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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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Generate CLI documentation files? #1524

Open victorlin opened 5 days ago

victorlin commented 5 days ago

Doc updates such as #1523 are tedious and prone to human error. It would be good if they can be auto-generated.

API docs can already be auto-generated, https://github.com/nextstrain/augur/pull/1525 adds that to CI.

victorlin commented 5 days ago

I don't think this is trivial since some doc files e.g. augur traits have custom text that isn't possible with auto-generation. If they were moved to docstrings such as distance.py it might be possible.

joverlee521 commented 5 days ago

I don't think this is trivial since some doc files e.g. augur traits have custom text that isn't possible with auto-generation.

Following the dev docs, I thought the doc files were auto-generated with 

sphinx-apidoc -T -f -MeT -o docs/api augur

Then any custom text is added manually?

We can at least run the sphinx-apidoc command to autogenerate the pages and they can get manually filled in with custom text as needed?

victorlin commented 5 days ago

Oh... I completely missed that section of dev docs 🤦 this person needs to read more