Add tool to identify CNS script dependencies

[rvhonorato]

This PR implements a tool to help us clean the CNS dependencies in the HADDOCK core modules and closes #42. It takes the main CNS script as input and the production protocols directory; Ex:

$  python tools/cns_dependency_tree.py src/haddock/modules/topology/cns/generate-topology.cns /Users/rodrigo/repos/haddock24/protocols 
[27/07/2021 11:27:21] L41 INFO - Protocols directory: /Users/rodrigo/repos/haddock24/protocols
[27/07/2021 11:27:21] L42 INFO - Retrieving dependencies of /Users/rodrigo/repos/haddock3/src/haddock/modules/topology/cns/generate-topology.cns
[27/07/2021 11:27:21] L47 INFO - First level dependencies: 9
[27/07/2021 11:27:21] L49 INFO - Looking for deeper dependencies
[27/07/2021 11:27:21] L76 INFO - Total dependencies found: 10
[27/07/2021 11:27:21] L78 INFO - generate-topology.cns depends on: patch-types-cg.cns patch-bb-cg.cns build-missing.cns prot_break.cns dna_break.cns covalheme.cns coval-ace-cys.cns auto-his.cns flex_segment_back.cns flexauto-neighbors.cns

This script is not very pretty but we can work on it later. :)

[joaomcteixeira]

That looks a nice idea. But we should make it part of the haddock CLI tools, not a simple script. Let me work on that since I pulled #28 .

[joaomcteixeira]

Question: why the script needs the /Users/rodrigo/repos/haddock24/protocols ? Is that because the haddock24/protocols is planned to be transferred to haddock3 but it is not yet here?

Will this dependency on HADDOCK24 disappear after #41 ? If that is so, maybe that second argument can be a fixed folder within haddock3 folder structure.

It would be nice to have the output also as you suggested on #42 😉 , looks much prettier.

[rvhonorato]

Question: why the script needs the /Users/rodrigo/repos/haddock24/protocols ?

Because this is where the CNS protocols are, haddock3 is building on top of it.

Will this dependency on HADDOCK24 disappear after #41 ? If that is so, maybe that second argument can be a fixed folder within haddock3 folder structure.

I'm afraid we will only keep relying on the production version (either 2.4 or 2.5) for a long time since it has many features that need to be implemented here; both ones that are already there as well as other that are being implement continuously.

[amjjbonvin]

We should start a haddock3 CNS protocol directory

…

On 27 Jul 2021, at 12:56, Rodrigo V Honorato ***@***.***> wrote: Question: why the script needs the /Users/rodrigo/repos/haddock24/protocols ? Because this is where the CNS protocols are, haddock3 is building on top of it. Will this dependency on HADDOCK24 disappear after #41 <#41> ? If that is so, maybe that second argument can be a fixed folder within haddock3 folder structure. I'm afraid we will only keep relying on the production version (either 2.4 or 2.5) for a long time since it has many features that need to be implemented here; both ones that are already there as well as other that are being implement continuously. — You are receiving this because your review was requested. Reply to this email directly, view it on GitHub <#43 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABOH5IDVLABSM33OKUWQH7TTZ2GHLANCNFSM5BB26X5Q>.

[rvhonorato]

Closing this one since I already used this script to implement the core modules, we don't need to have it in the repository anymore.