v3.0.0 #9
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…` argument to `group_cromwell`
- 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.
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
- Add module-level docstring - Use TYPE_CHECKING for optional imports - Improve parameter type hints - Add class-level docstrings
- Change default GCS root from `gs://encode-test-caper` to `gs://motrpac-test-caper` - Remove default value for `--gcp-prj` option to enforce explicit project specification - Add validation for GCS root URI format - Support `GOOGLE_CLOUD_PROJECT` environment variable as alternative to `--gcp-prj` - Update resource metadata path construction to use the configured GCS root - Improve code formatting and type hints for better clarity
- Add return type annotation to functions in test files for better code clarity - Update pytest parameter names to use tuples instead of variables for cleaner test definitions
- Update Java (>= 11) to Java >= 17 - Update Python from >=3.6 to >=3.12 - Replace pip install with uv/uvx for installation - Update troubleshooting link to DETAILS.md - Clarify MoTrPAC fork details in Introduction`
- Remove legacy JSON key file authentication in favor of VM-attached service accounts - Simplify positional arguments to require only instance name, project ID, and output directory - Add new optional argument for Batch worker service account - Update default Ubuntu image to 22.04 Jammy from 20.04 Focal - Improve documentation with clearer examples and authentication options - Change error messages from "Wrong parameter" to "Unknown parameter" - Update username description to clarify it's for SSH only - Add recommended authentication method example first
- Add GitHub Actions workflow file for test execution - Configure unit tests to run on Python 3.12, 3.13, and 3.14 - Add GCP integration tests requiring maintainer approval - Implement test splitting with environment-specific execution - Include proper cleanup for GCS artifacts after tests
- for better OmicsPipelines integration
- Add `gcp_network` and `gcp_subnetwork` parameters to backend configuration - Support custom subnet mode VPCs in GCP Batch backend - Update parameter documentation for new networking options - Implement VPC configuration in backend initialization
- Add gcp_dockerhub_mirror and gcp_dockerhub_mirror_address parameters - Enable Docker Hub mirroring through Google Artifact Registry by default - Allow customization of the mirror address with a configurable option
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--gcp-compute-service-accountto specify service accounts for Batch compute instances.