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v1.12.1

Getting Started

This maintenance release has no user-facing changes, but updates dependencies and modernizes the Python project tooling (#668) in preparation for the next development cycle.

v1.12.0

• Fix coercions of Array[File] and Array[Directory] to Array[String] (#669 @​john-smith, #681 @​markjschreiber)
• Ensure presence of optional fields in structs read from runner input JSON file (#686 @​adthrasher)
• miniwdl run: accept CLI inputs of compound types (pairs, maps, structs) as single-quoted JSON; also accept Array[Directory]
• miniwdl check: warn when a document of an older WDL version imports a document of a newer WDL version
• Dependency updates

v1.11.1

Getting Started

Maintenance release:

• miniwdl input-template: add --no-namespace option to omit the top-level workflow name prefix
• fix download caching when config [file_io] root is used (miniwdl-ext/miniwdl-aws#20 @​staskh)
• logging improvements and dependency updates

v1.11.0

No release notes provided.

v1.10.0

• WDL spec compatibility:
  • == and != accept optional operands (#634 @​jdidion)
  • fix resolution of imported struct type aliases when the original struct name is reused in current document (#635 @​jdidion)
  • WDL 1.1: allow placeholder options like sep= in string expressions outside of task commands (#633 @​adamnovak)
  • WDL 1.1: disable a few version development features that had been inadvertently enabled for version 1.1 (multi-line strings and optional call: keyword)
• allow extra JSON keys initializing structs (#524)
• fix bug in WDL.Env.merge() that could resurrect previously-shadowed bindings (#637 @​adamnovak)
• miniwdl zip --additional to include any specified file(s) in the zip (#641 @​rhpvorderman)

v1.9.1

• Change singularity invocation from singularity run to singularity exec (#628 @​adthrasher)
• WDL version development:
  • Make the input: keyword optional in calls (openwdl/wdl#524)
  • miniwdl check: reduce spurious warnings on env task inputs used as environment variables instead of WDL interpolations (openwdl/wdl#504)

v1.9.0

• Two potentially breaking changes:
  • Remove the default -l (login shell) flag that had been supplied to each task command bash interpreter starting in v1.5.3, but caused interoperability problems (#603). New config options mentioned below can restore this flag if necessary.
  • Disallow implicit coercions of Boolean? Int? Float? File? Directory? to (non-optional) String, which should never have been permitted (#596). These had been subject to miniwdl check deprecation warning since v1.7.1. They will still validate with --no-quant-check.
• New config options (see default.cfg)
  • [task_runtime] command_shell and [task_runtime] command_preamble customize the task command bash interpreter. For example, to restore the login shell flag, set [task_runtime] command_shell = /bin/bash -l or environment MINIWDL__TASK_RUNTIME__COMMAND_SHELL='/bin/bash -l'
  • [file_io] chown to opt-out of the post-task chown of the working directory
  • [podman] exe to customize the invocation for the podman backend (for example, to remove sudo)
• Relax PyYAML version requirements (#625 @​adamnovak)

... (truncated)

• 475dd3f update dependencies
• 148be2e fix readthedocs
• b00beec upgrade to pyproject.toml (#704)
• 5ccead0 migrate to ruff for linting & formatting (#697)
• 04ca37e migrate typechecker to mypy (#691)
• a34aa90 update wdlviz links
• dbfe115 update docker dependencies
• 3d02f41 update black
• 2086bb9 CLI: allow compound inputs as JSON (#688)
• c4db595 add test for nested interpolations (#679)
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