search

FHIBioGroup / fafoom-dev

Continuing development of genetic algorithm for biomolecules in different environments
GNU General Public License v3.0
4 stars 2 forks source link

Merge FAFOOM v2 #5

Open mahrossi opened 6 years ago

mahrossi commented 6 years ago

This is everything Dmitrii has done so far (and really essentially only Dmitrii coded everything and Carsten and I just discussed ideas and the architecture with him).

They include quite substantial changes deep inside FAFOOM. Some of them are the "independence" from RDkit in the code, inclusion of translational and rotational degrees of freedom, protomeric degree of freedom, and many many changes to the routines. Only pieces of the original implementation are still there. Testcases are provided. We suggest that any new developments are branched and based on this new master branch. I will leave the pull request here for a couple of days in case anyone wants to give a look.

mahrossi commented 6 years ago

Actually I started reviewing and I have a comment :) .pyc and .out files should not be pushed into the repo. We can talk about how to remove them.

mmarianski commented 6 years ago

When do you want to commit? I want to read the code before. I will try to review it this week but, being engaged in multiple tasks of spurious scientific importance, I can't promise.

On Tue, Feb 27, 2018 at 4:45 PM, Mariana Rossi notifications@github.com wrote:

Actually I started reviewing and I have a comment :) .pyc and .out files should not be pushed into the repo. We can talk about how to remove them.

— You are receiving this because your review was requested. Reply to this email directly, view it on GitHub https://github.com/FHIBioGroup/fafoom-dev/pull/5#issuecomment-369037356, or mute the thread https://github.com/notifications/unsubscribe-auth/ALS4ElFPGlAQHQrCPY0o4FGe0uJxsu6yks5tZHeBgaJpZM4SVr7t .

mahrossi commented 6 years ago

Hi Mateusz,

Given that the original FAFOOM is still alive in another completely separate repository, there isn't a massive need to review every line. General comments and improvements, or even testing the examples, would be more than welcome of course. However, detailed testing can even be done after the merge. Let us know what you can do until Friday and if you see any showstoppers (for us stuff works! :) ).

On Tue, Feb 27, 2018 at 10:48 PM, Mateusz Marianski < notifications@github.com> wrote:

When do you want to commit? I want to read the code before. I will try to review it this week but, being engaged in multiple tasks of spurious scientific importance, I can't promise.

On Tue, Feb 27, 2018 at 4:45 PM, Mariana Rossi notifications@github.com wrote:

Actually I started reviewing and I have a comment :) .pyc and .out files should not be pushed into the repo. We can talk about how to remove them.

— You are receiving this because your review was requested. Reply to this email directly, view it on GitHub <https://github.com/FHIBioGroup/fafoom-dev/pull/5#issuecomment-369037356 , or mute the thread https://github.com/notifications/unsubscribe-auth/ ALS4ElFPGlAQHQrCPY0o4FGe0uJxsu6yks5tZHeBgaJpZM4SVr7t .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/FHIBioGroup/fafoom-dev/pull/5#issuecomment-369038279, or mute the thread https://github.com/notifications/unsubscribe-auth/AGbkQlw0kkA1zVhdG20n5UCsco7p-igtks5tZHg-gaJpZM4SVr7t .