Merge 2.0 dev branch into main #1220
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…1033) * Starting to work on flexible spectral axis location Debugging initial spectrum creation Set private attribute here Working on debugging failing tests More things are temporarily broken, but I don't want to lose this work so I'm committing here Set spectral axis index to 0 if flux is None Working through test failures Fix codestyle Allow passing spectral_axis_index to wcs_fits loader Require specification of spectral_axis_index if WCS is 1D and flux is multi-D Decrement spectral_axis_index when slicing with integers Propagate spectral_axis_index through resampling Fix last test to account for spectral axis staying first Fix codestyle Specify spectral_axis_index in SDSS plate loader Greatly simply extract_bounding_spectral_region Account for variable spectral axis location in moment calculation, fix doc example Working on SpectrumCollection moment handling...not sure this is the way Need to add one to the axis index here Update narrative docs to reflect updates * Add back in the option to move the spectral axis to last, for back-compatibility Work around pixel unit slicing failure Change order on crop example Fix spectral slice handling in tuple input case (e.g. crop) Update output of crop example * Apply suggestions from code review Co-authored-by: Adam Ginsburg <[email protected]> Apply suggestion from code review Add helpful comment * Address review comment about move_spectral_axis, more docs * Add suggested line to docstring Co-authored-by: Erik Tollerud <[email protected]> * Add convenience method Make this a docstring * Add v2.0.0 changelog section --------- Co-authored-by: Erik Tollerud <[email protected]>
* Allow spectral axis to be anywhere, instead of forcing it to be last (#1033) * Starting to work on flexible spectral axis location Debugging initial spectrum creation Set private attribute here Working on debugging failing tests More things are temporarily broken, but I don't want to lose this work so I'm committing here Set spectral axis index to 0 if flux is None Working through test failures Fix codestyle Allow passing spectral_axis_index to wcs_fits loader Require specification of spectral_axis_index if WCS is 1D and flux is multi-D Decrement spectral_axis_index when slicing with integers Propagate spectral_axis_index through resampling Fix last test to account for spectral axis staying first Fix codestyle Specify spectral_axis_index in SDSS plate loader Greatly simply extract_bounding_spectral_region Account for variable spectral axis location in moment calculation, fix doc example Working on SpectrumCollection moment handling...not sure this is the way Need to add one to the axis index here Update narrative docs to reflect updates * Add back in the option to move the spectral axis to last, for back-compatibility Work around pixel unit slicing failure Change order on crop example Fix spectral slice handling in tuple input case (e.g. crop) Update output of crop example * Apply suggestions from code review Co-authored-by: Adam Ginsburg <[email protected]> Apply suggestion from code review Add helpful comment * Address review comment about move_spectral_axis, more docs * Add suggested line to docstring Co-authored-by: Erik Tollerud <[email protected]> * Add convenience method Make this a docstring * Add v2.0.0 changelog section --------- Co-authored-by: Erik Tollerud <[email protected]> * Prepare changelog for 1.10.0 release * Fix Changelog * Fixed issues with ndcube 2.1 docs * Fix incorrect fluxes and uncertainties returned by FluxConservingResampler, increase computation speed (#1060) * new implementation of flux conserving resample * removed unused method * handle multi dimensional flux inputs * . * Update CHANGES.rst Co-authored-by: Erik Tollerud <[email protected]> * omit removing units * added test to compare output to output from running SpectRes --------- Co-authored-by: Erik Tollerud <[email protected]> * Update changelog for 1.11.0 release * Changelog back to unreleased * Working on retaining full GWCS information in Spectrum1D rather than just spectral coords * Handle getting the spectral axis out of a GWCS Add changelog heading Remove debugging prints Fix changelog Fix codestyle * Add changelog entry * Delete the commented-out old wavelength parsing code * More accurate changelog --------- Co-authored-by: Erik Tollerud <[email protected]> Co-authored-by: Nabil Freij <[email protected]> Co-authored-by: Clare Shanahan <[email protected]>
* Rename Spectrum1D to Spectrum * Update name in analysis * Update name in fitting and manipulation * Update name in tests * Update name in io * Update name in io tests * Add changelog entry * Update class name in docs * Update schema ref in spectrum_list asdf * Replace instances of 'spectrum1d' * Properly (I think) version change to asdf schema * Add PR number to changelog entry * Remove unused import * Fix doc example output * Fix failing remote data test * Update url to MANGA data for tests * Fix RSS filename
Update SAMI test expected shape Fix moment 0 calculation for spectral axis that isn't last, and change non-spectral axis moments to use pixel values Raise error for invalid order, add note to docs Clean up instances of Spectrum1D after rebase to main Fix failing tests
* Working on constructing N dimensional GWCS for ND flux with only spectral axis provided * Get forward transform working for ND case * Convert other operator to Spectrum if needed in specutils where we have more control, rather than in astropy ndarithmetic * Don't pass extra arg to ndarithmetic * Use dimensionless instead of pix, remove unit conversion code that I think was unneeded and was causing errors * Fix two tests for multidimensional GWCS, remove debugging print * Working on debugging SpectrumCollection * Check for Spectrum specifically before arithmetic * Remove incorrect index from spectrum collection slice, cast operand as Spectrum even in 1D case * Don't pass multi-d WCS to collapsed spectrum * Fixing more test failures * Revamp arithmetic * Add changelog * remove debugging print * Handle creating dummy WCS and spectral axis when neither are provided, fix order of WCS * Codestyle * Remove debugging prints * Fixes for compatibility with up to date gwcs * Bump min version pins Bump min asdf Bump min astropy Bump min scipy Bump min asdf-astropy * Need gwcs 0.24 * Add note about arithmetic to changelog * Fix Spectrum1D references in doc page Fix skips in doc file
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #1220 +/- ##
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+ Coverage 86.89% 86.93% +0.03%
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Files 63 63
Lines 4572 4683 +111
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+ Hits 3973 4071 +98
- Misses 599 612 +13 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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* Handle pixel units correctly in gwcs_from_array, subtract fluxes as NDDataArrays * Update __add__ to be similar to new __sub__ * Consolidate arithmetic code
* Make WCS have unit of pixels to be consistent with spectral axis in this case, handle a couple bugs * Fix assumption that spectral axis is last in convolution smoothing * Make a couple reasonable assumptions in spectrum class * Keep original WCS in meta after _copy with spectral axis * Codestyle * Don't unnecessarily pass spectral axis in smoothing _copy, back to default None bin specification
* Allow -1 as spectral_axis_index * Add short note about 2.0 to README * Minor doc tweaks * Changelog
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Not to be merged yet, this is just to have an easy reference for the full diff between current
mainand thev2.0-devbranch.