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Marvin Beta 2.3.3

Marvin Beta 2.3.3

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@havok2063 havok2063 released this 09 Dec 03:07
2.3.3
83f4d3a

This release adds support for MaNGA DR16 data, expands access to new MaNGA VACs contributed to MaNGA for DR16, and adds a new VACs tool to access complete VAC FITS file. This release also now fully works on Windows machines. It expands the Map arithmetic operations, and enhances the web experience when viewing individual galaxies.

Added

  • Support for DR16. Updated datamodels and docs.
  • Added Galaxy Zoo VAC
  • Added GEMA VAC
  • Added Firefly VAC
  • Added Visual Morphology VAC
  • Merged :pr:678, richer support for VACs
  • Merged :pr:652, richer support for Windows
  • Merged :pr:677, updated documentation on issues with fuzzy string matching
  • Merged :pr:687, fixes map arithmetic with reflexive operators

Changed

  • all yaml.load uses new Loader to accommodate old and new yaml spec;
  • updated Runtime Issues documentation to include section on numpy.ufunc binary warnings
  • added to reprs for some db ModelClasses
  • all sdss_access.sync.RsyncAccess has been converted to sdss_access.sync.Access to allow for Linux/Windows switching
  • updates citation to Marvin paper
  • DAP Maps label on galaxy page now contains a pop up of links for more info

Fixed

  • Issue :issue:658 - modelcube datamodel units missing angstrom
  • Issue :issue:655 - added yaml loader to remove yaml warnings for 5.1 spec
  • Fixed bug when server tries to access NSA on cube when none exists and triggers remote authentication issue
  • Issue :issue:664 - Fixed link to MaNGA's Getting Started in docs.
  • Issue :issue:686 - added reflexive operators to EnhancedMap
  • Issue :issue:689 - added link to CSV file of Firefly stellar mass measurements needed for the Spatially-Resolved Mass-Metallicity Relation Tutorial
  • Issue :issue:682 - adds info links next to DAP Maps selection on galaxy page
  • Issue :issue:581 - makes MapSpecView button a session variable
  • Issuu :issue:208 - makes map selections session variable
  • Issue :issue:171 - fix y-min to 0 for spectrum web view
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Marvin Beta 2.3.2

Marvin Beta 2.3.2

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@havok2063 havok2063 released this 27 Feb 19:40
2.3.2
d51cbd9

This release primarily adds supports for MPL-8.

Added

  • Support for MPL-8

Fixed

  • Issue #629 - web table of search results broken
  • Issue #627 - web query displaying error message
  • Issue #630 - broken web links on query page
  • Issue #591 - broken query streaming return all results
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Marvin Beta 2.3.1

Marvin Beta 2.3.1

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@havok2063 havok2063 released this 10 Dec 23:04
2.3.1
95572fc

This release merges the refactored documentation into master.

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Marvin Beta 2.3.0

Marvin Beta 2.3.0

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@havok2063 havok2063 released this 07 Dec 22:22
2.3.0
d9a56eb

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.
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Marvin Beta 2.2.6

Marvin Beta 2.2.6

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@havok2063 havok2063 released this 14 Aug 15:29
2.2.6
cf843d1

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.
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Marvin Beta 2.2.5

Marvin Beta 2.2.5

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@havok2063 havok2063 released this 26 Apr 15:35
2.2.5
e348662

Changed

  • Galaxy Web page spaxel loading to be robust when no modelspaxels are present in the database.
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Marvin 2.2.4

Marvin 2.2.4

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@albireox albireox released this 04 Apr 21:03
2.2.4
e6d6dc5

Fixed

  • Issue #400: SII in BPT diagram should use sum of 6717 and 6732.
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Marvin Beta 2.2.3

Marvin Beta 2.2.3

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@havok2063 havok2063 released this 30 Mar 18:46
2.2.3
dc44439

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

Removed

  • The banner that showed up in Safari has been removed since most versions should now work properly.
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Marvin Beta 2.2.2

Marvin Beta 2.2.2

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@havok2063 havok2063 released this 25 Feb 19:01
2.2.2
e42bdeb

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>_
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Marvin Beta 2.2.1

Marvin Beta 2.2.1

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@havok2063 havok2063 released this 12 Jan 21:11
2.2.1
d7200fc

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

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