Cli protocol settings via yaml input

[richardjgowers]

Checklist

• Added a news entry

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[pep8speaks]

Hello @richardjgowers! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file openfe/setup/ligand_network_planning.py:

Line 100:80: E501 line too long (99 > 79 characters)
Line 102:80: E501 line too long (85 > 79 characters)

• In the file openfecli/parameters/plan_network_options.py:

Line 23:80: E501 line too long (82 > 79 characters)
Line 162:5: E265 block comment should start with '# '
Line 165:5: E265 block comment should start with '# '
Line 229:80: E501 line too long (86 > 79 characters)
Line 230:80: E501 line too long (90 > 79 characters)
Line 253:80: E501 line too long (82 > 79 characters)
Line 266:80: E501 line too long (80 > 79 characters)
Line 314:80: E501 line too long (80 > 79 characters)
Line 315:27: W291 trailing whitespace

• In the file openfecli/tests/parameters/test_plan_network_options.py:

Line 92:80: E501 line too long (86 > 79 characters)
Line 96:80: E501 line too long (85 > 79 characters)
Line 103:80: E501 line too long (86 > 79 characters)
Line 104:80: E501 line too long (83 > 79 characters)
Line 105:80: E501 line too long (89 > 79 characters)
Line 106:80: E501 line too long (86 > 79 characters)
Line 136:80: E501 line too long (116 > 79 characters)
Line 143:19: W291 trailing whitespace
Line 147:80: E501 line too long (106 > 79 characters)
Line 158:28: W291 trailing whitespace
Line 162:80: E501 line too long (96 > 79 characters)

Comment last updated at 2024-03-11 15:27:24 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 99.00990% with 1 line in your changes missing coverage. Please review.

Project coverage is 91.84%. Comparing base (c467874) to head (8df0b05).
Report is 395 commits behind head on main.

Files with missing lines	Patch %	Lines
openfecli/parameters/plan_network_options.py	98.21%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #770      +/-   ##
==========================================
- Coverage   93.57%   91.84%   -1.73%     
==========================================
  Files         133      133              
  Lines        9748     9839      +91     
==========================================
- Hits         9122     9037      -85     
- Misses        626      802     +176     

Flag	Coverage Δ
fast-tests	91.84% <99.00%> (?)
slow-tests	?

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.