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whirl

INFRA · APIS
Velocity0.0

R package whirl by NovoNordisk-OpenSource — release notes from GitHub.

github.com/NovoNordisk-OpenSource/whirl ↗

whirl turned script logging into a standardized provenance artifact regulators can read.

reproducibilityclinical reportingprovenanceloggingrenvr package
◆Current state
A parallel R script runner that produces execution logs, aimed at regulated analysis environments. The 0.3.0 release added write_biocompute(), emitting logs as BioCompute Objects in standardized JSON, and simplified the approved-package check to a plain package@version vector. Since then the work has been about what the log can be trusted to contain: an environment_secrets option to keep secret variables out of it, direct versus indirect package usage distinguished and highlighted against the approved list, and the same approval check extended to Python packages.
◆Where it's heading
The through-line is the log as evidence rather than as debugging output. Every recent addition either widens what the log proves — which packages were really used, in which language, against which approved list — or narrows what it must not leak. Setting options only through an explicit with_options argument to run() and getting renv library paths right for Quarto both point the same way: reproducible, auditable child sessions with nothing implicit.
◆Prediction
Expect the approved-package and provenance machinery to keep expanding across languages and environments, since Python approval checks followed the R ones and both feed the same log.

◆Recent moves

  1. 6mo ago

    Explicit option passing to child sessions; renv path fix

    Adds a with_options argument to run() as the only way options reach child sessions, and fixes Quarto startup under renv library paths. Tightens the isolation that makes the log trustworthy.

    View source ↗
  2. 11mo ago

    Logs flag package approval status and exclude secrets

    The log now separates directly from indirectly used packages and flags their approval status, an environment_secrets option keeps chosen variables out of it, and approved-package checks extend to Python. Log content becomes something an auditor can act on.

    View source ↗
  3. 1y ago

    whirl 0.3.0

    ⚡ SPARK

    write_biocompute() turns whirl's logs into BioCompute Objects — a standardized JSON provenance format — rather than a tool-specific report. The releases since have all been about making that record complete and trustworthy.

    View source ↗