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nextstrain / augur

Pipeline components for real-time phylodynamic analysis
https://docs.nextstrain.org/projects/augur/
GNU Affero General Public License v3.0
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CI: linkcheck fails occasionally due to fasttree link #1621

Closed corneliusroemer closed 2 months ago

corneliusroemer commented 2 months ago

Current Behavior

I've noticed that linkcheck occasionally makes CI fail.

The only broken link I could find in logs is this:

(installation/installation: line    9) broken    http://www.microbesonline.org/fasttree/ - 403 Client Error: Forbidden for url: http://www.microbesonline.org/fasttree/

https://github.com/nextstrain/augur/actions/runs/10706830674/job/29685454019#step:6:160

Update: seems just flaky, rerunning fixed it. Maybe we could wrap this step in a retry to deflake if it bothers us that CI fails stochastically.

tsibley commented 2 months ago

Yeah, see https://github.com/nextstrain/.github/issues/106.

corneliusroemer commented 2 months ago

Ah thanks. Why is this in the .github repo rather than here in the repo that's actually affected? This means I need to check 2 rather than 1 repo for duplicates?

Ah I see, because the code lives there - not sure we shouldn't just keep this open here pointing at upstream? .github/workflows/docs-ci.yaml

tsibley commented 2 months ago

Right, the code lives there and the issue is more broad than Augur (though Augur is where we're most noticing the failures right now). I don't see the need for an open issue here; a closed one serves fine for searching purposes and doesn't clutter the open list. But if you'd like to leave it open, that's fine with me.

This means I need to check 2 rather than 1 repo for duplicates?

Searching across the org, e.g., rather than within a repo would be easier than searching two repos.

corneliusroemer commented 2 months ago

Ah, the thing is the default of searching open issues is the easiest. I could search the org but it requires extra clicks I need to remember.

Same for closed issue potentially, I would have to alter the default query. I think in principle it should stay open and be marked as "blocked" or "upstream" but this is bikeshedding process and I'm happy with whatever you prefer 😀