Inspect dependencies are installed for thirdparty libraries

[joaomcteixeira]

Closes #29

concept

HADDOCK3 integrates third-party packages in its workflows. This PR implements a structure meant to assess if third-party packages are installed before executing the workflow. Hence, HADDOCK3 is not responsible for the proper installation of such packages.

detailed implementations

The BaseModuleHaddock class has now an @abstractclassmethod named confirm_installation that needs to be implemented on every subclass of BaseModuleHaddock. HADDOCK3's own modules must implement a dummy method with a simple return statement to bypass the required install confirmation. Third-party modules should implement whatever routines needed to properly check the module is functional with all third-party software installed. These confirmation steps take place while preparing the run and before executing the workflow. Any error raised by confirm_installation will be captured and raised as a problem with the installation.

I have implemented confirmation routines for both lightdock, gdock, and FCC, as well as for all other HADDOCK3 modules.

Updated installation instructions and dependencies.

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I think this implementation is a good example of both the modularity and extensibility of the prepare_run FP-based implementation as well as the OOP-based implementation of BaseModuleHaddock seeded by @brianjimenez . Taking profit from both realms 😉