doc: convert config guide to reST, document name restrictions for builds:
#896
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pandoc -f markdown -t rst --wrap=none docs/src/reference/configuration.md -o docs/src/reference/configuration.rst
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Thanks @victorlin! Looks good. Perhaps explicitly call out the fact that they cannot have a full stop? Also, the schema should be updated to avoid the build name ending with John & I talked about re-organising this file, and I'll try to do this in a separate PR on top of the tutorial branch. |
This is documented internally with [workflow config schema][1] and [various wildcard constraints][2]. [1]: https://github.com/nextstrain/ncov/blob/464041debc66a86a33d3c1c697026a1adeb1d326/workflow/schemas/config.schema.yaml [2]: https://github.com/nextstrain/ncov/blob/464041debc66a86a33d3c1c697026a1adeb1d326/Snakefile#L132-L138
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| Build names currently only allow alpha characters, underscores, and hyphens (``A-Z``, ``a-z``, ``_``, ``-``), but must not contain ``tip-frequencies`` as it is a special string used for Nextstrain builds. |
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I also noticed that just tip-frequencies passes the regex, is this fine? Or should it be matching for _tip-frequencies?
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We should err on the side of caution here and make sure the build name doesn't end with any of the 5 suffixes we filter out in the nextstrain server:
// All JSON files which aren't a sidecar file with a known suffix are assumed to
// be v2+ JSONs (aka "unified" JSONs)
const sidecarSuffixes = ["meta", "tree", "root-sequence", "seq", "tip-frequencies", "measurements"];
const datasets = jsonFiles
.filter((filename) => !sidecarSuffixes.some((suffix) => filename.endsWith(`_${suffix}.json`)))There was a problem hiding this comment.
Added this to issue #900
Description of proposed changes
This PR adds a warning message to the builds section:
This is documented internally with workflow config schema and various wildcard constraints.
To add the warning block, I first had to convert to reStructuredText.
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