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runner.conda: Comment on how to support activation scripts if necessa…
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…ry in the future

I was thinking about this for unrelated reasons today and tinkered with
it a little, so write down some clues for future me (or future you).
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tsibley committed Jan 13, 2023
1 parent 2b53cd4 commit 858ab5a
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12 changes: 12 additions & 0 deletions nextstrain/cli/runner/conda.py
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Expand Up @@ -83,6 +83,18 @@ def run(opts, argv, working_volume = None, extra_env = {}, cpus: int = None, mem
# memory, at least on POSIX systems.
# -trs, 21 May 2020 (copied from ./native.py on 30 Aug 2022)

# XXX TODO: If we need to support Conda activation scripts (e.g.
# …/env/etc/conda/activate.d/) in the future, we could probably switch to
# exec chaining thru `micromamba run` here (with carefully constructed
# options and environ akin to what we do in micromamba() below).
#
# Currently our env has a couple activation scripts, but they're not
# necessary due to 1) our particular usage of the related packages and 2)
# that this runtime, for reasons of package availability, can't support
# Windows at this time (where activation is more crucial than Unix due to
# DLL searching).
# -trs, 13 Jan 2023

extra_env.update({
"PATH": path_with_prefix(),
})
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