Merge remote-tracking branch 'upstream/main' into ehigham/simplify-ma…

…ke-struct
hail-is · Feb 2, 2024 · 65bf923 · 65bf923
2 parents af893e4 + d261554
commit 65bf923
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Showing 17 changed files with 336 additions and 189 deletions.
diff --git a/batch/batch/worker/worker.py b/batch/batch/worker/worker.py
@@ -14,7 +14,6 @@
 import tempfile
 import traceback
 import uuid
-import warnings
 from collections import defaultdict
 from contextlib import AsyncExitStack, ExitStack
 from typing import (
@@ -95,19 +94,6 @@
 with open('/subdomains.txt', 'r', encoding='utf-8') as subdomains_file:
     HAIL_SERVICES = [line.rstrip() for line in subdomains_file.readlines()]
 
-oldwarn = warnings.warn
-
-
-def deeper_stack_level_warn(*args, **kwargs):
-    if 'stacklevel' in kwargs:
-        kwargs['stacklevel'] = max(kwargs['stacklevel'], 5)
-    else:
-        kwargs['stacklevel'] = 5
-    return oldwarn(*args, **kwargs)
-
-
-warnings.warn = deeper_stack_level_warn
-
 
 class BatchWorkerAccessLogger(AccessLogger):
     def __init__(self, logger: logging.Logger, log_format: str):

diff --git a/batch/pinned-requirements.txt b/batch/pinned-requirements.txt
@@ -6,14 +6,14 @@
 #
 aiodocker==0.21.0
     # via -r hail/batch/requirements.txt
-aiohttp==3.9.1
+aiohttp==3.9.3
     # 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
     #   aiodocker
-aiorwlock==1.3.0
+aiorwlock==1.4.0
     # via -r hail/batch/requirements.txt
 aiosignal==1.3.1
     # via
@@ -30,7 +30,7 @@ async-timeout==4.0.3
     #   -c hail/batch/../web_common/pinned-requirements.txt
     #   -r hail/batch/requirements.txt
     #   aiohttp
-attrs==23.1.0
+attrs==23.2.0
     # via
     #   -c hail/batch/../gear/pinned-requirements.txt
     #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
@@ -39,7 +39,7 @@ attrs==23.1.0
     #   aiohttp
 dictdiffer==0.9.0
     # via -r hail/batch/requirements.txt
-frozenlist==1.4.0
+frozenlist==1.4.1
     # via
     #   -c hail/batch/../gear/pinned-requirements.txt
     #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
@@ -62,7 +62,7 @@ multidict==6.0.4
     #   -c hail/batch/../web_common/pinned-requirements.txt
     #   aiohttp
     #   yarl
-numpy==1.26.2
+numpy==1.26.3
     # via
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   pandas
@@ -71,7 +71,7 @@ packaging==23.2
     #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   plotly
-pandas==2.1.4
+pandas==2.2.0
     # via
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   -r hail/batch/requirements.txt
@@ -85,7 +85,7 @@ python-dateutil==2.8.2
     #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   pandas
-pytz==2023.3.post1
+pytz==2023.4
     # via
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   pandas
@@ -99,16 +99,16 @@ tenacity==8.2.3
     # via
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   plotly
-typing-extensions==4.8.0
+typing-extensions==4.9.0
     # via
     #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   aiodocker
-tzdata==2023.3
+tzdata==2023.4
     # via
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   pandas
-yarl==1.9.3
+yarl==1.9.4
     # 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
@@ -10,15 +10,15 @@ contourpy==1.2.0
     #   matplotlib
 cycler==0.12.1
     # via matplotlib
-fonttools==4.47.0
+fonttools==4.47.2
     # via matplotlib
 importlib-resources==6.1.1
     # via matplotlib
 kiwisolver==1.4.5
     # via matplotlib
 matplotlib==3.8.2
     # via -r hail/benchmark/python/requirements.txt
-numpy==1.26.2
+numpy==1.26.3
     # via
     #   -c hail/benchmark/python/../../hail/python/pinned-requirements.txt
     #   contourpy
@@ -28,7 +28,7 @@ packaging==23.2
     #   -c hail/benchmark/python/../../hail/python/dev/pinned-requirements.txt
     #   -c hail/benchmark/python/../../hail/python/pinned-requirements.txt
     #   matplotlib
-pillow==10.1.0
+pillow==10.2.0
     # via
     #   -c hail/benchmark/python/../../hail/python/dev/pinned-requirements.txt
     #   -c hail/benchmark/python/../../hail/python/pinned-requirements.txt

diff --git a/ci/pinned-requirements.txt b/ci/pinned-requirements.txt
@@ -26,7 +26,7 @@ click==8.1.7
     #   -c hail/ci/../hail/python/dev/pinned-requirements.txt
     #   -c hail/ci/../hail/python/pinned-requirements.txt
     #   zulip
-cryptography==41.0.7
+cryptography==42.0.2
     # via
     #   -c hail/ci/../hail/python/pinned-requirements.txt
     #   pyjwt
@@ -56,7 +56,7 @@ requests[security]==2.31.0
     #   -c hail/ci/../hail/python/dev/pinned-requirements.txt
     #   -c hail/ci/../hail/python/pinned-requirements.txt
     #   zulip
-typing-extensions==4.8.0
+typing-extensions==4.9.0
     # via
     #   -c hail/ci/../hail/python/dev/pinned-requirements.txt
     #   -c hail/ci/../hail/python/pinned-requirements.txt

diff --git a/gear/pinned-requirements.txt b/gear/pinned-requirements.txt
@@ -4,7 +4,7 @@
 #
 #    pip-compile --output-file=hail/gear/pinned-requirements.txt hail/gear/requirements.txt
 #
-aiohttp==3.9.1
+aiohttp==3.9.3
     # via
     #   -c hail/gear/../hail/python/dev/pinned-requirements.txt
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
@@ -27,7 +27,7 @@ async-timeout==4.0.3
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   aiohttp
-attrs==23.1.0
+attrs==23.2.0
     # via
     #   -c hail/gear/../hail/python/dev/pinned-requirements.txt
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
@@ -51,18 +51,18 @@ charset-normalizer==3.3.2
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   requests
-frozenlist==1.4.0
+frozenlist==1.4.1
     # 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
     #   aiosignal
-google-api-core==2.15.0
+google-api-core==2.16.1
     # via google-api-python-client
-google-api-python-client==2.111.0
+google-api-python-client==2.116.0
     # via google-cloud-profiler
-google-auth==2.23.4
+google-auth==2.27.0
     # via
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
@@ -98,7 +98,7 @@ multidict==6.0.4
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   aiohttp
     #   yarl
-orjson==3.9.10
+orjson==3.9.12
     # via
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
@@ -183,7 +183,7 @@ wrapt==1.16.0
     #   -c hail/gear/../hail/python/dev/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   prometheus-async
-yarl==1.9.3
+yarl==1.9.4
     # via
     #   -c hail/gear/../hail/python/dev/pinned-requirements.txt
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt