[query][hailtop] update dependencies (#13853)

batch/pinned-requirements.txt

@@ -6,7 +6,7 @@
 #
 aiodocker==0.21.0
     # via -r hail/batch/requirements.txt
-aiohttp==3.8.5
+aiohttp==3.8.6
     # via
     #   -c hail/batch/../gear/pinned-requirements.txt
     #   -c hail/batch/../hail/python/pinned-requirements.txt
@@ -34,7 +34,7 @@ attrs==23.1.0
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   -c hail/batch/../web_common/pinned-requirements.txt
     #   aiohttp
-charset-normalizer==3.3.0
+charset-normalizer==3.3.1
     # via
     #   -c hail/batch/../gear/pinned-requirements.txt
     #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
@@ -64,7 +64,7 @@ multidict==6.0.4
     #   -c hail/batch/../web_common/pinned-requirements.txt
     #   aiohttp
     #   yarl
-numpy==1.26.0
+numpy==1.26.1
     # via
     #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
     #   -c hail/batch/../hail/python/pinned-requirements.txt

ci/pinned-requirements.txt

@@ -15,7 +15,7 @@ cffi==1.16.0
     #   -c hail/ci/../hail/python/dev/pinned-requirements.txt
     #   -c hail/ci/../hail/python/pinned-requirements.txt
     #   cryptography
-charset-normalizer==3.3.0
+charset-normalizer==3.3.1
     # via
     #   -c hail/ci/../gear/pinned-requirements.txt
     #   -c hail/ci/../hail/python/dev/pinned-requirements.txt
@@ -71,7 +71,7 @@ uritemplate==4.1.1
     # via
     #   -c hail/ci/../gear/pinned-requirements.txt
     #   gidgethub
-urllib3==1.26.17
+urllib3==1.26.18
     # via
     #   -c hail/ci/../gear/pinned-requirements.txt
     #   -c hail/ci/../hail/python/dev/pinned-requirements.txt

gear/pinned-requirements.txt

@@ -6,7 +6,7 @@
 #
 aioconsole==0.6.2
     # via aiomonitor
-aiohttp==3.8.5
+aiohttp==3.8.6
     # via
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
@@ -50,7 +50,7 @@ certifi==2023.7.22
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   kubernetes-asyncio
     #   requests
-charset-normalizer==3.3.0
+charset-normalizer==3.3.1
     # via
     #   -c hail/gear/../hail/python/dev/pinned-requirements.txt
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
@@ -71,9 +71,9 @@ frozenlist==1.4.0
     #   aiosignal
 google-api-core==2.12.0
     # via google-api-python-client
-google-api-python-client==2.102.0
+google-api-python-client==2.104.0
     # via google-cloud-profiler
-google-auth==2.23.2
+google-auth==2.23.3
     # via
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
@@ -87,7 +87,7 @@ google-auth-httplib2==0.1.1
     #   google-cloud-profiler
 google-cloud-profiler==3.1.0
     # via -r hail/gear/requirements.txt
-googleapis-common-protos==1.60.0
+googleapis-common-protos==1.61.0
     # via google-api-core
 httplib2==0.22.0
     # via
@@ -123,7 +123,7 @@ multidict==6.0.4
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   aiohttp
     #   yarl
-orjson==3.9.7
+orjson==3.9.9
     # via
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
@@ -213,7 +213,7 @@ typing-extensions==4.8.0
     #   janus
 uritemplate==4.1.1
     # via google-api-python-client
-urllib3==1.26.17
+urllib3==1.26.18
     # via
     #   -c hail/gear/../hail/python/dev/pinned-requirements.txt
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt

hail/python/dev/pinned-requirements.txt

@@ -36,7 +36,7 @@ beautifulsoup4==4.12.2
     # via nbconvert
 black==22.12.0
     # via -r hail/hail/python/dev/requirements.txt
-bleach==6.0.0
+bleach==6.1.0
     # via nbconvert
 certifi==2023.7.22
     # via
@@ -48,7 +48,7 @@ cffi==1.16.0
     #   argon2-cffi-bindings
 cfgv==3.4.0
     # via pre-commit
-charset-normalizer==3.3.0
+charset-normalizer==3.3.1
     # via
     #   -c hail/hail/python/dev/../pinned-requirements.txt
     #   requests
@@ -68,7 +68,7 @@ contourpy==1.1.1
     #   matplotlib
 curlylint==0.13.1
     # via -r hail/hail/python/dev/requirements.txt
-cycler==0.12.0
+cycler==0.12.1
     # via matplotlib
 debugpy==1.8.0
     # via ipykernel
@@ -102,7 +102,7 @@ fastjsonschema==2.18.1
     # via nbformat
 filelock==3.12.4
     # via virtualenv
-fonttools==4.43.0
+fonttools==4.43.1
     # via matplotlib
 fqdn==1.5.1
     # via jsonschema
@@ -173,7 +173,7 @@ jsonschema-specifications==2023.7.1
     # via jsonschema
 jupyter==1.0.0
     # via -r hail/hail/python/dev/requirements.txt
-jupyter-client==8.3.1
+jupyter-client==8.4.0
     # via
     #   ipykernel
     #   jupyter-console
@@ -182,7 +182,7 @@ jupyter-client==8.3.1
     #   qtconsole
 jupyter-console==6.6.3
     # via jupyter
-jupyter-core==5.3.2
+jupyter-core==5.4.0
     # via
     #   ipykernel
     #   jupyter-client
@@ -193,11 +193,11 @@ jupyter-core==5.3.2
     #   nbconvert
     #   nbformat
     #   qtconsole
-jupyter-events==0.7.0
+jupyter-events==0.8.0
     # via jupyter-server
 jupyter-lsp==2.2.0
     # via jupyterlab
-jupyter-server==2.7.3
+jupyter-server==2.8.0
     # via
     #   jupyter-lsp
     #   jupyterlab
@@ -206,7 +206,7 @@ jupyter-server==2.7.3
     #   notebook-shim
 jupyter-server-terminals==0.4.4
     # via jupyter-server
-jupyterlab==4.0.6
+jupyterlab==4.0.7
     # via notebook
 jupyterlab-pygments==0.2.2
     # via nbconvert
@@ -260,13 +260,13 @@ nodeenv==1.8.0
     # via
     #   pre-commit
     #   pyright
-notebook==7.0.4
+notebook==7.0.6
     # via jupyter
 notebook-shim==0.2.3
     # via
     #   jupyterlab
     #   notebook
-numpy==1.26.0
+numpy==1.26.1
     # via
     #   -c hail/hail/python/dev/../pinned-requirements.txt
     #   contourpy
@@ -300,7 +300,7 @@ pexpect==4.8.0
     # via ipython
 pickleshare==0.7.5
     # via ipython
-pillow==10.0.1
+pillow==10.1.0
     # via
     #   -c hail/hail/python/dev/../pinned-requirements.txt
     #   -r hail/hail/python/dev/requirements.txt
@@ -313,15 +313,15 @@ platformdirs==3.11.0
     #   virtualenv
 pluggy==1.3.0
     # via pytest
-pre-commit==3.4.0
+pre-commit==3.5.0
     # via -r hail/hail/python/dev/requirements.txt
 prometheus-client==0.17.1
     # via jupyter-server
 prompt-toolkit==3.0.39
     # via
     #   ipython
     #   jupyter-console
-psutil==5.9.5
+psutil==5.9.6
     # via ipykernel
 ptyprocess==0.7.0
     # via
@@ -347,7 +347,7 @@ pylint==2.17.7
     # via -r hail/hail/python/dev/requirements.txt
 pyparsing==3.1.1
     # via matplotlib
-pyright==1.1.329
+pyright==1.1.332
     # via -r hail/hail/python/dev/requirements.txt
 pytest==7.4.2
     # via
@@ -369,7 +369,7 @@ pytest-instafail==0.5.0
     # via -r hail/hail/python/dev/requirements.txt
 pytest-metadata==3.0.0
     # via pytest-html
-pytest-timeout==2.1.0
+pytest-timeout==2.2.0
     # via -r hail/hail/python/dev/requirements.txt
 pytest-timestamper==0.0.9
     # via -r hail/hail/python/dev/requirements.txt
@@ -419,11 +419,11 @@ rfc3986-validator==0.1.1
     # via
     #   jsonschema
     #   jupyter-events
-rpds-py==0.10.4
+rpds-py==0.10.6
     # via
     #   jsonschema
     #   referencing
-ruff==0.0.292
+ruff==0.1.1
     # via -r hail/hail/python/dev/requirements.txt
 send2trash==1.8.2
     # via jupyter-server
@@ -467,7 +467,7 @@ sphinxcontrib-jquery==4.1
     # via sphinx-rtd-theme
 sphinxcontrib-jsmath==1.0.1
     # via sphinx
-sphinxcontrib-katex==0.9.7
+sphinxcontrib-katex==0.9.9
     # via -r hail/hail/python/dev/requirements.txt
 sphinxcontrib-qthelp==1.0.6
     # via sphinx
@@ -554,7 +554,7 @@ typing-extensions==4.8.0
     #   pylint
 uri-template==1.3.0
     # via jsonschema
-urllib3==1.26.17
+urllib3==1.26.18
     # via
     #   -c hail/hail/python/dev/../pinned-requirements.txt
     #   requests
@@ -568,7 +568,7 @@ webencodings==0.5.1
     # via
     #   bleach
     #   tinycss2
-websocket-client==1.6.3
+websocket-client==1.6.4
     # via jupyter-server
 widgetsnbextension==4.0.9
     # via ipywidgets

hail/python/hailtop/pinned-requirements.txt

@@ -6,7 +6,7 @@
 #
 aiodns==2.0.0
     # via -r hail/hail/python/hailtop/requirements.txt
-aiohttp==3.8.5
+aiohttp==3.8.6
     # via -r hail/hail/python/hailtop/requirements.txt
 aiosignal==1.3.1
     # via aiohttp
@@ -16,23 +16,23 @@ attrs==23.1.0
     # via aiohttp
 azure-common==1.1.28
     # via azure-mgmt-storage
-azure-core==1.29.4
+azure-core==1.29.5
     # via
     #   azure-identity
     #   azure-mgmt-core
     #   azure-storage-blob
     #   msrest
-azure-identity==1.14.0
+azure-identity==1.14.1
     # via -r hail/hail/python/hailtop/requirements.txt
 azure-mgmt-core==1.4.0
     # via azure-mgmt-storage
 azure-mgmt-storage==20.1.0
     # via -r hail/hail/python/hailtop/requirements.txt
-azure-storage-blob==12.18.2
+azure-storage-blob==12.18.3
     # via -r hail/hail/python/hailtop/requirements.txt
-boto3==1.28.61
+boto3==1.28.68
     # via -r hail/hail/python/hailtop/requirements.txt
-botocore==1.31.61
+botocore==1.31.68
     # via
     #   -r hail/hail/python/hailtop/requirements.txt
     #   boto3
@@ -47,7 +47,7 @@ cffi==1.16.0
     # via
     #   cryptography
     #   pycares
-charset-normalizer==3.3.0
+charset-normalizer==3.3.1
     # via
     #   aiohttp
     #   requests
@@ -68,7 +68,7 @@ frozenlist==1.4.0
     #   -r hail/hail/python/hailtop/requirements.txt
     #   aiohttp
     #   aiosignal
-google-auth==2.23.2
+google-auth==2.23.3
     # via
     #   -r hail/hail/python/hailtop/requirements.txt
     #   google-auth-oauthlib
@@ -108,7 +108,7 @@ nest-asyncio==1.5.8
     # via -r hail/hail/python/hailtop/requirements.txt
 oauthlib==3.2.2
     # via requests-oauthlib
-orjson==3.9.7
+orjson==3.9.9
     # via -r hail/hail/python/hailtop/requirements.txt
 portalocker==2.8.2
     # via msal-extensions
@@ -120,7 +120,7 @@ pyasn1==0.5.0
     #   rsa
 pyasn1-modules==0.3.0
     # via google-auth
-pycares==4.3.0
+pycares==4.4.0
     # via aiodns
 pycparser==2.21
     # via cffi
@@ -168,11 +168,11 @@ typing-extensions==4.8.0
     #   azure-storage-blob
     #   janus
     #   typer
-urllib3==1.26.17
+urllib3==1.26.18
     # via
     #   botocore
     #   requests
-uvloop==0.17.0 ; sys_platform != "win32"
+uvloop==0.19.0 ; sys_platform != "win32"
     # via -r hail/hail/python/hailtop/requirements.txt
 yarl==1.9.2
     # via aiohttp

hail/python/hailtop/requirements.txt

@@ -20,5 +20,5 @@ python-json-logger>=2.0.2,<3
 pyyaml>=6.0,<7.0
 sortedcontainers>=2.4.0,<3
 tabulate>=0.8.9,<1
-uvloop>=0.16.0,<1; sys_platform!='win32'
+uvloop>=0.19.0,<1; sys_platform!='win32'
 jproperties>=2.1.1,<3

hail/python/hailtop/utils/utils.py

@@ -60,7 +60,7 @@ def unpack_key_value_inputs(inputs: List[str]) -> Dict[str, str]:
     return {kv[0]: kv[1] for kv in key_values}
 
 
-def flatten(xxs: Iterable[List[T]]) -> List[T]:
+def flatten(xxs: Iterable[Iterable[T]]) -> List[T]:
     return [x for xs in xxs for x in xs]