Writing log file fails if only filename given

[Leighton Pritchard]

Summary:

When using -l <FILENAME> if <FILENAME> does not contain a valid directory path, a FileNotFoundError is thrown.

Description:

Attempting to open the log file splits the path to identify the parent directory/ies. If no leading path to a file in the current directory is given, e.g. myfile.log instead of ./myfile.log, os.makedirs() attempts to create a directory '', which fails.

The solution may be to move to pathlib for all filepath handling.

Reproducible Steps:

Any ncfp command with -l myfile.txt in the command.

Current Output:

A FileNotFound error

Expected Output:

No FileNotFound error

[Leighton Pritchard]

I am no longer able to reproduce this locally, but a related bug exists: the logfile is empty unless the -v flag is set.

% ncfp -l myfile.log -s ../tests/fixtures/sequences/input_uniprot_stockholm_small.fasta ncfp_out [e-mail]
% ls -ltrh myfile.log                                                                                                                   [11:37:25]
-rw-r--r--  1 lpritc  staff     0B 21 May 11:36 myfile.log
% ncfp -v -l myfile.log -s ../tests/fixtures/sequences/input_uniprot_stockholm_small.fasta ncfp_out [e-mail]
 ls -ltrh myfile.log                                                                                                                   [11:38:52]
-rw-r--r--  1 lpritc  staff   4.9K 21 May 11:38 myfile.log