patchsim 0.1.0b1__tar.gz

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Files changed (25) hide show
  1. patchsim-0.1.0b1/.gitignore +188 -0
  2. patchsim-0.1.0b1/LICENSE +674 -0
  3. patchsim-0.1.0b1/PKG-INFO +920 -0
  4. patchsim-0.1.0b1/README.md +192 -0
  5. patchsim-0.1.0b1/pyproject.toml +108 -0
  6. patchsim-0.1.0b1/src/patchsim/__init__.py +24 -0
  7. patchsim-0.1.0b1/src/patchsim/cli.py +246 -0
  8. patchsim-0.1.0b1/src/patchsim/core/__init__.py +0 -0
  9. patchsim-0.1.0b1/src/patchsim/core/model.py +237 -0
  10. patchsim-0.1.0b1/src/patchsim/core/model_runner.py +62 -0
  11. patchsim-0.1.0b1/src/patchsim/core/simulation.py +417 -0
  12. patchsim-0.1.0b1/src/patchsim/models/__init__.py +1 -0
  13. patchsim-0.1.0b1/src/patchsim/templates/models/seir.yaml +10 -0
  14. patchsim-0.1.0b1/src/patchsim/templates/models/sir.yaml +8 -0
  15. patchsim-0.1.0b1/src/patchsim/templates/models/sirs.yaml +10 -0
  16. patchsim-0.1.0b1/src/patchsim/templates/models/sis.yaml +8 -0
  17. patchsim-0.1.0b1/src/patchsim/templates/project/config.yaml +31 -0
  18. patchsim-0.1.0b1/src/patchsim/templates/project/data/networks/network-static.csv +5 -0
  19. patchsim-0.1.0b1/src/patchsim/templates/project/data/patch/patch-population.csv +3 -0
  20. patchsim-0.1.0b1/src/patchsim/templates/project/data/seeds/seed-initial.csv +3 -0
  21. patchsim-0.1.0b1/src/patchsim/templates/project/output/.gitkeep +0 -0
  22. patchsim-0.1.0b1/src/patchsim/utils/__init__.py +0 -0
  23. patchsim-0.1.0b1/src/patchsim/utils/loader.py +6 -0
  24. patchsim-0.1.0b1/src/patchsim/utils/logger.py +70 -0
  25. patchsim-0.1.0b1/src/patchsim/utils/viz.py +39 -0
patchsim-0.1.0b1/.gitignore ADDED
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+ # Byte-compiled / optimized / DLL files
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+ __pycache__/
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+ *.py[cod]
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+ *$py.class
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+
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+ *.vscode
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+
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+ # C extensions
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+ *.so
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+
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+ # Distribution / packaging
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+ .Python
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+ build/
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+ develop-eggs/
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+ dist/
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+ downloads/
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+ eggs/
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+ .eggs/
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+ lib/
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+ lib64/
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+ parts/
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+ sdist/
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+ var/
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+ wheels/
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+ pip-wheel-metadata/
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+ share/python-wheels/
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+ *.egg-info/
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+ .installed.cfg
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+ *.egg
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+ MANIFEST
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+
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+ # PyInstaller
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+ # Usually these files are written by a python script from a template
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+ # before PyInstaller builds the exe, so as to inject date/other infos into it.
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+ *.manifest
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+ *.spec
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+
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+ # Installer logs
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+ pip-log.txt
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+ pip-delete-this-directory.txt
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+
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+ # Unit test / coverage reports
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+ htmlcov/
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+ .tox/
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+ .nox/
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+ .coverage
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+ .coverage.*
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+ .cache
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+ nosetests.xml
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+ coverage.xml
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+ *.cover
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+ *.py,cover
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+ .hypothesis/
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+ .pytest_cache/
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+ pytest_cache/
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+
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+ # Translations
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+ *.mo
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+ *.pot
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+
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+ # Django stuff:
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+ *.log
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+ local_settings.py
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+ db.sqlite3
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+ db.sqlite3-journal
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+
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+ # Flask stuff:
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+ instance/
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+ .webassets-cache
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+
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+ # Scrapy stuff:
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+ .scrapy
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+
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+ # Sphinx documentation
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+ docs/_build/
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+
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+ # PyBuilder
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+ target/
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+
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+ # Jupyter Notebook
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+ .ipynb_checkpoints
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+
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+ # IPython
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+ profile_default/
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+ ipython_config.py
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+
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+ # pyenv
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+ # .python-version is tracked for CI reproducibility
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+
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+ # pipenv
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+ # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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+ # However, in case of collaboration, if having platform-specific dependencies or dependencies
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+ # having no cross-platform support, pipenv may install dependencies that don't work, or not
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+ # install all needed dependencies.
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+ #Pipfile.lock
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+
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+ # PEP 582; used by e.g. github.com/David-OConnor/pyflow
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+ __pypackages__/
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+
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+ # Celery stuff
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+ celerybeat-schedule
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+ celerybeat.pid
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+
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+ # SageMath parsed files
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+ *.sage.py
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+
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+ # Environments
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+ .env
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+ .venv
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+ env/
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+ venv/
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+ ENV/
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+ env.bak/
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+ venv.bak/
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+ .venv/
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+
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+ # Spyder project settings
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+ .spyderproject
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+ .spyproject
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+
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+ # Rope project settings
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+ .ropeproject
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+
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+ # mkdocs documentation
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+ /site
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+
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+ # mypy
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+ .mypy_cache/
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+ .dmypy.json
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+ dmypy.json
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+
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+ # Pyre type checker
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+ .pyre/
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+ **__pycache__
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+ **/__pycache__/
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+
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+ # PyCharm
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+ .idea/
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+
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+ # RStudio project files
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+ **.Rproj.user/
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+ **.Rproj.user*
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+ **.Rproj
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+ **.Rhistory
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+
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+ # MacOS
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+ .DS_Store
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+
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+ # Data file types
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+ *.csv
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+ *.txt
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+ *.xlsx
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+ output/**
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+
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+ # Keep package template scaffold files tracked
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+ !src/patchsim/templates/project/data/
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+ !src/patchsim/templates/project/data/networks/
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+ !src/patchsim/templates/project/data/networks/*.csv
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+ !src/patchsim/templates/project/data/patch/
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+ !src/patchsim/templates/project/data/patch/*.csv
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+ !src/patchsim/templates/project/data/seeds/
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+ !src/patchsim/templates/project/data/seeds/*.csv
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+ !src/patchsim/templates/project/output/.gitkeep
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+
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+ # Additions for GeoJSON, .zip files, and shapefiles
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+ *.geojson
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+ *.zip
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+ *.shp
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+ *.shx
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+ *.dbf
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+ *.prj
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+
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+ # Added entries for pytest cache, venv, pdm-build, and other relevant directories
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+ .pdm-build/
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+
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+ # Exception for .png files in assets/
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+ !assets/*.png
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+
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+ # Allow tracked data CSVs
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+ !data/
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+ !data/networks/
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+ !data/networks/*.csv
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+
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+ !data/patch/
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+ !data/patch/*.csv
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+
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+ !data/seeds/
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+ !data/seeds/*.csv