Please make pull requests if possible

[corneliusroemer]

When you identify that a recently designated lineage has been discussed in an issue, but the issues has not been mentioned in lineage_notes.txt as the person designating wasn't aware of the issue, it would be great if you could submit a PR adding that issue to lineage notes.

The same goes for other types of corrections to lineage_notes.txt, like typos. Pull requests speed up things a lot on the maintainer end. Thank you!

I've made a quick screen cast of the steps involved:

pr.mp4

[FedeGueli]

Thanks @corneliusroemer i think i have modified and committed the recent ones (beside the ones already committed by others) , but in the past have you always update the lineage notes with issue #? or i have to check further back?

[Memorablea]

Excuse me, does the green check mark indicate that I can close the pull request?

[corneliusroemer]

@Memorablea: Does the green check mark indicate that I can close the pull request?

Good question. No, it means that certain automatic checks passed successfully, like that there are no duplicate strains in lineages.csv, you can essentially ignore the tick.

You can read more about this Github feature here: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/collaborating-on-repositories-with-code-quality-features/about-status-checks

[FedeGueli]

I noticed that some of us have done separately the same changes, what happens in this case ? the last one overwrite the first right?? so it is not an issue at all, right?

[corneliusroemer]

@FedeGueli: I noticed that some of us have done separately the same changes, what happens in this case ? the last one overwrite the first right?? so it is not an issue at all, right?

That's a great question! This is a very common use case in software development so git/Github is very good at dealing with it: I manually select which changes to keep when merging. Not a problem at all.

[FedeGueli]

After the code from @avichzl1 we have still to update lineages notes manually??

[ryhisner]

Is there a link to get to the starting screen in the video posted above? I can't figure out how to get there.

[FedeGueli]

Is there a link to get to the starting screen in the video posted above? I can't figure out how to get there.

Just opem file limeages notes

[FedeGueli]

Touching the three points menu beside lineage_ notes_txt (on the right) and then clicking on view file thne on the right selecting for Master.

[FedeGueli]

@corneliusroemer @AngieHinrichs @aviczhl2 please could you write down the new rules cause i messed up things yesterday adding issues before the automatic update.

So i have just to add the milestone in the other repo right? the rest will be automatically updated right?

[aviczhl2]

@corneliusroemer @AngieHinrichs @aviczhl2 please could you write down the new rules cause i messed up things yesterday adding issues before the automatic update.

So i have just to add the milestone in the other repo right? the rest will be automatically updated right?

You only need to add milestones and my codes will automatically match milestones to lineages and issues if a lineage does not already has a reference but has a milestone attached on it.

The code will keep all manual refs and just skip those lineages. So manual refs will not do anything good or bad.

However, you need to keep your branch up-to-date before submiting a pull request. Otherwise there will be conflict.

[AngieHinrichs]

No worries @FedeGueli, any change in a process can be expected to cause some hiccups even when it's an improvement. 🙂 I think these steps should work (basically what @aviczhl2 said, but more verbose):

1. Cornelius designates new lineages
2. FedeGueli (and others?) add milestones to lineage-proposals and get Cornelius to add milestones to pango-designation
3. Wait for Cornelius to finish designations for now, wait for each other to have time to comment on designations and add milestones
4. @aviczhl2 runs automated update from milestones and does a PR in pango-designation
5. After the automated update PR is accepted, everybody updates their pango-designation/lineage_notes.txt. Then if manual edits are necessary (e.g. add missing geographical info, fix mutation typo), do the manual edits in one PR per person -- but please coordinate, so we don't get similar edits to the same line from multiple people. 😄

That's only my suggestion, feel free to correct any problems that you see with it, or scrap it and start over. 😄 @HynnSpylor adding you in case you aren't already watching this issue.

[And FYI I will be on vacation Aug. 3rd-13th so I won't reply to github messages during that time]

[FedeGueli]

Thank you @AngieHinrichs !

[HynnSpylor]

Thanks a lot @AngieHinrichs !

I strongly agree the auto-reference by @aviczhl2 is main path (if the references are missing), and then I'll make some supplements/patches if necessary.

Apologize if my works cause some chaos

[ciscorucinski]

@AngieHinrichs Thanks for laying out these details! It's been great to see others submit PRs

5. After the automated update PR is accepted, everybody updates their pango-designation/lineage_notes.txt. Then if manual edits are necessary (e.g. add missing geographical info, fix mutation typo), do the manual edits in one PR per person -- but please coordinate, so we don't get similar edits to the same line from multiple people. 😄

It seems the number of active maintainers reviewing and accepting pull requests has decreased over the past couple of months. I know you are on vacation (enjoy!). But do you think additional maintainers might be needed in the future or do you think that you two (??) will suffice?

[Memorablea]

O MY GOD

[ciscorucinski]

@Memorablea Your changes are most likely good.
PR #2306