Issue 373

[widdowquinn]

This initial PR fixes a number of niggling bugs that we needed to clear, before tackling #373 directly.

Due to scheduling/planning, we decided to make PR/merge of these smaller changes now, and merge the fastANI branch (after rebasing to master) at this point, so that we could consolidate the associated database changes for fastANI across branches.

This branch will remain live for fixing #340 after this PR/merge

Type of change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality not to work as expected)
• This change requires a documentation update
• This is a documentation update

Action Checklist

• Work on a single issue/concept (if there are multiple separate issues to address, please use a separate pull request for each)
• Fork the pyani repository under your own account (please allow write access for repository maintainers)
• Set up an appropriate development environment (please see CONTRIBUTING.md)
• Create a new branch with a short, descriptive name
• Work on this branch
  • style guidelines have been followed
  • new code is commented, especially in hard-to-understand areas
  • corresponding changes to documentation have been made
  • tests for the change have been added that demonstrate the fix or feature works
• Test locally with pytest -v non-passing code will not be merged
• Rebase against origin/master
• Check changes with flake8 and black before submission
• Commit branch
• Submit pull request, describing the content and intent of the pull request
• Request a code review
• Continue the discussion at Pull requests section in the pyani repository

[codecov]

Codecov Report

Merging #375 (7f76767) into master (8a59453) will increase coverage by 0.04%.
The diff coverage is 93.75%.

@@            Coverage Diff             @@
##           master     #375      +/-   ##
==========================================
+ Coverage   75.35%   75.40%   +0.04%     
==========================================
  Files          52       52              
  Lines        3421     3431      +10     
==========================================
+ Hits         2578     2587       +9     
- Misses        843      844       +1