v0.19.0

What's Changed

sprocket

Added

• Added run.task.cache and run.task.cache_dir settings to sprocket.toml
  for controlling call caching (#461).
• Added --no-call-cache option to sprocket run to disable use of the call
  cache for a specific run (#461).
• Added --azure-account-name and --azure-access-key CLI options to
  sprocket run (#454).
• New lint rule DocMetaStrings to ensure reserved meta and parameter_meta
  keys have string values (#407).
• A run.fail option was added to sprocket.toml for controlling the default
  failure mode (#444).
• Added the split standard library function in preparation for WDL v1.3 (#424).
• Added support for else if and else clauses in conditional statements (in
  support of WDL v1.3) (#411).
• Added feature flags support to enable experimental WDL versions (#411).
• Added shell expansion to the apptainer_images_dir config option, though
  this is an interim workaround for HPC path awkwardness pending the removal of
  this option entirely in the future (#435).
• Added experimental Slurm + Apptainer backend (#436).

Changed

• Sprocket now supports "slow" and "fast" failure modes for evaluation errors
  an interruptions (Ctrl-C) (#444).
• The wdl-analysis config flag that enables experimental WDL v1.3 features
  was renamed from experimental_versions to wdl_1_3 (#435).
• Removed the wdl-cli crate, absorbing its code into the sprocket library
  crate in preparation for future refactoring (#450).
• Apptainer-based backends now store converted container images within each run directory, rather than in a user-specified directory (#463).

Fixed

• Fixed a bug in sprocket config init where sprocket.toml was unnecessarily loaded and would fail if malformed (#473).
• Fixed Sprocket commands not always showing the full context of errors (#472).
• running sprocket run now writes a .sprocketignore file to the runs directory, which will tell subsequent Sprocket commands to ignore its contents (#469).
• Improved the portability of generated Apptainer scripts (#442).
• Fixed the handling of unusual filenames in generated Apptainer scripts (#459).

wdl

Removed

• Removed the cli feature and module (#450).
• Removed the codespan cargo feature in favor of enabling codespan reporting always (#462).

wdl-analysis

Added

• Added support for else if and else clauses in conditional statements (in support of WDL v1.3) (#411).
• Added feature flags support to enable experimental WDL versions (#411).
• Introduced pre-evaluation task type for all pre-evaluation contexts (task requirements, task hints, and task runtime sections) and expanded support of task.previous for post-evaluation sections in WDL v1.3 (#432).

Changed

• Refactored ScopeUnion to use ScopeRef instead of direct slice indexing, allowing it to be reused in the runtime engine for proper type reconciliation across conditional branches (#411).
• The wdl-analysis config flag that enables experimental WDL v1.3 features was renamed from experimental_versions to wdl_1_3 (#435).

Removed

• Removed the codespan cargo feature in favor of enabling codespan reporting always (#462).

wdl-ast

Added

• Added support for else if and else clauses in conditional statements (in support of WDL v1.3) (#411).

Removed

• Removed the codespan cargo feature in favor of enabling codespan reporting always (#462).

wdl-doc

No changes.

wdl-engine

Added

• Added call caching configuration to TaskConfig (#461).
• Implemented support for call caching
  in TaskEvaluator (#461).
• Added a new fail configuration option for controlling the default failure mode of the engine (#444).
• Added the split standard library function in preparation for WDL v1.3 (#424).
• Added support for else if and else clauses in conditional statements (in support of WDL v1.3) (#411).
• Added shell expansion to the apptainer_images_dir config option, though this is an interim workaround for HPC path awkwardness pending the removal of this option entirely in the future (#435).
• Added experimental Slurm + Apptainer backend (#436).
• Introduced pre-evaluation task type for all pre-evaluation contexts (task requirements, task hints, and task runtime sections) and expanded support of task.previous for post-evaluation sections in WDL v1.3 (#432).
• Added GPU support to the Docker backend (#439).

Changed

• Azure Storage authentication configuration has been changed to use shared key authentication rather than explicit SAS token authentication; SAS token authentication can still be used by directly adding the query parameters to any input URLs (#454).
• Changed how cancellation is supported by the engine; the engine can now wait for executing tasks to complete before canceling them (slow failure mode) or immediately cancel the executing tasks (fast failure mode) (#444).
• Added optional CPU and memory limits to the queue definitions in the LSF + Apptainer backend configuration. This is a breaking change for previous LSF configurations, as the queues are now a struct with a required name string field, rather than just a bare string (#429).
• Changed a number of types in the public interface in preparation for a larger refactoring (#460).
• Introduced a unified TopLevelEvaluator type as a common context for task and workflow evaluations (#463).
• Apptainer-based backends now store converted container images within each run directory, rather than in a user-specified directory (#463).

Fixed

• Improved the portability of generated Apptainer scripts (#442).
• Fixed the handling of unusual filenames in generated Apptainer scripts (#459).

Removed

• Removed the codespan cargo feature in favor of enabling codespan reporting always (#462).

wdl-format

Added

• Added support for else if and else clauses in conditional statements (in support of WDL v1.3) (#411).

wdl-grammar

Added

• Added support for else if and else clauses in conditional statements (in support of WDL v1.3) (#411).

Removed

• Removed the codespan cargo feature in favor of enabling codespan reporting always (#462).

wdl-lint

Removed

• Removed the codespan cargo feature in favor of enabling codespan reporting always (#462).

wdl-lsp

No changes.

New Contributors

• @srinidhisg88 made their first contribution in #473

Full Changelog: v0.18.0...v0.19.0