Handles python versioning

Author: snbianco

CHANGES.rst

@@ -7,6 +7,8 @@ Unreleased
   writing multiple cutouts into a single ZIP archive. [#167]
 - Added ``get_tess_sectors`` function to return TESS sector information for sectors whose footprints overlap with 
   the given sky coordinates and cutout size. [#168]
+- Cutouts of ASDF data in FITS format now include embedded ASDF metadata and cutout data in an "ASDF" extension within the FITS file for 
+  Python versions greater than or equal to 3.11. [#170]
 
 Breaking Changes
 ^^^^^^^^^^^^^^^^

astrocut/asdf_cutout.py

@@ -1,3 +1,4 @@
+import sys
 import warnings
 from copy import deepcopy
 from pathlib import Path
@@ -17,11 +18,10 @@
 from astropy.utils.decorators import deprecated_renamed_argument
 from astropy.wcs import WCS
 from s3path import S3Path
-from stdatamodels import asdf_in_fits
 
 from . import log, __version__
 from .image_cutout import ImageCutout
-from .exceptions import DataWarning, InvalidQueryError, InvalidInputError
+from .exceptions import DataWarning, ModuleWarning, InvalidQueryError, InvalidInputError
 
 
 class ASDFCutout(ImageCutout):
@@ -84,6 +84,9 @@ def __init__(self, input_files: List[Union[str, Path, S3Path]], coordinates: Uni
         # Superclass constructor 
         super().__init__(input_files, coordinates, cutout_size, fill_value, verbose=verbose)
 
+        # Must be using Python 3.11 or higher to support stdatamodels and ASDF-in-FITS embedding
+        self._supports_stdatamodels = sys.version_info >= (3, 11)
+
         # Assign AWS credential attributes
         self._key = key
         self._secret = secret
@@ -106,6 +109,18 @@ def fits_cutouts(self) -> List[fits.HDUList]:
         Return the cutouts as a list `astropy.io.fits.HDUList` objects.
         """
         if not self._fits_cutouts:
+            # Try to import stdatamodels for ASDF-in-FITS embedding
+            if self._supports_stdatamodels:
+                try:
+                    from stdatamodels import asdf_in_fits
+                except ModuleNotFoundError:
+                    warnings.warn('The `stdatamodels` package is required for ASDF-in-FITS embedding. Skipping embedding for these cutouts. '
+                                  'To install astrocut with optional `stdatamodels` support, run: pip install "astrocut[all]"', ModuleWarning)
+                    self._supports_stdatamodels = False
+            else:
+                warnings.warn('ASDF-in-FITS embedding requires Python 3.11 or higher. '
+                              'Skipping embedding for these cutouts.')
+
             fits_cutouts = []
             for i, (file, cutouts) in enumerate(self.cutouts_by_file.items()):                
                 cutout = cutouts[0]
@@ -119,8 +134,10 @@ def fits_cutouts(self) -> List[fits.HDUList]:
                 primary_hdu.header['ORIG_FLE'] = file  # Add original file to header
                 hdul = fits.HDUList([primary_hdu])
 
-                # Embed ASDF into FITS
-                hdul_embed = asdf_in_fits.to_hdulist(tree, hdul)
+                if self._supports_stdatamodels:
+                    hdul_embed = asdf_in_fits.to_hdulist(tree, hdul)
+                else:
+                    hdul_embed = hdul
                 fits_cutouts.append(hdul_embed)
             self._fits_cutouts = fits_cutouts
         return self._fits_cutouts

astrocut/exceptions.py

@@ -50,3 +50,10 @@ class DataWarning(AstropyWarning):
     Warnings to do with data content.
     """
     pass
+
+
+class ModuleWarning(AstropyWarning):
+    """
+    Warnings to do with optional modules.
+    """
+    pass

astrocut/tests/test_asdf_cutout.py

@@ -3,6 +3,7 @@
 import pytest
 import zipfile
 import io
+import importlib.util
 
 import asdf
 from astropy import coordinates as coord
@@ -14,7 +15,6 @@
 from astropy.io import fits
 from gwcs import wcs, coordinate_frames
 from PIL import Image
-from stdatamodels import asdf_in_fits
 
 from astrocut.asdf_cutout import ASDFCutout, asdf_cut, get_center_pixel
 from astrocut.exceptions import DataWarning, InvalidInputError, InvalidQueryError
@@ -196,9 +196,11 @@ def check_asdf_metadata(af, original_file, cutout_data):
             assert hdul[0].header['ORIG_FLE'] == test_images[i].as_posix()
             assert Path(fits_file).stat().st_size < Path(test_images[i]).stat().st_size
 
-        # Check ASDF extension contents
-        with asdf_in_fits.open(fits_file) as af:
-            check_asdf_metadata(af, test_images[i], cutout.cutouts[i].data)
+        # Check ASDF extension contents (stdatamodels optional)
+        if importlib.util.find_spec('stdatamodels') is not None:
+            from stdatamodels import asdf_in_fits
+            with asdf_in_fits.open(fits_file) as af:
+                check_asdf_metadata(af, test_images[i], cutout.cutouts[i].data)
 
 
 @pytest.mark.parametrize('output_format', ['.asdf', '.fits'])
@@ -224,7 +226,7 @@ def test_asdf_cutout_write_to_zip(tmpdir, test_images, center_coord, cutout_size
         else:
             with fits.open(io.BytesIO(data)) as hdul:
                 assert isinstance(hdul, fits.HDUList)
-                assert len(hdul) == 2  # primary + embedded ASDF extension
+                assert len(hdul) == 2 if importlib.util.find_spec('stdatamodels') is not None else 1
                 assert hdul[0].data.shape == (cutout_size, cutout_size)
 
 
@@ -254,13 +256,16 @@ def check_lite_metadata(af):
     # Write cutouts to HDUList objects in lite mode
     cutout = ASDFCutout(test_images, center_coord, cutout_size, lite=True)
     for hdul in cutout.fits_cutouts:
-        assert len(hdul) == 2  # primary HDU + embedded ASDF extension
+        has_stdatamodels = importlib.util.find_spec('stdatamodels') is not None
+        assert len(hdul) == 2 if has_stdatamodels else 1  # primary HDU + embedded ASDF extension
         assert hdul[0].name == 'PRIMARY'
-        assert hdul[1].name == 'ASDF'
 
-        # Check ASDF extension contents
-        with asdf_in_fits.open(hdul) as af:
-            check_lite_metadata(af)
+        # Check ASDF extension contents (stdatamodels optional)
+        if has_stdatamodels:
+            assert hdul[1].name == 'ASDF'
+            from stdatamodels import asdf_in_fits
+            with asdf_in_fits.open(hdul) as af:
+                check_lite_metadata(af)
 
 
 def test_asdf_cutout_partial(test_images, center_coord, cutout_size):

setup.cfg

@@ -25,7 +25,6 @@ install_requires =
     requests>=2.32.3 # for making HTTP requests
     spherical_geometry>=1.3.0
     gwcs>=0.21.0
-    stdatamodels>=4.1.0
     scipy
     Pillow
 
@@ -42,6 +41,8 @@ docs =
     docutils == 0.16
     sphinx-astropy
     sphinx_rtd_theme >= 0.5.2
+all =
+    stdatamodels>=4.1.0  # stdatamodels is optional; required for ASDF-in-FITS embedding (Python>=3.11)
 
 [options.package_data]
 astrocut.tests = data/*

tox.ini

@@ -51,6 +51,8 @@ deps =
 
     astroquery04: astroquery==0.4.*
 
+    stdatamodels; python_version >= "3.11"
+
     devdeps: git+https://github.com/numpy/numpy.git#egg=numpy
     devdeps: git+https://github.com/astropy/astropy.git#egg=astropy
     devdeps: git+https://github.com/astropy/astroquery.git