[all] Update python dependencies. (#14915)

This resolves new dependabot issues.

The only two explicit updates are:
- requests>=2.32.4
- azure-identity>=1.23.0

In addition, updating generate-pip-lockfiles.sh allows us to update
certain transitive dependencies, notably:
- tornado, now pinned to 6.5.1
- cryptography, now pinned to 45.0.4

## Security Assessment
- This change potentially impacts the Hail Batch instance as deployed by
Broad Institute in GCP

### Impact Rating
- This change has a low security impact

### Impact Description
Resolve dependabot alerts to newer and more secure versions.

### Appsec Review
- [x] Required: The impact has been assessed and approved by appsec

Author: chrisvittal

batch/pinned-requirements.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --python-version 3.9 --python-platform linux batch/requirements.txt --output-file=batch/pinned-requirements.txt
+#    uv pip compile --python-version 3.9.22 --python-platform linux batch/requirements.txt --output-file=batch/pinned-requirements.txt
 aiodocker==0.24.0
     # via -r batch/requirements.txt
 aiohappyeyeballs==2.6.1
@@ -9,7 +9,7 @@ aiohappyeyeballs==2.6.1
     #   -c batch/../hail/python/pinned-requirements.txt
     #   -c batch/../web_common/pinned-requirements.txt
     #   aiohttp
-aiohttp==3.11.18
+aiohttp==3.12.12
     # via
     #   -c batch/../gear/pinned-requirements.txt
     #   -c batch/../hail/python/dev/pinned-requirements.txt
@@ -42,7 +42,7 @@ attrs==25.3.0
     #   aiohttp
 dictdiffer==0.9.0
     # via -r batch/requirements.txt
-frozenlist==1.6.0
+frozenlist==1.7.0
     # via
     #   -c batch/../gear/pinned-requirements.txt
     #   -c batch/../hail/python/dev/pinned-requirements.txt
@@ -57,7 +57,7 @@ idna==3.10
     #   -c batch/../hail/python/pinned-requirements.txt
     #   -c batch/../web_common/pinned-requirements.txt
     #   yarl
-multidict==6.4.3
+multidict==6.4.4
     # via
     #   -c batch/../gear/pinned-requirements.txt
     #   -c batch/../hail/python/dev/pinned-requirements.txt
@@ -75,15 +75,15 @@ packaging==25.0
     #   -c batch/../hail/python/dev/pinned-requirements.txt
     #   -c batch/../hail/python/pinned-requirements.txt
     #   plotly
-pandas==2.2.3
+pandas==2.3.0
     # via
     #   -c batch/../hail/python/pinned-requirements.txt
     #   -r batch/requirements.txt
 plotly==5.24.1
     # via
     #   -c batch/../hail/python/pinned-requirements.txt
     #   -r batch/requirements.txt
-propcache==0.3.1
+propcache==0.3.2
     # via
     #   -c batch/../gear/pinned-requirements.txt
     #   -c batch/../hail/python/dev/pinned-requirements.txt
@@ -111,7 +111,7 @@ tenacity==9.1.2
     # via
     #   -c batch/../hail/python/pinned-requirements.txt
     #   plotly
-typing-extensions==4.13.2
+typing-extensions==4.14.0
     # via
     #   -c batch/../gear/pinned-requirements.txt
     #   -c batch/../hail/python/dev/pinned-requirements.txt
@@ -122,7 +122,7 @@ tzdata==2025.2
     # via
     #   -c batch/../hail/python/pinned-requirements.txt
     #   pandas
-yarl==1.20.0
+yarl==1.20.1
     # via
     #   -c batch/../gear/pinned-requirements.txt
     #   -c batch/../hail/python/dev/pinned-requirements.txt

ci/pinned-requirements.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --python-version 3.9 --python-platform linux ci/requirements.txt --output-file=ci/pinned-requirements.txt
+#    uv pip compile --python-version 3.9.22 --python-platform linux ci/requirements.txt --output-file=ci/pinned-requirements.txt
 certifi==2025.4.26
     # via
     #   -c ci/../gear/pinned-requirements.txt
@@ -22,13 +22,13 @@ click==8.1.8
     #   -c ci/../hail/python/dev/pinned-requirements.txt
     #   -c ci/../hail/python/pinned-requirements.txt
     #   zulip
-cryptography==43.0.3
+cryptography==45.0.4
     # via
     #   -c ci/../hail/python/pinned-requirements.txt
     #   pyjwt
 distro==1.9.0
     # via zulip
-gidgethub==5.3.0
+gidgethub==5.4.0
     # via -r ci/requirements.txt
 idna==3.10
     # via
@@ -46,20 +46,20 @@ pyjwt==2.10.1
     # via
     #   -c ci/../hail/python/pinned-requirements.txt
     #   gidgethub
-requests==2.32.3
+requests==2.32.4
     # via
     #   -c ci/../gear/pinned-requirements.txt
     #   -c ci/../hail/python/dev/pinned-requirements.txt
     #   -c ci/../hail/python/pinned-requirements.txt
     #   zulip
-typing-extensions==4.13.2
+typing-extensions==4.14.0
     # via
     #   -c ci/../gear/pinned-requirements.txt
     #   -c ci/../hail/python/dev/pinned-requirements.txt
     #   -c ci/../hail/python/pinned-requirements.txt
     #   -c ci/../web_common/pinned-requirements.txt
     #   zulip
-uritemplate==4.1.1
+uritemplate==4.2.0
     # via
     #   -c ci/../gear/pinned-requirements.txt
     #   gidgethub

gear/pinned-requirements.txt

@@ -1,12 +1,12 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --python-version 3.9 --python-platform linux gear/requirements.txt --output-file=gear/pinned-requirements.txt
+#    uv pip compile --python-version 3.9.22 --python-platform linux gear/requirements.txt --output-file=gear/pinned-requirements.txt
 aiohappyeyeballs==2.6.1
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   aiohttp
-aiohttp==3.11.18
+aiohttp==3.12.12
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
@@ -53,18 +53,18 @@ charset-normalizer==3.4.2
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   requests
-frozenlist==1.6.0
+frozenlist==1.7.0
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   aiohttp
     #   aiosignal
-google-api-core==2.24.2
+google-api-core==2.25.0
     # via google-api-python-client
-google-api-python-client==2.169.0
+google-api-python-client==2.172.0
     # via google-cloud-profiler
-google-auth==2.40.1
+google-auth==2.40.3
     # via
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
@@ -93,7 +93,7 @@ idna==3.10
     #   yarl
 kubernetes-asyncio==19.15.1
     # via -r gear/requirements.txt
-multidict==6.4.3
+multidict==6.4.4
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
@@ -102,12 +102,12 @@ multidict==6.4.3
     #   yarl
 prometheus-async==19.2.0
     # via -r gear/requirements.txt
-prometheus-client==0.21.1
+prometheus-client==0.22.1
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -r gear/requirements.txt
     #   prometheus-async
-propcache==0.3.1
+propcache==0.3.2
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
@@ -154,7 +154,7 @@ pyyaml==6.0.2
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   kubernetes-asyncio
-requests==2.32.3
+requests==2.32.4
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
@@ -166,7 +166,7 @@ rsa==4.9.1
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   google-auth
-setuptools==80.4.0
+setuptools==80.9.0
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   kubernetes-asyncio
@@ -182,13 +182,13 @@ sortedcontainers==2.4.0
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   -r gear/requirements.txt
-typing-extensions==4.13.2
+typing-extensions==4.14.0
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   multidict
-uritemplate==4.1.1
+uritemplate==4.2.0
     # via google-api-python-client
 urllib3==1.26.20
     # via
@@ -201,7 +201,7 @@ wrapt==1.17.2
     # via
     #   -c gear/../hail/python/pinned-requirements.txt
     #   prometheus-async
-yarl==1.20.0
+yarl==1.20.1
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt

generate-pip-lockfile.sh

@@ -7,6 +7,6 @@ set -ex
 
 package=$1
 uv pip compile \
-    --python-version 3.9 \
+    --python-version 3.9.22 \
     --python-platform linux \
     --upgrade $package/requirements.txt --output-file=$package/pinned-requirements.txt