Marvin Beta 2.3.1

This release merges the refactored documentation into master.

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.

Breaking changes

• 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

• 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.

Changed

• 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).

Fixed

• 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

Refactored

• 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.

Marvin Beta 2.2.6

This is a critical bugfix release that corrects a problem that could affect your science results. Please update as soon as possible and check whether your analysis has been impacted by this bug.

This version fixes a critical bug when retrieving the spaxels associated with a bin, as well as a problem with the calculation of the inverse variance for deredden datacubes. It also simplifies the library namespace allowing for easier access to the most used Tools.

This release also adds support for MPL-7

Added

• Added cheatsheet to docs.
• Map has a new method getSpaxel to retrieve an Spaxel using the parent Maps.

Changed

• 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).
• Moved yanny.py to extern/ and added a readme file for the external packages (:issue:468).
• ~marvin.tools.quantities.spectrum.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)

Fixed

• 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.
• Fixed typo in method name Spectrum.derredden -> Spectrum.deredden.
• Fixed #510 <https://github.com/sdss/marvin/issues/510>_ - fixes incorrect conversion to sky coordinates in map plotting.

Marvin Beta 2.2.5

Changed

• Galaxy Web page spaxel loading to be robust when no modelspaxels are present in the database.

Marvin 2.2.4

Fixed

• Issue #400: SII in BPT diagram should use sum of 6717 and 6732.

Marvin Beta 2.2.3

This patch release primarily fixes bugs found during the recent round of feedback vetting.

Added

• Added tests for emline_gflux_ha_6564 and fixed values in galaxy_test_data.

Fixed

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

Removed

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

Marvin Beta 2.2.2

Fixes critical bug with MPL-6 datamodel, where some H-alpha Marvin Maps channels are actually the maps from NII-6585 instead. The affected extensions channels are

emline_sflux_ha_6564
emline_sew_ha_6564
emline_gflux_ha_6564
emline_gew_ha_6564
emline_gsigma_ha_6564

The values in these maps are actually from the respective NII extension.

Additionally, the new R/Reff channel in the following extensions was absent in 2.2.1
spx_ellcoo
bin_lwellcoo_lum_weighted

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>_

Marvin Beta 2.2.1

This patch fixes a bug in the MPL-6 DAP datamodel.

Marvin Beta 2.2.0

This release is a new minor release of Marvin Beta which includes support for MPL-6.

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: 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
• Issue #99
• Issue #110
• Issue #111
• Issue #131
• Issue #133
• Issue #173
• Issue #178
• Issue #180
• Issue #190
• Issue #191
• Issue #233
• Issue #235
• Issue #246
• Issue #248
• Issue #261
• Issue #263
• Issue #269
• Issue #279
• Issue #281
• Issue #286
• Issue #287
• Issue #290
• Issue #291
• Issue #294
• Issue #295
• Issue #296
• Issue #297
• Issue #299
• Issue #301
• Issue #302
• Issue #303
• Issue #304
• Issue #308
• Issue #311
• Issue #312

Marvin Beta 2.1.4

This patch release includes

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: Improvements to "Go to CAS" link. Changed to Go To SkyServer and updated link to public up-to-date link

Fixed:

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