requirements.txt

#
# This file is autogenerated by pip-compile with Python 3.11
# by the following command:
#
#    pip-compile --output-file=requirements.txt pyproject.toml
#
aiohttp==3.8.6
    # 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
amqp==5.1.1
    # via kombu
antlr4-python3-runtime==4.9.3
    # via
    #   hydra-core
    #   omegaconf
anyio==3.7.1
    # via
    #   fastapi
    #   httpcore
    #   starlette
appdirs==1.4.4
    # via iterative-telemetry
asttokens==2.4.0
    # via stack-data
async-timeout==4.0.3
    # via aiohttp
asyncssh==2.14.0
    # via scmrepo
atpublic==4.0
    # via flufl-lock
attrs==23.1.0
    # via
    #   aiohttp
    #   dvc-data
    #   jsonschema
    #   referencing
    #   sqltrie
backcall==0.2.0
    # via ipython
billiard==4.1.0
    # via celery
bio==1.5.9
    # via predict-drug-target (pyproject.toml)
biopython==1.81
    # via bio
biothings-client==0.3.0
    # via mygene
bmt==1.1.2
    # via trapi-predict-kit
cached-property==1.5.2
    # via mlem
cachetools==5.3.1
    # via tox
celery==5.3.4
    # via dvc-task
certifi==2023.7.22
    # via
    #   httpcore
    #   httpx
    #   requests
cffi==1.16.0
    # via
    #   cryptography
    #   pygit2
chardet==5.2.0
    # via tox
charset-normalizer==3.3.0
    # via
    #   aiohttp
    #   requests
click==8.1.7
    # via
    #   celery
    #   click-didyoumean
    #   click-plugins
    #   click-repl
    #   json-flattener
    #   linkml-runtime
    #   mlem
    #   prefixcommons
    #   prefixmaps
    #   typer
    #   uvicorn
click-didyoumean==0.3.0
    # via celery
click-plugins==1.1.1
    # via celery
click-repl==0.3.0
    # via celery
cloudpickle==3.0.0
    # via mlem
colorama==0.4.6
    # via
    #   dvc
    #   tox
comm==0.1.4
    # via ipykernel
configobj==5.0.8
    # via dvc
contourpy==1.1.1
    # via matplotlib
cryptography==41.0.4
    # via asyncssh
curies==0.6.6
    # via
    #   linkml-runtime
    #   prefixmaps
cycler==0.12.1
    # via matplotlib
debugpy==1.8.0
    # via ipykernel
decorator==5.1.1
    # via ipython
deprecated==1.2.14
    # via linkml-runtime
deprecation==2.1.0
    # via bmt
dictdiffer==0.9.0
    # via dvc-data
dill==0.3.7
    # via mlem
diskcache==5.6.3
    # via dvc-data
distlib==0.3.7
    # via virtualenv
distro==1.8.0
    # via
    #   dvc
    #   iterative-telemetry
dpath==2.1.6
    # via dvc
dulwich==0.21.6
    # via
    #   dvc-studio-client
    #   scmrepo
dvc==3.26.2
    # via trapi-predict-kit
dvc-data==2.18.1
    # via dvc
dvc-http==2.30.2
    # via dvc
dvc-objects==1.0.1
    # via dvc-data
dvc-render==0.6.0
    # via dvc
dvc-studio-client==0.15.0
    # via dvc
dvc-task==0.3.0
    # via dvc
entrypoints==0.4
    # via
    #   gto
    #   mlem
executing==2.0.0
    # via stack-data
fair-esm==2.0.0
    # via predict-drug-target (pyproject.toml)
fastapi==0.103.2
    # via trapi-predict-kit
filelock==3.12.4
    # via
    #   iterative-telemetry
    #   torch
    #   tox
    #   triton
    #   virtualenv
flatdict==4.0.1
    # via mlem
flatten-dict==0.4.2
    # via dvc
flufl-lock==7.1.1
    # via dvc
fonttools==4.43.1
    # via matplotlib
frozenlist==1.4.0
    # via
    #   aiohttp
    #   aiosignal
fsspec[http]==2023.9.2
    # via
    #   dvc-http
    #   dvc-objects
    #   mlem
    #   scmrepo
    #   torch
funcy==2.0
    # via
    #   dvc
    #   dvc-data
    #   dvc-objects
    #   dvc-task
    #   gto
    #   scmrepo
gitdb==4.0.10
    # via gitpython
gitpython==3.1.38
    # via
    #   mlem
    #   scmrepo
gprofiler-official==1.0.0
    # via bio
grandalf==0.8
    # via dvc
grpcio==1.59.0
    # via
    #   grpcio-tools
    #   qdrant-client
grpcio-tools==1.59.0
    # via qdrant-client
gto==1.4.0
    # via dvc
gunicorn==21.2.0
    # via trapi-predict-kit
h11==0.14.0
    # via
    #   httpcore
    #   uvicorn
h2==4.1.0
    # via httpx
hbreader==0.9.1
    # via
    #   jsonasobj2
    #   linkml-runtime
hpack==4.0.0
    # via h2
httpcore==0.18.0
    # via httpx
httpx[http2]==0.25.0
    # via qdrant-client
hydra-core==1.3.2
    # via dvc
hyperframe==6.0.1
    # via h2
idna==3.4
    # via
    #   anyio
    #   httpx
    #   requests
    #   yarl
importlib-metadata==6.8.0
    # via mlem
iniconfig==2.0.0
    # via pytest
ipykernel==6.25.2
    # via predict-drug-target (pyproject.toml)
ipython==8.16.1
    # via ipykernel
isodate==0.6.1
    # via rdflib
isort==5.12.0
    # via mlem
iterative-telemetry==0.0.8
    # via
    #   dvc
    #   mlem
jedi==0.19.1
    # via ipython
jinja2==3.1.2
    # via
    #   aiohttp-swagger
    #   mlem
    #   torch
joblib==1.3.2
    # via scikit-learn
json-flattener==0.1.9
    # via linkml-runtime
jsonasobj2==1.0.4
    # via linkml-runtime
jsonschema==4.19.1
    # via linkml-runtime
jsonschema-specifications==2023.7.1
    # via jsonschema
jupyter-client==8.4.0
    # via ipykernel
jupyter-core==5.4.0
    # via
    #   ipykernel
    #   jupyter-client
kiwisolver==1.4.5
    # via matplotlib
kombu==5.3.2
    # via
    #   celery
    #   dvc-task
linkml-runtime==1.6.0
    # via bmt
markdown-it-py==3.0.0
    # via rich
markupsafe==2.1.3
    # via jinja2
matplotlib==3.8.0
    # via predict-drug-target (pyproject.toml)
matplotlib-inline==0.1.6
    # via
    #   ipykernel
    #   ipython
mdurl==0.1.2
    # via markdown-it-py
mlem==0.4.14
    # via trapi-predict-kit
mpmath==1.3.0
    # via sympy
multidict==6.0.4
    # via
    #   aiohttp
    #   yarl
mygene==3.2.2
    # via bio
nest-asyncio==1.5.8
    # via ipykernel
networkx==3.1
    # via
    #   dvc
    #   torch
numpy==1.26.1
    # via
    #   biopython
    #   contourpy
    #   matplotlib
    #   pandas
    #   predict-drug-target (pyproject.toml)
    #   qdrant-client
    #   scikit-learn
    #   scipy
nvidia-cublas-cu12==12.1.3.1
    # via
    #   nvidia-cudnn-cu12
    #   nvidia-cusolver-cu12
    #   torch
nvidia-cuda-cupti-cu12==12.1.105
    # via torch
nvidia-cuda-nvrtc-cu12==12.1.105
    # via torch
nvidia-cuda-runtime-cu12==12.1.105
    # via torch
nvidia-cudnn-cu12==8.9.2.26
    # via torch
nvidia-cufft-cu12==11.0.2.54
    # via torch
nvidia-curand-cu12==10.3.2.106
    # via torch
nvidia-cusolver-cu12==11.4.5.107
    # via torch
nvidia-cusparse-cu12==12.1.0.106
    # via
    #   nvidia-cusolver-cu12
    #   torch
nvidia-nccl-cu12==2.18.1
    # via torch
nvidia-nvjitlink-cu12==12.2.140
    # via
    #   nvidia-cusolver-cu12
    #   nvidia-cusparse-cu12
nvidia-nvtx-cu12==12.1.105
    # via torch
omegaconf==2.3.0
    # via hydra-core
orjson==3.9.9
    # via sqltrie
packaging==23.2
    # via
    #   deprecation
    #   dvc
    #   dvc-objects
    #   gunicorn
    #   hydra-core
    #   ipykernel
    #   matplotlib
    #   pooch
    #   pyproject-api
    #   pytest
    #   tox
pandas==2.1.1
    # via bio
parso==0.8.3
    # via jedi
pathspec==0.11.2
    # via
    #   dvc
    #   scmrepo
pexpect==4.8.0
    # via ipython
pickleshare==0.7.5
    # via ipython
pillow==10.1.0
    # via matplotlib
platformdirs==3.11.0
    # via
    #   dvc
    #   jupyter-core
    #   pooch
    #   tox
    #   virtualenv
pluggy==1.3.0
    # via
    #   pytest
    #   tox
pooch==1.7.0
    # via bio
portalocker==2.8.2
    # via qdrant-client
prefixcommons==0.1.12
    # via linkml-runtime
prefixmaps==0.1.6
    # via linkml-runtime
prompt-toolkit==3.0.39
    # via
    #   click-repl
    #   ipython
protobuf==4.24.4
    # via grpcio-tools
psutil==5.9.6
    # via
    #   dvc
    #   flufl-lock
    #   ipykernel
ptyprocess==0.7.0
    # via pexpect
pubchempy==1.0.4
    # via predict-drug-target (pyproject.toml)
pure-eval==0.2.2
    # via stack-data
pycparser==2.21
    # via cffi
pydantic==1.10.13
    # via
    #   curies
    #   fastapi
    #   gto
    #   linkml-runtime
    #   mlem
    #   prefixmaps
    #   qdrant-client
    #   reasoner-pydantic
    #   trapi-predict-kit
pydot==1.4.2
    # via dvc
pygit2==1.13.1
    # via scmrepo
pygments==2.16.1
    # via
    #   ipython
    #   rich
pygtrie==2.5.0
    # via
    #   dvc
    #   dvc-data
    #   scmrepo
    #   sqltrie
pyparsing==3.1.1
    # via
    #   dvc
    #   grandalf
    #   matplotlib
    #   mlem
    #   pydot
    #   rdflib
pyproject-api==1.6.1
    # via tox
pytest==7.4.2
    # via pytest-logging
pytest-logging==2015.11.4
    # via prefixcommons
python-dateutil==2.8.2
    # via
    #   celery
    #   jupyter-client
    #   matplotlib
    #   pandas
python-gitlab==3.15.0
    # via mlem
python-multipart==0.0.6
    # via mlem
pytrie==0.4.0
    # via curies
pytz==2023.3.post1
    # via pandas
pyyaml==6.0.1
    # via
    #   aiohttp-swagger
    #   json-flattener
    #   linkml-runtime
    #   omegaconf
    #   prefixcommons
    #   prefixmaps
pyzmq==25.1.1
    # via
    #   ipykernel
    #   jupyter-client
qdrant-client==1.6.3
    # via predict-drug-target (pyproject.toml)
rdflib==7.0.0
    # via
    #   linkml-runtime
    #   trapi-predict-kit
reasoner-pydantic==4.1.4
    # via trapi-predict-kit
referencing==0.30.2
    # via
    #   jsonschema
    #   jsonschema-specifications
requests==2.31.0
    # via
    #   bio
    #   biothings-client
    #   curies
    #   dvc
    #   dvc-studio-client
    #   fsspec
    #   gprofiler-official
    #   iterative-telemetry
    #   linkml-runtime
    #   mlem
    #   pooch
    #   predict-drug-target (pyproject.toml)
    #   prefixcommons
    #   python-gitlab
    #   requests-toolbelt
    #   trapi-predict-kit
requests-toolbelt==1.0.0
    # via python-gitlab
rich==13.6.0
    # via
    #   dvc
    #   gto
    #   mlem
rpds-py==0.10.6
    # via
    #   jsonschema
    #   referencing
ruamel-yaml==0.17.35
    # via
    #   dvc
    #   gto
ruamel-yaml-clib==0.2.8
    # via ruamel-yaml
scikit-learn==1.3.1
    # via predict-drug-target (pyproject.toml)
scipy==1.11.3
    # via
    #   predict-drug-target (pyproject.toml)
    #   scikit-learn
scmrepo==1.4.0
    # via
    #   dvc
    #   gto
semver==3.0.2
    # via gto
shortuuid==1.0.11
    # via
    #   dvc
    #   dvc-data
    #   dvc-objects
    #   dvc-task
    #   scmrepo
shtab==1.6.4
    # via dvc
six==1.16.0
    # via
    #   asttokens
    #   configobj
    #   flatten-dict
    #   isodate
    #   python-dateutil
smmap==5.0.1
    # via gitdb
sniffio==1.3.0
    # via
    #   anyio
    #   httpcore
    #   httpx
sortedcontainers==2.4.0
    # via pytrie
sqltrie==0.8.0
    # via dvc-data
stack-data==0.6.3
    # via ipython
starlette==0.27.0
    # via fastapi
stringcase==1.2.0
    # via bmt
sympy==1.12
    # via torch
tabulate==0.9.0
    # via
    #   dvc
    #   gto
threadpoolctl==3.2.0
    # via scikit-learn
tomlkit==0.12.1
    # via dvc
torch==2.1.0
    # via predict-drug-target (pyproject.toml)
tornado==6.3.3
    # via
    #   ipykernel
    #   jupyter-client
tox==4.11.3
    # via prefixmaps
tqdm==4.66.1
    # via
    #   bio
    #   dvc
    #   dvc-objects
traitlets==5.11.2
    # via
    #   comm
    #   ipykernel
    #   ipython
    #   jupyter-client
    #   jupyter-core
    #   matplotlib-inline
# trapi-predict-kit[web] @ git+https://github.com/MaastrichtU-IDS/trapi-predict-kit.git
    # via predict-drug-target (pyproject.toml)
triton==2.1.0
    # via torch
typer==0.9.0
    # via
    #   gto
    #   mlem
typing-extensions==4.8.0
    # via
    #   asyncssh
    #   dvc-objects
    #   fastapi
    #   pydantic
    #   pydantic-core
    #   torch
    #   typer
tzdata==2023.3
    # via
    #   celery
    #   pandas
urllib3==1.26.17
    # via
    #   dulwich
    #   qdrant-client
    #   requests
uvicorn==0.23.2
    # via trapi-predict-kit
vine==5.0.0
    # via
    #   amqp
    #   celery
    #   kombu
virtualenv==20.24.5
    # via tox
voluptuous==0.13.1
    # via
    #   dvc
    #   dvc-studio-client
wcwidth==0.2.8
    # via prompt-toolkit
wrapt==1.15.0
    # via deprecated
yarl==1.9.2
    # via aiohttp
zc-lockfile==3.0.post1
    # via dvc
zipp==3.17.0
    # via importlib-metadata

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