Initial ASDF extension and tests by nden · Pull Request #2211 · astropy/photutils

nden · 2026-03-04T07:03:59Z

This PR is a contribution to astropy/astropy-project#527 . It implements the initial setup for serializing photutils PSF and aperture objects to ASDF. The proposal mentioned the implementation will be in asdf-astropy. However, after discussion with the ASDF developers we decided to include the implementation in photutils in order to keep the library code in sync with the serialization more easily. This PR adds

ASDF extension
Schemas for one PSF model and one aperture
Converters for the obkects
Sets up testing of schemas and adds tests for the converters

I am not able to request reviewers so tagging here @larrybradley @perrygreenfield @braingram

larrybradley · 2026-03-04T13:36:05Z

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nden · 2026-03-05T09:05:44Z

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nden · 2026-03-05T09:10:55Z

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nden · 2026-03-06T08:31:04Z

Bumping the min version of astropy to v 7.2 fixed the oldestdeps test. Is this an acceptable change?

larrybradley · 2026-03-06T15:27:34Z

@nden Is astropy 7.2 (released Nov 2025) the only version that works? Requiring only the latest release of astropy does seem to be a bit restrictive. That would also put constraints on all photutils dependencies, like jwst, romancal, drizzlepac/hap, etc.

nden · 2026-03-07T08:23:19Z

The failing tests were using astropy 6.1.4. It appears there was a follow up bug fix release, 6.1.7, which works.

braingram

I do not have enough experience with photutils to test if real instances of these classes roundtrip so I only looked at this from an asdf extension perspective. I left a few comments, questions and suggestions.

Overall looks like it's on the right track. Aside from the one suggested schema change the rest of the comments are mostly questions or test changes.

braingram · 2026-03-10T17:27:22Z

pyproject.toml

 filterwarnings = [
    'error',  # turn warnings into exceptions
 ]
+asdf_schema_root = 'photutils/resources/schemas'


Is this sufficient to run these tests in the CI? So far I see lots of --pyargs photutils in the CI jobs which result in unpredictable file paths which typically result in the pytest-asdf-plugin failing to find schemas to tests: asdf-format/pytest-asdf-plugin#8

It's unclear to me if it's helpful to test schemas as part of all CI jobs (for example oldestdeps or macos vs linux) so one thing to consider is delegating schema testing to 1 CI job (either an existing one or a new one).

FWIW if I run pytest locally it is picking up these tests. However I'm not familiar enough with the photutils CI to know what to expect here. For example, considering the py313-all-deps job:

on main: 3038 passed, 30 skipped

this pr: 2858 passed, 28 skipped

Most of that difference appears to be from this PR having a base commit older than HEAD on main.

braingram · 2026-03-10T17:29:33Z

pyproject.toml

+    'to_yaml_tree',  # ASDF converter
+    'from_yaml_tree',  # ASDF converter


It seems useful to include these in the coverage measurement. Aren't they covered by the converter tests?

braingram · 2026-03-10T17:49:25Z

photutils/resources/manifests/photutils-1.0.0.yaml

+- tag_uri: tag:astropy.org:photutils/aperture/circular_aperture-1.0.0
+  schema_uri: asdf://astropy.org/photutils/schemas/aperture/circular_aperture-1.0.0
+  title: CircularAperture
+  description: ASDF schema for serializing a photutils CircularAperture.


Suggested change

description: ASDF schema for serializing a photutils CircularAperture.

description: Circular aperture with one or more positions.

This is a nitpick. Since this is a tag definition I don't think "ASDF schema" fits. I'm also on the fence about adding "photutils" since that's already in the URI (and in other context). If this is updated would you update the other descriptions to match?

braingram · 2026-03-10T17:59:35Z

photutils/resources/schemas/aperture/circular_aperture-1.0.0.yaml

+          anyOf:
+            - type: number
+              maxItems: 2
+              minItems: 2


Suggested change

minItems: 2

These keywords don't apply to number

braingram · 2026-03-10T18:02:42Z

photutils/resources/schemas/aperture/circular_aperture-1.0.0.yaml

+    anyOf:
+      - type: array
+        items:
+          anyOf:
+            - type: number
+              maxItems: 2
+              minItems: 2
+            - type: array
+              items:
+                type: number
+              maxItems: 2
+              minItems: 2
+      - tag: "tag:stsci.edu:asdf/core/ndarray-1.*"


Suggested change

anyOf:

- type: array

items:

anyOf:

- type: number

maxItems: 2

minItems: 2

- type: array

items:

type: number

maxItems: 2

minItems: 2

- tag: "tag:stsci.edu:asdf/core/ndarray-1.*"

anyOf:

- type: array

minItems: 2

maxItems: 2

items:

type: number

- tag: "tag:stsci.edu:asdf/core/ndarray-1.*"

Is there any condition where this can be a list of lists? I think the converter can currently only produce:

a ndarray

a 2 item list of numbers

braingram · 2026-03-10T18:04:39Z

photutils/converters/apertures.py

+
+class CircularApertureConverter(Converter):
+    """
+    Base class for aperture converters.


Are there (or is there a plan to add) child classes?

braingram · 2026-03-10T18:05:39Z

photutils/converters/apertures.py

+    Base class for aperture converters.
+    """
+
+    tags = ['tag:astropy.org:photutils/aperture/circular_aperture-*']  # noqa: RUF012, E501


Suggested change

tags = ['tag:astropy.org:photutils/aperture/circular_aperture-*'] # noqa: RUF012, E501

tags = ('tag:astropy.org:photutils/aperture/circular_aperture-*',) # noqa: E501

Making this a tuple would allow removing the noqa for RUF012. Same applies to the other tags and types.

braingram · 2026-03-10T18:07:21Z

photutils/converters/tests/test_apertures.py

+
+        assert np.all(aperture.positions == aperture2.positions)
+        assert aperture.r == aperture2.r


Suggested change

assert np.all(aperture.positions == aperture2.positions)

assert aperture.r == aperture2.r

assert np.all(aperture.positions == aperture2.positions)

assert aperture.r == aperture2.r

These should be in the with since asdf is using lazy loading and aperature2.positions may be a ndarray.

braingram · 2026-03-10T18:08:32Z

photutils/converters/tests/test_psf.py

+        assert psf.flux == psf2.flux
+        assert psf.x_0 == psf2.x_0
+        assert psf.y_0 == psf2.y_0
+        assert psf.radius == psf2.radius
+        assert psf.bbox_factor == psf2.bbox_factor


Suggested change

assert psf.flux == psf2.flux

assert psf.x_0 == psf2.x_0

assert psf.y_0 == psf2.y_0

assert psf.radius == psf2.radius

assert psf.bbox_factor == psf2.bbox_factor

assert psf.flux == psf2.flux

assert psf.x_0 == psf2.x_0

assert psf.y_0 == psf2.y_0

assert psf.radius == psf2.radius

assert psf.bbox_factor == psf2.bbox_factor

Similar to https://github.com/astropy/photutils/pull/2211/changes#r2913554434 asdf is lazy loading and psf2 is coming from a file.

larrybradley added aperture psf asdf_serialization labels Mar 4, 2026

nden added 5 commits March 5, 2026 11:04

initial ASDF extension and tests

0c4dfb0

fix style

fc9e972

fix pre-commit errors

d768014

make asdf-astropy required

091e20f

appease ruff

3800369

nden force-pushed the asdf-init branch from e0ac31b to 3800369 Compare March 5, 2026 09:04

line length fix

069993b

nden force-pushed the asdf-init branch from c0104e3 to 069993b Compare March 5, 2026 09:10

pre-commit-ci bot and others added 2 commits March 5, 2026 09:11

[pre-commit.ci] auto fixes from pre-commit.com hooks

8edfdf0

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bump min version of astropy to 7.2

5251c03

fix test and increase code cov

4e46695

nden added 2 commits March 7, 2026 08:58

try another way to fix olddeps test

c1710f2

one more attempt

c94835f

braingram reviewed Mar 10, 2026

View reviewed changes

		'to_yaml_tree', # ASDF converter
		'from_yaml_tree', # ASDF converter

	description: ASDF schema for serializing a photutils CircularAperture.
	description: Circular aperture with one or more positions.

	tags = ['tag:astropy.org:photutils/aperture/circular_aperture-*'] # noqa: RUF012, E501
	tags = ('tag:astropy.org:photutils/aperture/circular_aperture-*',) # noqa: E501


		assert np.all(aperture.positions == aperture2.positions)
		assert aperture.r == aperture2.r

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nden commented Mar 4, 2026 •

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