Haddock3 restraints

[mgiulini]

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---

Closes #734 by adding a new CLI, haddock3-restraints, with four subcommands (validate_tbl, restrain_bodies, passive_from_active, active_passive_to_ambig) that can be used to generate, validate, and handle restraints.

this adds the freesasa dependency (necessary for passive_from_active).

For the sake of time I didn't rewrite these scripts completely, but at least now they are properly tested.

[codecov]

Codecov Report

Attention: 89 lines in your changes are missing coverage. Please review.

Comparison is base (1e307a0) 75.48% compared to head (d260fc6) 75.92%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #732      +/-   ##
==========================================
+ Coverage   75.48%   75.92%   +0.43%     
==========================================
  Files         115      121       +6     
  Lines        8204     8723     +519     
==========================================
+ Hits         6193     6623     +430     
- Misses       2011     2100      +89     

Files	Coverage Δ
tests/test_cli_restraints.py	98.66% <98.66%> (ø)
src/haddock/restraints/active_passive_to_ambig.py	58.33% <58.33%> (ø)
src/haddock/restraints/restrain_bodies.py	70.00% <70.00%> (ø)
src/haddock/restraints/validate_tbl.py	68.42% <68.42%> (ø)
src/haddock/restraints/passive_from_active.py	60.37% <60.37%> (ø)
src/haddock/libs/librestraints.py	85.29% <85.29%> (ø)

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[rvhonorato]

I see quite a lot of minor issues but those are related to the legacy script rather than this port. I'd suggest you add a disclaimer/warning/big comment somewhere that this was ported from old code and there is room for improvment.

[mgiulini]

I see quite a lot of minor issues but those are related to the legacy script rather than this port. I'd suggest you add a disclaimer/warning/big comment somewhere that this was ported from old code and there is room for improvment.

makes sense, I will add it in the main CLI. I won't print the disclaimer though, as the output of these scripts is typically redirected

[rvhonorato]

Nicely ported!