search

MolSSI / covid

MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store
https://covid.molssi.org
28 stars 49 forks source link

Create nsp14_nsp10_namd_trajectories_dry_amarolab.yml #251

Closed ozlemd78 closed 2 years ago

ozlemd78 commented 2 years ago

Description

Provide a brief description of the data being added here.

Status

Lnaden commented 2 years ago

@ozlemd78 can you please set the trajectory URL to the actual trajectory URL and not just the lab homepage? I'm going to hold off on merging any of the other files right now until thats resolved.

ozlemd78 commented 2 years ago

Hi Levi,

The exact link for this trajectory is https://amarolab.ucsd.edu/files/covid19/CoV2_ExoN/nsp14_nsp10/trajectories_nsp14_nsp10_namd_dry_amarolab.dcd.gz

I couldn't find where to edit the file and make this change. Can you help please?

Best, Ozlem

On Tue, Feb 8, 2022 at 11:10 AM Levi Naden @.***> wrote:

@ozlemd78 https://github.com/ozlemd78 can you please set the trajectory URL to the actual trajectory URL and not just the lab homepage? I'm going to hold off on merging any of the other files right now until thats resolved.

— Reply to this email directly, view it on GitHub https://github.com/MolSSI/covid/pull/251#issuecomment-1032965526, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJZYLCAMV2DVJFLK4PDUAKTU2FTDLANCNFSM5N3KMEYA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

Lnaden commented 2 years ago

What you have done here is make a PR to the repository using the GitHub web interface. That's fine for making very short or small changes/edits to single file, but runs into the issue you have where if you then need to edit it, it gets to be more problematic.

When you made a PR through the web here, GitHub automatically made a fork of this central repository in your personal user repo here: https://github.com/ozlemd78/covid. It then also made a branch called patch-X where X is just an increment of how many times you've used the website to open PR's on this central repo. Its a default name, you could have called it whatever.

One option is to go to the patch-10 branch on your fork, edit the file there directly, and commit the file directly to your fork without opening as a PR, it should be a radio button at the bottom before you click submit (or something). That will automatically update this PR as well on the main repo.

The more complete approach is to use git from your local computer, do a git pull of your fork and branch to your local filesystem, edit the files as normal, do a git add and git commit to confirm your changes to the local git repository, and finally do a git push to upload those changes to the repository on GitHub. This option is more complete because it allows multiple and arbitrary amounts of changes to any number of files, and you can verify everything before you upload. Then any modifications you need, you can just repeat the process of editing the files locally, add/committing them, then pushing to update the PR.

ozlemd78 commented 2 years ago

Hi Levi,

I have made the changes using patch-10 link you sent for nsp14_amber_trajectories_dry_amarolab.yml .

I don't see the changes yet when I look at the public files though, does it take some time or am I missing something?

Best, Ozlem

On Tue, Feb 8, 2022 at 11:34 AM Levi Naden @.***> wrote:

What you have done here is make a PR to the repository using the GitHub web interface. That's fine for making very short or small changes/edits to single file, but runs into the issue you have where if you then need to edit it, it gets to be more problematic.

When you made a PR through the web here, GitHub automatically made a fork https://docs.github.com/en/get-started/quickstart/fork-a-repo of this central repository in your personal user repo here: https://github.com/ozlemd78/covid. It then also made a branch https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches called patch-X where X is just an increment of how many times you've used the website to open PR's on this central repo. Its a default name, you could have called it whatever.

One option is to go to the patch-10 branch on your fork https://github.com/ozlemd78/covid/tree/patch-10, edit the file there directly, and commit the file directly to your fork without opening as a PR, it should be a radio button at the bottom before you click submit (or something). That will automatically update this PR as well on the main repo.

The more complete approach is to use git from your local computer, do a git pull https://github.com/git-guides/git-pull of your fork and branch to your local filesystem, edit the files as normal, do a git add https://github.com/git-guides/git-add and git commit https://github.com/git-guides/git-commit to confirm your changes to the local git repository, and finally do a git push https://github.com/git-guides/git-push to upload those changes to the repository on GitHub. This option is more complete because it allows multiple and arbitrary amounts of changes to any number of files, and you can verify everything before you upload. Then any modifications you need, you can just repeat the process of editing the files locally, add/committing them, then pushing to update the PR.

— Reply to this email directly, view it on GitHub https://github.com/MolSSI/covid/pull/251#issuecomment-1032986263, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJZYLCEHB5ULWCPMQDCCYVLU2FV3JANCNFSM5N3KMEYA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

Lnaden commented 2 years ago

I don't see the changes yet when I look at the public files though,

Public files is a bit ambiguous here.

The only place the changes will have occurred so far are on your fork, and only on the specific branch this PR is drawing from. Until the Pull request is approved and merged into the main repository here, there are no changes committed the the main repo. Similarly, your main/master branch on your fork won't have the changes either because the changes are only on your branch.

Because the files have not been committed yet, they are not visible on the live website yet which is based on the current main branch of the original repo (this one). There is a preview build of the website generated from the checks of this PR, but I don't think thats what you wanted either.

Also, your new file: nsp14_nsp10_namd_trajectories_dry_amarolab.yml is still using the lab's main URL instead of the actual trajectory. I think most of your PR's, including the ones I already merged have this problem as well.

ozlemd78 commented 2 years ago

Hi Levi,

Could you please cancel/reject all 6 of my pull requests today? Or do I have to delete them? I'd like to go ahead and generate fresh files with complete info and make a pull request then.

Thanks much for your help, Ozlem

On Tue, Feb 8, 2022 at 11:54 AM Levi Naden @.***> wrote:

I don't see the changes yet when I look at the public files though,

Public files is a bit ambiguous here.

The only place the changes will have occurred so far are on your fork, and only on the specific branch this PR is drawing from. Until the Pull request is approved and merged into the main repository here, there are no changes committed the the main repo. Similarly, your main/master branch on your fork won't have the changes either because the changes are only on your branch.

Because the files have not been committed yet, they are not visible on the live website yet which is based on the current main branch of the original repo (this one). There is a preview build of the website generated from the checks of this PR, but I don't think thats what you wanted either.

Also, your new file: nsp14_nsp10_namd_trajectories_dry_amarolab.yml https://github.com/MolSSI/covid/pull/251/files#diff-64007d351bbfc7cba55b2e48e2711cefcf75ac369b6f41bf04835cc4ccbd939e is still using the lab's main URL instead of the actual trajectory. I think most of your PR's, including the ones I already merged have this problem as well.

— Reply to this email directly, view it on GitHub https://github.com/MolSSI/covid/pull/251#issuecomment-1033002898, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJZYLCEOMG2YBXRKELUG2ZLU2FYHFANCNFSM5N3KMEYA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

Lnaden commented 2 years ago

Could you please cancel/reject all 6 of my pull requests today

Not a problem. I can close all the open ones.

Thanks much for your help,

No problem, happy to help; especially when it comes to helping people learn git.