# # 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==3.1.29 # 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==1.16.1 # 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