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Spectral-cube uses astropy.coordinates.angle_utilities which is removed in Astropy 6 #892

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olebole opened this issue Nov 28, 2023 · 6 comments · Fixed by #893
Closed

Spectral-cube uses astropy.coordinates.angle_utilities which is removed in Astropy 6 #892

olebole opened this issue Nov 28, 2023 · 6 comments · Fixed by #893

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@olebole
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olebole commented Nov 28, 2023 •
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With Astropy 6.0, the CI tests of spectral-cube no longer pass; there are now many failures like

______________________ test_casa_read_basic[False-False] _______________________

memmap = False, bigendian = False

    @pytest.mark.parametrize(('memmap', 'bigendian'), product((False, True), (False, True)))
    def test_casa_read_basic(memmap, bigendian):
        […]
>       cube.moment0()

/usr/lib/python3/dist-packages/spectral_cube/tests/test_casafuncs.py:133: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/usr/lib/python3/dist-packages/spectral_cube/spectral_cube.py:1702: in moment0
    return self.moment(axis=axis, order=0, how=how)
/usr/lib/python3/dist-packages/spectral_cube/dask_spectral_cube.py:1069: in moment
    pix_cen = self._pix_cen()[axis]
/usr/lib/python3/dist-packages/spectral_cube/utils.py:18: in wrapper
    self._cache[(func, args)] = func(self, *args)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = DaskSpectralCube with shape=(3, 4, 5) and unit=Jy / beam and chunk size (3, 4, 5):
 n_x:      5  type_x: RA---SIN  uni...9.934094 deg:   29.935778 deg
 n_s:      3  type_s: FREQ      unit_s: Hz     range: 1421917021.146 Hz:1421929254.325 Hz

    @cached
    def _pix_cen(self):
        """…"""
        # Start off by extracting the world coordinates of the pixels
        _, lat, lon = self.world[0, :, :]
        spectral, _, _ = self.world[:, 0, 0]
        spectral -= spectral[0] # offset from first pixel
    
        # Convert to radians
        lon = np.radians(lon)
        lat = np.radians(lat)
    
        # Find the dx and dy arrays
>       from astropy.coordinates.angle_utilities import angular_separation
E       ModuleNotFoundError: No module named 'astropy.coordinates.angle_utilities'

/usr/lib/python3/dist-packages/spectral_cube/spectral_cube.py:1456: ModuleNotFoundError

full test log

Reason is that angle_utilities was deprecated in Astropy 4.2 and removed in 6.0:

Removed deprecated angle parsing and formatting utilities from angle_utilities. Use the functions from angle_formats instead. [#14675]
@keflavich
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See also astropy/astropy#15666

@keflavich keflavich mentioned this issue Dec 2, 2023
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@neutrinoceros neutrinoceros mentioned this issue Dec 4, 2023
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keflavich added a commit that referenced this issue Dec 5, 2023
@keflavich @e-koch
Fix deprecated import path [#892] (#893)
9847cf1 
* fix deprecated import path

* Drop "docs" builds based on changed in the tox file

* Update rtd build to fix it

* Change to a normal python install

---------

Co-authored-by: e-koch <koch.eric.w@gmail.com>
@NithyaSathyan
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While doing FERMI LAT data analysis using fermipy , I encountered similar error which is given below :
WARNING: FITSFixedWarning: RADECSYS= 'FK5 '
the RADECSYS keyword is deprecated, use RADESYSa. [astropy.wcs.wcs]
WARNING: FITSFixedWarning: 'datfix' made the change 'Set DATEREF to '2001-01-01T00:01:04.184' from MJDREF.
Set MJD-OBS to 54682.655283 from DATE-OBS.
Set MJD-END to 59852.000000 from DATE-END'. [astropy.wcs.wcs]
Traceback (most recent call last):
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/fermipy/gtanalysis.py", line 5196, in setup
self._bexp = Map.read(self.files['bexpmap'], hdu=hpxhduname)
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py", line 240, in read
return Map.from_hdulist(
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py", line 308, in from_hdulist
map_type = Map._get_map_type(hdulist, hdu)
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py", line 339, in _get_map_type
header = hdu_list[hdu_name].header
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/astropy/io/fits/hdu/hdulist.py", line 390, in getitem
super().getitem, self._positive_index_of(key)
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/astropy/io/fits/hdu/hdulist.py", line 857, in _positive_index_of
index = self.index_of(key)
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/astropy/io/fits/hdu/hdulist.py", line 839, in index_of
raise KeyError(f"Extension {key!r} not found.")
KeyError: "Extension 'HPXEXPOSURES' not found."

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/dell/data backup ubuntu dell mint/Documents/low_z_BLLACs/1ES1959+650/xx.py", line 3, in
gta.setup()
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/fermipy/gtanalysis.py", line 1087, in setup
c.setup(overwrite=overwrite)
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/fermipy/gtanalysis.py", line 5198, in setup
self._bexp = Map.read(self.files['bexpmap'])
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py", line 240, in read
return Map.from_hdulist(
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py", line 315, in from_hdulist
return cls_out.from_hdulist(
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/wcs/core.py", line 142, in from_hdulist
wcs_map = cls.from_hdu(hdu, hdu_bands, format=format)
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/wcs/ndmap.py", line 88, in from_hdu
geom = WcsGeom.from_header(hdu.header, hdu_bands, format=format)
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/wcs/geom.py", line 485, in from_header
axes = MapAxes.from_table_hdu(hdu_bands, format=format)
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/axes.py", line 1962, in from_table_hdu
return cls.from_table(table, format=format)
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/axes.py", line 1980, in from_table
from gammapy.irf.io import IRF_DL3_AXES_SPECIFICATION
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/irf/init.py", line 6, in
from .background import Background2D, Background3D
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/irf/background.py", line 10, in
from .core import IRF
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/irf/core.py", line 17, in
from .io import IRF_DL3_HDU_SPECIFICATION, IRF_MAP_HDU_SPECIFICATION, gadf_is_pointlike
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/irf/io.py", line 4, in
from gammapy.data.hdu_index_table import HDUIndexTable
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/data/init.py", line 3, in
from .data_store import DataStore
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/data/data_store.py", line 15, in
from .observations import Observation, ObservationChecker, Observations
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/data/observations.py", line 22, in
from .event_list import EventList, EventListChecker
File "/home/dell/miniconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/data/event_list.py", line 8, in
from astropy.coordinates.angle_utilities import angular_separation
ModuleNotFoundError: No module named 'astropy.coordinates.angle_utilities'

@Firestar-Reimu
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Firestar-Reimu commented May 9, 2024 •
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Same issue, still not fixed?

Sorry, the spectral-cube on conda-forge is still 0.6.3, it needs to be updated to 0.6.5

Do you maintain the conda-forge package?

@keflavich
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@Firestar-Reimu indeed, see conda-forge/spectral-cube-feedstock#16

@Firestar-Reimu
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Firestar-Reimu commented May 9, 2024 •
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Quick Reply, Thanks!

I can change /home/firestar/.miniconda/lib/python3.12/site-packages/spectral_cube/spectral_cube.py manually for now.

Bash exited with code '1'.

I still do not know why it cannot be merged, what a pity.

@Firestar-Reimu
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https://anaconda.org/conda-forge/spectral-cube

now its good.

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Fix deprecated import path [#892] keflavich/spectral-cube
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@keflavich @olebole @Firestar-Reimu @NithyaSathyan