Facilitates use of pdb-tools as a library

joaomcteixeira commented 3 years ago

What was done

pdbtools can now be easily used as a library from which users can import individual functions/modules to execute the tool logic.
no additional code or functionality is introduced.
maintains full backwards compatibility with the command line interface.
Extensive library documentation.
I did not introduce any object-like Structure class interface. That is not the intent of this PR, nor the intent of this repository.

How was done

All tools have now three equally named functions that serve the same purposes: check_input, run, main.
The original functions holding the tool logic were renamed to run.
A reference to the original name was maintained. This can be dropped eventually in future version 3.

Note!

The only break in backwards compatibility introduced here is the order of the tuples returned by check_input. Tuples (where they are) were swapped such that the file handler is at index 0, instead of index -1. This was done to allow chaining check_input with run; see docs. I believe this does not create problems with version 2 because no one is expected to be importing check_input. Is this right for all HADDOCK services?

Please read the documentation now on init.

Examples

more at the docs

import pdbtools
from pdbtools import *
from pdbtools import pdb_selchain

with open('dummy.pdb') as fin:
    print(''.join(pdb_selchain.run(fin, ['A'])))

version bump

I suggest [FEATURE].

Closes #106

joaomcteixeira commented 3 years ago

I greped both haddock2.4 and haddock2.5 branches for check_input and no output returned. So I am positive no module is importing check_input from pdb-tools. check_input return values was the only API that changes in this PR.

amjjbonvin commented 3 years ago

Indeed - no pdb-tools dependencies in the haddock2.4/2.5 code

On 12 Jul 2021, at 10:59, João M.C. Teixeira @.***> wrote:

I greped both haddock2.4 and haddock2.5 branches for check_input and no output returned. So I am positive no module is importing check_input from pdb-tools. check_input return values was the only API that changes in this PR.

— You are receiving this because your review was requested. Reply to this email directly, view it on GitHub https://github.com/haddocking/pdb-tools/pull/107#issuecomment-878100304, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABOH5IBP4CGK6WHB2YLVBMLTXKVGRANCNFSM473FXYCQ.

joaomcteixeira commented 3 years ago

Great you could double check it. Apart form the return tuple on some of the check_input functions, no other API is broken. The older function names link to the new run.

I like we will be able to do this:

https://github.com/haddocking/pdb-tools/pull/107/files#diff-fdf5a6300e07e6be609fca3db7f1a755e0f519a25476ca4b3aa65db2d0cf4d1fR46-R52

joaomcteixeira commented 3 years ago

Hi all, if anyone has objections on this PR, I will merge it by the end of today. :+1: I will raise version 2.4 despite it should be version 3 by definition, because there is no reported use of the check_input API, there is no need to upgrade to 3. Special cases are also acceptable in SV2.0.

haddocking / pdb-tools