adds trjconv command

[richardjgowers]

allows FEReader to take negative state_id and replica_id kwargs (to access final states/replicas)

[codecov]

Codecov Report

Attention: Patch coverage is 50.00000% with 19 lines in your changes are missing coverage. Please review.

Project coverage is 59.45%. Comparing base (75d8af5) to head (10ec9ae).
Report is 1 commits behind head on main.

Files	Patch %	Lines
src/openfe_analysis/cli.py	34.48%	19 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #28      +/-   ##
==========================================
- Coverage   60.06%   59.45%   -0.61%     
==========================================
  Files           6        6              
  Lines         298      333      +35     
==========================================
+ Hits          179      198      +19     
- Misses        119      135      +16     

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[richardjgowers]

@mikemhenry mentioned that we should have some sort of 'all' option that iterates over replicas

[pep8speaks]

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

• In the file src/openfe_analysis/cli.py:

Line 48:41: E128 continuation line under-indented for visual indent
Line 49:41: E128 continuation line under-indented for visual indent
Line 50:41: E128 continuation line under-indented for visual indent
Line 51:25: E127 continuation line over-indented for visual indent