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Data format: TSV #238

Merged
merged 4 commits into from
Dec 3, 2024
Merged

Data format: TSV #238

merged 4 commits into from
Dec 3, 2024

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joverlee521
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@joverlee521 joverlee521 commented Nov 26, 2024

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Description of proposed changes

Add TSV section to the Data Format docs, based on discussion in nextstrain/augur#1566.

Related issue(s)

Resolves #237

Checklist

  • Checks pass (failing rtd redirect unrelated to changes in this PR)

Preparing to add a separate section for TSV files.
Proper handling of TSVs with `csvtk`/`tsv-utils` was originally
recommended by @tsibley

<nextstrain/augur#1566 (comment)>
@joverlee521
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Hmm, both rtd redirects and docs build failed with 403 Client Error...maybe related to readthedocs/readthedocs.org#11763.

Adding User-Agent as an attempt to fix the 403 Client Errors returned
from requests to GitHub.
@joverlee521
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Hooray, c561b61 seems to fix the docs build.

Looking into rtd redirects, which I believe will require updating/releasing https://github.com/nextstrain/readthedocs-cli

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@genehack genehack left a comment

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+1 from me; the "be more definitive" comment is not a blocker, just a suggestion.

src/reference/data-formats.rst Outdated Show resolved Hide resolved
@joverlee521
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Created issue to track rtd redirect error, but that should not block this PR since I'm not making any changes to the redirect paths:

paths:
- redirects.yml
- .github/workflows/sync-redirects.yaml

@joverlee521 joverlee521 merged commit 38d42fd into master Dec 3, 2024
2 of 3 checks passed
@joverlee521 joverlee521 deleted the data-format-tsv branch December 3, 2024 22:15
@jameshadfield
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Is this the correct place to document suggested python code for reading/writing? Would be great to have snippets to reuse

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Is this the correct place to document suggested python code for reading/writing? Would be great to have snippets to reuse

Ah, that's true! I'll add it tomorrow.

joverlee521 added a commit that referenced this pull request Dec 4, 2024
Prompted by @jameshadfield's request
<#238 (comment)>

Snippets are simplified versions of TSV handling in Augur.
joverlee521 added a commit that referenced this pull request Dec 5, 2024
Prompted by @jameshadfield's request
<#238 (comment)>

Snippets are simplified versions of TSV handling in Augur.
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Document TSV data format and proper handling
3 participants