Requre photutils 3+ by larrybradley · Pull Request #10471 · spacetelescope/jwst

larrybradley · 2026-04-20T19:10:09Z

This PR uses a context manager for locally-scoped changes instead of relying on or potentially mutating a global photutils variable.

CC: @braingram

Tasks

braingram · 2026-04-20T19:14:38Z

Thanks! @tapastro mentioned bumping the pin to >=3. Since it's now out, would that be easier (perhaps using the same approach as you added in romancal)?

larrybradley · 2026-04-20T19:20:49Z

Sure, I can do that. I wasn't sure if jwst was ready for that (romancal needs photutils 3+). I'll update this PR.

codecov · 2026-04-20T19:37:22Z

Codecov Report

❌ Patch coverage is 91.66667% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 86.44%. Comparing base (4c7ca23) to head (9704d47).

Files with missing lines	Patch %	Lines
jwst/extract_1d/ifu.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main   #10471      +/-   ##
==========================================
+ Coverage   86.38%   86.44%   +0.05%     
==========================================
  Files         373      373              
  Lines       40095    40033      -62     
==========================================
- Hits        34638    34608      -30     
+ Misses       5457     5425      -32

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larrybradley · 2026-04-20T20:39:09Z

I also bumped numpy >= 2.0 and astropy >= 6.1.4. Those are required for photutils >= 3.0.

larrybradley · 2026-04-20T20:58:16Z

Regression tests:
https://github.com/spacetelescope/RegressionTests/actions/runs/24690043180

larrybradley · 2026-04-21T16:28:10Z

The oldestdeps CI failures are unrelated -- due to PyparsingDeprecationWarning and ValueError: numpy.dtype size changed.

melanieclarke · 2026-04-22T13:36:24Z

It looks like there are some significant differences in the regression tests, for the MIRI and NIRCam image3 results, looks like because the source catalog found some extra sources in both cases. Is that expected with the changes here?

Also, we'll need to update the oldest dependencies allowed to get the oldestdeps tests passing.

larrybradley · 2026-04-22T19:40:45Z

Thanks, @melanieclarke . I updated the min versions of packaging and scikit-image and now the oldestdeps tests pass.

For the regression tests, it appears that the FGS, MIRI, and NIRCam i2d images have differences, which could lead to a slightly different number of sources in the downstream catalogs. Are the differences in the i2d images expected from other recent pipeline changes or dependency updates? For example, there are many differences in the MIRI image (https://github.com/spacetelescope/RegressionTests/actions/runs/24690043180/job/72209316131#step:42:1371), including the WCS (https://github.com/spacetelescope/RegressionTests/actions/runs/24690043180/job/72209316131#step:42:1270).

melanieclarke · 2026-04-22T19:51:03Z

Thanks, @melanieclarke . I updated the min versions of packaging and scikit-image and now the oldestdeps tests pass.

Thank you!

For the regression tests, it appears that the FGS, MIRI, and NIRCam i2d images have differences, which could lead to a slightly different number of sources in the downstream catalogs. Are the differences in the i2d images expected from other recent pipeline changes or dependency updates? For example, there are many differences in the MIRI image (https://github.com/spacetelescope/RegressionTests/actions/runs/24690043180/job/72209316131#step:42:1371), including the WCS (https://github.com/spacetelescope/RegressionTests/actions/runs/24690043180/job/72209316131#step:42:1270).

Our regression tests are clean with current dependencies, so it's not likely other pipeline changes. I expect a few pixels different from upgrading numpy and scipy, but nothing on the scale of the differences for the regtests on the branch here.

I think the i2d differences are because the tweakreg solution is slightly different in the image3 run, so all the pixels are shifted a little compared to the regtest truth files. So, not directly because of the source catalog differences (sorry I misspoke!), but presumably because the sources chosen in tweakreg are a little different with the changes here.

larrybradley · 2026-04-22T20:08:44Z

Thanks. I'll need to investigate the tweakreg differences.

emolter

Looks good, thanks for handling this! I had just a few small comments.

emolter · 2026-05-04T18:29:01Z

+        if isinstance(ellipticity, u.Quantity):
+            ellipticity = ellipticity.value


why is an if...else necessary here? Shouldn't it always be one or the other, a Quantity or not?

emolter · 2026-05-04T18:35:05Z

        JWSTSourceCatalog.convert_mjysr_to_jy(output_model)

+        min_separation = (
+            max(2, int(self.minsep_fwhm * self.kernel_fwhm + 0.5)) if self.minsep_fwhm else None


Won't self.minsep_fwhm always be set as an attribute since it's in the spec, so there's no need for the None setting if undefined?

emolter · 2026-05-04T18:36:05Z

 # The tweakreg catalog output always uses 'xcentroid'/'ycentroid',
 # but _rename_catalog_columns and user-supplied catalogs may use
 # either the old or new photutils column names.


Is this comment still relevant?

emolter · 2026-05-04T18:39:11Z

    def _find_sources(self, image_model):
+        # preserve original behavior
+        min_separation = (
+            max(2, int(self.minsep_fwhm * self.kernel_fwhm + 0.5)) if self.minsep_fwhm else None


same here as for source catalog

pllim · 2026-05-05T21:25:32Z

Can you also do this change? Thanks!

Update photutils requirement from <3,>=2.1.0 to >=2.1.0,<4 #10498

larrybradley requested a review from a team April 20, 2026 19:10

larrybradley requested review from emolter and mcara as code owners April 20, 2026 19:10

github-actions Bot added the tweakreg label Apr 20, 2026

larrybradley requested review from jemorrison and melanieclarke as code owners April 20, 2026 20:38

larrybradley changed the title ~~Use context manager instead of global variable for photutils 3+~~ Requre photutils 3+ Apr 20, 2026

github-actions Bot added source catalog extract_1d testing Wide Field Slitless Spec (WFSS) installation wfss_contam labels Apr 20, 2026

larrybradley force-pushed the photutils-future branch 2 times, most recently from 76c4598 to 68bee8d Compare April 20, 2026 20:42

larrybradley requested review from penaguerrero, pllim and tapastro as code owners April 20, 2026 20:54

github-actions Bot added NIRISS regression_testing labels Apr 20, 2026

larrybradley force-pushed the photutils-future branch from b9ed068 to 4382d19 Compare April 20, 2026 20:58

melanieclarke added this to the Build 13.0 milestone Apr 22, 2026

larrybradley force-pushed the photutils-future branch from 4382d19 to a5b02a4 Compare April 22, 2026 18:31

braingram mentioned this pull request Apr 28, 2026

Update photutils requirement from <3,>=2.1.0 to >=2.1.0,<4 #10481

Closed

larrybradley added 6 commits May 1, 2026 12:21

Use context manager instead of global variable

d637ba0

Require photutils 3+; bump dependent versions

2e860aa

Remove support for photutils 2.x

25bc5d6

Add changelog entry

82fb4f2

Update regtests

b60e3de

Bump min version of packaging and scikit-image to prevent warnings

9704d47

larrybradley force-pushed the photutils-future branch from a5b02a4 to 9704d47 Compare May 1, 2026 16:21

emolter reviewed May 4, 2026

View reviewed changes

pllim mentioned this pull request May 5, 2026

Update photutils requirement from <3,>=2.1.0 to >=2.1.0,<4 #10498

Closed

pllim reviewed May 5, 2026

View reviewed changes

		if isinstance(ellipticity, u.Quantity):
		ellipticity = ellipticity.value

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larrybradley commented Apr 20, 2026 •

edited by melanieclarke

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