Astrobase

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

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

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

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

Fixes

- moved notebooks to their own
[astrobase-notebooks](https://github.com/waqasbhatti/astrobase-notebooks)
repository
- tests: updated test light curve path

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