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Improved and expanded runtime documentation #303

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merged 10 commits into from
Aug 17, 2023
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Commits on Aug 2, 2023

  1. 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.
    tsibley committed Aug 2, 2023
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Commits on Aug 3, 2023

  1. 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>.
    tsibley committed Aug 3, 2023
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  2. docs: Document config file variables and path configuration

    Previously undocumented!
    tsibley committed Aug 3, 2023
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  3. 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.
    tsibley committed Aug 3, 2023
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  5. 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.
    tsibley committed Aug 3, 2023
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Commits on Aug 17, 2023

  1. docs: Reiterate how to report runtime version info in ¶ about switchi…

    …ng/updating runtimes
    
    A good suggestion by @joverlee521 in review.
    tsibley committed Aug 17, 2023
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  2. 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.
    tsibley committed Aug 17, 2023
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  3. 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.
    tsibley committed Aug 17, 2023
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