diff --git a/batch/batch/worker/worker.py b/batch/batch/worker/worker.py index 83b7ac96ef1..1a7a865b5bc 100644 --- a/batch/batch/worker/worker.py +++ b/batch/batch/worker/worker.py @@ -36,7 +36,6 @@ import aiodocker.images import aiohttp import aiohttp.client_exceptions -import aiomonitor import aiorwlock import async_timeout import orjson @@ -3473,25 +3472,24 @@ async def async_main(): await network_allocator.reserve() worker = Worker(httpx.client_session()) - with aiomonitor.start_monitor(asyncio.get_event_loop(), locals=locals()): - try: - async with AsyncExitStack() as cleanup: - cleanup.push_async_callback(docker.close) - cleanup.push_async_callback(network_allocator_task_manager.shutdown_and_wait) - cleanup.push_async_callback(CLOUD_WORKER_API.close) - cleanup.push_async_callback(worker.shutdown) - await worker.run() - finally: - asyncio.get_event_loop().set_debug(True) - other_tasks = [t for t in asyncio.all_tasks() if t != asyncio.current_task()] - if other_tasks: - log.warning('Tasks immediately after docker close') - dump_all_stacktraces() - _, pending = await asyncio.wait(other_tasks, timeout=10 * 60, return_when=asyncio.ALL_COMPLETED) - for t in pending: - log.warning('Dangling task:') - t.print_stack() - t.cancel() + try: + async with AsyncExitStack() as cleanup: + cleanup.push_async_callback(docker.close) + cleanup.push_async_callback(network_allocator_task_manager.shutdown_and_wait) + cleanup.push_async_callback(CLOUD_WORKER_API.close) + cleanup.push_async_callback(worker.shutdown) + await worker.run() + finally: + asyncio.get_event_loop().set_debug(True) + other_tasks = [t for t in asyncio.all_tasks() if t != asyncio.current_task()] + if other_tasks: + log.warning('Tasks immediately after docker close') + dump_all_stacktraces() + _, pending = await asyncio.wait(other_tasks, timeout=10 * 60, return_when=asyncio.ALL_COMPLETED) + for t in pending: + log.warning('Dangling task:') + t.print_stack() + t.cancel() loop = asyncio.get_event_loop() diff --git a/batch/pinned-requirements.txt b/batch/pinned-requirements.txt index 35dadef8203..68d136e5a1e 100644 --- a/batch/pinned-requirements.txt +++ b/batch/pinned-requirements.txt @@ -6,7 +6,7 @@ # aiodocker==0.21.0 # via -r hail/batch/requirements.txt -aiohttp==3.8.6 +aiohttp==3.9.1 # via # -c hail/batch/../gear/pinned-requirements.txt # -c hail/batch/../hail/python/dev/pinned-requirements.txt @@ -37,13 +37,6 @@ attrs==23.1.0 # -c hail/batch/../hail/python/pinned-requirements.txt # -c hail/batch/../web_common/pinned-requirements.txt # aiohttp -charset-normalizer==3.3.2 - # via - # -c hail/batch/../gear/pinned-requirements.txt - # -c hail/batch/../hail/python/dev/pinned-requirements.txt - # -c hail/batch/../hail/python/pinned-requirements.txt - # -c hail/batch/../web_common/pinned-requirements.txt - # aiohttp dictdiffer==0.9.0 # via -r hail/batch/requirements.txt frozenlist==1.4.0 @@ -54,7 +47,7 @@ frozenlist==1.4.0 # -c hail/batch/../web_common/pinned-requirements.txt # aiohttp # aiosignal -idna==3.4 +idna==3.6 # via # -c hail/batch/../gear/pinned-requirements.txt # -c hail/batch/../hail/python/dev/pinned-requirements.txt @@ -69,7 +62,7 @@ multidict==6.0.4 # -c hail/batch/../web_common/pinned-requirements.txt # aiohttp # yarl -numpy==1.26.1 +numpy==1.26.2 # via # -c hail/batch/../hail/python/pinned-requirements.txt # pandas @@ -78,7 +71,7 @@ packaging==23.2 # -c hail/batch/../hail/python/dev/pinned-requirements.txt # -c hail/batch/../hail/python/pinned-requirements.txt # plotly -pandas==2.1.2 +pandas==2.1.3 # via # -c hail/batch/../hail/python/pinned-requirements.txt # -r hail/batch/requirements.txt @@ -108,7 +101,6 @@ tenacity==8.2.3 # plotly typing-extensions==4.8.0 # via - # -c hail/batch/../gear/pinned-requirements.txt # -c hail/batch/../hail/python/dev/pinned-requirements.txt # -c hail/batch/../hail/python/pinned-requirements.txt # aiodocker @@ -116,7 +108,7 @@ tzdata==2023.3 # via # -c hail/batch/../hail/python/pinned-requirements.txt # pandas -yarl==1.9.2 +yarl==1.9.3 # via # -c hail/batch/../gear/pinned-requirements.txt # -c hail/batch/../hail/python/dev/pinned-requirements.txt diff --git a/benchmark/python/pinned-requirements.txt b/benchmark/python/pinned-requirements.txt index 9fc6c11ba50..20502345bd1 100644 --- a/benchmark/python/pinned-requirements.txt +++ b/benchmark/python/pinned-requirements.txt @@ -10,15 +10,15 @@ contourpy==1.2.0 # matplotlib cycler==0.12.1 # via matplotlib -fonttools==4.44.0 +fonttools==4.45.1 # via matplotlib importlib-resources==6.1.1 # via matplotlib kiwisolver==1.4.5 # via matplotlib -matplotlib==3.8.1 +matplotlib==3.8.2 # via -r hail/benchmark/python/requirements.txt -numpy==1.26.1 +numpy==1.26.2 # via # -c hail/benchmark/python/../../hail/python/pinned-requirements.txt # contourpy diff --git a/ci/ci/build.py b/ci/ci/build.py index 7a6a75d98ef..3232ea73dd5 100644 --- a/ci/ci/build.py +++ b/ci/ci/build.py @@ -3,7 +3,7 @@ import logging from collections import Counter, defaultdict from shlex import quote as shq -from typing import Dict, List, Optional, Sequence, TypedDict +from typing import Dict, List, Optional, Sequence, Set, TypedDict import jinja2 import yaml @@ -217,8 +217,8 @@ def deps_parents(self): return flatten([d.wrapped_job() for d in self.deps]) def all_deps(self): - visited = set([self]) - frontier = [self] + visited: Set[Step] = set([self]) + frontier: List[Step] = [self] while frontier: current = frontier.pop() diff --git a/ci/pinned-requirements.txt b/ci/pinned-requirements.txt index 7acf28dbfd2..6ada8c4918f 100644 --- a/ci/pinned-requirements.txt +++ b/ci/pinned-requirements.txt @@ -4,7 +4,7 @@ # # pip-compile --output-file=hail/ci/pinned-requirements.txt hail/ci/requirements.txt # -certifi==2023.7.22 +certifi==2023.11.17 # via # -c hail/ci/../gear/pinned-requirements.txt # -c hail/ci/../hail/python/dev/pinned-requirements.txt @@ -20,15 +20,13 @@ charset-normalizer==3.3.2 # -c hail/ci/../gear/pinned-requirements.txt # -c hail/ci/../hail/python/dev/pinned-requirements.txt # -c hail/ci/../hail/python/pinned-requirements.txt - # -c hail/ci/../web_common/pinned-requirements.txt # requests click==8.1.7 # via - # -c hail/ci/../gear/pinned-requirements.txt # -c hail/ci/../hail/python/dev/pinned-requirements.txt # -c hail/ci/../hail/python/pinned-requirements.txt # zulip -cryptography==41.0.5 +cryptography==41.0.7 # via # -c hail/ci/../hail/python/pinned-requirements.txt # pyjwt @@ -36,15 +34,13 @@ distro==1.8.0 # via zulip gidgethub==5.3.0 # via -r hail/ci/requirements.txt -idna==3.4 +idna==3.6 # via # -c hail/ci/../gear/pinned-requirements.txt # -c hail/ci/../hail/python/dev/pinned-requirements.txt # -c hail/ci/../hail/python/pinned-requirements.txt # -c hail/ci/../web_common/pinned-requirements.txt # requests -matrix-client==0.4.0 - # via zulip pycparser==2.21 # via # -c hail/ci/../hail/python/dev/pinned-requirements.txt @@ -59,11 +55,9 @@ requests[security]==2.31.0 # -c hail/ci/../gear/pinned-requirements.txt # -c hail/ci/../hail/python/dev/pinned-requirements.txt # -c hail/ci/../hail/python/pinned-requirements.txt - # matrix-client # zulip typing-extensions==4.8.0 # via - # -c hail/ci/../gear/pinned-requirements.txt # -c hail/ci/../hail/python/dev/pinned-requirements.txt # -c hail/ci/../hail/python/pinned-requirements.txt # zulip @@ -76,7 +70,6 @@ urllib3==1.26.18 # -c hail/ci/../gear/pinned-requirements.txt # -c hail/ci/../hail/python/dev/pinned-requirements.txt # -c hail/ci/../hail/python/pinned-requirements.txt - # matrix-client # requests -zulip==0.8.2 +zulip==0.9.0 # via -r hail/ci/requirements.txt diff --git a/gear/pinned-requirements.txt b/gear/pinned-requirements.txt index 11492abab7e..535766454e9 100644 --- a/gear/pinned-requirements.txt +++ b/gear/pinned-requirements.txt @@ -4,20 +4,15 @@ # # pip-compile --output-file=hail/gear/pinned-requirements.txt hail/gear/requirements.txt # -aioconsole==0.6.2 - # via aiomonitor -aiohttp==3.8.6 +aiohttp==3.9.1 # via # -c hail/gear/../hail/python/dev/pinned-requirements.txt # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt # -c hail/gear/../hail/python/pinned-requirements.txt # aiohttp-session - # aiomonitor # kubernetes-asyncio aiohttp-session==2.12.0 # via -r hail/gear/requirements.txt -aiomonitor==0.6.0 - # via -r hail/gear/requirements.txt aiomysql==0.2.0 # via -r hail/gear/requirements.txt aiosignal==1.3.1 @@ -38,15 +33,12 @@ attrs==23.1.0 # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt # -c hail/gear/../hail/python/pinned-requirements.txt # aiohttp - # aiomonitor -backports-strenum==1.2.8 - # via aiomonitor cachetools==5.3.2 # via # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt # -c hail/gear/../hail/python/pinned-requirements.txt # google-auth -certifi==2023.7.22 +certifi==2023.11.17 # via # -c hail/gear/../hail/python/dev/pinned-requirements.txt # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt @@ -58,14 +50,7 @@ charset-normalizer==3.3.2 # -c hail/gear/../hail/python/dev/pinned-requirements.txt # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt # -c hail/gear/../hail/python/pinned-requirements.txt - # aiohttp # requests -click==8.1.7 - # via - # -c hail/gear/../hail/python/dev/pinned-requirements.txt - # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt - # -c hail/gear/../hail/python/pinned-requirements.txt - # aiomonitor frozenlist==1.4.0 # via # -c hail/gear/../hail/python/dev/pinned-requirements.txt @@ -73,9 +58,9 @@ frozenlist==1.4.0 # -c hail/gear/../hail/python/pinned-requirements.txt # aiohttp # aiosignal -google-api-core==2.13.0 +google-api-core==2.14.0 # via google-api-python-client -google-api-python-client==2.107.0 +google-api-python-client==2.108.0 # via google-cloud-profiler google-auth==2.23.4 # via @@ -97,30 +82,15 @@ httplib2==0.22.0 # via # google-api-python-client # google-auth-httplib2 -idna==3.4 +idna==3.6 # via # -c hail/gear/../hail/python/dev/pinned-requirements.txt # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt # -c hail/gear/../hail/python/pinned-requirements.txt # requests # yarl -janus==1.0.0 - # via - # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt - # -c hail/gear/../hail/python/pinned-requirements.txt - # aiomonitor -jinja2==3.1.2 - # via - # -c hail/gear/../hail/python/dev/pinned-requirements.txt - # -c hail/gear/../hail/python/pinned-requirements.txt - # aiomonitor kubernetes-asyncio==19.15.1 # via -r hail/gear/requirements.txt -markupsafe==2.1.3 - # via - # -c hail/gear/../hail/python/dev/pinned-requirements.txt - # -c hail/gear/../hail/python/pinned-requirements.txt - # jinja2 multidict==6.0.4 # via # -c hail/gear/../hail/python/dev/pinned-requirements.txt @@ -135,22 +105,18 @@ orjson==3.9.10 # -r hail/gear/requirements.txt prometheus-async==19.2.0 # via -r hail/gear/requirements.txt -prometheus-client==0.18.0 +prometheus-client==0.19.0 # via # -c hail/gear/../hail/python/dev/pinned-requirements.txt # -r hail/gear/requirements.txt # prometheus-async -prompt-toolkit==3.0.39 - # via - # -c hail/gear/../hail/python/dev/pinned-requirements.txt - # aiomonitor protobuf==3.20.2 # via # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt # -c hail/gear/../hail/python/pinned-requirements.txt # google-api-core # google-cloud-profiler -pyasn1==0.5.0 +pyasn1==0.5.1 # via # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt # -c hail/gear/../hail/python/pinned-requirements.txt @@ -203,17 +169,6 @@ sortedcontainers==2.4.0 # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt # -c hail/gear/../hail/python/pinned-requirements.txt # -r hail/gear/requirements.txt -terminaltables==3.1.10 - # via aiomonitor -trafaret==2.1.1 - # via aiomonitor -typing-extensions==4.8.0 - # via - # -c hail/gear/../hail/python/dev/pinned-requirements.txt - # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt - # -c hail/gear/../hail/python/pinned-requirements.txt - # aiomonitor - # janus uritemplate==4.1.1 # via google-api-python-client urllib3==1.26.18 @@ -223,16 +178,12 @@ urllib3==1.26.18 # -c hail/gear/../hail/python/pinned-requirements.txt # kubernetes-asyncio # requests -wcwidth==0.2.9 - # via - # -c hail/gear/../hail/python/dev/pinned-requirements.txt - # prompt-toolkit -wrapt==1.15.0 +wrapt==1.16.0 # via # -c hail/gear/../hail/python/dev/pinned-requirements.txt # -c hail/gear/../hail/python/pinned-requirements.txt # prometheus-async -yarl==1.9.2 +yarl==1.9.3 # via # -c hail/gear/../hail/python/dev/pinned-requirements.txt # -c hail/gear/../hail/python/hailtop/pinned-requirements.txt diff --git a/gear/requirements.txt b/gear/requirements.txt index 91f2f5d581b..a75dd5cb217 100644 --- a/gear/requirements.txt +++ b/gear/requirements.txt @@ -7,7 +7,6 @@ -c ../hail/python/dev/pinned-requirements.txt aiohttp_session>=2.7,<2.13 -aiomonitor>=0.4.5,<1 aiomysql>=0.0.20,<1 google-cloud-profiler<4.0.0 kubernetes-asyncio>=19.15.1,<20 diff --git a/hail/python/dev/pinned-requirements.txt b/hail/python/dev/pinned-requirements.txt index 759e4be5ad9..2fff21408a2 100644 --- a/hail/python/dev/pinned-requirements.txt +++ b/hail/python/dev/pinned-requirements.txt @@ -4,11 +4,11 @@ # # pip-compile --output-file=hail/hail/python/dev/pinned-requirements.txt hail/hail/python/dev/requirements.txt # -aiohttp==3.8.6 +aiohttp==3.9.1 # via # -c hail/hail/python/dev/../pinned-requirements.txt # aiohttp-devtools -aiohttp-devtools==1.1 +aiohttp-devtools==1.1.1 # via -r hail/hail/python/dev/requirements.txt aiosignal==1.3.1 # via @@ -16,7 +16,7 @@ aiosignal==1.3.1 # aiohttp alabaster==0.7.13 # via sphinx -anyio==4.0.0 +anyio==4.1.0 # via # jupyter-server # watchfiles @@ -55,7 +55,7 @@ black==22.12.0 # via -r hail/hail/python/dev/requirements.txt bleach==6.1.0 # via nbconvert -certifi==2023.7.22 +certifi==2023.11.17 # via # -c hail/hail/python/dev/../pinned-requirements.txt # requests @@ -68,7 +68,6 @@ cfgv==3.4.0 charset-normalizer==3.3.2 # via # -c hail/hail/python/dev/../pinned-requirements.txt - # aiohttp # requests click==8.1.7 # via @@ -104,7 +103,7 @@ docutils==0.18.1 # nbsphinx # sphinx # sphinx-rtd-theme -exceptiongroup==1.1.3 +exceptiongroup==1.2.0 # via # anyio # ipython @@ -115,7 +114,7 @@ executing==2.0.1 # via # devtools # stack-data -fastjsonschema==2.18.1 +fastjsonschema==2.19.0 # via nbformat filelock==3.13.1 # via virtualenv @@ -128,9 +127,9 @@ frozenlist==1.4.0 # aiosignal fswatch==0.1.1 # via -r hail/hail/python/dev/requirements.txt -identify==2.5.31 +identify==2.5.32 # via pre-commit -idna==3.4 +idna==3.6 # via # -c hail/hail/python/dev/../pinned-requirements.txt # anyio @@ -149,13 +148,13 @@ importlib-metadata==6.8.0 # sphinx iniconfig==2.0.0 # via pytest -ipykernel==6.26.0 +ipykernel==6.27.1 # via # jupyter # jupyter-console # jupyterlab # qtconsole -ipython==8.17.2 +ipython==8.18.1 # via # ipykernel # ipywidgets @@ -181,12 +180,12 @@ json5==0.9.14 # via jupyterlab-server jsonpointer==2.4 # via jsonschema -jsonschema[format-nongpl]==4.19.2 +jsonschema[format-nongpl]==4.20.0 # via # jupyter-events # jupyterlab-server # nbformat -jsonschema-specifications==2023.7.1 +jsonschema-specifications==2023.11.1 # via jsonschema jupyter==1.0.0 # via -r hail/hail/python/dev/requirements.txt @@ -212,9 +211,9 @@ jupyter-core==5.5.0 # qtconsole jupyter-events==0.9.0 # via jupyter-server -jupyter-lsp==2.2.0 +jupyter-lsp==2.2.1 # via jupyterlab -jupyter-server==2.10.0 +jupyter-server==2.11.1 # via # jupyter-lsp # jupyterlab @@ -223,11 +222,11 @@ jupyter-server==2.10.0 # notebook-shim jupyter-server-terminals==0.4.4 # via jupyter-server -jupyterlab==4.0.8 +jupyterlab==4.0.9 # via notebook -jupyterlab-pygments==0.2.2 +jupyterlab-pygments==0.3.0 # via nbconvert -jupyterlab-server==2.25.0 +jupyterlab-server==2.25.2 # via # jupyterlab # notebook @@ -308,13 +307,13 @@ pathspec==0.11.2 # via # black # curlylint -pexpect==4.8.0 +pexpect==4.9.0 # via ipython pillow==10.1.0 # via # -c hail/hail/python/dev/../pinned-requirements.txt # -r hail/hail/python/dev/requirements.txt -platformdirs==3.11.0 +platformdirs==4.0.0 # via # black # jupyter-core @@ -324,9 +323,9 @@ pluggy==1.3.0 # via pytest pre-commit==3.5.0 # via -r hail/hail/python/dev/requirements.txt -prometheus-client==0.18.0 +prometheus-client==0.19.0 # via jupyter-server -prompt-toolkit==3.0.39 +prompt-toolkit==3.0.41 # via # ipython # jupyter-console @@ -344,7 +343,7 @@ pycparser==2.21 # via # -c hail/hail/python/dev/../pinned-requirements.txt # cffi -pygments==2.16.1 +pygments==2.17.2 # via # -c hail/hail/python/dev/../pinned-requirements.txt # aiohttp-devtools @@ -356,7 +355,7 @@ pygments==2.16.1 # sphinx pylint==2.17.7 # via -r hail/hail/python/dev/requirements.txt -pyright==1.1.334 +pyright==1.1.337 # via -r hail/hail/python/dev/requirements.txt pytest==7.4.3 # via @@ -405,11 +404,11 @@ pyzmq==25.1.1 # jupyter-console # jupyter-server # qtconsole -qtconsole==5.5.0 +qtconsole==5.5.1 # via jupyter qtpy==2.4.1 # via qtconsole -referencing==0.30.2 +referencing==0.31.0 # via # jsonschema # jsonschema-specifications @@ -427,11 +426,11 @@ rfc3986-validator==0.1.1 # via # jsonschema # jupyter-events -rpds-py==0.12.0 +rpds-py==0.13.1 # via # jsonschema # referencing -ruff==0.1.4 +ruff==0.1.6 # via -r hail/hail/python/dev/requirements.txt send2trash==1.8.2 # via jupyter-server @@ -483,7 +482,7 @@ sphinxcontrib-serializinghtml==1.1.9 # via sphinx stack-data==0.6.3 # via ipython -terminado==0.17.1 +terminado==0.18.0 # via # jupyter-server # jupyter-server-terminals @@ -497,7 +496,7 @@ tomli==2.0.1 # jupyterlab # pylint # pytest -tomlkit==0.12.2 +tomlkit==0.12.3 # via pylint tornado==6.3.3 # via @@ -508,7 +507,7 @@ tornado==6.3.3 # jupyterlab # notebook # terminado -traitlets==5.13.0 +traitlets==5.14.0 # via # comm # ipykernel @@ -542,7 +541,7 @@ types-pyyaml==6.0.12.12 # via -r hail/hail/python/dev/requirements.txt types-requests==2.31.0.6 # via -r hail/hail/python/dev/requirements.txt -types-setuptools==68.2.0.0 +types-setuptools==68.2.0.2 # via -r hail/hail/python/dev/requirements.txt types-six==1.16.21.9 # via -r hail/hail/python/dev/requirements.txt @@ -566,11 +565,11 @@ urllib3==1.26.18 # via # -c hail/hail/python/dev/../pinned-requirements.txt # requests -virtualenv==20.24.6 +virtualenv==20.24.7 # via pre-commit watchfiles==0.21.0 # via aiohttp-devtools -wcwidth==0.2.9 +wcwidth==0.2.12 # via prompt-toolkit webcolors==1.13 # via jsonschema @@ -584,11 +583,11 @@ wheel==0.41.3 # via -r hail/hail/python/dev/requirements.txt widgetsnbextension==4.0.9 # via ipywidgets -wrapt==1.15.0 +wrapt==1.16.0 # via # -c hail/hail/python/dev/../pinned-requirements.txt # astroid -yarl==1.9.2 +yarl==1.9.3 # via # -c hail/hail/python/dev/../pinned-requirements.txt # aiohttp diff --git a/hail/python/hailtop/pinned-requirements.txt b/hail/python/hailtop/pinned-requirements.txt index 220a3440e19..70adf3f3f6e 100644 --- a/hail/python/hailtop/pinned-requirements.txt +++ b/hail/python/hailtop/pinned-requirements.txt @@ -6,7 +6,7 @@ # aiodns==2.0.0 # via -r hail/hail/python/hailtop/requirements.txt -aiohttp==3.8.6 +aiohttp==3.9.1 # via -r hail/hail/python/hailtop/requirements.txt aiosignal==1.3.1 # via aiohttp @@ -28,18 +28,18 @@ 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==12.18.3 +azure-storage-blob==12.19.0 # via -r hail/hail/python/hailtop/requirements.txt -boto3==1.28.80 +boto3==1.33.1 # via -r hail/hail/python/hailtop/requirements.txt -botocore==1.31.80 +botocore==1.33.1 # via # -r hail/hail/python/hailtop/requirements.txt # boto3 # s3transfer cachetools==5.3.2 # via google-auth -certifi==2023.7.22 +certifi==2023.11.17 # via # msrest # requests @@ -48,14 +48,12 @@ cffi==1.16.0 # cryptography # pycares charset-normalizer==3.3.2 - # via - # aiohttp - # requests + # via requests click==8.1.7 # via typer commonmark==0.9.1 # via rich -cryptography==41.0.5 +cryptography==41.0.7 # via # azure-identity # azure-storage-blob @@ -76,7 +74,7 @@ google-auth-oauthlib==0.8.0 # via -r hail/hail/python/hailtop/requirements.txt humanize==1.1.0 # via -r hail/hail/python/hailtop/requirements.txt -idna==3.4 +idna==3.6 # via # requests # yarl @@ -114,7 +112,7 @@ portalocker==2.8.2 # via msal-extensions protobuf==3.20.2 # via -r hail/hail/python/hailtop/requirements.txt -pyasn1==0.5.0 +pyasn1==0.5.1 # via # pyasn1-modules # rsa @@ -124,7 +122,7 @@ pycares==4.4.0 # via aiodns pycparser==2.21 # via cffi -pygments==2.16.1 +pygments==2.17.2 # via rich pyjwt[crypto]==2.8.0 # via msal @@ -148,7 +146,7 @@ rich==12.6.0 # via -r hail/hail/python/hailtop/requirements.txt rsa==4.9 # via google-auth -s3transfer==0.7.0 +s3transfer==0.8.0 # via boto3 six==1.16.0 # via @@ -174,5 +172,5 @@ urllib3==1.26.18 # requests uvloop==0.19.0 ; sys_platform != "win32" # via -r hail/hail/python/hailtop/requirements.txt -yarl==1.9.2 +yarl==1.9.3 # via aiohttp diff --git a/hail/python/hailtop/requirements.txt b/hail/python/hailtop/requirements.txt index a62016b2f52..a7d7f2f1899 100644 --- a/hail/python/hailtop/requirements.txt +++ b/hail/python/hailtop/requirements.txt @@ -1,5 +1,5 @@ aiodns>=2.0.0,<3 -aiohttp>=3.8.1,<4 +aiohttp>=3.9,<4 azure-identity>=1.6.0,<2 azure-mgmt-storage==20.1.0 azure-storage-blob>=12.11.0,<13 diff --git a/hail/python/pinned-requirements.txt b/hail/python/pinned-requirements.txt index db965402254..d7af149ca74 100644 --- a/hail/python/pinned-requirements.txt +++ b/hail/python/pinned-requirements.txt @@ -8,7 +8,7 @@ aiodns==2.0.0 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # -r hail/hail/python/hailtop/requirements.txt -aiohttp==3.8.6 +aiohttp==3.9.1 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # -r hail/hail/python/hailtop/requirements.txt @@ -49,17 +49,17 @@ azure-mgmt-storage==20.1.0 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # -r hail/hail/python/hailtop/requirements.txt -azure-storage-blob==12.18.3 +azure-storage-blob==12.19.0 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # -r hail/hail/python/hailtop/requirements.txt -bokeh==3.3.0 +bokeh==3.3.1 # via -r hail/hail/python/requirements.txt -boto3==1.28.80 +boto3==1.33.1 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # -r hail/hail/python/hailtop/requirements.txt -botocore==1.31.80 +botocore==1.33.1 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # -r hail/hail/python/hailtop/requirements.txt @@ -69,7 +69,7 @@ cachetools==5.3.2 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # google-auth -certifi==2023.7.22 +certifi==2023.11.17 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # msrest @@ -82,7 +82,6 @@ cffi==1.16.0 charset-normalizer==3.3.2 # via # -c hail/hail/python/hailtop/pinned-requirements.txt - # aiohttp # requests click==8.1.7 # via @@ -94,7 +93,7 @@ commonmark==0.9.1 # rich contourpy==1.2.0 # via bokeh -cryptography==41.0.5 +cryptography==41.0.7 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # azure-identity @@ -128,7 +127,7 @@ humanize==1.1.0 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # -r hail/hail/python/hailtop/requirements.txt -idna==3.4 +idna==3.6 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # requests @@ -177,7 +176,7 @@ nest-asyncio==1.5.8 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # -r hail/hail/python/hailtop/requirements.txt -numpy==1.26.1 +numpy==1.26.2 # via # -r hail/hail/python/requirements.txt # bokeh @@ -196,7 +195,7 @@ packaging==23.2 # via # bokeh # plotly -pandas==2.1.2 +pandas==2.1.3 # via # -r hail/hail/python/requirements.txt # bokeh @@ -217,7 +216,7 @@ protobuf==3.20.2 # -r hail/hail/python/requirements.txt py4j==0.10.9.5 # via pyspark -pyasn1==0.5.0 +pyasn1==0.5.1 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # pyasn1-modules @@ -234,7 +233,7 @@ pycparser==2.21 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # cffi -pygments==2.16.1 +pygments==2.17.2 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # rich @@ -283,11 +282,11 @@ rsa==4.9 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # google-auth -s3transfer==0.7.0 +s3transfer==0.8.0 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # boto3 -scipy==1.11.3 +scipy==1.11.4 # via -r hail/hail/python/requirements.txt six==1.16.0 # via @@ -330,11 +329,11 @@ uvloop==0.19.0 ; sys_platform != "win32" # via # -c hail/hail/python/hailtop/pinned-requirements.txt # -r hail/hail/python/hailtop/requirements.txt -wrapt==1.15.0 +wrapt==1.16.0 # via deprecated xyzservices==2023.10.1 # via bokeh -yarl==1.9.2 +yarl==1.9.3 # via # -c hail/hail/python/hailtop/pinned-requirements.txt # aiohttp diff --git a/web_common/pinned-requirements.txt b/web_common/pinned-requirements.txt index 7fa1d0ff664..d72a068dba2 100644 --- a/web_common/pinned-requirements.txt +++ b/web_common/pinned-requirements.txt @@ -4,13 +4,13 @@ # # pip-compile --output-file=hail/web_common/pinned-requirements.txt hail/web_common/requirements.txt # -aiohttp==3.8.6 +aiohttp==3.9.1 # via # -c hail/web_common/../gear/pinned-requirements.txt # -c hail/web_common/../hail/python/dev/pinned-requirements.txt # -c hail/web_common/../hail/python/pinned-requirements.txt # aiohttp-jinja2 -aiohttp-jinja2==1.5.1 +aiohttp-jinja2==1.6 # via -r hail/web_common/requirements.txt aiosignal==1.3.1 # via @@ -30,12 +30,6 @@ attrs==23.1.0 # -c hail/web_common/../hail/python/dev/pinned-requirements.txt # -c hail/web_common/../hail/python/pinned-requirements.txt # aiohttp -charset-normalizer==3.3.2 - # via - # -c hail/web_common/../gear/pinned-requirements.txt - # -c hail/web_common/../hail/python/dev/pinned-requirements.txt - # -c hail/web_common/../hail/python/pinned-requirements.txt - # aiohttp frozenlist==1.4.0 # via # -c hail/web_common/../gear/pinned-requirements.txt @@ -43,7 +37,7 @@ frozenlist==1.4.0 # -c hail/web_common/../hail/python/pinned-requirements.txt # aiohttp # aiosignal -idna==3.4 +idna==3.6 # via # -c hail/web_common/../gear/pinned-requirements.txt # -c hail/web_common/../hail/python/dev/pinned-requirements.txt @@ -51,7 +45,6 @@ idna==3.4 # yarl jinja2==3.1.2 # via - # -c hail/web_common/../gear/pinned-requirements.txt # -c hail/web_common/../hail/python/dev/pinned-requirements.txt # -c hail/web_common/../hail/python/pinned-requirements.txt # -r hail/web_common/requirements.txt @@ -60,7 +53,6 @@ libsass==0.22.0 # via -r hail/web_common/requirements.txt markupsafe==2.1.3 # via - # -c hail/web_common/../gear/pinned-requirements.txt # -c hail/web_common/../hail/python/dev/pinned-requirements.txt # -c hail/web_common/../hail/python/pinned-requirements.txt # jinja2 @@ -71,7 +63,7 @@ multidict==6.0.4 # -c hail/web_common/../hail/python/pinned-requirements.txt # aiohttp # yarl -yarl==1.9.2 +yarl==1.9.3 # via # -c hail/web_common/../gear/pinned-requirements.txt # -c hail/web_common/../hail/python/dev/pinned-requirements.txt