Marvin’s Change Log¶

[2.2.5] - 2018/04/26¶

[2.2.4] - 2018/04/04¶

[2.2.3] - 2018/03/20¶

[2.2.2] - 2018/02/25¶

[2.2.1] - 2018/01/12¶

• bugfix in MPL-6 datamodel for gew OII lines

[2.2.0] - 2018/01/12¶

• 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

• 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

• 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

[2.1.4] - 2017/08/02¶

• 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 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

• 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

[2.1.3] - 2017/05/18¶

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

• Issue #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: Moved map plotting methods from tools/map to utils/plot/map
• Issue #229 and Issue #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: Move plot defaults to datamodel (i.e., bitmasks, colormaps, percentile clips, symmetric, minimum SNR).
• Issue #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.

• Interactive prompt for username in sdss_access now works for Python 3.
• Fixed #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: prevents access mode to go in to remote if filename is present.
• Fixed #213: shortcuts are now only applied on full words, to avoid blind replacements.
• Fixed #206: no longer masks spaxels close to zero velocity contour in web and tools map plots
• Fixed #229: corrects web bitmask parsing for map plots
• Fixed #231: hatch regions within IFU but without data in map plots
• Fixed #255: Lean tutorial code cells did not work with the ipython directive, so they now use the python directive.
• Highcharts draggable legend cdn.

• Issue #232 and Issue #251: Automatic setting of matplotlib style sheets via seaborn import or plt.style.use().

[2.1.2] - 2017/03/17¶

• API and Web argument validation using webargs and marshmallow. If parameters invalid, returns 422 status.

• Per Issue #186: Switched to using the elpetro version of stellar mass, absolute magnitude i-band, and i-band mass-to-light ratio for NSA web display, from sersic values. (elpetro_logmass, elpetro_absmag_i, elpetro_mtol_i)
• Issue #188: deprecated snr in favour of snr_min for get_bpt. snr can still be used.
• Issue #187: Renamed NSA Display tab in web to Galaxy Properties. Added a link to the NASA-Sloan Atlas catalogue to the table title.
• Moved our documentation to readthedocs for version control. Updated all Marvin web documenation links to point to readthedocs.

• A bug in the calculation of the composite mask for BPT.
• Issue #179: Fixed a python 2/3 exception error compatibility with the 2.1 release.

[2.1.1] - 2017/02/18¶

• Added query runtime output in search page html. And a warning if query is larger than 20 seconds.

• Removed the python 3 raise Exception in the check_marvin bin
• Reverted the api/query return output from jsonify back to json.dumps
  • This is an issue with python 2.7.3 namedtuple vs 2.7.11+

• Issue #181: web display of maps were inverted; changed to xyz[jj, ii, val] in heatmap.js
• Added more code to handle MarvinSentry exceptions to fix #179.

[2.1.0] - 2017/02/16¶

• Restructured documentation index page.
• Improved installation documentation:
  • Removed old installation text
  • Added section on marvin SDSS dependencies and SAS_BASE_DIR
  • Added section for FAQ about installation
  • Added web browser cache issue into FAQ
• Added traceback info in the API calls
  • Added traceback attribute in Brain config
  • Added hidden _traceback attribute in Marvin config
  • Only implemented in two Query API calls at the moment
  • Added a few tests for traceback
  • see usage in cube_query in marvin/api/query.py
• Added the Ha_to_Hb ratio the DAP ModelClasses for querying
• Added new script to perform somce basic system, os, and Marvin checks: bin/check_marvin
• Added an alert banner when the user is using Safari. See #94.
• Issue #122: added ra/dec to spaxel
• Issue #145: Limited the number of query parameters in the web
• Added more tests to Results for sorting, paging, and getting subsets
• Added kwargs input for Spaxel when using Result.convertToTool
• Added automatic Sentry error logging #147 into MarvinError, and Sentry in Flask for production mode
• Added custom error handlers for the web, with potential user feedback form
• Added Sentry tool for grabbing and displaying Sentry statistics
• Added text to MarvinError with a Github Issues link and description of how to submit and issue
• Added Results option to save to CSV
• Added new parameters in Marvin Config to turn off Sentry error handling and Github Issue message
• Added Python example code for getting a spectrum in galaxy page of web.
• Added new test for image utilities getRandomImages, getImagesByPlate, getImagesByList
• Added new documentation on Image Utilities
• Added new image utility function showImage, which displays images from your local SAS
• Added the Kewley+06 implementation of the BPT classification as Maps.get_bpt()
• Added quick access to the NSA information for a Cube/Maps either from mangaSampleDB or drpall.

• When marvin is running from source (not dist), marvin.__version__ is dev.
• Removed the cleanUpQueries method to assess db stability
• Switched dogpile.cache from using a file to python-memcached
• Syntax changes and bug fixes to get Marvin Web working when Marvin run on 3.5
• Got Queries and Results working in 3.5
• Changed all convertToTool options in Results from mangaid to plateifu
• Added release explicitly into api query routes
• Modified the decision tree in query to throw an error in local mode
• Modified convertToTool to accept a mode keyword
• Modifed the MarvinError for optional Sentry exception catching, and github issue inclusion
• Updated all Marvin tests to turn off Sentry exception catching and the github message
• Updated some of the Tools Snippets on the web
• Overhauled Map plotting
  • uses DAP bitmasks (NOVALUE, BADVALUE, MATHERROR, BADFIT, and DONOTUSE)
  • adds percentile and sigma clipping
  • adds hatching for regions with data (i.e., a spectrum) but no measurement by the DAP
  • adds Linear Lab color map
  • adds option for logarithmic colorbar
  • adds option to use sky coordinates
  • adds map property name as title
  • makes plot square
  • sets plotting defaults:
    • cmap is linear_Lab (sequential)
    • cmap is RdBu_r (diverging) for velocity plots (Note: this is reversed from the sense of the default coolwarm colormap in v2.0—red for positive velocities and blue for negative velocities)
    • cmap is inferno (sequential) for sigma plots
    • clips at 5th and 95th percentiles
    • clips at 10th and 90th percentiles for velocity and sigma plots
    • velocity plots are symmetric about 0
    • uses DAP bitmasks NOVALUE, BADVALUE, MATHERROR, BADFIT, and DONOTUSE
    • also masks spaxels with ivar=0
    • minimum SNR is 1
• Changed Marvin Plate path back to the standard MarvinToolsClass use
• Made sdss_access somewhat more Python 3 compatible
• Modified the image utilities to return local paths in local/remote modes and url paths when as_url is True
• downloadList utility function now downloads images
• updated the limit-as parameter in the uwsgi ini file to 4096 mb from 1024 mb for production environment

• Issue #115: drpall does not get updated when a tool sets a custom release.
• Issue #107: missing os library under save function of Map class
• Issue #117: hybrid colours were incorrect as they were being derived from petroth50_el.
• Issue #119: test_get_spaxel_no_db fails
• Issue #121: bugfix with misspelled word in downloadList utility function
• Issue #105: query results convertToTool not robust when null/default parameters not present
• Issue #136: BinTest errors when nose2 run in py3.5 and marvin server in 3.5
• Issue #137: PIL should work in py2.7 and py3.5
• Issue #172: broken mode=auto in image utilities
• Issue #158: version discrepancy in setup.py

[2.0.9] - 2016/11/19¶

• Docs now use marvin.__version__.

• Fixed #100, #103: problem with getMap for properties without ivar.
• Fixed #101: problem with marvin query.

[2.0.8] - 2016/11/18¶

• Now really fixing #98

[2.0.7] - 2016/11/18¶

• Fixed issue #98

[2.0.6] - 2016/11/17¶

• Bug in Queries with dap query check running in remote mode. Param form is empty.

[2.0.5] - 2016/11/17¶

• Added netrc configuration to installation documentation.
• Added netrc check on init.

• Added mask to model spaxel.
• Bug in Cube tool when a galaxy loaded from db does not have NSA info; no failure with redshift
• Two bugs in index.py on KeyErrors: Sentry issues 181369719,181012809
• Bug on plate web page preventing meta-data from rendering
• Fixed installation in Python 3.
• Fixed long_description in setup.py to work with PyPI.
• Fixed a problem that made marvin always use the modules in extern

[The dark ages] - multiple versions not logged.¶

[1.90.0]¶

• Full refactoring of Marvin 1.0
• Refactored web

• Marvin Tools
• Queries (only global properties, for now)
• Point-and-click for marvin-web
• RESTful API
• Many more changes

• Issue albireox/marvin#2: Change how matplotlib gets imported.