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I am running a python code on jupyter notebook and I wanted to import and use the specutils package to plot a doppler-shifted spectrum from my data.
This is the part of the code I want to run:
_from astropy.io import ascii
spec1 = ascii.read('NH2CHO_1147_1148.dat') #spectrum data with x = radio velocity [km/s], y = flux [K]
t_mol_s2 = ascii.read('NH2CHO_s1.dat') #Table containing parameters of fitted spectral lines
from specutils import Spectrum1D
print(spec1)
wavelengths = spec1['Velocity']
spectrum = Spectrum1D(spectral_axis=wavelengths, flux=spec1['Flux'])
shift = t_mol_s2['Deltav'][0] #Row in the table containing the shifting quantity for my spectrum
new_spec = Spectrum1D(spectral_axis=spectrum.spectral_axis + shift, flux=spectrum.flux)
print(new_spec)_
and this is the raising error:
_ContextualVersionConflict Traceback (most recent call last)
Input In [48], in <cell line: 1>()
----> 1 from specutils import Spectrum1D
2 print(spec1)
3 wavelengths = spec1['Velocity']
File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/specutils/__init__.py:23, in <module>
19 test.__test__ = False
22 # Allow loading spectrum object from top level module
---> 23 from .spectra import * # noqa
25 # Load the IO functions
26 from .io.default_loaders import * # noqa
File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/specutils/spectra/__init__.py:5, in <module>
1 """
2 The core specutils data objects package. This contains the
3 `~astropy.nddata.NDData`-inherited classes used for storing the spectrum data.
4 """
----> 5 from .spectrum1d import * # noqa
6 from .spectral_region import * # noqa
7 from .spectrum_collection import * # noqa
File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/specutils/spectra/spectrum1d.py:11, in <module>
8 from astropy.nddata import NDUncertainty, NDIOMixin, NDArithmeticMixin
10 from .spectral_axis import SpectralAxis
---> 11 from .spectrum_mixin import OneDSpectrumMixin
12 from .spectral_region import SpectralRegion
13 from ..utils.wcs_utils import gwcs_from_array
File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/specutils/spectra/spectrum_mixin.py:8, in <module>
5 from astropy import units as u
6 from astropy.utils.decorators import deprecated
----> 8 from specutils.utils.wcs_utils import gwcs_from_array
10 DOPPLER_CONVENTIONS = {}
11 DOPPLER_CONVENTIONS['radio'] = u.doppler_radio
File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/specutils/utils/wcs_utils.py:7, in <module>
5 from astropy.modeling.models import Shift
6 from astropy.modeling.tabular import Tabular1D
----> 7 from gwcs import WCS as GWCS
8 from gwcs import coordinate_frames as cf
11 def refraction_index(wavelength, method='Griesen2006', co2=None):
File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/gwcs/__init__.py:66, in <module>
63 raise ImportError("GWCS supports Python versions 3.6 and above.") # pragma: no cover
65 try:
---> 66 __version__ = get_distribution(__name__).version
67 except DistributionNotFound: # pragma: no cover
68 # package is not installed
69 pass # pragma: no cover
File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pkg_resources/__init__.py:466, in get_distribution(dist)
464 dist = Requirement.parse(dist)
465 if isinstance(dist, Requirement):
--> 466 dist = get_provider(dist)
467 if not isinstance(dist, Distribution):
468 raise TypeError("Expected string, Requirement, or Distribution", dist)
File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pkg_resources/__init__.py:342, in get_provider(moduleOrReq)
340 """Return an IResourceProvider for the named module or requirement"""
341 if isinstance(moduleOrReq, Requirement):
--> 342 return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0]
343 try:
344 module = sys.modules[moduleOrReq]
File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pkg_resources/__init__.py:886, in WorkingSet.require(self, *requirements)
877 def require(self, *requirements):
878 """Ensure that distributions matching `requirements` are activated
879
880 `requirements` must be a string or a (possibly-nested) sequence
(...)
884 included, even if they were already activated in this working set.
885 """
--> 886 needed = self.resolve(parse_requirements(requirements))
888 for dist in needed:
889 self.add(dist)
File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pkg_resources/__init__.py:777, in WorkingSet.resolve(self, requirements, env, installer, replace_conflicting, extras)
774 if dist not in req:
775 # Oops, the "best" so far conflicts with a dependency
776 dependent_req = required_by[req]
--> 777 raise VersionConflict(dist, req).with_context(dependent_req)
779 # push the new requirements onto the stack
780 new_requirements = dist.requires(req.extras)[::-1]
ContextualVersionConflict: (importlib-metadata 4.11.3 (/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages), Requirement.parse('importlib-metadata>=4.11.4'), {'asdf'})_
I am using a MacBook Air (M1, 2020) with macOS Monterey version 12.3.1 and I have installed python 3.9.7, pip 23.1.2, jupyter notebook 6.4.10 and, looking at pip list, specutils 1.11.0, importlib-metadata 4.11.4 and:
asdf 2.15.0
asdf-astropy 0.4.0
asdf-coordinates-schemas 0.2.0
asdf-standard 1.0.3
asdf-transform-schemas 0.3.0
asdf-unit-schemas 0.1.0
asdf-wcs-schemas 0.1.1
(given that, if I well interpreted the error message, it's the asdf dependency of both import lib-metadata and specutils to raise it)
Can you help me? Thank you in advance.
The text was updated successfully, but these errors were encountered:
The ContextualVersionConflict is coming from pkg_resources, which is attempting to validate that "importlib_metadata>=4.11.4" is present as required by "asdf", but importlib_metadata is only available at 4.11.3.
You say you have importlib-metadata 4.11.4 installed, but pkg_resources disagrees. You'll need to install importlib_metadata>=4.11.4 to fix the issue.
This report is not a bug with importlib_metadata and there's nothing this project can do to help with the situation. Please reach out on StackOverflow or other user support for Python packaging for help with your environment.
I am running a python code on jupyter notebook and I wanted to import and use the specutils package to plot a doppler-shifted spectrum from my data.
This is the part of the code I want to run:
and this is the raising error:
I am using a MacBook Air (M1, 2020) with macOS Monterey version 12.3.1 and I have installed python 3.9.7, pip 23.1.2, jupyter notebook 6.4.10 and, looking at pip list, specutils 1.11.0, importlib-metadata 4.11.4 and:
asdf 2.15.0
asdf-astropy 0.4.0
asdf-coordinates-schemas 0.2.0
asdf-standard 1.0.3
asdf-transform-schemas 0.3.0
asdf-unit-schemas 0.1.0
asdf-wcs-schemas 0.1.1
(given that, if I well interpreted the error message, it's the asdf dependency of both import lib-metadata and specutils to raise it)
Can you help me? Thank you in advance.
The text was updated successfully, but these errors were encountered: