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Strauss hack jt #17

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james-trayford@09c3cc6

To show the sonification changes alone - I this incorporates some of the later BUGFIXes from the spacetelescope main branch

Description

This pull request is to address ...

Fixes #

Change log entry

  • Is a change log needed? If yes, is it added to CHANGES.rst? If you want to avoid merge conflicts,
    list the proposed change log here for review and add to CHANGES.rst before merge. If no, maintainer
    should add a no-changelog-entry-needed label.

Checklist for package maintainer(s)

This checklist is meant to remind the package maintainer(s) who will review this pull request of some common things to look for. This list is not exhaustive.

  • Are two approvals required? Branch protection rule does not check for the second approval. If a second approval is not necessary, please apply the trivial label.
  • Do the proposed changes actually accomplish desired goals? Also manually run the affected example notebooks, if necessary.
  • Do the proposed changes follow the STScI Style Guides?
  • Are tests added/updated as required? If so, do they follow the STScI Style Guides?
  • Are docs added/updated as required? If so, do they follow the STScI Style Guides?
  • Did the CI pass? If not, are the failures related?
  • Is a milestone set? Set this to bugfix milestone if this is a bug fix and needs to be released ASAP; otherwise, set this to the next major release milestone.
  • After merge, any internal documentations need updating (e.g., JIRA, Innerspace)?

maartenbreddels and others added 30 commits July 9, 2024 14:19
Unclear what the real underlying issue is. Code comments give a
possible explanation.
…otlib_standalone_compat

fix: make standalone work with matplotlib >= 3.9.0
…cope#2934)

* support exporting a plot from an unopened/inactive plugin
* prevent clearing plot selection (under most conditions)
Sync notebook github links in HTML docs to the git commit used to build them
* BUG: Specviz to respect local_path and timeout when provided

---------

Co-authored-by: Katherine Carver <[email protected]>
Co-authored-by: P. L. Lim <[email protected]>
Co-authored-by: Kyle Conroy <[email protected]>
Co-authored-by: Ricky O'Steen <[email protected]>
…orientation-dropdown

Exclude subsets from WCS-only layer filter
* Use normalize_filename and overwrite_warn for plugin plots

* Clear overwrite warning overlay after confirming

* Changelog

* Codestyle
* Markers: Save to CSV

* Mark block as uncovered for coverage

* Remove unused entries from _dict

* Update CHANGES.rst

Co-authored-by: Kyle Conroy <[email protected]>

---------

Co-authored-by: Kyle Conroy <[email protected]>
…escope#2941)

* Create private method for importing spectral region objects

* Address review comments

* Add tests for list of modes and single SpectralRegion

* Fix style
…-test

Fix for Imviz parser romandeps test after update to defaults
…extract

Bugfix for flux unit conversion in spectral cubes
* UI functioning unit conversion, need to reconcile tests

* update syntax, remove unnecessary logic

* tests now pass, API functionality improved

* add additional equivalencies for coords info

* first pass at disabling specviz translations

* Remove dev flag, consolidate untranslatable units, multi-config support, styling changes

* Refactor moment map unit conversion
to not require spectrum, so nothing to centralize now.

Fix devdeps

Simplify flux_conversion logic
and other minor fixes. Add flux conversion tests.

Clarify which one should be reverted
in the future

* Remove SB/flux conversion for moment map
because moment map always in SB

* add os import

* remove duplicate import from rebase

* reconcile tests, change hints/docs, handle dimensionless case

* emit GlobalDisplayUnitChanged msg when toggling SB<>flux

* resolve most tests

* temporarily remove translation message

* add comments, reenable global display message, resolve tests

* force sb unit for line flux test

* add comments, clarify naming, add case handling for args

* remove args and loop, replaced with msg

* consolidate 2 translator functions into 1, consolidate _translate and _on_flux_unit_changed

* address test failures

* update marks.py equivalencies, resolving UnitConversion errors

* make sure not only translation equivalencies are in marks.py but also conversions

* add test coverage

* use astropy units, small logic tweaks, cache untranslatable units

* technical review changes

* add warning message in tray if PIXAR_SR not present in FITS header

* second pass at technical changes

* move flux_unit checks to beginning of _on_flux_unit_changed

* change _unit to flux.unit

---------

Co-authored-by: P. L. Lim <[email protected]>
Co-authored-by: Kyle Conroy <[email protected]>
…telescope#3101)

* TST: Also run slow test in non-dev env

* BUG: Fix table I/O in Catalog Search

* ID as string always

* Force ID to be always str even from file
…ope#3114)

* MNT: Remove unnecessary astropy version checks

* TST: Update model doctest
…pacetelescope#3113)

* Enabling model fitting results to convert between flux and surface brightness

* Switch to using selected_obj, clean up pixel scale retrieval

* Changelog

* Don't store pixel scale factor

* Fix missing variable

* Update test value due to updated pixel scale factor
kecnry and others added 18 commits July 30, 2024 10:11
* generalize use of term "spectrum"
* move code to allow importing slice mixins without circular imports
* is_slice_indicator filter for extract results instead of relying on a spectrum viewer existing and being set
* attach marks to slice_indicator_viewers[0] instead of spectrum_viewer (temporarily to just the first instance, later we'll make this more flexible to allow any number of slice indicator viewers)
* remove reliance on loaded_flux_cube
* rename (internal) spectral_cube -> cube
* generalize logic for setting disabled_msg
* generalize internal marks names
* generalize some internal traitlet names
* update disabled message to specify cube
* update tests for renamed marks/method
* generalize logic within live-preview and extract
* allow skipping wavelength-dependence
* hide aperture masking method for entire cube and no bg
* fix (and allow disabling) bg export
* fix updating live preview on change to subset
* skip updating marks if not tray instance
MNT: Remove unnecessary astropy check.
…escope#3121)

* remove "Imviz" from "Line Profiles XY" plugin name with deprecation

* changelog entry
spacetelescope#2931)

* Respond to changed unit and display on the UI

* Convert all sb<>sb units listed in the dropdown menu

* Use the default current unit from the cube

* Apply only for relevant configs

* Update current_unit setting logic

* Fix failing tests

* Add tests

* Add a changelog

* Move conversion logic to utils

* Move the conversion to utils

* Pass when unable to convert

* Update tests

* Update based on the feedback

* Only subscribe to cubeviz

* Check for equivalency rather than image dimension

* Refactor conversion logic

Co-authored-by: P. L. Lim <[email protected]>

* Rename unit and broadcast 'sb' as part of msg

* Code style

---------

Co-authored-by: P. L. Lim <[email protected]>
TST: Fix tests downloading data into source dir, MNT: Remove unnecessary astropy check
Cubeviz to use wcs1d-fits from specutils to write out fitted cube
* Avoid checking selected_obj before it's available

* Changelog

* Added a test that fails on main
- Fix sigcube alignment with other cubes [get rid of transpose]
- Add percentile cut option that enables some rough feature isolation without full continuum subtraction
- Protect against cubes w/NaNs
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10 participants