search

lorenzo-rovigatti / oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings
https://dna.physics.ox.ac.uk/
GNU General Public License v3.0
38 stars 26 forks source link

DNA-RNA hybrid model #68

Closed eryykr closed 9 months ago

ErikPoppleton commented 9 months ago

Excited to see this update! It looks like you've got a bunch of test files in analysis/test. There is a script in there called cleanup.sh which will remove all the generated files to clean up the commit. Can you please run that to remove the files?

eryykr commented 9 months ago

Sure, just did it!

On Wed, Sep 20, 2023 at 9:58 AM Erik Poppleton @.***> wrote:

Excited to see this update! It looks like you've got a bunch of test files in analysis/test. There is a script in there called cleanup.sh which will remove all the generated files to clean up the commit. Can you please run that to remove the files?

— Reply to this email directly, view it on GitHub https://github.com/lorenzo-rovigatti/oxDNA/pull/68#issuecomment-1727279713, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASQGARMUY7Z6MRCIPYXEVVDX3KV3BANCNFSM6AAAAAA46PSWKU . You are receiving this because you authored the thread.Message ID: @.***>

lorenzo-rovigatti commented 9 months ago

Thanks for the PR, this will be a great addition to the code! I'm trying to make sense of the changes so that I can make sure that we are not going to break anything. In the meantime, can you resolve MCBackend.cpp's conflict? I have the impression that you didn't make any changes to the file yourself, but it's just a bit outdated with respect to the master one.

lorenzo-rovigatti commented 9 months ago

Sorry for the multiple messages. The other issue I see is that you are trying to merge with master a branch that was merged with new_topology. I think we need to first merge that into master, and then we can go ahead with this one.

ErikPoppleton commented 9 months ago

Sorry for the multiple messages. The other issue I see is that you are trying to merge with master a branch that was merged with new_topology. I think we need to first merge that into master, and then we can go ahead with this one.

We also need to merge oat_dev into new_topology first since I also rewrote convert.py and the oat data structures/readers to work with the new topology.

lorenzo-rovigatti commented 9 months ago

Erik and I are working on the new topology branch. We plan to merge it later this week and then I'll start working on this one. However, since there are some core files that are involved, I think it would be better if we could merge your code into a non-master branch. I don't know if you can change that after you created the PR or you have to make a new one. If you can't edit this one then I'll close it and you can make a new one.

eryykr commented 9 months ago

Looks like this can be easily done - I've now changed the base branch of the PR to the new topology one.

On Mon, Sep 25, 2023 at 12:21 PM Lorenzo Rovigatti @.***> wrote:

Erik and I are working on the new topology branch. We plan to merge it later this week and then I'll start working on this one. However, since there are some core files that are involved, I think it would be better if we could merge your code into a non-master branch. I don't know if you can change that after you created the PR or you have to make a new one. If you can't edit this one then I'll close it and you can make a new one.

— Reply to this email directly, view it on GitHub https://github.com/lorenzo-rovigatti/oxDNA/pull/68#issuecomment-1733468584, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASQGARNCC34I24S33CH45BLX4FSJXANCNFSM6AAAAAA46PSWKU . You are receiving this because you authored the thread.Message ID: @.***>

lorenzo-rovigatti commented 9 months ago

Thanks! I have created a new branch (dna_rna) and make this PR point to that one instead. Can you resolve the conflicts so that I merge it and then test it appropriately?

lorenzo-rovigatti commented 9 months ago

@eryykr thanks again for the PR! I have merged it into a separate branch and will work on merging it to master as soon as I'm done with oat_dev.