Sdss-marvin

--------------------

Added
^^^^^

- Added tests for `emline_gflux_ha_6564` and fixed values in galaxy_test_data.

Fixed
^^^^^

- Issue `182 <https://github.com/sdss/marvin/issues/182>`_
- Issue `202 <https://github.com/sdss/marvin/issues/202>`_
- Issue `319 <https://github.com/sdss/marvin/issues/319>`_
- Issue `322 <https://github.com/sdss/marvin/issues/322>`_
- Issue `334 <https://github.com/sdss/marvin/issues/334>`_
- Issue `339 <https://github.com/sdss/marvin/issues/339>`_
- Issue `341 <https://github.com/sdss/marvin/issues/341>`_
- Issue `342 <https://github.com/sdss/marvin/issues/342>`_
- Issue `348 <https://github.com/sdss/marvin/issues/348>`_
- Issue `352 <https://github.com/sdss/marvin/issues/352>`_
- Issue `354 <https://github.com/sdss/marvin/issues/354>`_
- Issue `355 <https://github.com/sdss/marvin/issues/355>`_
- Issue `362 <https://github.com/sdss/marvin/issues/362>`_
- Issue `366 <https://github.com/sdss/marvin/issues/366>`_
- Issue `367 <https://github.com/sdss/marvin/issues/367>`_
- Issue `368 <https://github.com/sdss/marvin/issues/368>`_
- Issue `369 <https://github.com/sdss/marvin/issues/369>`_
- Issue `372 <https://github.com/sdss/marvin/issues/372>`_
- Issue `375 <https://github.com/sdss/marvin/issues/375>`_
- Issue `378 <https://github.com/sdss/marvin/issues/378>`_
- Issue `379 <https://github.com/sdss/marvin/issues/379>`_
- Issue `383 <https://github.com/sdss/marvin/issues/383>`_
- Issue `385 <https://github.com/sdss/marvin/issues/385>`_
- Issue `386 <https://github.com/sdss/marvin/issues/386>`_
- Issue `374 <https://github.com/sdss/marvin/issues/374>`_: Cube units do not persist under axis reordering.
- Fixed some problems with test_spaxel tests.
- Issue `382 <https://github.com/sdss/marvin/issues/382>`_: Is fuzzywuzzy too fuzzy?
- Fixed an issue with Astropy 3 in `get_nsa_data()`.
- Fixed some issues with query results tests
- Issue `391 <https://github.com/sdss/marvin/issues/391>`_
- Issue `387 <https://github.com/sdss/marvin/issues/387>`_
- Issue `384 <https://github.com/sdss/marvin/issues/384>`_
- Issue `380 <https://github.com/sdss/marvin/issues/380>`_
- Issue `376 <https://github.com/sdss/marvin/issues/376>`_
- Issue `373 <https://github.com/sdss/marvin/issues/373>`_
- Issue `371 <https://github.com/sdss/marvin/issues/371>`_
- Issue `370 <https://github.com/sdss/marvin/issues/370>`_
- Issue `363 <https://github.com/sdss/marvin/issues/363>`_
- Issue `361 <https://github.com/sdss/marvin/issues/361>`_
- Issue `360 <https://github.com/sdss/marvin/issues/360>`_
- Issue `359 <https://github.com/sdss/marvin/issues/359>`_
- Issue `358 <https://github.com/sdss/marvin/issues/358>`_
- Issue `357 <https://github.com/sdss/marvin/issues/357>`_
- Issue `353 <https://github.com/sdss/marvin/issues/353>`_
- Issue `351 <https://github.com/sdss/marvin/issues/351>`_
- Issue `349 <https://github.com/sdss/marvin/issues/349>`_
- Issue `346 <https://github.com/sdss/marvin/issues/346>`_
- Issue `345 <https://github.com/sdss/marvin/issues/345>`_
- Issue `344 <https://github.com/sdss/marvin/issues/344>`_
- Issue `343 <https://github.com/sdss/marvin/issues/343>`_
- Issue `340 <https://github.com/sdss/marvin/issues/340>`_
- Issue `337 <https://github.com/sdss/marvin/issues/337>`_
- Issue `336 <https://github.com/sdss/marvin/issues/336>`_
- Issue `335 <https://github.com/sdss/marvin/issues/335>`_
- Issue `333 <https://github.com/sdss/marvin/issues/333>`_
- Issue `331 <https://github.com/sdss/marvin/issues/331>`_
- Issue `330 <https://github.com/sdss/marvin/issues/330>`_
- Issue `329 <https://github.com/sdss/marvin/issues/329>`_
- Issue `328 <https://github.com/sdss/marvin/issues/328>`_
- Issue `327 <https://github.com/sdss/marvin/issues/327>`_
- Issue `326 <https://github.com/sdss/marvin/issues/326>`_
- Issue `325 <https://github.com/sdss/marvin/issues/325>`_
- Issue `324 <https://github.com/sdss/marvin/issues/324>`_
- Issue `320 <https://github.com/sdss/marvin/issues/320>`_
- Issue `307 <https://github.com/sdss/marvin/issues/307>`_
- Issue `395 <https://github.com/sdss/marvin/issues/395>`_
- Issue `390 <https://github.com/sdss/marvin/issues/390>`_


Removed
^^^^^^^

- The banner that showed up in Safari has been removed since most versions should now work properly.

--------------------

Fixed
^^^^^

- MPL-6 issue with all H-alpha extensions mapped to NII instead. Indexing issue in MPL-6 datamodel.
- MPL-6 issue with elliptical coordinate extensions; missing R/Reff channel in MPL-6 datamodel.
- Issue `324 <https://github.com/sdss/marvin/issues/324>`_
- Issue `325 <https://github.com/sdss/marvin/issues/325>`_
- Issue `326 <https://github.com/sdss/marvin/issues/326>`_
- Issue `327 <https://github.com/sdss/marvin/issues/327>`_
- Issue `330 <https://github.com/sdss/marvin/issues/330>`_
- Issue `333 <https://github.com/sdss/marvin/issues/333>`_
- Issue `335 <https://github.com/sdss/marvin/issues/335>`_
- Issue `336 <https://github.com/sdss/marvin/issues/336>`_
- Issue `343 <https://github.com/sdss/marvin/issues/343>`_
- Issue `351 <https://github.com/sdss/marvin/issues/351>`_
- Issue `353 <https://github.com/sdss/marvin/issues/353>`_
- Issue `357 <https://github.com/sdss/marvin/issues/357>`_
- Issue `358 <https://github.com/sdss/marvin/issues/358>`_
- Issue `360 <https://github.com/sdss/marvin/issues/360>`_
- Issue `363 <https://github.com/sdss/marvin/issues/363>`_
- Issue `373 <https://github.com/sdss/marvin/issues/373>`_

--------------------

Fixed
^^^^^

- bugfix in MPL-6 datamodel for gew OII lines

--------------------

Added
^^^^^

- Added ``Maskbit`` class for easy conversion between mask values, bits, and
labels.
- Better BPT documentation, in particular in the ``Modifying the plot``
section.
- A hack function ``marvin.utils.plot.utils.bind_to_figure()`` that
replicate the contents of a matplotlib axes in another figure.
- New scatter and histogram plotting utility functions
- Integrated scatter and histogram plotting into query Results
- New methods for easier query Results handling
- New Pythonic DRP, DAP, and Query DataModels
- Access to DAPall data

Changed
^^^^^^^

- Issue `190 <https://github.com/sdss/marvin/issues/190>`_: ``Maps.get_bpt()`` and
``marvin.utils.dap.bpt.bpt_kewley06()`` now also return a list of
axes. Each axes contains a method pointing to the
``marvin.utils.plot.utils.bind_to_figure()`` function, for easily
transfer the axes to a new figure.
- All Cubes, Maps, and Modelcubes use Astropy Quantities
- Refactored to the Bin class
- Bin and Spaxel are now subclassed from SpaxelBase

Fixed
^^^^^

- Issue `24 <https://github.com/sdss/marvin/issues/24>`_
- Issue `99 <https://github.com/sdss/marvin/issues/99>`_
- Issue `110 <https://github.com/sdss/marvin/issues/110>`_
- Issue `111 <https://github.com/sdss/marvin/issues/111>`_
- Issue `131 <https://github.com/sdss/marvin/issues/131>`_
- Issue `133 <https://github.com/sdss/marvin/issues/133>`_
- Issue `173 <https://github.com/sdss/marvin/issues/173>`_
- Issue `178 <https://github.com/sdss/marvin/issues/178>`_
- Issue `180 <https://github.com/sdss/marvin/issues/180>`_
- Issue `190 <https://github.com/sdss/marvin/issues/190>`_
- Issue `191 <https://github.com/sdss/marvin/issues/191>`_
- Issue `233 <https://github.com/sdss/marvin/issues/233>`_
- Issue `235 <https://github.com/sdss/marvin/issues/235>`_
- Issue `246 <https://github.com/sdss/marvin/issues/246>`_
- Issue `248 <https://github.com/sdss/marvin/issues/248>`_
- Issue `261 <https://github.com/sdss/marvin/issues/261>`_
- Issue `263 <https://github.com/sdss/marvin/issues/263>`_
- Issue `269 <https://github.com/sdss/marvin/issues/269>`_
- Issue `279 <https://github.com/sdss/marvin/issues/279>`_
- Issue `281 <https://github.com/sdss/marvin/issues/281>`_
- Issue `286 <https://github.com/sdss/marvin/issues/286>`_
- Issue `287 <https://github.com/sdss/marvin/issues/287>`_
- Issue `290 <https://github.com/sdss/marvin/issues/290>`_
- Issue `291 <https://github.com/sdss/marvin/issues/291>`_
- Issue `294 <https://github.com/sdss/marvin/issues/294>`_
- Issue `295 <https://github.com/sdss/marvin/issues/295>`_
- Issue `296 <https://github.com/sdss/marvin/issues/296>`_
- Issue `297 <https://github.com/sdss/marvin/issues/297>`_
- Issue `299 <https://github.com/sdss/marvin/issues/299>`_
- Issue `301 <https://github.com/sdss/marvin/issues/301>`_
- Issue `302 <https://github.com/sdss/marvin/issues/302>`_
- Issue `303 <https://github.com/sdss/marvin/issues/303>`_
- Issue `304 <https://github.com/sdss/marvin/issues/304>`_
- Issue `308 <https://github.com/sdss/marvin/issues/308>`_
- Issue `311 <https://github.com/sdss/marvin/issues/311>`_
- Issue `312 <https://github.com/sdss/marvin/issues/312>`_

--------------------

Added
^^^^^

- Added new query_params object, for easier navigation of available
query parameters. Added new tests.
- Added a new guided query builder using Jquery Query Builder to the
Search page
- Added a View Galaxies link on the web results to view postage stamps
of the galaxies in the results
- Added Route Rate Limiting. Adopts a limit of 200/min for all api
routes and 60/minute for query api calls and web searches

Changed
^^^^^^^

- Changed call signature for
:meth:``marvin.utils.plot.map.no_coverage_mask`` (removed ``value``
arg because unused, added ``None`` as default value ``ivar``
(``None``), and re-ordered args and kwargs).
- Changed call signature for
:meth:``marvin.utils.plot.map.bad_data_mask`` (removed ``value`` arg
because unused).
- Changed the Marvin web search page to use the new query_params and
parameter grouping. Removed the autocomplete input box.
- Updated the documentation on query and query_params.
- Modified Guided Search operator options to remove options that could
not be parsed by SQLA boolean_search
- Refactored the web settings, route registration, extensions to enable
extensibility
- Issue `282 <https://github.com/sdss/marvin/issues/282>`_: Improvements to "Go to CAS" link. Changed to Go To
SkyServer and updated link to public up-to-date link

Fixed
^^^^^

- Issue `102 <https://github.com/sdss/marvin/issues/102>`_: problem with urllib package when attempting to retrieve
the Marvin URLMap
- Issue `93 <https://github.com/sdss/marvin/issues/93>`_: safari browser does not play well with marvin
- Issue `155 <https://github.com/sdss/marvin/issues/155>`_: Contrails in Web Map
- Issue `174 <https://github.com/sdss/marvin/issues/174>`_: sdss_access may not be completely python 3 compatible
- Issue `196 <https://github.com/sdss/marvin/issues/196>`_: Bin not loading from local sas
- Issue `207 <https://github.com/sdss/marvin/issues/207>`_: Get Maps in MapSpecView of Galaxy page sometimes fails to
return selected maps
- Issue `210 <https://github.com/sdss/marvin/issues/210>`_: pip upgrade may not install new things as fresh install
- Issue `209 <https://github.com/sdss/marvin/issues/209>`_: marvin version from pip install is incorrect
- Issue `268 <https://github.com/sdss/marvin/issues/268>`_: Cube flux from file error
- Issue `85 <https://github.com/sdss/marvin/issues/85>`_: Python does not start in Python 3
- Issue `273 <https://github.com/sdss/marvin/issues/273>`_: ha.value bug
- Issue `277 <https://github.com/sdss/marvin/issues/277>`_: Ticks for log normalized colorbar
- Issue `275 <https://github.com/sdss/marvin/issues/275>`_: logger crashes on warning when other loggers try to log
- Issue `258 <https://github.com/sdss/marvin/issues/258>`_: 422 Invalid Parameters
- Issue `271 <https://github.com/sdss/marvin/issues/271>`_: Problem in dowloading image.
- Issue `97 <https://github.com/sdss/marvin/issues/97>`_: sqlalchemy-boolean-search not found when installed from
pip source
- Issue `227 <https://github.com/sdss/marvin/issues/227>`_: Marvin installation in python 3.6 (update setuptools to
36)
- Issue `262 <https://github.com/sdss/marvin/issues/262>`_: problem with marvin update
- Issue `270 <https://github.com/sdss/marvin/issues/270>`_: BPT array sizing not compatible
- Issue `88 <https://github.com/sdss/marvin/issues/88>`_: Deployment at Utah requires automatisation
- Issue `234 <https://github.com/sdss/marvin/issues/234>`_: Add (and use) functions to the datamodel to determine
plotting parameters
- Issue `278 <https://github.com/sdss/marvin/issues/278>`_: marvin_test_if decorator breaks in python 2.7
- Issue `274 <https://github.com/sdss/marvin/issues/274>`_: cube slicing to get a spaxel fails with maps error
- Issue `39 <https://github.com/sdss/marvin/issues/39>`_: implement more complete testing framework
- Issue `242 <https://github.com/sdss/marvin/issues/242>`_: Result object representation error with 0 query results
- Issue `159 <https://github.com/sdss/marvin/issues/159>`_: Marvin issues multiple warnings in PY3
- Issue `149 <https://github.com/sdss/marvin/issues/149>`_: Improve integrated flux maps display in web

--------------------

Added
^^^^^

- Issue `204 <https://github.com/sdss/marvin/issues/204>`_: added elpetro_absmag colours to mangaSampleDB models.
- Issue `253 <https://github.com/sdss/marvin/issues/253>`_: Plotting tutorial.
- Issue `223 <https://github.com/sdss/marvin/issues/223>`_: Easy multi-panel map plotting (with correctly placed
colorbars).
- Issue 232 and Issue `251 <https://github.com/sdss/marvin/issues/251>`_: Uses matplotlib style sheets context
managers for plotting (map, spectrum, and BPT) and restores previous
defaults before methods finish.
- Issue `189 <https://github.com/sdss/marvin/issues/189>`_: Map plotting accepts user-defined value, ivar, and/or
mask (including BPT masks).
- Issue `252 <https://github.com/sdss/marvin/issues/252>`_: Quantile clipping for properties other than velocity,
sigma, or flux in web.
- Added ``utils.plot.map`` doc page.
- Added ``tools.map`` doc page.

Changed
^^^^^^^

- Issue `243 <https://github.com/sdss/marvin/issues/243>`_: inverted ``__getitem__`` behaviour for
Cube/Maps/ModelCube and fixed tests.
- Modified Flask Profiler File to always point to
$MARVIN_DIR/flask_profiler.sql
- Issue `241 <https://github.com/sdss/marvin/issues/241>`_: Moved map plotting methods from tools/map to
utils/plot/map
- Issue 229 and Issue `231 <https://github.com/sdss/marvin/issues/231>`_: Switch to new gray/hatching scheme (in
tools and web):

- gray: spaxels with NOCOV.
- hatched: spaxels with bad data (UNRELIABLE and DONOTUSE) or S/N
below some minimum value.
- colored: good data.

- Issue `238 <https://github.com/sdss/marvin/issues/238>`_: Move plot defaults to datamodel (i.e., bitmasks,
colormaps, percentile clips, symmetric, minimum SNR).
- Issue `206 <https://github.com/sdss/marvin/issues/206>`_: SNR minimum to None (effectively 0) for velocity maps so
that they aren't hatched near the zero velocity contour.
- Simplified default colormap name to "linearlab."
- Decreased map plot title font size in web so that it does not run
onto second line and overlap plot.

Fixed
^^^^^

- Interactive prompt for username in sdss_access now works for Python
3.
- Fixed `195 <https://github.com/sdss/marvin/issues/195>`_: The data file for the default colormap for ``Map.plot()``
("linear_Lab") is now included in pip version of Marvin and does not
throw invalid ``FileNotFoundError`` if the data file is missing.
- Fixed `143 <https://github.com/sdss/marvin/issues/143>`_: prevents access mode to go in to remote if filename is
present.
- Fixed `213 <https://github.com/sdss/marvin/issues/213>`_: shortcuts are now only applied on full words, to avoid
blind replacements.
- Fixed `206 <https://github.com/sdss/marvin/issues/206>`_: no longer masks spaxels close to zero velocity contour in
web and tools map plots
- Fixed `229 <https://github.com/sdss/marvin/issues/229>`_: corrects web bitmask parsing for map plots
- Fixed `231 <https://github.com/sdss/marvin/issues/231>`_: hatch regions within IFU but without data in map plots
- Fixed `255 <https://github.com/sdss/marvin/issues/255>`_: Lean tutorial code cells did not work with the ipython
directive, so they now use the python directive.
- Highcharts draggable legend cdn.

Removed
^^^^^^^

- Issue 232 and Issue `251 <https://github.com/sdss/marvin/issues/251>`_: Automatic setting of matplotlib style
sheets via seaborn import or ``plt.style.use()``.