graphviz
jsonschema<4.18
pyyaml
requests
mergedeep
networkx
cwl-utils>=0.32
typeguard
pydantic>=2.6
pydantic-settings
docker
podman
toil[cwl]
fastapi
python-jose
uvicorn

[all_except_runner_src]
sophios[cyto,doc,mypy-types,plots,test]

[cyto]
ipycytoscape

[doc]
sphinx
myst-parser
sphinx-autodoc-typehints

[mypy-types]
lxml-stubs
types-Pillow
types-PyYAML
types-Pygments
types-colorama
types-decorator
types-docutils
types-html5lib
types-jsonschema
types-psutil
types-python-jose
types-pytz
types-redis
types-requests
types-setuptools
types-six
types-urllib3

[plots]
matplotlib

[runners]
toil[cwl]
cwl-utils

[test]
pre-commit
py
pytest
pytest-cov
pytest-parallel
coverage
mypy
numpy
scipy
pylint
autopep8
hypothesis
hypothesis-jsonschema
