We are currently using astropy's log to print color-coded information to screen. However, this does not save a file with those warnings.

Astropy allows to write to file, but I think it's cumbersome as it requires a with statement for every log entry:
with log.log_to_file('myfile.log'):
# your code here

I much prefer a function or class.

GNIRS's nsextract is not an ideal extraction code. It cannot handle individual emission lines so well. I decided to create a separate module to extract (Extract1D) and a code to compute the distortion-based extraction solution from bright continuum source. The latter is called distort_trace.py.

A replace() method should fix the option

Codes is unable to distinguish different sets of telluric data. Must split them in create_list.py and update reduce.py to loop over each instance of telluric data.

Recommend using filename to split.