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Improved and expanded runtime documentation #303
Commits on Aug 2, 2023
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docs: Note on the "upgrade Nextstrain CLI" page how to update the run…
…time I'd like to make this distinction even clearer in the future, but it'll have to wait for another doc push. For now, at least provide a pointer to anyone coming to this page wanting to update the runtime.
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Commits on Aug 3, 2023
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docs: Document runtimes more comprehensively and centrally
Trying to provide a more useful resource to point people to than a smattering of scattered doc snippets. There's still some places this could be better cross-referenced (e.g. in --help output) and more that could be said about runtimes in general and each runtime specifically… but that can all come in due time. I needed to find a stopping point for this work _somewhere_. A big gain here is that now there's clear places to attach additional documentation in the future. Like the recent switch from dynamically- to statically-generated rST for command documentation, it may also sooner-than-later make sense to ditch the "automodule" directive and do something static instead. Resolves <#288>.
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docs: Document config file variables and path configuration
Previously undocumented!
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runner.singularity: Clean up caches during update and setup
Since we immediately convert the Docker/OCI image to SIF, the Docker/OCI image layer caches end up being duplicative. Not keeping them cached means the cache can't be used to avoid downloading layers that haven't changed in subsequent updates, but I think when choosing between minimizing transfer or storage for our users, we should minimize storage. If we want to have our cake and eat it to (i.e. minimize both), we might be able to change tack to newer Singularity features where (I think) OCI images can be used directly without first converting to SIF. Then, like with our Docker runtime, the image we use and layer caches are one and the same. That's a larger change for a future time, though.
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docs: Replace reference to "runtime" term in our umbrella doc's gloss…
…ary with ours More internally consistent now that we have the glossary term, which in turn links to our overview page about them for more details.
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Commits on Aug 17, 2023
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docs: Reiterate how to report runtime version info in ¶ about switchi…
…ng/updating runtimes A good suggestion by @joverlee521 in review.
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docs: Link to our conda-base repo in the Conda runtime description
à la how we do it for the docker-base repo and the Docker runtime. A good suggestion by @joverlee521 in review.
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docs: Refer to our general installation page from the setup section o…
…f our ambient runtime The general installation page contains a good example of ambient setup. A good suggestion by @victorlin in review.
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