v3.0.0#9

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mihirsamdarshi wants to merge 93 commits intomasterfrom

Commits on Mar 28, 2025

fix: move deprecated strtobool import to a local function [fixes ENCODE-DCC/caper#207]
mihirsamdarshi
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Commits on Jan 28, 2026

Merge pull request #1 from MoTrPAC/fix/python312-compatibility
mihirsamdarshi
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feat: add Google Batch backend support
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fix: remove fully deprecated Genomics/Life Sciences APIs
mihirsamdarshi
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refactor: continue removing Life Sciences API support, update for Batch API usage
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docs: update documentation and other scripts to remove Life Sciences references
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feat: add support for customizing Google Batch compute service account
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feat: add GCP compute service account support in tests and update test parameters
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feat: add GCP logging policy support and update Cromwell/Womtool versions
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chore: move pytest configuration file
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chore: add `slow` marker to tests and update pytest configuration
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fix: GCS URL formatting in test and add `slow` marker to test
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refactor: migrate to pyproject.toml, use uv as the package manager
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refactor: complete migration to pyproject.toml/uv
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docs: update GCP docs to remove Life Sciences API references and reflect Batch API usage
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test: add `google_cloud` markers to GCP-related resource analysis tests
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chore: bump required Python to 3.10
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fix: remove incorrect group reassignment, relocate `--cromwell-stdout` argument to `group_cromwell`
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fix: add missing required service-account config option
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feat: add type annotations and improve error handling
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chore: update python version and dependencies, update Ruff config
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Ignore VS Code workspace files

biodavidjm
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mihirsamdarshi
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chore: ignore additional IDE folders
mihirsamdarshi
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Set 'auth' to 'service-account' for GCP backend

biodavidjm
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mihirsamdarshi
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refactor: update CromwellMetadata internals for readability
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feat: modernize type hints and docstrings
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refactor: improve code organization and documentation
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refactor: improve type hints and error handling
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refactor: improve code structure and type hints
mihirsamdarshi
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refactor: improve error handling and type annotations
mihirsamdarshi
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refactor: improve type hints and documentation
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feat: update test configuration for new GCS bucket and project
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refactor: fix lint errors, add type annotations to functions
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chore: update supported Python to 3.12
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docs: update documentation and installation requirements
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refactor: update instance creation script
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build: add CI workflow for unit and GCP integration tests
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test: fix CI failures with ls return code
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chore: add pyright config for type-checking
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feat: add optional callbacks for server events and status changes
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chore: add class variable for Cromwell version, bump default version to 91
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feat: add GCP VPC network and subnetwork configuration support
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feat: add Docker Hub mirroring configuration
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chore(release): bump version
mihirsamdarshi
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Commits on Jan 29, 2026

Remove unused config keys from GCP backend
biodavidjm
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Commits on Jan 30, 2026

Print metadata in subcmd_metadata function
biodavidjm
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Commits on Jan 31, 2026