#
# This file is autogenerated by pip-compile with Python 3.9
# by the following command:
#
#    pip-compile --annotation-style=line --extra=pipeline,test --output-file=requirements.txt --strip-extras pyproject.toml
#

aiohttp==3.9.5            # via gcsfs
aiosignal==1.3.1          # via aiohttp
alabaster==0.7.16         # via sphinx
annotated-types==0.7.0    # via pydantic
antlr4-python3-runtime==4.9.3  # via omegaconf
async-timeout==4.0.3      # via aiohttp
attrs==23.2.0             # via aiohttp, jsonschema, pytest, referencing
babel==2.15.0             # via sphinx
biotite==0.39.0           # via hydride, plinder (pyproject.toml)
boto3==1.34.134           # via metaflow
botocore==1.34.134        # via boto3, s3transfer
build==0.9.0              # via plinder (pyproject.toml)
cachetools==5.3.3         # via google-auth, tox
certifi==2024.7.4         # via kubernetes, requests
cffi==1.16.0              # via cryptography
chardet==5.2.0            # via tox
charset-normalizer==3.3.2  # via requests
click==8.1.7              # via mmpdb
cloudpathlib==0.18.1      # via plinder (pyproject.toml)
colorama==0.4.6           # via tox
coverage==7.5.4           # via pytest-cov
cryptography==42.0.8      # via (pyproject.toml)
decorator==5.1.1          # via gcsfs
distlib==0.3.8            # via virtualenv
docutils==0.17.1          # via pdb2pqr, sphinx
duckdb==1.0.0             # via plinder (pyproject.toml)
eval-type-backport==0.2.0  # via plinder (pyproject.toml)
exceptiongroup==1.2.1     # via pytest
fastjsonschema==2.20.0    # via nbformat
filelock==3.15.4          # via tox, virtualenv
frozenlist==1.4.1         # via aiohttp, aiosignal
fsspec==2024.6.0          # via gcsfs
future==1.0.0             # via mmcif
gcsfs==2024.6.0           # via plinder (pyproject.toml)
gemmi==0.6.6              # via pdbeccdutils, plinder (pyproject.toml)
google-api-core==2.19.1   # via google-cloud-core, google-cloud-secret-manager, google-cloud-storage
google-auth==2.30.0       # via gcsfs, google-api-core, google-auth-oauthlib, google-cloud-core, google-cloud-secret-manager, google-cloud-storage, kubernetes
google-auth-oauthlib==1.2.0  # via gcsfs
google-cloud-core==2.4.1  # via google-cloud-storage
google-cloud-secret-manager==2.20.0  # via (pyproject.toml)
google-cloud-storage==2.17.0  # via gcsfs, plinder (pyproject.toml)g
google-crc32c==1.5.0      # via google-cloud-storage, google-resumable-media
google-resumable-media==2.7.1  # via google-cloud-storage
googleapis-common-protos==1.63.2  # via google-api-core, grpc-google-iam-v1, grpcio-status
grpc-google-iam-v1==0.13.1  # via google-cloud-secret-manager
grpcio==1.64.1            # via google-api-core, googleapis-common-protos, grpc-google-iam-v1, grpcio-status
grpcio-status==1.62.2     # via google-api-core
hydride==1.1.2            # via plinder (pyproject.toml)
idna==3.7                 # via requests, yarl
imagesize==1.4.1          # via sphinx
importlib-metadata==8.0.0  # via sphinx
iniconfig==2.0.0          # via pytest
jinja2==3.1.4             # via numpydoc, sphinx
jmespath==1.0.1           # via boto3, botocore
joblib==1.4.2             # via oddt, scikit-learn
jsonschema==4.22.0        # via nbformat
jsonschema-specifications==2023.12.1  # via jsonschema
jupyter-core==5.7.2       # via nbformat
kubernetes==30.1.0        # via (pyproject.toml)
lxml==5.2.2               # via pdb-validation
markupsafe==2.1.5         # via jinja2
metaflow==2.11.15         # via (pyproject.toml)
mmcif==0.88.0             # via pdb-validation, plinder (pyproject.toml)
mmcif-pdbx==2.0.1         # via pdb2pqr
mmpdb @ git+https://github.com/rdkit/mmpdb.git  # via plinder (pyproject.toml)
molecular-rectifier==1.0.1  # via plinder (pyproject.toml)
msgpack==1.0.8            # via biotite, mmcif
multidict==6.0.5          # via aiohttp, yarl
nbformat==5.10.4          # via plinder (pyproject.toml)
networkit==11.0.0         # via plinder (pyproject.toml)
networkx==3.2.1           # via biotite, pdbeccdutils
numpy==1.26.4             # via biotite, hydride, oddt, pandas, pdb2pqr, pdbeccdutils, plinder (pyproject.toml), posebusters, pyarrow, rdkit, scikit-learn, scipy
numpydoc==1.6.0           # via oddt
oauthlib==3.2.2           # via kubernetes, requests-oauthlib
oddt==0.7                 # via plinder (pyproject.toml)
omegaconf==2.3.0          # via plinder (pyproject.toml)
packaging==24.1           # via build, plotly, pyproject-api, pytest, setuptools-scm, sphinx, tox
pandas==2.2.2             # via oddt, pdb-validation, plinder (pyproject.toml), posebustersg
pdb-validation @ git+https://git.scicore.unibas.ch/schwede/ligand-validation.git  # via plinder (pyproject.toml)
pdb2pqr==3.6.2            # via plinder (pyproject.toml)
pdbeccdutils==0.8.5       # via plinder (pyproject.toml)
peewee==3.17.5            # via mmpdb
pep517==0.13.1            # via build
pillow==10.3.0            # via pdbeccdutils, rdkit
platformdirs==4.2.2       # via jupyter-core, tox, virtualenv
plotly==5.22.0            # via plinder (pyproject.toml)
pluggy==1.5.0             # via pytest, tox
posebusters==0.2.14       # via plinder (pyproject.toml)
propka==3.5.1             # via pdb2pqr
proto-plus==1.24.0        # via google-api-core, google-cloud-secret-manager
protobuf==4.25.3          # via google-api-core, google-cloud-secret-manager, googleapis-common-protos, grpc-google-iam-v1, grpcio-status, proto-plus
pyarrow==16.1.0           # via plinder (pyproject.toml)
pyasn1==0.6.0             # via pyasn1-modules, rsa
pyasn1-modules==0.4.0     # via google-auth
pycparser==2.22           # via cffi
pydantic==2.7.4           # via plinder (pyproject.toml)g
pydantic-core==2.18.4     # via pydantic
pygments==2.18.0          # via sphinx
pyjwt==2.8.0              # via (pyproject.toml)
pyproject-api==1.7.1      # via tox
pytest==7.2.0             # via plinder (pyproject.toml), pytest-cov
pytest-cov==4.0.0         # via plinder (pyproject.toml)
python-dateutil==2.9.0.post0  # via botocore, kubernetes, pandas
pytz==2024.1              # via pandas
pyyaml==6.0.1             # via kubernetes, omegaconf, posebustersg
rdkit==2024.3.1           # via molecular-rectifier, plinder (pyproject.toml), posebusters
referencing==0.35.1       # via jsonschema, jsonschema-specifications
requests==2.32.3          # via biotite, gcsfs, google-api-core, google-cloud-storage, kubernetes, metaflow, mmcif, pdb2pqr, pdbeccdutils, requests-oauthlib, sphinxg
requests-oauthlib==2.0.0  # via google-auth-oauthlib, kubernetes
rpds-py==0.18.1           # via jsonschema, referencing
rsa==4.9                  # via google-auth
s3transfer==0.10.2        # via boto3
scikit-learn==1.5.0       # via oddt
scipy==1.13.1             # via mmpdb, oddt, pdbeccdutils, scikit-learn
setuptools-scm==7.0.5     # via plinder (pyproject.toml)
six==1.16.0               # via kubernetes, mmcif, oddt, python-dateutil
snowballstemmer==2.2.0    # via sphinx
sphinx==5.3.0             # via numpydoc
sphinxcontrib-applehelp==1.0.8  # via sphinx
sphinxcontrib-devhelp==1.0.6  # via sphinx
sphinxcontrib-htmlhelp==2.0.5  # via sphinx
sphinxcontrib-jsmath==1.0.1  # via sphinx
sphinxcontrib-qthelp==1.0.7  # via sphinx
sphinxcontrib-serializinghtml==1.1.10  # via sphinx
tabulate==0.9.0           # via numpydoc, plinder (pyproject.toml)
tenacity==8.4.2           # via plotly
threadpoolctl==3.5.0      # via scikit-learn
tomli==2.0.1              # via build, coverage, numpydoc, pep517, pyproject-api, pytest, setuptools-scm, tox
tox==4.15.1               # via plinder (pyproject.toml)
tqdm==4.66.4              # via plinder (pyproject.toml)
traitlets==5.14.3         # via jupyter-core, nbformat
typing-extensions==4.12.2  # via cloudpathlib, plinder (pyproject.toml), pydantic, pydantic-core, setuptools-scm
tzdata==2024.1            # via pandas
urllib3==1.26.19          # via botocore, kubernetes, requests
virtualenv==20.26.3       # via tox
websocket-client==1.8.0   # via kubernetes
yarl==1.9.4               # via aiohttp
zipp==3.19.2              # via importlib-metadata

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