sdss/marvin: Marvin Beta 2.3.0

This release represents a major overhaul of Marvin for the DR15 public data release. It introduces a new token authentication system, a public versus collaboration access modes, and many other new and refactored changes. With this version change on the server-side, all Marvin versions 2.2.x will no longer be compatible.

• Removed Bin class. Bin information is now available on a per-quantity basis (:issue:109). See :ref:What's new? <whats-new> and documentation for details.
• Syntax on the inputs to the Query and Results tools has been changed.
• DAP spaxel queries have been disabled due to performance issues. We expect to bring them back soon. Metadata queries (those querying the NSA or DAPall tables) are still available.
• getSpaxel now only loads the quantities from the parent object (that means that, for example, Maps.getSpaxel only loads Maps properties by default). Additional quantities can be loaded using ~marvin.tools.spaxel.Spaxel.load.
• getSpaxel accepted arguments have been changed to cube, maps, and modelcube. The formerly accepted arguments (drp, properties, model(s)) now raise a deprecation error.

• Added cheatsheet to docs.
• New Web authentication using Flask-Login
• New API authentication using Flask-JWT-Extended
• Adds MPL-7 / DR15 datamodel
• New config.access attribute indicating public or collab access
• New config.login method to handle token-based login
• New marvin.yml config file for customization of configuration options
• Adds User table into the history schema of mangadb. Tracks user logins.
• Map has a new method getSpaxel to retrieve an Spaxel using the parent Maps.
• New configuration option in marvin.yml, default_release, to set the release to be used when Marvin gets imported (:issue:463).
• Applying a NumPy ufunc (except np.log10()) raises NotImplementedError because ivar propagation is not implemented yet.
• New Marvin Image Tool to load optical images using the MMA (:issue:22)
• New Bundle and Cutout utility classes
• New MMAMixIn for providing multi-modal data access
• qual_flag and pixmask_flag are now stored in the datamodel (:issue:479,482).
• Query tool now accepts a new targets and quality keyword argument which enables querying on target or quality maskbit labels. (:issue:485)
• Added a new API route for streaming large query results. This uses a generator to stream large results back to the client to minimize memory usage and bulk responses.

• Integrated datamodel plotting params into actual datamodel structures
• Moved netrc checks into the Brain
• Expanded sasurl into public and collab urls
• Changes personal emails to sdss helpdesk email in web
• Added rawsql and return_params columns to history.query table in mangadb
• Extra keyword arguments passed to Spectrum.plot are now forwarded to Axes.plot.
• Tools (e.g., Cube, Maps) can now be accessed from the marvin namespace (e.g., marvin.tools.Cube or marvin.tools.cube.Cube).
• Map plotting ax_setup() function is now hidden.
• Moved yanny.py to extern/ and added a readme file for the external packages (:issue:468).
• ~marvin.tools.quantities.Spectrum.plot now only masks part of the spectrum that have the DONOTUSE maskbit set (:issue:455).
• pixmask is now available for all quantities (except AnalysisProprty). The property masked now uses the bit DONOTUSE to determine what values must be masked out (:issue:462).
• Raises error when applying inst_sigma_correction on stellar_sigma MPL-6 maps. Applies correction to stellar_sigma and emline_sigma for web maps with added 'Corrected' title (:issue:478)
• Removes targeting bits from Spaxel and Bin (:issue:465).
• The name of the channel is now shown in the Property description (:issue:424).
• Replaced inconsistent parameter model in ~marvin.tools.maps.Maps.getSpaxel. Use models instead.
• MarvinError now accepts an optional ignore_git keyword to locally turn off the git addition to the message
• Using the return_all keyword in Query or getAll in Results now calls the streaming API route instead.
• When ~marvin.tool.cube.Cube or ~marvin.tool.modelcube.ModelCube are instantiated from file, gunzip the file to a temporary location to speed up subsequent access (:issue:525).
• Convert MMA warnings to debug messages (:issues:580).

• Issue :issue:421 - query returning spaxel props returns wrong total count
• Bugfix - Python 3 xrange syntax bug in buildImageDict
• Bin._create_spaxels instantiating spaxels with the wrong (i,j) values for the bin. The (i, j) values from the binid map were being swapped twice before sending them to SpaxelBase (:issue:457).
• A bug in the calculation of the deredden inverse variance in a ~marvin.tools.quantities.datacube.DataCube.
• Issue with setting drpall path on initial import/set of release before tree has been planted
• Issue :issue:456 - spectrum web display shows incorrect RA, Dec
• Issue :issue:422 - ensuring config auto checks access to netrc
• Issue :issue:423 - adding marvin.yml documentation
• Issue :issue:431 - adding login documentation
• Issue :issue:151 - adding web spectrum tooltips
• Issue :issue:548 - failed to retrieve ModelCube extension in remote mode
• Fixed typo by in method name Spectrum.derredden -> Spectrum.deredden.
• Fixed #305 <https://github.com/sdss/marvin/issues/305>_ - adding ivar propogation for np.log10(Map)
• A bug when explicitly returning default parameters in a query (:issue:484)
• Fixed #510 <https://github.com/sdss/marvin/issues/510>_ - fixes incorrect conversion to sky coordinates in map plotting.
• Fixed #563 <https://github.com/sdss/marvin/issues/563>_ - fail retrieving Query datamodels in Python 3.6+.
• Fixes bug with sasurl not properly being set to api.sdss.org on initial import
• Incorrect setting of the default bintype to download from web (:issue:531).
• Fixed :issue:536, :issue:537, :issue:538. Added modelcube to downloadList.
• Incorrect mismatch warning between MPL-7 and DR15 (:issue:495).
• Incorrect handling of maskbits when the mask does not contain any of the bits in the list (:issue:507).
• Fixed :issue:534 - flipped axes in NSA scatterplot when plotting absmag colors
• Fixed :issue:559 - bug in check_marvin when marvindb is None
• Fixed :issue:579 - bug in MMA with marvindb preventing files from opening
• Fixed :issue:543, :issue:552, :issue:553 - bugs with various Query handlings
• Fixed :issue:575 - cannot access maps due to bug in login and authentication in Interaction class
• Fixed :issue:539 - print downloadList target directory
• Fixed :issue:566 - made error message for web query with non-unique parameters name more specific

• Moved marvin.core.core to marvin.tools.core and split the mixins into marvin.tools.mixins.
• Reimplemented ~marvin.tools.mixins.aperture.GetApertureMixIn.getAperture as a mixin using photutils apertures (:issue:3,315).
• Reimplemented ~marvin.tools.rss.RSS as a list of ~marvin.tools.rss.RSSFiber objects (:issue:27,504).
• Moved pieces of MarvinToolsClass into marvin.tools.mixins.
• Reimplemented ~marvin.tools.query.Query to remove local query dependencies from remote mode usage.