Code

Singularity compatibility fixes#283

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tsibley merged 10 commits intomasternextstrain/cli:masterfrom trs/singularity/compatnextstrain/cli:trs/singularity/compatCopy head branch name to clipboardMay 26, 2023

+188-8

Commits

Commits on May 24, 2023

• shell: Note which runtime is being entered

  Show description for 9c4c65b
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  9c4c65b

Commits on May 25, 2023

• debug: Emit log lines for calls to capture_output() and exec_or_return()

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  c0ee999

• runner.singularity: Extend commentary on isolation flags compatibility

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  13149ef

• runner.singularity: Check for minimum Singularity version during check-setup

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  6feda73

• runner.singularity: Allow writes to HOME on the container filesystem

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  d014415

• runner.singularity: Restore our customized shell prompt on Singularity ≥3.5.3

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  91e079e

• runner.singularity: Avoid pre-exec evaluation of entrypoint command line…

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  dee8903

• dev: Add type stubs for boto3 and botocore

  Show description for 845f067
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  845f067

• dev: Work around some mypy limitation when type checking a lambda

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  31d708f

Commits on May 26, 2023

• CHANGES: Document the Singularity (and Conda) fixes since the last release

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  3215a5f