v3.0.0-beta.2

What's Changed since v3.0.0-beta.1

• Refactor caprieval by @rvhonorato in #441
• Generate .rst documentation page for .yaml default configuration files by @joaomcteixeira in #436
• Add user documentation on configuration files by @joaomcteixeira in #445
• Update MANIFEST.in by @joaomcteixeira in #455
• Enhance clustering protocols by @rvhonorato in #454
• amended clt_threshold behavior by @mgiulini in #460
• Add md5 property to libontology by @rvhonorato in #459
• Populate mol_ expandable parameters when using --extend-run by @joaomcteixeira in #450
• Allows single entries in molecules parameter by @joaomcteixeira in #439
• add cluster name to seletopclusts.txt by @rvhonorato in #462
• add tests to topoaa by @rvhonorato in #461
• add haddock3-docs to .gitignore by @joaomcteixeira in #463
• remove duplicated entry in clustfcc.txt by @rvhonorato in #465
• Corrects bug in --restart option by @joaomcteixeira in #467
• Add missing header to seletopclusts.txt by @rvhonorato in #471
• Implements clean output - compress/archive output files by @joaomcteixeira in #468
• Corrects check modules names in config on startup by @joaomcteixeira in #477
• Update CI workflows by @joaomcteixeira in #478
• Improve reading md5 from REMARK lines by @joaomcteixeira in #475
• Allows topoaa to run in different parts of the workflow by @joaomcteixeira in #474
• Adds parameter validation to general parameters by @joaomcteixeira in #479
• Improves mandatory parameter check by @joaomcteixeira in #481
• added chain-matching AlignError by @mgiulini in #483
• added single linkage as clustrmsd default by @mgiulini in #486
• added check on tolerance in clustrmsd by @mgiulini in #489
• run analysis modules after topoaa by @mgiulini in #484
• Add general parameters to haddock3-cfg client by @joaomcteixeira in #476

Full Changelog: v3.0.0-beta.1...v3.0.0-beta.2