Add "1m" timespan in Nextstrain profiles #1027
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victorlin
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Here are the job ids so one can check logs, open should be done by now but isn't... Jobs failed @victorlin Some errors I don't understand: Open seems to have worked apart from some uploads that failed. GISAID meanwhile failed like this: We should probably have an option |
corneliusroemer
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Nov 3, 2022
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Thanks for digging into that @corneliusroemer. I'm about to sign out for the day, so feel free to make changes on the PR branch to your desire. Otherwise I can pick up on it tomorrow. |
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As @trvrb mentioned in Slack, logistic growth is set to 6 weekly pivots which is too much when frequencies is limited by |
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Also @corneliusroemer it's the same error for both GISAID and open. |
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Excellent, now it works. I think we can make the bucket size bigger to get more recent sequences for the open build. We only have 1.3k sequences from last 1M and 2k sequences in total. A build with 4k sequences is a good size, so we can add another 2k sequences from the most recent month to make it as useful as possible. |
Fixes some copy errors.
Everything is copied from entries defining the existing "2m" timespan. Comments and other timespan references updated accordingly.
This avoids an uncaught IndexError that had occurred with pivots[first_pivot_index] when first_pivot_index was out of bounds.
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@corneliusroemer I've just rebased onto latest master so it has your changes to upload builds as they are done. I think it'd be best if you take over this branch now and tweak to your desire. Would you be willing to do that? |
docs/src/reference/change_log.md
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| @@ -5,6 +5,10 @@ We also use this change log to document new features that maintain backward comp | |||
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| ## New features since last version update | |||
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| - X November 2022: Add "2m" timespan in Nextstrain profile builds. [PR 1027](https://github.com/nextstrain/ncov/pull/1027) | |||
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Suggested change
| - X November 2022: Add "2m" timespan in Nextstrain profile builds. [PR 1027](https://github.com/nextstrain/ncov/pull/1027) | |
| - 8 November 2022: Add "1m" timespan in Nextstrain profile builds. [PR 1027](https://github.com/nextstrain/ncov/pull/1027) | |
docs/src/reference/change_log.md
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| @@ -5,6 +5,10 @@ We also use this change log to document new features that maintain backward comp | |||
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| ## New features since last version update | |||
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| - X November 2022: Add "2m" timespan in Nextstrain profile builds. [PR 1027](https://github.com/nextstrain/ncov/pull/1027) | |||
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| - X November 2022: calculate_delta_frequency: Allow script to work with fewer pivots available than requested with `--delta-pivots`. [PR 1027](https://github.com/nextstrain/ncov/pull/1027) | |||
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Suggested change
| - X November 2022: calculate_delta_frequency: Allow script to work with fewer pivots available than requested with `--delta-pivots`. [PR 1027](https://github.com/nextstrain/ncov/pull/1027) | |
| - 8 November 2022: calculate_delta_frequency: Allow script to work with fewer pivots available than requested with `--delta-pivots`. [PR 1027](https://github.com/nextstrain/ncov/pull/1027) | |
corneliusroemer
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Nov 8, 2022
rneher
approved these changes
Nov 11, 2022
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@corneliusroemer FYI, I'm deleting your branch |
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Description of proposed changes
Motivated by this Slack thread.
Everything is copied from entries defining the existing "2m" timespan. Comments and other timespan references updated accordingly.
Preview staging builds
Note that these won't be ready until the trial runs have finished uploading.
Related issue(s)
N/A
Testing
Release checklist
If this pull request introduces backward incompatible changes, complete the following steps for a new release of the workflowN/AIf this pull request introduces new features, complete the following steps:
docs/src/reference/change_log.mdin this pull request to document these changes by the date they were added.