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@mihirsamdarshi mihirsamdarshi commented Jul 27, 2025

  • Replaced the deprecated Google Cloud Life Sciences API with the Google Cloud Batch API and adjusted all related arguments and documentation.
  • Introduced a new argument --gcp-compute-service-account to specify service accounts for Batch compute instances.
  • Updated default Cromwell and Womtool versions used by the project.
  • Added integration tests for Google Cloud Batch API.
  • Removed unused arguments and code related to the deprecated APIs.
  • Updated documentation to reflect changes in API usage and supported regions.

@mihirsamdarshi mihirsamdarshi force-pushed the dev branch 6 times, most recently from 4ddbb44 to 2bfd0f9 Compare December 24, 2025 08:13
mihirsamdarshi and others added 22 commits December 25, 2025 00:23
fix: move deprecated strtobool import to a local function
- Add type hints to all methods and attributes
- Improve docstrings with more detailed descriptions
- Enhance error handling in the read method
- Add proper return type annotations
- Fix typo in interval_update_heartbeat parameter
- Convert heartbeat_file to string path
- Check file existence before reading
- Use more specific exception handling
- restrict supported python versions to 3.10 through 3.14
- update argcomplete from 3.6.2 to 3.6.3
- update awscli from 1.41.9 to 1.44.4
- update boto3 from 1.39.9 to 1.42.14
- include all scripts in package-data instead of only gcp_caper_server
- add ruff configuration for linting and formatting
- set line-length to 96 characters
- enable all ruff rules except explicitly ignored ones
Added '*.code-workspace' to .gitignore to prevent committing VS Code workspace configuration files.
biodavidjm and others added 7 commits December 25, 2025 00:23
Adds explicit setting of 'auth' to 'service-account' in the batch configuration when a GCP service account key JSON is provided. Ensures correct authentication method is used for Google Cloud Platform workflows.
- Add comprehensive type hints throughout the module
- Introduce new `_CallContext` dataclass for internal tracking
- Enhance function signatures with proper return types
- Improve docstrings for all public methods
- Add error handling for edge cases in parsing functions
- Update class attributes with type information
- Replace legacy `MutableMapping` import with direct `collections.abc`
- Introduce new type variables `T`, `U`, and `W` for better type coverage
- Add overloads to `flatten_dict()` for optional reducer support
- Extend type hints across all function signatures
- Standardize docstring formatting throughout the module
- Clarify argument descriptions in function documentation
- Restructure argument parsing functions into smaller, focused methods
- Add type hints and docstrings to improve code clarity
- Separate localization arguments into dedicated function
- Update enum definition with descriptive docstring and uppercase naming
- Maintain existing functionality while making code more maintainable
- Add type hints throughout the module
- Replace string formatting with f-strings
- Improve error handling for HTTP and connection errors
- Increase default timeout to 300 seconds
- Add module docstring
- Update function signatures with proper typing
- Improve UUID validation logic
- Enhance wildcard detection for strings and iterables
- Add module docstring for clarity
- Restructure WorkflowStatusTransition with detailed docstrings
- Improve type hints and formatting throughout
- Consolidate regex patterns using WORKFLOW_UUID_REGEX constant
- Enhance logging format for consistency
- Replace string formatting in error messages with f-strings
- Add type hints to functions and methods
- Use named variables for error messages
- Improve docstrings with type information
- Add noqa comments where necessary
- Simplify conditional logic in subcmd_hpc
- Standardize error message formatting across the file
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3 participants