error importing lime

[albertfxwang]

Hi Vital,

Thanks so much for bringing this awesome spectral fitting tool to the community. I installed the latest version using pip install lime-stable but when I try to import the package, I got the following error message. Could you please help take a look? Thanks so much!

In [1]: import lime

ImportError Traceback (most recent call last)
Cell In [1], line 1
----> 1 import lime

File ~/local/anaconda3/envs/xwang-jwst/lib/python3.10/site-packages/lime/init.py:38
35 class Error(Exception):
36 """LiMe exception function"""
---> 38 from .treatment import Spectrum, Sample, Cube
39 from .io import *
40 from .tools import *

File ~/local/anaconda3/envs/xwang-jwst/lib/python3.10/site-packages/lime/treatment.py:8
5 from astropy.io import fits
7 import lime
----> 8 from .tools import LineFinder, UNITS_LATEX_DICT, DISPERSION_UNITS,
9 FLUX_DENSITY_UNITS, unit_convertor, define_masks, extract_fluxes, relative_fluxes, compute_line_ratios
11 from .plots import SpectrumFigures, SampleFigures, CubeFigures
12 from .plots_interactive import SpectrumCheck, CubeCheck, SampleCheck

File ~/local/anaconda3/envs/xwang-jwst/lib/python3.10/site-packages/lime/tools.py:19
17 from pathlib import Path
18 from scipy import signal
---> 19 from .io import LiMe_Error
21 _logger = logging.getLogger('LiMe')
23 try:

File ~/local/anaconda3/envs/xwang-jwst/lib/python3.10/site-packages/lime/io.py:24
22 from pathlib import Path
23 from distutils.util import strtobool
---> 24 from collections import Sequence
26 from astropy.io import fits
27 from astropy.table import Table

ImportError: cannot import name 'Sequence' from 'collections' (/Users/wangxin/local/anaconda3/envs/xwang-jwst/lib/python3.10/collections/init.py)

[Vital-Fernandez]

Hello @albertfxwang for your post and sorry for the delay.

I think this error is due to the python version (skorch-dev/skorch#895). Can you try to run this command in your terminal to see if it works?

from collections.abc import Sequence

I can modify to command to make it work for you.

(This week and the next one I am updating the documentation to show the definitive LiMe workflow, Until them I recommend you follow the scripts on the github examples folder to follow the definitive version)

[albertfxwang]

Hi @Vital-Fernandez , I checked that both the following lines of code work for me.
python3.10 -c "from collections.abc import Sequence"
python3.9 -c "from collections.abc import Sequence"
However, when trying to import lime, in Python 3.10 environment, it seems that from collections import Sequence will inflict an error.

[Vital-Fernandez]

Ty @albertfxwang very much for checking. I have modified that import in the 0.9.16 version. You should be able to get it with this command:

pip install lime-stable --upgrade

Please tell me if you have any issue.