While using the default settings of the pipeline I have found a problem that wasn't happening before. I'm having this issue since the last time I updated ubuntu.
In a virtual machine from other pc I have installed ubuntu from scratch with only what's needed to run this pipeline, but I get exactly the same error.
I can "bypass" this problem if I add the following text to hdulist.py, from the astropy package, in the line 967.
This file is located in ... /lib/python3.7/site-packages/astropy/io/fits/hdu. I know that I shouldn't touch this files but, for now with that change, the pipeline actually finishes without errors.
Here I attach a copy of the main error.
Extracting cutouts with SWARP../home/john/anaconda3/lib/python3.7/site-packages/tqdm/std.py:666: FutureWarning: The Panel class is removed from pandas. Accessing it from the top-level namespace will also be removed in the next version
from pandas import Panel
Creating cutouts: 0%| | 2/666 [00:00<02:40, 4.12cutouts/
Exception occurred during analysis:
Traceback (most recent call last):
File "/home/john/anaconda3/bin/ssos", line 8, in
sys.exit(main())
File "/home/john/anaconda3/lib/python3.7/site-packages/ssos/main.py", line 105, in main
pipeline.execute_analysis(step)
File "/home/john/anaconda3/lib/python3.7/site-packages/ssos/core.py", line 815, in execute_analysis
self.args)
File "/home/john/anaconda3/lib/python3.7/site-packages/ssos/opt.py", line 205, in extract_cutouts
sources.progress_apply(lambda row: _call_swarp(row, settings, log, paths, args), axis=1)
File "/home/john/anaconda3/lib/python3.7/site-packages/tqdm/std.py", line 765, in inner
return getattr(df, df_function)(wrapper, **kwargs)
File "/home/john/anaconda3/lib/python3.7/site-packages/pandas/core/frame.py", line 6878, in apply
return op.get_result()
File "/home/john/anaconda3/lib/python3.7/site-packages/pandas/core/apply.py", line 186, in get_result
return self.apply_standard()
File "/home/john/anaconda3/lib/python3.7/site-packages/pandas/core/apply.py", line 296, in apply_standard
values, self.f, axis=self.axis, dummy=dummy, labels=labels
File "pandas/_libs/reduction.pyx", line 620, in pandas._libs.reduction.compute_reduction
File "pandas/_libs/reduction.pyx", line 128, in pandas._libs.reduction.Reducer.get_result
File "/home/john/anaconda3/lib/python3.7/site-packages/tqdm/std.py", line 760, in wrapper
return func(*args, **kwargs)
File "/home/john/anaconda3/lib/python3.7/site-packages/ssos/opt.py", line 205, in
sources.progress_apply(lambda row: _call_swarp(row, settings, log, paths, args), axis=1)
File "/home/john/anaconda3/lib/python3.7/site-packages/ssos/opt.py", line 182, in _call_swarp
utils.create_clean_image(cutout_filename, cutout_filename, update=True)
File "/home/john/anaconda3/lib/python3.7/site-packages/ssos/utils.py", line 332, in create_clean_image
exp.flush()
File "/home/john/anaconda3/lib/python3.7/site-packages/astropy/io/fits/hdu/hdulist.py", line 389, in exit
self.close(output_verify=output_verify)
File "/home/john/anaconda3/lib/python3.7/site-packages/astropy/io/fits/hdu/hdulist.py", line 971, in close
self.flush(output_verify=output_verify, verbose=verbose)
File "/home/john/anaconda3/lib/python3.7/site-packages/astropy/io/fits/util.py", line 241, in wrapped
func(*args, **kwargs)
File "/home/john/anaconda3/lib/python3.7/site-packages/astropy/io/fits/hdu/hdulist.py", line 829, in flush
self.verify(option=output_verify)
File "/home/john/anaconda3/lib/python3.7/site-packages/astropy/io/fits/verify.py", line 66, in verify
opt = option.lower()
AttributeError: 'bool' object has no attribute 'lower'