Drops support for Python < 3.10 and MySQL < 8.0#1287
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bump python version in docker compose to ensure that tests pass
…tings-management-adsuG
- Remove ConfigWrapper class and backward compatibility layer - Use direct pydantic BaseSettings with typed nested models - Change context manager from config(...) to config.override(...) - Add validate_assignment=True for runtime type checking - Improve store spec validation with clear error messages - Update all tests to use new API - Preserve dict-style access via __getitem__/__setitem__ for convenience
Config file search: - Search for datajoint.json recursively up from cwd - Stop at .git/.hg boundaries or filesystem root - Warn if no config file found (instead of silently using defaults) Secrets management: - Add .secrets/ directory support (next to datajoint.json) - Support /run/secrets/datajoint/ for Docker/Kubernetes - Use SecretStr for password and aws_secret_access_key - Secrets masked in repr/logs, excluded from save() - Dict access automatically unwraps SecretStr for compatibility Breaking changes: - Config file renamed from dj_local_conf.json to datajoint.json - No more ~/.datajoint_config.json (project-only config) - Secrets should be in env vars or .secrets/ directory
Credentials should be managed via environment variables or .secrets/ directory, not stored in config files.
Config files should be created/edited manually and version controlled, not generated programmatically.
- Rewrite settings.md with new config structure and secrets management - Update credentials.md to remove set_password and save methods - Update quick-start.md with new config file name and patterns - Add documentation for .secrets/ directory and environment variables
- Update pyproject.toml to require Python >=3.10 (was >=3.9) - Update ruff target-version to py310 - Update pixi Python version constraint - Modernize type hints to use Python 3.10+ union syntax (X | Y instead of Union[X, Y], X | None instead of Optional[X]) - Use built-in dict, list, tuple for generics instead of typing imports - Update MySQL documentation reference from 5.7 to 8.0
Documentation updates: - docs/src/client/install.md: Update Python requirement from 3.4+ to 3.10+ - docs/src/quick-start.md: Update Python requirement from 3.8+ to 3.10+ - docs/src/quick-start.md: Update MySQL doc link from 5.7 to 8.0 - docs/src/develop.md: Update Python requirement from 3.9+ to 3.10+ - docs/src/develop.md: Fix version.py path (datajoint/ -> src/datajoint/) Configuration updates: - docker-compose.yaml: Update default PY_VER from 3.9 to 3.10 - .github/workflows/test.yaml: Remove Python 3.9 and MySQL 5.7 from test matrix - .github/workflows/post_draft_release_published.yaml: Update to Python 3.10 - .github/workflows/post_draft_release_published.yaml: Fix version.py path
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d-v-b
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| sed -i "s/^__version__ = .*/__version__ = \"$VERSION\"/" src/datajoint/version.py | ||
| cat src/datajoint/version.py |
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out of scope for this PR but you might find it simpler to tie your library version to git tags instead of manually updating a version file. See https://setuptools-scm.readthedocs.io/en/latest/
d-v-b
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Dec 21, 2025
d-v-b
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Dec 21, 2025
d-v-b
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Dec 21, 2025
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| ├── aws.access_key_id | ||
| └── aws.secret_access_key |
Contributor
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why encourage people to copy aws credentials here?
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
d-v-b
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Dec 22, 2025
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Summary
This PR drops support for Python < 3.10 and MySQL < 8.0, enabling use of modern Python syntax and simplifying the codebase and CI configuration.
Merge #1282 first.
Changes
Python Version Requirements
pyproject.tomltarget-versionfrompy39topy310>=3.10,<3.14Type Hint Modernization (Python 3.10+ syntax)
Optional[X]withX | NoneUnion[X, Y]withX | YDict[K, V]withdict[K, V]List[X]withlist[X]Tuple[X, ...]withtuple[X, ...]typingmoduleFiles updated:
src/datajoint/settings.pysrc/datajoint/condition.pysrc/datajoint/table.pyDocumentation Updates
docs/src/client/install.md: Updated Python requirement from 3.4+ to 3.10+docs/src/quick-start.md: Updated Python requirement from 3.8+ to 3.10+docs/src/develop.md: Updated Python requirement from 3.9+ to 3.10+version.pypath references (datajoint/→src/datajoint/)CI/CD Updates
.github/workflows/test.yaml: Removed Python 3.9 and MySQL 5.7 from test matrix.github/workflows/post_draft_release_published.yaml: Updated build Python version to 3.10docker-compose.yaml: Updated defaultPY_VERfrom 3.9 to 3.10MySQL Reference Updates
src/datajoint/connection.pydocstring link from MySQL 5.7 to 8.0 documentation