[R] Upgrade dependencies 2024-03-18 (#6064, #6072, PR #6078)

DataBiosphere · Mar 27, 2024 · f0576a3 · f0576a3
2 parents be78a54 + 696f620
commit f0576a3
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diff --git a/...common_protos-1.62.0-py2.py3-none-any.whl → ...common_protos-1.63.0-py2.py3-none-any.whl b/...common_protos-1.62.0-py2.py3-none-any.whl → ...common_protos-1.63.0-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/grpcio-1.62.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/bin/wheels/runtime/grpcio-1.62.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/bin/wheels/runtime/grpcio-1.62.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/bin/wheels/runtime/grpcio-1.62.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/...ime/grpcio_status-1.62.0-py3-none-any.whl → ...ime/grpcio_status-1.62.1-py3-none-any.whl b/...ime/grpcio_status-1.62.0-py3-none-any.whl → ...ime/grpcio_status-1.62.1-py3-none-any.whl
diff --git a/bin/wheels/runtime/packaging-23.2-py3-none-any.whl b/bin/wheels/runtime/packaging-23.2-py3-none-any.whl
diff --git a/bin/wheels/runtime/packaging-24.0-py3-none-any.whl b/bin/wheels/runtime/packaging-24.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/pyOpenSSL-24.0.0-py3-none-any.whl b/bin/wheels/runtime/pyOpenSSL-24.0.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/pyOpenSSL-24.1.0-py3-none-any.whl b/bin/wheels/runtime/pyOpenSSL-24.1.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/pyasn1-0.5.1-py2.py3-none-any.whl b/bin/wheels/runtime/pyasn1-0.5.1-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/pyasn1-0.6.0-py2.py3-none-any.whl b/bin/wheels/runtime/pyasn1-0.6.0-py2.py3-none-any.whl
diff --git a/...pyasn1_modules-0.3.0-py2.py3-none-any.whl → ...ime/pyasn1_modules-0.4.0-py3-none-any.whl b/...pyasn1_modules-0.3.0-py2.py3-none-any.whl → ...ime/pyasn1_modules-0.4.0-py3-none-any.whl
diff --git a/environment.boot b/environment.boot
@@ -1,4 +1,4 @@
 azul_python_version=3.11.8
 azul_python_image=docker.io/library/python:3.11.8-bullseye
-azul_docker_version=24.0.9
+azul_docker_version=25.0.5
 azul_terraform_version=1.6.6
diff --git a/environment.py b/environment.py
@@ -227,7 +227,7 @@ def env() -> Mapping[str, Optional[str]]:
         # and pushing the executor image (see terraform/gitlab/runner/Dockerfile
         # for how).
         #
-        'azul_docker_version': '24.0.9',
+        'azul_docker_version': '25.0.5',
 
         # The version of Python used throughout the system.
         #
@@ -273,10 +273,10 @@ def env() -> Mapping[str, Optional[str]]:
                 'ref': 'docker.io/library/python:{azul_python_version}-bullseye'
             },
             'pycharm': {
-                'ref': 'docker.io/ucscgi/azul-pycharm:2023.3.4-15'
+                'ref': 'docker.io/ucscgi/azul-pycharm:2023.3.5-17'
             },
             'elasticsearch': {
-                'ref': 'docker.io/ucscgi/azul-elasticsearch:7.17.18-13'
+                'ref': 'docker.io/ucscgi/azul-elasticsearch:7.17.18-14'
             },
             'bigquery_emulator': {
                 'ref': 'ghcr.io/hannes-ucsc/bigquery-emulator:azul'
@@ -289,10 +289,10 @@ def env() -> Mapping[str, Optional[str]]:
                 'ref': 'docker.io/clamav/clamav:1.2.1-27'
             },
             'gitlab': {
-                'ref': 'docker.io/gitlab/gitlab-ce:16.9.1-ce.0'
+                'ref': 'docker.io/gitlab/gitlab-ce:16.10.0-ce.0'
             },
             'gitlab_runner': {
-                'ref': 'docker.io/gitlab/gitlab-runner:ubuntu-v16.9.1'
+                'ref': 'docker.io/gitlab/gitlab-runner:ubuntu-v16.10.0'
             },
             'dind': {
                 'ref': 'docker.io/library/docker:{azul_docker_version}-dind'

diff --git a/image_manifests.json b/image_manifests.json
@@ -1,60 +1,60 @@
 {
-    "docker.io/library/docker:24.0.9": {
-        "digest": "sha256:bfca615a14787f7cc15c962b644745888a949efeae0460e2da29db20be4884bf",
+    "docker.io/library/docker:25.0.5": {
+        "digest": "sha256:b1ac36e3c085b33768515badcfbc3cd2b7469bd2f5973a744dd27ea7d9167fa5",
         "manifests": {
             "linux/amd64": {
-                "digest": "sha256:53ca3e4d3f8f15b32989cf657b41f2ce8d8531b3b894ac10ad65788459409420",
-                "id": "sha256:365b8ddc1c23c15cc09f30bc3ae8bd78fbfa816346f33faf5483397780737303",
+                "digest": "sha256:903a787733992d0c8a48a689f80e7ca944e702a717d55d1ebb19515c4f41b9f5",
+                "id": "sha256:7eae861439b92d694a60f38a548238e692e0c86984b63ba66897c11bdd319f5a",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:d6737d3da09e6b38bb68f6f17995372440b20dfecc7428df5cee599f140492bc",
-                "id": "sha256:753424ef4156d4f336bab004c19f01ad2e3be5596192b92c9a718a3bc0a8c65d",
+                "digest": "sha256:85df2ff7363ca81370b6bae99ff323ed917a8d990de22a330fc062a13b46f3d8",
+                "id": "sha256:556bec2898f5aa2a7f075e816ea95c4849a63316f582ca045726080ad4d01245",
                 "platform": "linux/arm64"
             }
         }
     },
     "docker.io/library/python:3.11.8-bullseye": {
-        "digest": "sha256:a2263067985a930a9479d6ae0835d3402d9ad7862f5fcac81ee4b221b77f2245",
+        "digest": "sha256:5bd29274bdd04975459c397f3817956f0e013cdccaea419070a03d2a11dc899f",
         "manifests": {
             "linux/amd64": {
-                "digest": "sha256:3fae413a110d4146b6ce8edd847c99169972edfa50c0177713586a75919f3cd4",
-                "id": "sha256:a6892da4cf9a3064d88802450fd96bc53cf5bc812df043156f5497fd2ca9d297",
+                "digest": "sha256:1e78b46bd49050a8176ef2ee3897be71ee3e9d2610883de98ad955076b8365cc",
+                "id": "sha256:bb7e04c2081ba98bfe4a8bc0ff39037426e3770e7b3864b8d0dcbac2a7bb0a9a",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:65c5428b66c2dca1ab1c35ae6c982281eab58ce63ee2807690221ec838572f25",
-                "id": "sha256:dc8302f92a480c3ce102bb8a24f5b1f7db13de1a773363d4c80b6993b9911df7",
+                "digest": "sha256:9b33daa086f51c7806662105836f0dcb8eb8d5dc6d1e36af25d9e3e5cfc5b0bf",
+                "id": "sha256:57e81b68a880cb3755a8afbf1920d7ca5565470d9ec12460c774319d8ad7a8e1",
                 "platform": "linux/arm64"
             }
         }
     },
-    "docker.io/ucscgi/azul-pycharm:2023.3.4-15": {
-        "digest": "sha256:50c9923d2a2c1fedc560f6b33834786780d5664533e539810546718f9e8e3220",
+    "docker.io/ucscgi/azul-pycharm:2023.3.5-17": {
+        "digest": "sha256:607e6f80549a2a1ea0ac5cf540df20facf1d48a431aab3075dd9a36689b433f9",
         "manifests": {
             "linux/amd64": {
-                "digest": "sha256:910633642a8d244213c1be37810ecd6c88ac805ff50a5e2ab3c4e20652f50c32",
-                "id": "sha256:abba54e163416026fb894d8154e1dd0eb6893e27fdf5e41b786b8c1179e0c8ee",
+                "digest": "sha256:78b1fd44ca91bdffb5a65c46e02f5b7095004438494660771fff09c9ca8e19e5",
+                "id": "sha256:9d123f753cf4e61c3fecd67e3ff06b0a89f2c9a0267e00b3ef0c794f4dd5b12d",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:908c28e4e270336cf9b87182f9e444d9ada5b920c7765d8b0ae4cf6fdcbbcdea",
-                "id": "sha256:e1b79f2eb1882f99c1517c1e991e9aa6cfb3400d316697cda557680376e8adc7",
+                "digest": "sha256:e14fd221ed242ef3f34326f23cfa1cd0de1fbfdfcdaf9ae5bcc161825f057081",
+                "id": "sha256:03062b8401247e591170b44d3a1cd6d0094be795781ebc24e3357291d069365d",
                 "platform": "linux/arm64"
             }
         }
     },
-    "docker.io/ucscgi/azul-elasticsearch:7.17.18-13": {
-        "digest": "sha256:e70754d35aa2410cefbea5e5e4970c36772f1cb936c171b2625ec2715e32c30f",
+    "docker.io/ucscgi/azul-elasticsearch:7.17.18-14": {
+        "digest": "sha256:e0646ade3ad24d3f258e569afd443e0fc945a09b1d9a0150099567850a7523da",
         "manifests": {
             "linux/amd64": {
-                "digest": "sha256:8249a2f2de38ddfc668eff6f064a51c306381b4ed1e8e335a3a8bb1467bfae91",
-                "id": "sha256:4f818dbc8a286c11baa3291b955d9aa6fc9c9d583345d669b2530c49f7f787c5",
+                "digest": "sha256:dfdf97fb1a62475db35015446b26b8e153ccde05358f4232fee2cc0dd8804d15",
+                "id": "sha256:1a164b325452274fad1399ccb49d5463c810235a58cfaea867d97cbadd816929",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:cd88714ef95935983b8b1198ac2b593fe89bf97ae2420c8e4ada6e9d8eaa814b",
-                "id": "sha256:043ddf0a10eae880c92d822dbd244e2cd03407ed42257e3d693b40fb9f2709fa",
+                "digest": "sha256:3fbb7dd1bb79c6c70216599d420802e948a4d14a2ff1ecf9a633222c68162600",
+                "id": "sha256:8234e8b1de04e793e9e58508ab90af04481465e8ce58e8938910c6e50d1e94e6",
                 "platform": "linux/arm64"
             }
         }
@@ -69,37 +69,37 @@
         "id": "sha256:b56c8c4aa940277a4dc17599b610ce55ab09d3d882fee0e3bb6ecabd2748a5ee",
         "platform": "linux/amd64"
     },
-    "docker.io/gitlab/gitlab-ce:16.9.1-ce.0": {
-        "digest": "sha256:78b2cd7392c957d8c7631b1fbf911aaaa4327add3c1aa43cab595f5a8a66bf2e",
-        "id": "sha256:e9cb66792d94678011684a5f092c83d89a088f095b45d9a82024a5e063d5a29f",
+    "docker.io/gitlab/gitlab-ce:16.10.0-ce.0": {
+        "digest": "sha256:bf67edce97f03c5584d5ad3f1681c2817b9f80b3da4b1a930a3c4aecb3c4a950",
+        "id": "sha256:68bac8106068b2a341af2db21c93710999259d9339703d0123daaac9755449c1",
         "platform": "linux/amd64"
     },
-    "docker.io/gitlab/gitlab-runner:ubuntu-v16.9.1": {
-        "digest": "sha256:938a20776072c5ca0d42ebb5e437f27b7dcbd000fa0290e572d6194e35ad40d9",
+    "docker.io/gitlab/gitlab-runner:ubuntu-v16.10.0": {
+        "digest": "sha256:38a8c56774c909978aa38bf5f3d4312bbd7f723fb9a21f428138cee28adedea1",
         "manifests": {
             "linux/amd64": {
-                "digest": "sha256:53252861ec0f11f07185224f788e55ba961608e4f37bac5b7b3ea1f8d2acab66",
-                "id": "sha256:5364b8e4b4ea3a0c9954c813131efe07aaa479c2b34e8d45b31398cdb39d6190",
+                "digest": "sha256:55bca1632350b23863c1a735ddffb0997c5c8490ec87d4ed639a6f340dc27f77",
+                "id": "sha256:992232bc99f20799db607998e0c8b8fe0ada107fc591799912bc26cb10c9d618",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:ca098e49b45954948839ec2f65e33e7e013c71463f47bfa47395f33f3bb27022",
-                "id": "sha256:b9aa63fdd2b101b6aeedb0ab77a895dc6abd7702b9be10714eb9fcc868b12c4a",
+                "digest": "sha256:87773d8e4869f4207cf084d06993ea645d57fa674130012ed23104bed464941c",
+                "id": "sha256:c772a6c1fdeb8cdfce1c24639734b21722dc38f466888c223583b7bc9f5d1de5",
                 "platform": "linux/arm64"
             }
         }
     },
-    "docker.io/library/docker:24.0.9-dind": {
-        "digest": "sha256:bfca615a14787f7cc15c962b644745888a949efeae0460e2da29db20be4884bf",
+    "docker.io/library/docker:25.0.5-dind": {
+        "digest": "sha256:b1ac36e3c085b33768515badcfbc3cd2b7469bd2f5973a744dd27ea7d9167fa5",
         "manifests": {
             "linux/amd64": {
-                "digest": "sha256:53ca3e4d3f8f15b32989cf657b41f2ce8d8531b3b894ac10ad65788459409420",
-                "id": "sha256:365b8ddc1c23c15cc09f30bc3ae8bd78fbfa816346f33faf5483397780737303",
+                "digest": "sha256:903a787733992d0c8a48a689f80e7ca944e702a717d55d1ebb19515c4f41b9f5",
+                "id": "sha256:7eae861439b92d694a60f38a548238e692e0c86984b63ba66897c11bdd319f5a",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:d6737d3da09e6b38bb68f6f17995372440b20dfecc7428df5cee599f140492bc",
-                "id": "sha256:753424ef4156d4f336bab004c19f01ad2e3be5596192b92c9a718a3bc0a8c65d",
+                "digest": "sha256:85df2ff7363ca81370b6bae99ff323ed917a8d990de22a330fc062a13b46f3d8",
+                "id": "sha256:556bec2898f5aa2a7f075e816ea95c4849a63316f582ca045726080ad4d01245",
                 "platform": "linux/arm64"
             }
         }

diff --git a/requirements.all.txt b/requirements.all.txt
@@ -10,7 +10,7 @@ blinker==1.7.0
 boto3==1.28.63
 boto3-stubs==1.28.63
 botocore==1.31.63
-botocore-stubs==1.34.58
+botocore-stubs==1.34.69
 brotli==1.1.0
 cachetools==5.3.3
 certifi==2024.2.2
@@ -36,7 +36,7 @@ flask-basicauth==0.2.0
 flask-cors==4.0.0
 furl==2.1.3
 gevent==23.9.1
-geventhttpclient==2.0.11
+geventhttpclient==2.0.12
 gitdb==4.0.11
 gitpython==3.1.41
 google-api-core==2.12.0
@@ -49,10 +49,10 @@ google-cloud-core==2.4.1
 google-cloud-storage==2.12.0
 google-crc32c==1.5.0
 google-resumable-media==2.7.0
-googleapis-common-protos==1.62.0
+googleapis-common-protos==1.63.0
 greenlet==3.0.3
-grpcio==1.62.0
-grpcio-status==1.62.0
+grpcio==1.62.1
+grpcio-status==1.62.1
 http-message-signatures==0.4.4
 http_sfv==0.9.9
 httplib2==0.22.0
@@ -86,23 +86,23 @@ openapi-schema-validator==0.3.4
 openapi-spec-validator==0.5.1
 openpyxl==3.0.6
 orderedmultidict==1.0.1
-packaging==23.2
+packaging==24.0
 pathable==0.4.3
 pip==23.3.2
 posix-ipc==1.1.1
 proto-plus==1.23.0
 protobuf==4.25.3
 psutil==5.9.8
 py-partiql-parser==0.3.3
-pyasn1==0.5.1
-pyasn1-modules==0.3.0
+pyasn1==0.6.0
+pyasn1_modules==0.4.0
 pycodestyle==2.9.1
 pycparser==2.21
 pyflakes==2.5.0
 pygithub==1.56
 pyjwt==2.8.0
 pynacl==1.5.0
-pyopenssl==24.0.0
+pyopenssl==24.1.0
 pyparsing==3.1.2
 pyrsistent==0.20.0
 python-dateutil==2.9.0.post0
@@ -112,7 +112,7 @@ python-gitlab==3.13.0
 pytz==2024.1
 pyyaml==6.0.1
 pyzmq==25.1.2
-readchar==4.0.5
+readchar==4.0.6
 requests==2.31.0
 requests-toolbelt==1.0.0
 requirements-parser==0.2.0+1
@@ -129,7 +129,7 @@ toml==0.10.2
 tqdm==4.66.2
 types-awscrt==0.20.5
 types-s3transfer==0.10.0
-types-toml==0.10.8.7
+types-toml==0.10.8.20240310
 typing_extensions==4.10.0
 tzlocal==2.1
 uritemplate==4.1.1

diff --git a/requirements.dev.trans.txt b/requirements.dev.trans.txt
@@ -1,6 +1,6 @@
 blessed==1.20.0
 blinker==1.7.0
-botocore-stubs==1.34.58
+botocore-stubs==1.34.69
 brotli==1.1.0
 click==8.1.7
 colorama==0.4.4
@@ -10,7 +10,7 @@ et-xmlfile==1.1.0
 flask==3.0.2
 flask-basicauth==0.2.0
 flask-cors==4.0.0
-geventhttpclient==2.0.11
+geventhttpclient==2.0.12
 gitdb==4.0.11
 google-auth-httplib2==0.2.0
 greenlet==3.0.3
@@ -45,15 +45,15 @@ pyparsing==3.1.2
 pyrsistent==0.20.0
 python-editor==1.0.4
 pyzmq==25.1.2
-readchar==4.0.5
+readchar==4.0.6
 requests-toolbelt==1.0.0
 roundrobin==0.0.4
 smmap==5.0.1
 toml==0.10.2
 tqdm==4.66.2
 types-awscrt==0.20.5
 types-s3transfer==0.10.0
-types-toml==0.10.8.7
+types-toml==0.10.8.20240310
 uritemplate==4.1.1
 wcwidth==0.2.13
 websocket-client==1.7.0

diff --git a/requirements.trans.txt b/requirements.trans.txt
@@ -8,20 +8,20 @@ cryptography==42.0.5
 google-cloud-core==2.4.1
 google-crc32c==1.5.0
 google-resumable-media==2.7.0
-googleapis-common-protos==1.62.0
-grpcio==1.62.0
-grpcio-status==1.62.0
+googleapis-common-protos==1.63.0
+grpcio==1.62.1
+grpcio-status==1.62.1
 http_sfv==0.9.9
 idna==3.6
 markupsafe==2.1.5
 orderedmultidict==1.0.1
-packaging==23.2
+packaging==24.0
 proto-plus==1.23.0
 protobuf==4.25.3
-pyasn1==0.5.1
-pyasn1-modules==0.3.0
+pyasn1==0.6.0
+pyasn1_modules==0.4.0
 pycparser==2.21
-pyopenssl==24.0.0
+pyopenssl==24.1.0
 python-dateutil==2.9.0.post0
 pytz==2024.1
 s3transfer==0.7.0