Move fastANI to a separate requirements

[baileythegreen]

Sidesteps macOS/Python3.9 issues with the fastANI conda recipe.

Closes #377.

Please include a summary of the change and which issue is fixed. Please also include the motivation and context, and note the tests that apply to these changes.

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 #384 (9108d01) into master (6d669d1) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #384   +/-   ##
=======================================
  Coverage   75.60%   75.60%           
=======================================
  Files          55       55           
  Lines        3735     3735           
=======================================
  Hits         2824     2824           
  Misses        911      911           

[widdowquinn]

The changes to the docs are going in the right direction (addition of fastani in the early section, noting the issue with Python 3.9)

Removing fastani from the requirements-thirdparty.txt file is the right thing to do, but I don't think there's any advantage to having the extra requirements-fastani.txt file. A user can more simply and explicitly execute:

conda install fastani

than

conda install --file requirements-fastani.txt

and that should be our advice. Please remove the requirements-fastani.txt file.

As far as how to compile fastANI goes, I think we should use the docs to point and link users to #377 in the repository, where improvements/additions can be shared for others to read, rather than making a single suggestion concrete in the text (and imposing further documentation maintenance on ourselves to keep up). Please reword that section.

[widdowquinn]

After discussion I recall our reasons for having the extra requirements-fastani.txt file. For the record, they are:

• stylistic consistency
• we can add other dependencies that are fastani specific to this file if we need them
• convenience for the Makefile
• arguably easier for users

[widdowquinn]

Just a couple of notes about minor extra detail in the docs.