Code

Environment variables#289

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tsibley merged 12 commits intomasternextstrain/cli:masterfrom trs/envnextstrain/cli:trs/envCopy head branch name to clipboardJun 21, 2023

+528-86

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Commits on Jun 21, 2023

• devel: Replace realpath from GNU coreutils with cd …; pwd

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• runner.singularity: Use hostenv.forwarded_values() instead of reimplementing it

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• runner: Annotate all extra_env parameters with a type

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• runner.conda: Fix inadvertent mutation of extra_env

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• Support removal of env vars via Env (e.g. extra_env) keys valued None

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• runner: Add --env=<name>[=<value>] and --envdir=<path> options

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• view: Override HOST inside a Docker container with an alternative method

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• runner.{docker,aws_batch}: Pass env into the container via /nextstrain/env.d…

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• runner: Centralize handling of hostenv and pass it via extra_env

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• runner: Don't pass automatic hostenv if --env or --envdir are used

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• runner: Slightly better prose list formatting in the description of --env

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• CHANGES: Document --env and --envdir and more secure env handling for Docker and AWS Batch

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