Fix Log Entry to Config File Bug

[Lilferrit]

Fixed a bug that would write the log entries to the config file instead of the log file when running the configure command.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.56%. Comparing base (17bb3f2) to head (b9d8b25).
Report is 1 commits behind head on dev.

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #406      +/-   ##
==========================================
- Coverage   94.61%   94.56%   -0.05%     
==========================================
  Files          14       14              
  Lines        1282     1289       +7     
==========================================
+ Hits         1213     1219       +6     
- Misses         69       70       +1     

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[bittremieux]

Looks good, just some considerations.

As you mentioned on Slack, I think it would also be good to add an integration test that checks whether the produced config file is actually compatible (i.e. you can run Casanovo with it).

[Lilferrit]

Sounds good, I added additional test cases for the configure sub-command as well splitting the file IO options into a different class.