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Address shared snippets/code in pathogen builds #2

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tsibley opened this issue Jun 30, 2018 · 2 comments
Open

Address shared snippets/code in pathogen builds #2

tsibley opened this issue Jun 30, 2018 · 2 comments

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@tsibley
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tsibley commented Jun 30, 2018

Not sure what the best approach is here, there are several, but we should eventually address things like: https://github.com/nextstrain/zika/blob/master/Snakefile#L4-L23
@tsibley tsibley self-assigned this Jun 30, 2018
@jameshadfield jameshadfield mentioned this issue Jul 2, 2018
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@tsibley
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tsibley commented Jul 2, 2018

After consideration, my current thought is to create a nextstrain-build Python package which provides a module structure like:

nextstrain/
  build/
    __init__.py
    config.py
    ...

which is expected to be installed. This would let Snakefiles import useful functions like:

from nextstrain.build.config import field_map

Thoughts?

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tsibley commented Jul 2, 2018

augur version checking could be wrapped up into a routine in this nextstrain-build package, for example:

from nextstrain.build.util import assert_augur_version

assert_augur_version("3.0.0")

tsibley added a commit that referenced this issue Jul 2, 2018
@tsibley
wip! Remove credentials from config in favor of environment variables
2d14707 
This is more standard (e.g. follows the 12 factor app pattern) and, as
Trevor noted¹, is encouraged by lots of services like Travis CI and
Heroku and EC2.  It also means credentials are not visible in the output
of `ps`, which is important for running on shared hosts.

Unresolved is how to programmatically describe the requirements on the
"envdir" module.  This is an unresolved question for build requirements
in general.²  It may be that we sidestep that by accessing envdir
through a nextstrain.build module that's always required to be
available, as described in a proposal for refactoring shared functions.³

¹ #4
² #3
³ #2
@tsibley tsibley removed their assignment May 10, 2019
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@tsibley