requirements.txt

#
# This file is autogenerated by pip-compile with Python 3.11
# by the following command:
#
#    pip-compile --unsafe-package=annoy --unsafe-package=protobuf requirements.in
#
aiodns==2.0.0
    # via hail
aiofiles==24.1.0
    # via -r requirements.in
aiohappyeyeballs==2.6.1
    # via aiohttp
aiohttp==3.11.16
    # via
    #   hail
    #   slackclient
aiosignal==1.3.2
    # via aiohttp
annotated-types==0.7.0
    # via pydantic
anyio==4.9.0
    # via jupyter-server
appnope==0.1.4
    # via ipykernel
argon2-cffi==23.1.0
    # via
    #   jupyter-server
    #   notebook
argon2-cffi-bindings==21.2.0
    # via argon2-cffi
asttokens==3.0.0
    # via stack-data
attrs==25.3.0
    # via
    #   aiohttp
    #   bioutils
    #   hgvs
    #   jsonschema
avro==1.11.3
    # via hail
azure-common==1.1.28
    # via azure-mgmt-storage
azure-core==1.32.0
    # via
    #   azure-identity
    #   azure-mgmt-core
    #   azure-storage-blob
    #   msrest
azure-identity==1.21.0
    # via hail
azure-mgmt-core==1.5.0
    # via azure-mgmt-storage
azure-mgmt-storage==20.1.0
    # via hail
azure-storage-blob==12.25.1
    # via hail
beautifulsoup4==4.13.3
    # via nbconvert
biocommons-seqrepo==0.6.11
    # via
    #   ga4gh-vrs
    #   hgvs
bioutils==0.6.1
    # via
    #   biocommons-seqrepo
    #   ga4gh-vrs
    #   hgvs
bleach==6.2.0
    # via nbconvert
bokeh==3.3.4
    # via hail
boto3==1.37.27
    # via hail
botocore==1.37.27
    # via
    #   boto3
    #   hail
    #   s3transfer
cachetools==5.5.2
    # via google-auth
canonicaljson==2.0.0
    # via ga4gh-vrs
certifi==2025.1.31
    # via
    #   msrest
    #   requests
cffi==1.17.1
    # via
    #   argon2-cffi-bindings
    #   cryptography
    #   pycares
charset-normalizer==3.4.1
    # via requests
click==8.1.8
    # via
    #   ga4gh-vrs
    #   typer
coloredlogs==15.0.1
    # via
    #   biocommons-seqrepo
    #   ga4gh-vrs
    #   onnxruntime
comm==0.2.2
    # via ipykernel
commonmark==0.9.1
    # via rich
configparser==7.2.0
    # via hgvs
contourpy==1.3.1
    # via bokeh
cryptography==44.0.2
    # via
    #   azure-identity
    #   azure-storage-blob
    #   msal
    #   pyjwt
debugpy==1.8.13
    # via ipykernel
decorator==4.4.2
    # via
    #   hail
    #   ipython
defusedxml==0.7.1
    # via nbconvert
deprecated==1.2.18
    # via hail
dill==0.3.9
    # via hail
entrypoints==0.4
    # via jupyter-client
executing==2.2.0
    # via stack-data
fastjsonschema==2.21.1
    # via nbformat
flatbuffers==25.2.10
    # via onnxruntime
frozenlist==1.5.0
    # via
    #   aiohttp
    #   aiosignal
    #   hail
ga4gh-vrs[extras]==0.8.4
    # via gnomad
gnomad==0.8.0
    # via -r requirements.in
gnomad-qc @ git+https://github.com/broadinstitute/gnomad_qc.git@v4.1
    # via -r requirements.in
google-auth==2.38.0
    # via
    #   google-auth-oauthlib
    #   hail
google-auth-oauthlib==0.8.0
    # via hail
hail==0.2.133
    # via -r requirements.in
hdbscan==0.8.40
    # via gnomad
hgvs==1.5.4
    # via ga4gh-vrs
humanfriendly==10.0
    # via coloredlogs
humanize==4.12.2
    # via hail
idna==3.10
    # via
    #   anyio
    #   requests
    #   yarl
importlib-metadata==8.6.1
    # via yoyo-migrations
inflection==0.5.1
    # via python-jsonschema-objects
ipykernel==6.22.0
    # via
    #   -r requirements.in
    #   ipywidgets
    #   nbclassic
    #   notebook
ipython==8.34.0
    # via
    #   biocommons-seqrepo
    #   hgvs
    #   ipykernel
    #   ipywidgets
ipython-genutils==0.2.0
    # via
    #   nbclassic
    #   notebook
ipywidgets==8.0.6
    # via
    #   -r requirements.in
    #   gnomad
isodate==0.7.2
    # via
    #   azure-storage-blob
    #   msrest
janus==1.0.0
    # via hail
jedi==0.19.2
    # via ipython
jinja2==3.1.6
    # via
    #   bokeh
    #   jupyter-server
    #   nbconvert
    #   notebook
jmespath==1.0.1
    # via
    #   boto3
    #   botocore
joblib==1.4.2
    # via
    #   hdbscan
    #   scikit-learn
jproperties==2.1.2
    # via hail
jsonschema[format-nongpl]==3.2.0
    # via
    #   ga4gh-vrs
    #   jupyter-events
    #   nbformat
    #   python-jsonschema-objects
jupyter-client==7.4.9
    # via
    #   ipykernel
    #   jupyter-server
    #   nbclient
    #   notebook
jupyter-core==5.7.2
    # via
    #   ipykernel
    #   jupyter-client
    #   jupyter-server
    #   nbclient
    #   nbconvert
    #   nbformat
    #   notebook
jupyter-events==0.6.3
    # via jupyter-server
jupyter-server==2.10.0
    # via notebook-shim
jupyter-server-terminals==0.5.3
    # via jupyter-server
jupyterlab-pygments==0.3.0
    # via nbconvert
jupyterlab-widgets==3.0.13
    # via ipywidgets
lockfile==0.12.2
    # via python-daemon
luigi==3.5.2
    # via -r requirements.in
markdown==3.7
    # via python-jsonschema-objects
markupsafe==3.0.2
    # via
    #   jinja2
    #   nbconvert
matplotlib-inline==0.1.7
    # via
    #   ipykernel
    #   ipython
mistune==2.0.5
    # via nbconvert
mpmath==1.3.0
    # via sympy
msal==1.32.0
    # via
    #   azure-identity
    #   msal-extensions
msal-extensions==1.3.1
    # via azure-identity
msrest==0.7.1
    # via azure-mgmt-storage
multidict==6.3.2
    # via
    #   aiohttp
    #   yarl
nbclassic==1.2.0
    # via notebook
nbclient==0.10.2
    # via nbconvert
nbconvert==7.3.1
    # via
    #   -r requirements.in
    #   jupyter-server
    #   notebook
nbformat==5.10.4
    # via
    #   jupyter-server
    #   nbclient
    #   nbconvert
    #   notebook
nest-asyncio==1.6.0
    # via
    #   hail
    #   ipykernel
    #   jupyter-client
    #   nbclassic
    #   notebook
networkx==3.4.2
    # via gnomad
notebook==6.5.6
    # via -r requirements.in
notebook-shim==0.2.4
    # via nbclassic
numpy==1.26.4
    # via
    #   bokeh
    #   contourpy
    #   ga4gh-vrs
    #   hail
    #   hdbscan
    #   onnx
    #   onnxconverter-common
    #   onnxruntime
    #   pandas
    #   patsy
    #   scikit-learn
    #   scipy
    #   statsmodels
oauthlib==3.2.2
    # via requests-oauthlib
onnx==1.17.0
    # via
    #   gnomad
    #   onnxconverter-common
    #   skl2onnx
onnxconverter-common @ git+https://github.com/microsoft/onnxconverter-common.git@f7a8eb699caa6f6a78d3bdfbcaf5dfbd43569ebd
    # via
    #   -r requirements.in
    #   skl2onnx
onnxruntime==1.21.0
    # via gnomad
orjson==3.10.16
    # via hail
overrides==7.7.0
    # via jupyter-server
packaging==24.2
    # via
    #   bokeh
    #   ipykernel
    #   jupyter-server
    #   nbconvert
    #   onnxconverter-common
    #   onnxruntime
    #   plotly
    #   statsmodels
pandas==2.2.3
    # via
    #   bokeh
    #   hail
    #   statsmodels
pandocfilters==1.5.1
    # via nbconvert
parsimonious==0.10.0
    # via hail
parsley==1.3
    # via hgvs
parso==0.8.4
    # via jedi
patsy==1.0.1
    # via statsmodels
pexpect==4.9.0
    # via ipython
pillow==11.1.0
    # via bokeh
platformdirs==4.3.7
    # via jupyter-core
plotly==5.24.1
    # via hail
prometheus-client==0.21.1
    # via
    #   jupyter-server
    #   notebook
prompt-toolkit==3.0.50
    # via ipython
propcache==0.3.1
    # via
    #   aiohttp
    #   yarl
psutil==7.0.0
    # via ipykernel
psycopg2==2.9.10
    # via hgvs
psycopg2-binary==2.9.10
    # via ga4gh-vrs
ptyprocess==0.7.0
    # via
    #   pexpect
    #   terminado
pure-eval==0.2.3
    # via stack-data
py4j==0.10.9.7
    # via pyspark
pyasn1==0.6.1
    # via
    #   pyasn1-modules
    #   rsa
pyasn1-modules==0.4.2
    # via google-auth
pycares==4.5.0
    # via aiodns
pycparser==2.22
    # via cffi
pydantic==2.8.2
    # via -r requirements.in
pydantic-core==2.20.1
    # via pydantic
pygments==2.19.1
    # via
    #   ipython
    #   nbconvert
    #   rich
pyjwt[crypto]==2.10.1
    # via msal
pyrsistent==0.20.0
    # via jsonschema
pysam==0.23.0
    # via biocommons-seqrepo
pyspark==3.5.5
    # via hail
python-daemon==3.1.2
    # via luigi
python-dateutil==2.9.0.post0
    # via
    #   botocore
    #   jupyter-client
    #   luigi
    #   pandas
python-json-logger==2.0.7
    # via
    #   hail
    #   jupyter-events
python-jsonschema-objects==0.4.6
    # via ga4gh-vrs
pytz==2025.2
    # via pandas
pyyaml==6.0.2
    # via
    #   bokeh
    #   ga4gh-vrs
    #   hail
    #   jupyter-events
pyzmq==24.0.1
    # via
    #   ipykernel
    #   jupyter-client
    #   jupyter-server
    #   notebook
regex==2024.11.6
    # via parsimonious
requests==2.32.3
    # via
    #   azure-core
    #   biocommons-seqrepo
    #   bioutils
    #   ga4gh-vrs
    #   hail
    #   msal
    #   msrest
    #   requests-oauthlib
requests-oauthlib==2.0.0
    # via
    #   google-auth-oauthlib
    #   msrest
rfc3339-validator==0.1.4
    # via jupyter-events
rfc3986-validator==0.1.1
    # via jupyter-events
rich==12.6.0
    # via
    #   hail
    #   typer
rsa==4.9
    # via google-auth
s3transfer==0.11.4
    # via boto3
scikit-learn==1.6.1
    # via
    #   gnomad
    #   hdbscan
    #   skl2onnx
scipy==1.11.4
    # via
    #   hail
    #   hdbscan
    #   scikit-learn
    #   statsmodels
send2trash==1.8.3
    # via
    #   jupyter-server
    #   notebook
setuptools==78.1.0
    # via jsonschema
shellingham==1.5.4
    # via typer
six==1.17.0
    # via
    #   azure-core
    #   hgvs
    #   jproperties
    #   jsonschema
    #   python-dateutil
    #   python-jsonschema-objects
    #   rfc3339-validator
skl2onnx==1.18.0
    # via gnomad
slackclient==2.5.0
    # via gnomad
sniffio==1.3.1
    # via anyio
sortedcontainers==2.4.0
    # via hail
soupsieve==2.6
    # via beautifulsoup4
sqlparse==0.5.3
    # via yoyo-migrations
stack-data==0.6.3
    # via ipython
statsmodels==0.14.4
    # via gnomad
sympy==1.13.3
    # via onnxruntime
tabulate==0.9.0
    # via
    #   hail
    #   yoyo-migrations
tenacity==8.5.0
    # via
    #   luigi
    #   plotly
terminado==0.18.1
    # via
    #   jupyter-server
    #   jupyter-server-terminals
    #   notebook
threadpoolctl==3.6.0
    # via scikit-learn
tinycss2==1.4.0
    # via nbconvert
tornado==6.4.2
    # via
    #   bokeh
    #   ipykernel
    #   jupyter-client
    #   jupyter-server
    #   luigi
    #   notebook
    #   terminado
tqdm==4.67.1
    # via biocommons-seqrepo
traitlets==5.14.3
    # via
    #   comm
    #   ipykernel
    #   ipython
    #   ipywidgets
    #   jupyter-client
    #   jupyter-core
    #   jupyter-events
    #   jupyter-server
    #   matplotlib-inline
    #   nbclient
    #   nbconvert
    #   nbformat
    #   notebook
typer==0.15.2
    # via hail
typing-extensions==4.13.1
    # via
    #   anyio
    #   azure-core
    #   azure-identity
    #   azure-storage-blob
    #   beautifulsoup4
    #   biocommons-seqrepo
    #   ipython
    #   janus
    #   pydantic
    #   pydantic-core
    #   typer
tzdata==2025.2
    # via pandas
urllib3==2.3.0
    # via
    #   botocore
    #   requests
uvloop==0.21.0
    # via hail
wcwidth==0.2.13
    # via prompt-toolkit
webencodings==0.5.1
    # via
    #   bleach
    #   tinycss2
websocket-client==1.8.0
    # via jupyter-server
widgetsnbextension==4.0.13
    # via ipywidgets
wrapt==1.17.2
    # via deprecated
xyzservices==2025.1.0
    # via bokeh
yarl==1.18.3
    # via aiohttp
yoyo-migrations==9.0.0
    # via biocommons-seqrepo
zipp==3.21.0
    # via importlib-metadata

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