requirements.txt

#
# This file is autogenerated by pip-compile with Python 3.8
# by the following command:
#
#    pip-compile --extra=dev --extra=test --extra=train --output-file=requirements.txt pyproject.toml
#
aiohttp==3.8.3
    # via
    #   aiohttp-retry
    #   aiohttp-swagger
    #   fsspec
    #   mlem
aiohttp-retry==2.8.3
    # via dvc-http
aiohttp-swagger==1.0.16
    # via mlem
aiosignal==1.3.1
    # via aiohttp
alabaster==0.7.12
    # via sphinx
amqp==5.1.1
    # via kombu
antlr4-python3-runtime==4.9.3
    # via
    #   hydra-core
    #   linkml
    #   omegaconf
    #   pyjsg
    #   pyshexc
anyio==3.6.2
    # via httpcore
appdirs==1.4.4
    # via
    #   black
    #   dvc
    #   iterative-telemetry
arrow==1.2.3
    # via isoduration
async-timeout==4.0.2
    # via aiohttp
asyncssh==2.12.0
    # via scmrepo
atpublic==3.1.1
    # via flufl-lock
attrs==22.1.0
    # via
    #   aiohttp
    #   dvc-data
    #   jsonlines
    #   jsonschema
    #   pytest
babel==2.11.0
    # via sphinx
billiard==3.6.4.0
    # via celery
black==21.6b0
    # via
    #   bmt
    #   kgx
bmt==0.8.12
    # via
    #   kgx
    #   trapi-predict-kit
build==1.0.3
    # via pip-tools
cached-property==1.5.2
    # via mlem
cachetools==5.2.0
    # via kgx
celery==5.2.7
    # via dvc-task
certifi==2022.12.7
    # via
    #   httpcore
    #   httpx
    #   requests
cffi==1.15.1
    # via
    #   cryptography
    #   pygit2
cfgraph==0.2.1
    # via pyshex
cfgv==3.3.1
    # via pre-commit
chardet==5.1.0
    # via
    #   pyshex
    #   pyshexc
charset-normalizer==2.1.1
    # via
    #   aiohttp
    #   requests
click==8.1.3
    # via
    #   black
    #   celery
    #   click-didyoumean
    #   click-plugins
    #   click-repl
    #   json-flattener
    #   kgx
    #   linkml
    #   linkml-runtime
    #   mlem
    #   pip-tools
    #   prefixcommons
    #   sphinx-click
    #   typer
click-didyoumean==0.3.0
    # via celery
click-plugins==1.1.1
    # via celery
click-repl==0.2.0
    # via celery
cloudpickle==2.2.0
    # via
    #   mlem
    #   shap
colorama==0.4.6
    # via dvc
commonmark==0.9.1
    # via
    #   recommonmark
    #   rich
configobj==5.0.6
    # via dvc
coverage[toml]==6.5.0
    # via pytest-cov
cryptography==38.0.4
    # via asyncssh
cycler==0.11.0
    # via matplotlib
cython==0.29.32
    # via openpredict (pyproject.toml)
decorator==5.1.1
    # via
    #   jsonpath-ng
    #   validators
deprecated==1.2.13
    # via linkml-runtime
deprecation==2.1.0
    # via
    #   bmt
    #   kgx
dictdiffer==0.9.0
    # via dvc-data
dill==0.3.6
    # via mlem
diskcache==5.4.0
    # via dvc-data
distlib==0.3.6
    # via virtualenv
distro==1.8.0
    # via
    #   dvc
    #   iterative-telemetry
docker==5.0.3
    # via
    #   kgx
    #   tox-docker
docutils==0.16
    # via
    #   kgx
    #   myst-parser
    #   recommonmark
    #   sphinx
    #   sphinx-click
    #   sphinx-rtd-theme
dpath==2.1.3
    # via dvc
dulwich==0.20.50
    # via scmrepo
dvc==2.38.1
    # via
    #   dvc-http
    #   openpredict (pyproject.toml)
    #   trapi-predict-kit
dvc-data==0.28.4
    # via dvc
dvc-http==2.27.2
    # via dvc
dvc-objects==0.14.0
    # via dvc-data
dvc-render[table]==0.0.15
    # via
    #   dvc
    #   dvclive
dvc-task==0.1.8
    # via dvc
dvclive==1.2.2
    # via dvc
entrypoints==0.4
    # via mlem
et-xmlfile==1.1.0
    # via openpyxl
exceptiongroup==1.0.4
    # via pytest
fastapi==0.68.2
    # via
    #   openpredict (pyproject.toml)
    #   trapi-predict-kit
filelock==3.8.2
    # via
    #   iterative-telemetry
    #   tox
    #   virtualenv
flake8==5.0.4
    # via
    #   bmt
    #   kgx
flatdict==4.0.1
    # via mlem
flatten-dict==0.4.2
    # via dvc
flufl-lock==7.1.1
    # via dvc
fqdn==1.5.1
    # via jsonschema
frozenlist==1.3.3
    # via
    #   aiohttp
    #   aiosignal
fsspec[http]==2022.11.0
    # via
    #   dvc-http
    #   dvc-objects
    #   mlem
    #   scmrepo
funcy==1.17
    # via
    #   dvc
    #   dvc-data
    #   dvc-objects
    #   dvc-task
    #   scmrepo
future==0.18.2
    # via grandalf
gensim==3.8.3
    # via
    #   openpredict (pyproject.toml)
    #   pyrdf2vec
gitdb==4.0.10
    # via gitpython
gitpython==3.1.30
    # via
    #   mlem
    #   scmrepo
grandalf==0.6
    # via dvc
graphviz==0.20.1
    # via linkml
greenlet==2.0.1
    # via sqlalchemy
h11==0.14.0
    # via httpcore
hbreader==0.9.1
    # via
    #   jsonasobj2
    #   linkml
    #   linkml-runtime
httpcore==0.18.0
    # via httpx
httpx==0.25.0
    # via openpredict (pyproject.toml)
hydra-core==1.3.0
    # via dvc
identify==2.5.10
    # via pre-commit
idna==3.4
    # via
    #   anyio
    #   httpx
    #   jsonschema
    #   requests
    #   yarl
ijson==3.1.4
    # via kgx
imagesize==1.4.1
    # via sphinx
importlib-metadata==4.13.0
    # via
    #   build
    #   mlem
    #   prefixmaps
    #   sphinx
importlib-resources==6.1.0
    # via
    #   dvc
    #   hydra-core
    #   jsonschema
iniconfig==1.1.1
    # via pytest
isodate==0.6.1
    # via
    #   linkml
    #   rdflib
isoduration==20.11.0
    # via jsonschema
isort==5.11.2
    # via mlem
iterative-telemetry==0.0.6
    # via
    #   dvc
    #   mlem
jinja2==3.1.2
    # via
    #   aiohttp-swagger
    #   linkml
    #   linkml-dataops
    #   mlem
    #   myst-parser
    #   sphinx
joblib==1.2.0
    # via scikit-learn
json-flattener==0.1.9
    # via linkml-runtime
jsonasobj==1.3.1
    # via
    #   pyjsg
    #   pyshexc
jsonasobj2==1.0.4
    # via
    #   linkml
    #   linkml-runtime
jsonlines==3.1.0
    # via kgx
jsonpatch==1.32
    # via linkml-dataops
jsonpath-ng==1.5.3
    # via linkml-dataops
jsonpointer==2.3
    # via
    #   jsonpatch
    #   jsonschema
jsonschema[format]==4.17.3
    # via
    #   linkml
    #   linkml-runtime
jsonstreams==0.6.0
    # via kgx
kgx==1.7.2
    # via openpredict (pyproject.toml)
kiwisolver==1.4.4
    # via matplotlib
kombu==5.2.4
    # via
    #   celery
    #   dvc-task
linkml==1.3.16
    # via
    #   bmt
    #   kgx
linkml-dataops==0.1.0
    # via linkml
linkml-runtime==1.3.7
    # via
    #   bmt
    #   kgx
    #   linkml
    #   linkml-dataops
llvmlite==0.36.0
    # via numba
markdown-it-py==2.1.0
    # via
    #   mdit-py-plugins
    #   myst-parser
markupsafe==2.1.1
    # via jinja2
matplotlib==3.4.3
    # via
    #   openpredict (pyproject.toml)
    #   pyrdf2vec
mccabe==0.7.0
    # via flake8
mdit-py-plugins==0.3.3
    # via myst-parser
mdurl==0.1.2
    # via markdown-it-py
mlem==0.4.14
    # via
    #   openpredict (pyproject.toml)
    #   trapi-predict-kit
multidict==6.0.3
    # via
    #   aiohttp
    #   yarl
mypy==0.991
    # via kgx
mypy-extensions==0.4.3
    # via
    #   black
    #   mypy
myst-parser==0.18.1
    # via linkml
nanotime==0.5.2
    # via dvc-data
neo4j==4.3.0
    # via kgx
networkx==2.8.8
    # via
    #   dvc
    #   kgx
    #   openpredict (pyproject.toml)
    #   pyrdf2vec
    #   python-louvain
nodeenv==1.7.0
    # via pre-commit
numba==0.53.1
    # via shap
numpy==1.19.5
    # via
    #   gensim
    #   matplotlib
    #   numba
    #   openpredict (pyproject.toml)
    #   pandas
    #   pyrdf2vec
    #   python-louvain
    #   scikit-learn
    #   scipy
    #   shap
nvidia-cublas-cu11==11.10.3.66
    # via
    #   nvidia-cudnn-cu11
    #   torch
nvidia-cuda-nvrtc-cu11==11.7.99
    # via torch
nvidia-cuda-runtime-cu11==11.7.99
    # via torch
nvidia-cudnn-cu11==8.5.0.96
    # via torch
omegaconf==2.3.0
    # via hydra-core
openpyxl==3.0.10
    # via linkml
ordered-set==4.1.0
    # via kgx
packaging==22.0
    # via
    #   build
    #   deprecation
    #   dvc
    #   hydra-core
    #   pytest
    #   shap
    #   sphinx
    #   tox
pandas==1.1.1
    # via
    #   kgx
    #   openpredict (pyproject.toml)
    #   pyrdf2vec
    #   shap
parse==1.19.0
    # via linkml
pathspec==0.9.0
    # via
    #   black
    #   dvc
    #   scmrepo
pillow==9.3.0
    # via matplotlib
pip-tools==7.3.0
    # via openpredict (pyproject.toml)
pkgutil-resolve-name==1.3.10
    # via jsonschema
platformdirs==2.6.0
    # via virtualenv
pluggy==1.0.0
    # via
    #   pytest
    #   tox
ply==3.11
    # via jsonpath-ng
pockets==0.9.1
    # via sphinxcontrib-napoleon
pre-commit==3.5.0
    # via openpredict (pyproject.toml)
prefixcommons==0.1.12
    # via
    #   kgx
    #   linkml
    #   linkml-runtime
prefixmaps==0.1.4
    # via linkml
prologterms==0.0.6
    # via kgx
prompt-toolkit==3.0.36
    # via click-repl
psutil==5.9.4
    # via
    #   dvc
    #   flufl-lock
py==1.11.0
    # via tox
py4j==0.10.9
    # via pyspark
pycodestyle==2.9.1
    # via flake8
pycparser==2.21
    # via cffi
pydantic==1.10.2
    # via
    #   fastapi
    #   linkml
    #   mlem
    #   openpredict (pyproject.toml)
    #   reasoner-pydantic
    #   trapi-predict-kit
pydot==1.4.2
    # via dvc
pyflakes==2.5.0
    # via flake8
pygit2==1.11.1
    # via scmrepo
pygments==2.13.0
    # via
    #   rich
    #   sphinx
pygtrie==2.5.0
    # via
    #   dvc
    #   dvc-data
    #   scmrepo
pyjsg==0.11.10
    # via
    #   linkml
    #   pyshexc
    #   shexjsg
pyparsing==3.0.9
    # via
    #   dvc
    #   grandalf
    #   matplotlib
    #   mlem
    #   pydot
    #   rdflib
pyproject-hooks==1.0.0
    # via build
pyrdf2vec==0.0.5
    # via openpredict (pyproject.toml)
pyrsistent==0.19.2
    # via jsonschema
pyshex==0.8.1
    # via linkml
pyshexc==0.9.1
    # via
    #   linkml
    #   pyshex
pyspark==3.1.1
    # via openpredict (pyproject.toml)
pytest==7.2.0
    # via
    #   bmt
    #   kgx
    #   openpredict (pyproject.toml)
    #   pytest-cov
    #   pytest-logging
pytest-cov==3.0.0
    # via openpredict (pyproject.toml)
pytest-logging==2015.11.4
    # via prefixcommons
python-dateutil==2.8.2
    # via
    #   arrow
    #   kgx
    #   linkml
    #   matplotlib
    #   pandas
python-gitlab==3.12.0
    # via mlem
python-louvain==0.16
    # via pyrdf2vec
python-multipart==0.0.5
    # via
    #   mlem
    #   openpredict (pyproject.toml)
pytz==2022.6
    # via
    #   babel
    #   celery
    #   neo4j
    #   pandas
pyyaml==6.0
    # via
    #   aiohttp-swagger
    #   json-flattener
    #   kgx
    #   linkml
    #   linkml-runtime
    #   myst-parser
    #   omegaconf
    #   pre-commit
    #   prefixcommons
    #   prefixmaps
rdflib==6.2.0
    # via
    #   cfgraph
    #   kgx
    #   linkml
    #   linkml-runtime
    #   openpredict (pyproject.toml)
    #   pyrdf2vec
    #   rdflib-jsonld
    #   rdflib-shim
    #   sparqlslurper
    #   sparqlwrapper
    #   trapi-predict-kit
rdflib-jsonld==0.6.1
    # via rdflib-shim
rdflib-shim==1.0.3
    # via
    #   pyshex
    #   pyshexc
    #   sparqlslurper
reasoner-pydantic==4.1.4
    # via
    #   openpredict (pyproject.toml)
    #   trapi-predict-kit
recommonmark==0.7.1
    # via
    #   bmt
    #   kgx
regex==2022.10.31
    # via black
requests==2.28.1
    # via
    #   docker
    #   dvc
    #   fsspec
    #   iterative-telemetry
    #   linkml
    #   linkml-runtime
    #   mlem
    #   openpredict (pyproject.toml)
    #   prefixcommons
    #   pyshex
    #   python-gitlab
    #   requests-toolbelt
    #   sphinx
    #   trapi-predict-kit
requests-toolbelt==0.10.1
    # via python-gitlab
rfc3339-validator==0.1.4
    # via jsonschema
rfc3987==1.3.8
    # via jsonschema
rich==12.6.0
    # via
    #   dvc
    #   mlem
ruamel-yaml==0.17.21
    # via
    #   dvc
    #   dvclive
    #   linkml-dataops
ruamel-yaml-clib==0.2.7
    # via ruamel-yaml
scikit-learn==0.23.1
    # via
    #   openpredict (pyproject.toml)
    #   pyrdf2vec
    #   shap
scipy==1.5.4
    # via
    #   gensim
    #   openpredict (pyproject.toml)
    #   scikit-learn
    #   shap
scmrepo==0.1.4
    # via dvc
shap==0.41.0
    # via openpredict (pyproject.toml)
shexjsg==0.8.2
    # via
    #   kgx
    #   pyshex
    #   pyshexc
shortuuid==1.0.11
    # via
    #   dvc
    #   dvc-data
    #   dvc-objects
    #   dvc-task
shtab==1.5.8
    # via dvc
six==1.16.0
    # via
    #   click-repl
    #   configobj
    #   flatten-dict
    #   gensim
    #   isodate
    #   jsonpath-ng
    #   jsonstreams
    #   pockets
    #   python-dateutil
    #   python-multipart
    #   rfc3339-validator
    #   sphinxcontrib-napoleon
    #   tox
slicer==0.0.7
    # via shap
smart-open==6.3.0
    # via gensim
smmap==5.0.0
    # via gitdb
sniffio==1.3.0
    # via
    #   anyio
    #   httpcore
    #   httpx
snowballstemmer==2.2.0
    # via sphinx
sparqlslurper==0.5.1
    # via pyshex
sparqlwrapper==2.0.0
    # via
    #   kgx
    #   openpredict (pyproject.toml)
    #   pyshex
    #   sparqlslurper
sphinx==5.3.0
    # via
    #   bmt
    #   kgx
    #   myst-parser
    #   recommonmark
    #   sphinx-click
    #   sphinx-rtd-theme
sphinx-click==4.4.0
    # via
    #   kgx
    #   linkml
sphinx-rtd-theme==1.1.1
    # via
    #   bmt
    #   kgx
    #   linkml
sphinxcontrib-applehelp==1.0.2
    # via sphinx
sphinxcontrib-devhelp==1.0.2
    # via sphinx
sphinxcontrib-htmlhelp==2.0.0
    # via sphinx
sphinxcontrib-jsmath==1.0.1
    # via sphinx
sphinxcontrib-napoleon==0.7
    # via bmt
sphinxcontrib-qthelp==1.0.3
    # via sphinx
sphinxcontrib-serializinghtml==1.1.5
    # via sphinx
sqlalchemy==1.4.45
    # via linkml
starlette==0.14.2
    # via fastapi
stringcase==1.2.0
    # via
    #   bmt
    #   kgx
tabulate==0.9.0
    # via
    #   dvc
    #   dvc-render
terminaltables==3.1.10
    # via kgx
threadpoolctl==3.1.0
    # via scikit-learn
toml==0.10.2
    # via black
tomli==2.0.1
    # via
    #   build
    #   coverage
    #   mypy
    #   pip-tools
    #   pyproject-hooks
    #   pytest
    #   tox
tomlkit==0.11.6
    # via dvc
torch==1.13.1
    # via openpredict (pyproject.toml)
tox==3.27.1
    # via
    #   bmt
    #   kgx
    #   linkml
    #   tox-docker
tox-docker==3.1.0
    # via kgx
tqdm==4.64.1
    # via
    #   dvc
    #   dvc-objects
    #   pyrdf2vec
    #   shap
trapi-predict-kit==0.2.2
    # via openpredict (pyproject.toml)
typer==0.7.0
    # via
    #   mlem
    #   openpredict (pyproject.toml)
types-requests==2.28.11.5
    # via openpredict (pyproject.toml)
types-urllib3==1.26.25.4
    # via types-requests
typing-extensions==4.4.0
    # via
    #   asyncssh
    #   dvc
    #   dvc-objects
    #   mypy
    #   myst-parser
    #   pydantic
    #   rich
    #   torch
uri-template==1.2.0
    # via jsonschema
urllib3==1.26.13
    # via
    #   dulwich
    #   pyshex
    #   requests
validators==0.20.0
    # via kgx
vine==5.0.0
    # via
    #   amqp
    #   celery
    #   kombu
virtualenv==20.17.1
    # via
    #   pre-commit
    #   tox
voluptuous==0.13.1
    # via dvc
watchdog==2.2.0
    # via linkml
wcwidth==0.2.5
    # via prompt-toolkit
webcolors==1.12
    # via jsonschema
websocket-client==1.4.2
    # via docker
wheel==0.38.4
    # via
    #   nvidia-cublas-cu11
    #   nvidia-cuda-runtime-cu11
    #   pip-tools
wrapt==1.14.1
    # via deprecated
yarl==1.8.2
    # via aiohttp
zc-lockfile==2.0
    # via dvc
zipp==3.11.0
    # via
    #   importlib-metadata
    #   importlib-resources

# The following packages are considered to be unsafe in a requirements file:
# pip
# setuptools