Add 4 autoref from main page and 31 from lineage-proposals

[aviczhl2]

Also modified the code to priortize milestones on main page.

@AngieHinrichs
If there's a milestone on both main page and sars-cov-2, it will prioritize main page now.

@ciscorucinski
Please take a look at the new code now, may be helpful.

[FedeGueli]

Also modified the code to priortize milestones on main page.

@AngieHinrichs If there's a milestone on both main page and sars-cov-2, it will prioritize main page now.

@ciscorucinski Please take a look at the new code now, may be helpful.

Thank you. so i can add all the milestones in the secondary page without fearing to mess things right?

[ciscorucinski]

I can't really see the diff for automated-issue-ref.ipynb. Notebook diffs are not supported well on GitHub it seems like. However, in lineage_notes.txt, there are some differences between what this PR suggests for linked issues and what @FedeGueli has suggested in his PRs.

[FedeGueli]

I can't really see the diff for automated-issue-ref.ipynb. Notebook diffs are not supported well on GitHub it seems like. However, in lineage_notes.txt, there are some differences between what this PR suggests for linked issues and what @FedeGueli has suggested in his PRs.

Maybe for the fact i added milestones to secondary page ?

[aviczhl2]

Thank you. so i can add all the milestones in the secondary page without fearing to mess things right?

If there's a milestone on main page, milestones on the secondary page won't influence the result.

However it will take milestones from secondary pages if there's no milestone on main page.

[ciscorucinski]

If there's a milestone on main page, milestones on the secondary page won't influence the result.

Not quite. The opposite is happening within some lineages within this PR.

There are 5 lineages that convert his cov-lineage/pango-designation issue to a sars-cov-2-variants/lineage-proposals issue. And there is one lineage where it converts his sars-cov-2-variants/lineage-proposals issue to a different sars-cov-2-variants/lineage-proposals issue

This is the same issue I discovered earlier this week with auto generating this. It's why I am changing direction.

[ciscorucinski]

I believe that he shouldn't have to worry at all about milestoning issues. In fact, I think he should be encouraged to milestone every single connection; worry-free.

@FedeGueli I am working on a new workflow that I hope to PR here soon. It will collect ALL lineage-milestone-issue connections and document them rather than needing to narrow it down to just one issue as with lineage_notes.txt.

I plan on creating a supplementary file to go along with lineage_notes.txt. You can check out my repo's mapping.json file, which can be updated daily. The existing JSON file will be used for verification purposes anyways with my new workflow, and a simple JSON to table transformation could be applied to create this supplementary file. It might look possibly something like the following...

Lineage	Milestone	Issues	Repository
...
EG.5.1.3	24	222	sars-cov-2-variants/lineage-proposals
EG.5.1.4	801	2117	cov-lineages/pango-designation
EG.5.1.4	18	428	sars-cov-2-variants/lineage-proposals
...

With this supplementary file, there will be no lost information; The only way to lose information is to not milestone and label enough.

[aviczhl2]

Not quite. The opposite is happening within some lineages within this PR.

There are 5 lineages that convert his cov-lineage/pango-designation issue to a sars-cov-2-variants/lineage-proposals issue. And there is one lineage where it converts his sars-cov-2-variants/lineage-proposals issue to a different sars-cov-2-variants/lineage-proposals issue

This is the same issue I discovered earlier this week with auto generating this. It's why I am changing direction.

What are they? Each autoref shall not have any prior refs in lineage_notes.txt. So such conversion won't happen.

[ciscorucinski]

I was not talking about that aspect.

Based on @FedeGueli 's PR and your PR, there are 5 lineages that have issues within the main repo where your PR didn't use those main repo issues, but the secondary repos issues.

The reason is because the main repo hasn't had it's milestones updated in 2 days. So they aren't milestoned yet, but @FedeGueli had identified these currently non-milestoned issues. The major issue is that since autoref does not modify existing references, all of these need to be correctly identified and fixed after each autoref update. But the 5 issues are what has been identified so far. This number could go up.

However, if autoref were to update existing references, then that would have it's own problems. This is why I'm focused on validation and continuously updating information now.

The following have been identified within the main repo...

• HC.2
• HK.3.1
• JF.1
• XBB.1.16.23
• GE.1.3

[aviczhl2]

The following have been identified within the main repo...

• HC.2
• HK.3.1
• JF.1
• XBB.1.16.23
• GE.1.3

I see. In the next version I'll come up with a fix of this by checking main page milestones for lineages with secondary page refs. Assuming they eventually get their milestones on main page they eventually will be linked to their main page ref.

Currently autorefs and manual refs are actually distinguishable (manual refs use “from" while autoref uses "From"), so it's not hard to detect and remove autorefs and update with new ones.

So @FedeGueli feel free for milestone on the secondary page.

[ciscorucinski]

Ah sorry, it was the PR from @Over-There-Is, not @FedeGueli. Maybe that led to some confusion.

Assuming they eventually get their milestones on main page they eventually will be linked to their main page ref.

This will be good,. This sounds like that autoref will be changed to overwrite existing references, right?

manual refs use “from" while autoref uses "From")

This isn't currently consistent within lineage_notes.txt, though. There are PRs that have already "corrected" some references that use From to use from instead. There are at least 4 examples of this in @Over-There-Is 's current PR. If this autoref identification feature is not imperative, then this doesn't matter.

[AngieHinrichs]

Thanks @aviczhl2! I had to manually resolve some conflicts, and there was a warning that I would be changing a master branch (probably yours since this still requires merging) -- so you might want to check your local master branch vs. github. I hope that doesn't create an inconvenience for you.