> fakelcs.generation
- fakelcrecovery -> fakelcs.recovery
- varbase.features -> varclass.varfeatures
- hatds -> services.hatds
new modules:
- varclass.periodicfeatures
- varclass.starfeatures
- varclass.rfclass
- services.dust
- services.gaia
- services.skyview
- services.trilegal
checkplot: arbitrary lspmethods in priority order for neighbors
checkplotlist: use '|' to separate filter/sort ops/operands, not '_'
fakelcs.generation: add in cepheids as a fakevar class
fakelcs.recovery: added grid-search for optimizing per-magbin varidx
fakelcs.recovery: added plotting for optimization results
lcfit: additional guards against leastsq failure
lcfit: handle case where covxmatrix isn't returned
lcmodels.eclipses: add secondaryphase as another param
lcproc: added get_starfeatures, serial and parallel drivers
lcproc: added parallel_periodicfeatures, _lcdir
lcproc: adding in per-magbin variable index thresholds
lcproc: fix glob for parallel_runcp_pfdir
lcproc: added star, periodic_feature parallel and serial drivers
lcproc.runpf: remove BLS, add AoVMH + specwindow L-S as default PF
periodbase, plotbase: add specwindow function to registries
periodbase.zgls: add specwindow_lsp to check for peaks caused by time-sampling
many other bugfixes

Work that may be in progress

added lcproc_batch.py for running LC processing on AWS, GKE, etc.
added Dockerfiles to run astrobase from a Docker container

v0.2.9

Fixes

moved notebooks to their own astrobase-notebooks repository
tests: updated test light curve path

v0.2.8

Fixes

checkplot: add a short cp2png function for convenience
checkplot/hplc: add gzip support
checkplot, hplc, lcproc: fix binary mode opening for gzipped pickles
checkplot: remove stray re-raise so things won't break if no finder
fakelcgen.add_fakelc_variability: don't add variability if it exists
fakelcgen: add generate_transit_lightcurve, add_fakelc_variability fns
fakelcgen: add timecols, magcols, errcols to fakelcdict; transit stuff
fakelcgen: finished up add_variability_to_fakelc_collection
fakelcgen: fixed bugs in generate_[eb|flare]_lightcurve
fakelcgen: fixing generate_transit_lightcurve
fakelcgen: fix random declination range
fakelcgen: handle non-variables in add_fakelc_variability
fakelcgen/lcproc: chosen random mag -> scalar; feature arrays -> 1-d
fakelcgen: use the correct bin count dist for random mag assignments
hplc: read gzipped pklc transparently
lcproc: add parallel_runcp for list of periodfinding result pickles
lcproc: HP gzipped pklc glob update

Work that may be in progress

[WIP] varclass.fakelcrecovery: TBD

v0.2.7

Fixes

checkplot: use axes_grid1 because axes_grid is deprecated apparently
features.all_nonperiodic_features: add back magsarefluxes kwarg
lcmath: add (optional for now) iterative sigclip to sigclip_magseries
lcmodels.eclipses: fixes to docstring
lcmodels.eclipses, lcfit: implemented invgauss_eclipses model & fit fns
lcproc.plot_variability_thresholds: yscale -> log
lcproc: stetson_threshold -> variability_threshold, now per mag-bin
lcproc: stupid bug fix
lcproc.variability_threshold: get and plot LC RMS as well
recoverysim: added make_fakelc_collection
recoverysim: fixed up make_fakelc, make_fakelc_collection
varbase.features: some more measures added
varbase.lcfit: fix confusing fourierorder, fourierparams kwargs. GH PR #27
varbase.signals: fixes for GH PR #25 and #29
varbase/signals: fix long-broken gls_prewhiten iterative prewhiten function
varclass.recoverysim -> two modules: fakelcgen and fakelcrecovery
Wrapped LOGWARNING in if verbose: statement

Work that may be in progress

[WIP] moved various LC models into lcmodels, TODO: finish these
[WIP] recoverysim: redo make_fakelc, now gets mag-rms from previous results
[WIP] setting up the varclass package
[WIP] various implementation notes
[WIP] working on recoverysim

v0.2.6

Fixes

lcfit: fix error handling
lcfit: implement traptransit_fit_magseries, to be tested
lcfit: tested/fixed traptransit_fit_magseries, seems to work OK
lcfit.traptransit_fit_magseries: get formal 1-sig errs for final params
lcfit.traptransit_fit_magseries: get formal 1-sig errs for fit as well
lcproc/checkplot: use full lcfpath in makelclist, getlclist, nbr procs
lcproc, features: fix broken beyond1std, add bestmagcol to results
lcproc.makelclist: add maxlcs kwarg
lcproc.makelclist: fixing bugs
lcproc, periodbase: update period-finder registry dicts
periodbase: fix falsealarmprob for PDM
periodbase.make_combined_periodogram: addmethods kwarg
README: added zenodo DOI badge
smav: bump up default nharmonics to 6 from 4
smav: use correct dot product function (np.vdot not np.dot)

v0.2.5

Fixes

checkplot: add neighbor stuff to checkplot png as well
checkplot.checkplot_pickle_to_png: actually fix mistaken pkl outfile ext
checkplot: fix handling of no neighbors case
checkplot: get neighbors of target, their radecs, xys, and lcfpaths
checkplotlist: added some TODOs for multi-checkplot-per-object stuff
checkplotlist: more notes on planned features
finally added coding: utf-8 to everything
glsp: remove because all moved to zgls.py
lcmath: added a fill_magseries_gaps function
lcmath, autocorr: add some guards against weirdness
lcmath.fill_magseries_gaps: fix normalization of fluxes
lcmath.fill_magseries_gaps: use 0.0 to fill gaps instead of noiselevel by default
lcmath.fill_magseries_gaps: use scipy's perfectly cromulent mode fn
lcmath.fill_magseries_gaps: use scipy's perfectly cromulent mode fn instead
lcproc: added update_checkplotdict_nbrlcs to get neighbor LCs
lcproc: add neighbor stuff to parallel_cp workers and driver
lcproc: add serial_varfeatures
lcproc: better kwargs for xmatchexternal
lcproc: fix default fileglobs for HAT and HPX LCs
lcproc.makelclist: do concurrent (threaded) info collection instead
lcproc.makelclist: do parallel info collection instead
lcproc.makelclist: get actual ndets per magnitude column
lcproc.makelclist: remove useless fileglob from tasklist
lcproc.parallel_cp_lcdir: make output directory if it's doesn't exist
lcproc.parallel_varfeatures: use ProcessPoolExecutor instead of mp.Pool
lcproc.runpf: bugfix
lcproc.runpf: make BLS SNR optional because it takes forever
lcproc.runpf/runcp: allow any of the period-finders from periodbase
lcproc: simplify parallel task list for makelclist
macf: added macf_period_find; seems to work, TODO: more testing
macf: added plot_acf_results to see smoothed/unsmoothed ACF and peaks
macf: fixed, tested; reproduces McQuillian+ (2014) results on KeplerLCs
macf: fix handling of kwargs
macf: fix peak detection
macf: search interval for ACF peaks now depends on smoothing
macf: some more docstring work
macf: update docstrings
periodbase: add a make_combined_periodogram fn
periodbase: add macf to base namespace
periodbase.macf: initial bits for McQuillian+ (2013a, 2014) period-finder
plotbase: get the FITS header for the cutout for WCS purposes later
README: updated for some new stuff
README, various: add links to ADS for period-finders, fix spelling of names
smav: bugs fixed, seems to be working OK
smav: implemented aovhm_periodfind, to be tested
smav: initial bits
smav: some more progress
varbase.autocorr: actually return acf as np.array
varbase.autocorr: autocorr_magseries fn using lcmath.fill_magseries_gaps
varbase.autocorr: fix _autocorr_func3 and set as default
varbase.autocorr: return acf as np.array
varbase.autocorr: use 0.0 to fill gaps instead of noiselevel by default
varbase.features: fix annoyingly subtle bug causing np.polyfit crashes
varbase.features: np.nonzero -> npnonzero
zgls, lcfit: guard against zero errors here too
zgls: move the glsp functions into here

v0.2.4

Fixes

lcproc: add external cross-matching to getlclist
lcproc.getlclist: also copy matching light curves to requested dir
lcproc: getlclist, makelclist now have column-filtering and cone-search

v0.2.3

Fixes

lcproc: don't crash runpf if BLS SNR fails

v0.2.2

Fixes

cplist: add 'ne' -> not-equal-to filter operator for --filter arg
cplist/cpserver: now takes multiple filters to be ANDed together; yet to test
cplist: fix docstring
cplist: fixed multiple filter keyword arguments
cplist: fix incorrect filtering
cplist: fixing multiple filter args

v0.2.0

Fixes

checkplot: add check for overwritten pkl when converting to png
checkplot: added kwarg for findercachedir to checkplot fns
checkplot: added verbose kwarg
checkplot: add in extra BLS info if available
checkplot: add in markeredgewidth for older matplotlibs
checkplot: astroquery_skyview_stamp -> internal_skyview_stamp
checkplot: calculate varfeatures, add other keys required by cpserver tools
checkplot.checkplot_pickle: can now overplot external LC fit fn
checkplot: direct return mode for _pkl_phased_magseries_plot
checkplot: docstring fixes
checkplot: handle case of no explicitly provided lspmethod
checkplotlist: added chunked output if too many checkplots
checkplotlist: add optional prefixes to output JSON filelists
checkplotlist: auto-add output JSON prefix if sortby is provided
checkplotlist: better messaging if more than 1 output JSON
checkplotlist: can now index into arrays when sorting on cpd properties
checkplotlist: can now specify sortkey/sortorder when making the pkl list
checkplotlist: faster custom sorting with mp.Pool
checkplotlist: fix docstring
checkplotlist: guard against missing sortkey items
checkplotlist: remove non-finite vals from filters
checkplotlist: use argparse instead of hacked together cmdline parsing
checkplot: make varfeatures optional
checkplot, plotbase: astroquery_skyview_stamp -> skyview_stamp
checkplot: pyplot.scatter -> pyplot.plot for speed, also use rasterized=True
checkplot: return lcfit per phased LC, not just the last one
checkplot: slightly smaller marker size for binned mag series
checkplot: turn off bestperiodhighlight by default
checkplot.twolsp_checkplot_png: don't break if bestperiodhighlight is None
cplist: added filtering options for checkplotserver input JSON
cplist: fix incorrect filtering because we didn't take sort order into account
cpserver: add check for checkplot-filelist-00.json as default
cpserver: added sortorder/sortkey UI elem in sidebar list
cpserver/cplist: add support for filtered list JSONs
cpserver: enable gzip
cpserver.js: fix case where observing stations aren't strings
cpserver: slightly better display of sortkey/sortorder
cpserver: turn off cplist sorting since checkplotlist handles it
cpserver UI: add a filter control to the reviewed checkplot sidebar list
cpserver UI: disable bokeh; will use server-side plotting for now
hplc: added HPX binned LC reader functions
hplc: added parallel LC concatenator
hplc: added pklc_fovcatalog_objectinfo to fill in objectinfo
hplc: fix station names
hplc: use gzipped fovcatalogs if available
imageutils: added frame_radecbox_to_jpeg function
imageutils: handle weird input better
imageutils: various fixes
kbls: add alternate SNR calculation
kbls: add support for max number of frequencies to search
kbls: don't crash if spline fit to find a minimum fails
lcfit: fourier_fit_magseries now accepts fourierorder as a scalar
lcfit: initfourierparams -> fourierparams
lcfit.spline_fit...: maxknots reduced to 30 for better min-finding
lcmath.time_bin_magseries_with_errs: return jdbins as array
lcproc: add a LC binning function
lcproc: added maxobjects to be processed per driver invocation
lcproc: added pf driver for all LC formats
lcproc: adding makelclist
lcproc: adding support for multiple lc types
lcproc: add overrideable time, mag, err cols for all function drivers
lcproc: add parallel LC binning functions
lcproc: add register func for custom LC format
lcproc: also get objects above stetson threshold across all magcols
lcproc: bugfixes
lcproc/checkplot: add in BLS snr if available
lcproc: dereference columns for different lctypes correctly
lcproc: fix bug where bls result was replaced instead of updated
lcproc: more bug fixes
lcproc: more fixes
lcproc: use last deferenced mcol val to correctly process astrokep lcs
plotbase: added internal_skyview_stamp fn to remove astroquery dep
plotbase: plot the binned plot over the unbinned one
plotbase.skyview_stamp: add provenance, use sha256 instead of md5
signals: fix mask_signal
signals: more fixes
signals: return a BytesIO/StringIO object as fitplotfile if provided
signals: whiten_magseries now accepts fourierorder as a scalar
varbase.lcfit: added verbose kwarg
varbase.signals: fix gls_prewhiten
varbase.signals: fix various horrendous problems in prewhiten_magseries

Work that may be in progress

[WIP] added lcproc.py to drive large HAT LC processing jobs
[WIP] cpserver: added some TODOs
[WIP] cpserver, checkplot: some plot fixes
[WIP] cpserver: continuing work
[WIP] cpserver: finishing up backend work, to be tested
[WIP] cpserver: fix async err handling, some lctools now working
[WIP] cpserver: fixed various lctool bugs after testing
[WIP] cpserver: fix parsing of argument types
[WIP] cpserver: fix saving to tempfpath, fix circular ref in var-varfeatures
[WIP] cpserver: implemented lctools: phasedlc-newplot, var-varfeatures
[WIP] cpserver.js: added skeleton for cptools
[WIP] cpserver lctools: added a reset function and a lcfit subtract function
[WIP] cpserver: more fixes
[WIP] cpserver: more work on UI
[WIP] cpserver: screenshot updated with near-final UI for v0.2
[WIP] cpserver: some notes for stuff
[WIP] cpserver: still WIP
[WIP] cpserver: still working on LC tools backend
[WIP] cpserver UI: added period-search, variability-tools, lcfit tabs
[WIP] cpserver UI: added some phased LC plot options
[WIP] cpserver UI: adding controls to JS, working on periodsearch
[WIP] cpserver UI: phasedlc-newplot, var-varfeatures, work queues
[WIP] cpserver UI: still working on JS for lctools
[WIP] cpserver UI: various CSS fixes
[WIP] cpserver: various fixes to JSON decoding and checkplot loading
[WIP] cpserver: various fixes to UI
[WIP] cpserver: various UI fixes
[WIP] cpserver: working on hooking up signal and fitting functions
[WIP] cpserver: working on LC tools handlers
[WIP] cpserver: write tool results to temp pkl, keep orig pkl load fast
[WIP] lcfit: add a simple trapezoid function for eclipses

v0.1.22

Fixes

checkplot.checkplot_pickle_to_png: fix breakage if pickle has no objectinfo

v0.1.21

Fixes

astrokep: add onormalize kwarg to read and consolidate MASTLC fns
astrokep: add recursive kwarg for glob
astrokep.consolidate_kepler_fitslc: use recursive glob for speed if Py>3.5
astrokep: docstring fixes
astrokep: trying fnmatch
astrokep: trying recursive glob
astrokep: use fnmatch instead of glob
checkplotlist: appending bugs fixed
checkplotlist: append to an existing list JSON if it exists
checkplot: make sure it still works with matplotlib < v2.0.0
checkplot: try hard to get an objectid out of the input kwargs
hatlc: added normalization fns to docstring, more fixes for sqlitecurve compression
hatlc: added OS independent sqlite.gz read/write
hatlc: first crack at normalizing by instrument properties
hatlc: keep the input sqlitecurves until done with (de)compression
hatlc: make less talkative
hatlc: normalize_lcdict_byinst function sort of working
hatlc.normalize_lcdict_byinst: more fixes
hatlc.normalize_lcdict_instruments: fixing bugs
hatlc: warning if gzip < 1.6
hatpilc: add column defs to lcdict
hatpilc: added concatenation and pickle writing
hatpilc: added concat rollup fn
hatpilc: add recursive kwarg for glob
hatpilc: bug fixing
hatpilc.concatenate...: use recursive glob on Py3.5+ for speed
hatpilc: improved a bit
hatpilc: make a bit more organized
hatpilc: reorganization
hatpilc: use empty ndarrays if no dets
hplc: added normalization across light curves
hplc: added pklc reader, breaking out framekeys to elems
hplc: addeed non-recursive LC search mode
hplc: concatenation: fix lc index
hplc: concatenation: fix recursive search to include only specific postfixed files
hplc: fix docstrings
hplc: fixing normalization
hplc: fixing pklc output
hplc: more fixes for non-recursive LC search
hplc: return a normalized LC even if there's only one to return
hplc: sort concatenated light curves by time
init: add a version
varbase.features: added a roll-up function

v0.1.20

Fixes

astrokep: making read_kepler_fitslc work with K2 LCs
astrokep: more fixes for K2 LC reading
kbls.bls_snr: add check for rare case when minepoch is an array
README.md: added k2hat.py and expanded some descriptions
README.md: some more fixes
setup.py: require astropy>=1.3 and numpy>=1.4

v0.1.19

Fixes

astrokep: added appendto mode to read_kepler_fitslc
astrokep: better naming scheme for output pickles
astrokep.filter_kepler_lcdict: fix timestoignore for new lcdict format
astrokep: fixing appendto mode
astrokep: fixing consolidate_kepler_fitslc
astrokep: implemented consolidate_kepler_fitslc, will test soon
astrokep: make sklearn dependency optional
astrokep: pickle export now uses HIGHEST_PROTOCOL, docstring fixes
astrokep: stitch_lightcurve -> stitch_kepler_lcdict (TBD)

v0.1.18

Fixes

checkplot: added minbinelems kwarg
varbase/features: implemented CDPP as in Gilliland+ 2011

v0.1.15

Fixes

checkplot: added checkplot_pickle_to_png
checkplot: added externalplots kwarg to checkplot_pickle
checkplot: add missing finderconvolve kwarg to [twolsp_]checkplot_png fn
checkplot: fix extrarows functionality in checkplot_pickle_to_png
checkplot: parse the variable flag correctly for PNG export
checkplot_pickle_to_png: fix extra row handling
checkplot_pickle_to_png: fix extra row handling again
checkplotserver: some style improvements to PNG export UI
lcmath: fixed import for datetime
notebooks: updated lightcurves-and-checkplots for latest checkplot version

v0.1.13

Fixes

checkplot.checkplot_pickle_update: fixed some python 3 vs 2.7 breakage
checkplotserver: fixed up readonly mode
cpserver.js: moved readonly alert to end of load cycle
README.md: add fancy test status icons
tests: added a case for checkplot_pickle_update

v0.1.12

Fixes

.gitignore: ignore test results
MANIFEST.in: include tests
setup.py: fixed testing imports and launch
test_endtoend.py: fixed various things
test_endtoend: updated test procedure docstring
tests: added test_endtoend.py

v0.1.10

Fixes

kbls.py: added bootstrap false-alarm probability and an SNR calculation
periodbase.bootstrap_falsealarmprob: get kwargs from lspdict
periodbase: return a dict of results instead
periodbase: return bootstrap trial values for diagnostics, etc.

v0.1.9

Fixes

checkplot: fix issue with pickles breaking if times, mags, errs are astropy.table.Column objects

Files

CHANGELOG.md

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v0.5.3

New stuff

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v0.5.2

Fixes

v0.5.1

Fixes

v0.5.0

New stuff

Fixes

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Removed

v0.4.3

New stuff

Fixes

v0.4.2

Changes

Fixes

Removed

v0.4.1

New stuff

Changes

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v0.4.0

New stuff

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v0.3.20

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v0.3.19

New stuff

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Fixes

v0.3.18

New stuff

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v0.3.17

New stuff

Changes

Fixes

v0.3.16

Fixes

v0.3.15

New stuff

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v0.3.14

New stuff

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Fixes

v0.3.13

New stuff

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v0.3.12

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v0.3.11

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v0.3.10

Fixes

v0.3.9

New stuff

Changes

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v0.3.8

Fixes