[R] Upgrade dependencies 2025-02-03 (#6874, PR #6892)

DataBiosphere · Feb 13, 2025 · d04474e · d04474e
2 parents 40c3bcb + a71087e
commit d04474e
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diff --git a/OPERATOR.rst b/OPERATOR.rst
@@ -302,9 +302,13 @@ separately.
 
 There are ways to dynamically determine the latest AMI released by CIS under the
 subscription but in the spirit of reproducible builds, we would rather pin the
-AMI ID and adopt updates at our own discretion to avoid unexpected failures. To
-obtain the latest compatible AMI ID, select the desired ``….gitlab`` component,
-say, ``_select dev.gitlab`` and run
+AMI ID and adopt updates at our own discretion to avoid unexpected failures.
+
+Note that the AMI versioning scheme (e.g., ``v01``, ``v11``) indicates the month
+of release, and is not a monotonically increasing value.
+
+To obtain the latest compatible AMI ID, select the desired ``….gitlab``
+component, say, ``_select dev.gitlab`` and run
 
 ::
 

diff --git a/...me/Deprecated-1.2.15-py2.py3-none-any.whl → ...me/Deprecated-1.2.18-py2.py3-none-any.whl b/...me/Deprecated-1.2.15-py2.py3-none-any.whl → ...me/Deprecated-1.2.18-py2.py3-none-any.whl
diff --git a/...els/runtime/attrs-24.3.0-py3-none-any.whl → ...els/runtime/attrs-25.1.0-py3-none-any.whl b/...els/runtime/attrs-24.3.0-py3-none-any.whl → ...els/runtime/attrs-25.1.0-py3-none-any.whl
diff --git a/...els/runtime/boto3-1.36.5-py3-none-any.whl → ...ls/runtime/boto3-1.36.14-py3-none-any.whl b/...els/runtime/boto3-1.36.5-py3-none-any.whl → ...ls/runtime/boto3-1.36.14-py3-none-any.whl
diff --git a/.../runtime/botocore-1.36.5-py3-none-any.whl → ...runtime/botocore-1.36.14-py3-none-any.whl b/.../runtime/botocore-1.36.5-py3-none-any.whl → ...runtime/botocore-1.36.14-py3-none-any.whl
diff --git a/...eels/runtime/cryptography-44.0.0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/...eels/runtime/cryptography-44.0.0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/...eels/runtime/cryptography-44.0.1-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/...eels/runtime/cryptography-44.0.1-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/...e/google_api_core-2.24.0-py3-none-any.whl → ...e/google_api_core-2.24.1-py3-none-any.whl b/...e/google_api_core-2.24.0-py3-none-any.whl → ...e/google_api_core-2.24.1-py3-none-any.whl
diff --git a/bin/wheels/runtime/googleapis_common_protos-1.66.0-py2.py3-none-any.whl b/bin/wheels/runtime/googleapis_common_protos-1.66.0-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/googleapis_common_protos-1.67.0-py2.py3-none-any.whl b/bin/wheels/runtime/googleapis_common_protos-1.67.0-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/tzlocal-5.2-py3-none-any.whl b/bin/wheels/runtime/tzlocal-5.2-py3-none-any.whl
diff --git a/bin/wheels/runtime/tzlocal-5.3-py3-none-any.whl b/bin/wheels/runtime/tzlocal-5.3-py3-none-any.whl
diff --git a/docker_images.json b/docker_images.json
@@ -1,87 +1,87 @@
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+        "digest": "sha256:ba55987d5a560d321a148e9e33b9d465b9badf0400c5e3fa06b38c0048062294",
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                 "platform": "linux/arm64"
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                 "platform": "linux/arm64"
             }
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-    "docker.io/ucscgi/azul-bigquery-emulator:0.4.4-22": {
-        "digest": "sha256:73136ff0770d78a319ea0ffccac33bca59febba3e37dd887fde0ccc4155fb740",
-        "id": "sha256:5cc13d4dc2a08872dbdb8beb19d28b13cbd2b8d233326e6760465fcee760a94f",
+    "docker.io/ucscgi/azul-bigquery-emulator:0.4.4-23": {
+        "digest": "sha256:7cc2a338d78f06e5ac397faa2e7f7524c375d8e63ca7ea6f6f863c8be4088a43",
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         "platform": "linux/amd64"
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-    "docker.io/clamav/clamav:1.4.2-23": {
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-        "mirror_digest": "sha256:fc06903f721674437eb0cc61e38535c37f2825daddb82126a689c7fbef7401fa",
+    "docker.io/clamav/clamav:1.4.2-25": {
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                 "platform": "linux/amd64"
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-    "docker.io/gitlab/gitlab-ce:17.8.1-ce.0": {
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-        "id": "sha256:3f90d34496bc70ec361f1c784125fa114c3eafc0d3e933d8485d0f43c59a9984",
+    "docker.io/gitlab/gitlab-ce:17.8.2-ce.0": {
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         "platform": "linux/amd64"
     },
     "docker.io/gitlab/gitlab-runner:ubuntu-v17.8.3": {
@@ -101,17 +101,17 @@
         }
     },
     "docker.io/library/docker:27.5.1-dind": {
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-        "mirror_digest": "sha256:501efe65bf84c7f49bece11906638c033361e027d87ea8f14014e976dccd2db6",
+        "digest": "sha256:ba55987d5a560d321a148e9e33b9d465b9badf0400c5e3fa06b38c0048062294",
+        "mirror_digest": "sha256:ce4c9b281dd8d2f7c021edc2312490ac85e2c60458ace1fb381641c192497dda",
         "parts": {
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-                "id": "sha256:49fc2acb217f861e371ee204f2aa3cebfbc95d8fc16368fecc17d0f23504a6cd",
+                "digest": "sha256:ca45170b1042819f5e8d4b621bc6a07bb4316ecf224ae84f42bb26c2073e9b84",
+                "id": "sha256:7a9eec921ea39b46e656790825d7044ac6e9b19f4cd7ad6283df2100c00ca695",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:2829f189d5a6aac3b136e4d3a8dfa34ae79253a93212d69c60c5736da2e7c328",
-                "id": "sha256:6dc60435e40e3d1cf5fb9331daf6986eec111350622161f68f8053f1b4980013",
+                "digest": "sha256:ad1ba35907f26bf56daa85924daeaf50eade0014bb8b7a6ce997efa04723f6c9",
+                "id": "sha256:de2de1cbb81f5dee9eb76552bb9224c9325b41ac158e786315a46d4b1119b090",
                 "platform": "linux/arm64"
             }
         }

diff --git a/environment.boot b/environment.boot
@@ -1,4 +1,4 @@
 azul_python_version=3.12.8
-azul_python_image=docker.io/library/python@sha256:2666f95b070d02be2689a2ec66adbac8b2df7d3e6f2b5f8205bd1a6d1c113c44
+azul_python_image=docker.io/library/python@sha256:556871eba0de3018f8cd267ee10f4ebf2fdf09cbbc7102eaf474296ecfe906ae
 azul_docker_version=27.5.1
 azul_terraform_version=1.10.5
diff --git a/environment.py b/environment.py
@@ -296,28 +296,28 @@ def env() -> Mapping[str, Optional[str]]:
                 'url': 'https://hub.docker.com/_/python',
             },
             'pycharm': {
-                'ref': 'docker.io/ucscgi/azul-pycharm:2024.3.1.1-43',
+                'ref': 'docker.io/ucscgi/azul-pycharm:2024.3.2-44',
                 'url': 'https://hub.docker.com/repository/docker/ucscgi/azul-pycharm',
                 'is_custom': True
             },
             'elasticsearch': {
-                'ref': 'docker.io/ucscgi/azul-elasticsearch:7.17.27-36',
+                'ref': 'docker.io/ucscgi/azul-elasticsearch:7.17.27-37',
                 'url': 'https://hub.docker.com/repository/docker/ucscgi/azul-elasticsearch',
                 'is_custom': True
             },
             'bigquery_emulator': {
-                'ref': 'docker.io/ucscgi/azul-bigquery-emulator:0.4.4-22',
+                'ref': 'docker.io/ucscgi/azul-bigquery-emulator:0.4.4-23',
                 'url': 'https://hub.docker.com/repository/docker/ucscgi/azul-bigquery-emulator',
                 'is_custom': True
             },
             # Updating any of the four images below additionally requires
             # redeploying the `gitlab` TF component.
             'clamav': {
-                'ref': 'docker.io/clamav/clamav:1.4.2-23',
+                'ref': 'docker.io/clamav/clamav:1.4.2-25',
                 'url': 'https://hub.docker.com/r/clamav/clamav'
             },
             'gitlab': {
-                'ref': 'docker.io/gitlab/gitlab-ce:17.8.1-ce.0',
+                'ref': 'docker.io/gitlab/gitlab-ce:17.8.2-ce.0',
                 'url': 'https://hub.docker.com/r/gitlab/gitlab-ce'
             },
             'gitlab_runner': {

diff --git a/requirements.all.txt b/requirements.all.txt
@@ -1,16 +1,16 @@
 atomicwrites==1.4.1
-attrs==24.3.0
+attrs==25.1.0
 aws-requests-auth==0.4.3
-awscli==1.37.5
+awscli==1.37.14
 bagit==1.8.1
 bagit-profile==1.3.1
 bdbag==1.7.3
 blessed==1.20.0
 blinker==1.9.0
-boto3==1.36.5
-boto3-stubs-lite==1.36.5
-botocore==1.36.5
-botocore-stubs==1.36.15
+boto3==1.36.14
+boto3-stubs-lite==1.36.14
+botocore==1.36.14
+botocore-stubs==1.36.18
 brotli==1.1.0
 cachetools==5.5.1
 certifi==2025.1.31
@@ -22,8 +22,8 @@ click==8.1.8
 colorama==0.4.6
 configargparse==1.7
 coverage==7.6.10
-cryptography==44.0.0
-deprecated==1.2.15
+cryptography==44.0.1
+deprecated==1.2.18
 docker==7.1.0
 docutils==0.16
 editor==1.6.6
@@ -40,17 +40,17 @@ gevent==24.11.1
 geventhttpclient==2.3.3
 gitdb==4.0.12
 gitpython==3.1.44
-google-api-core==2.24.0
-google-api-python-client==2.159.0
+google-api-core==2.24.1
+google-api-python-client==2.160.0
 google-auth==2.38.0
 google-auth-httplib2==0.2.0
 google-cloud-bigquery==3.13.0
 google-cloud-bigquery-reservation==1.15.0
 google-cloud-core==2.4.1
-google-cloud-storage==2.19.0
+google-cloud-storage==3.0.0
 google-crc32c==1.6.0
 google-resumable-media==2.7.2
-googleapis-common-protos==1.66.0
+googleapis-common-protos==1.67.0
 greenlet==3.1.1
 grpcio==1.70.0
 grpcio-status==1.62.3
@@ -67,18 +67,18 @@ jsonschema==4.23.0
 jsonschema-path==0.3.4
 jsonschema-specifications==2024.10.1
 lazy-object-proxy==1.10.0
-locust==2.32.6
+locust==2.32.8
 markupsafe==3.0.2
 mccabe==0.7.0
 more-itertools==10.6.0
-moto==5.0.27
+moto==5.0.28
 msgpack==1.1.0
-mypy==1.14.1
+mypy==1.15.0
 mypy-boto3-apigateway==1.36.0
 mypy-boto3-cloudwatch==1.36.0
 mypy-boto3-dynamodb==1.36.0
-mypy-boto3-ec2==1.36.8
-mypy-boto3-ecr==1.36.10
+mypy-boto3-ec2==1.36.18
+mypy-boto3-ecr==1.36.16
 mypy-boto3-es==1.36.0
 mypy-boto3-iam==1.36.13
 mypy-boto3-kms==1.36.0
@@ -116,7 +116,7 @@ pyopenssl==25.0.0
 pyparsing==3.2.1
 python-dateutil==2.9.0.post0
 python-dxf==12.1.0
-python-gitlab==5.3.1
+python-gitlab==5.6.0
 pytz==2025.1
 pyyaml==6.0.2
 pyzmq==26.2.1
@@ -137,12 +137,12 @@ six==1.17.0
 smmap==5.0.2
 strict-rfc3339==0.7
 tqdm==4.67.1
-types-awscrt==0.23.9
+types-awscrt==0.23.10
 types-chevron==0.14.2
 types-s3transfer==0.11.2
 types-urllib3==1.26.20
 typing_extensions==4.12.2
-tzlocal==5.2
+tzlocal==5.3
 uritemplate==4.1.1
 urllib3==1.26.20
 watchdog==6.0.0

diff --git a/requirements.dev.trans.txt b/requirements.dev.trans.txt
@@ -1,6 +1,6 @@
 blessed==1.20.0
 blinker==1.9.0
-botocore-stubs==1.36.15
+botocore-stubs==1.36.18
 brotli==1.1.0
 click==8.1.8
 colorama==0.4.6
@@ -27,8 +27,8 @@ mccabe==0.7.0
 mypy-boto3-apigateway==1.36.0
 mypy-boto3-cloudwatch==1.36.0
 mypy-boto3-dynamodb==1.36.0
-mypy-boto3-ec2==1.36.8
-mypy-boto3-ecr==1.36.10
+mypy-boto3-ec2==1.36.18
+mypy-boto3-ecr==1.36.16
 mypy-boto3-es==1.36.0
 mypy-boto3-iam==1.36.13
 mypy-boto3-kms==1.36.0
@@ -60,7 +60,7 @@ rpds-py==0.22.3
 runs==1.2.2
 smmap==5.0.2
 tqdm==4.67.1
-types-awscrt==0.23.9
+types-awscrt==0.23.10
 types-s3transfer==0.11.2
 uritemplate==4.1.1
 wcwidth==0.2.13

diff --git a/requirements.dev.txt b/requirements.dev.txt
@@ -1,26 +1,26 @@
 atomicwrites==1.4.1
-awscli==1.37.5
-boto3-stubs-lite[apigateway,cloudwatch,dynamodb,ec2,ecr,es,iam,kms,lambda,s3,secretsmanager,securityhub,sns,sqs,ssm,stepfunctions,sts]==1.36.5  # match this with the version of the `boto3` runtime dendency
+awscli==1.37.14
+boto3-stubs-lite[apigateway,cloudwatch,dynamodb,ec2,ecr,es,iam,kms,lambda,s3,secretsmanager,securityhub,sns,sqs,ssm,stepfunctions,sts]==1.36.14  # match this with the version of the `boto3` runtime dendency
 coverage==7.6.10
 docker==7.1.0
 flake8==7.1.1
 gevent==24.11.1
 git+https://github.com/DataBiosphere/[email protected]+16#egg=chalice
 git+https://github.com/hannes-ucsc/[email protected]+1#egg=requirements-parser
 gitpython==3.1.44
-google-api-python-client==2.159.0
+google-api-python-client==2.160.0
 google-cloud-bigquery-reservation==1.15.0
-google-cloud-storage==2.19.0
+google-cloud-storage==3.0.0
 jq==1.8.0
-locust==2.32.6
-moto[s3,sqs,sns,dynamodb,iam]==5.0.27  # match the extras with the backends listed in AzulUnitTestCase._reset_moto
-mypy==1.14.1
+locust==2.32.8
+moto[s3,sqs,sns,dynamodb,iam]==5.0.28  # match the extras with the backends listed in AzulUnitTestCase._reset_moto
+mypy==1.15.0
 openapi-spec-validator==0.7.1
 openpyxl==3.1.5
 posix_ipc==1.1.1
 pygithub==2.5
 python-dxf==12.1.0
-python-gitlab==5.3.1
+python-gitlab==5.6.0
 pyyaml==6.0.2
 responses==0.25.6
 strict-rfc3339==0.7

diff --git a/requirements.trans.txt b/requirements.trans.txt
@@ -4,11 +4,11 @@ cachetools==5.5.1
 certifi==2025.1.31
 cffi==1.17.1
 charset-normalizer==3.4.1
-cryptography==44.0.0
+cryptography==44.0.1
 google-cloud-core==2.4.1
 google-crc32c==1.6.0
 google-resumable-media==2.7.2
-googleapis-common-protos==1.66.0
+googleapis-common-protos==1.67.0
 grpcio==1.70.0
 grpcio-status==1.62.3
 http_sfv==0.9.9
@@ -28,5 +28,5 @@ s3transfer==0.11.2
 setuptools-scm==5.0.2
 six==1.17.0
 typing_extensions==4.12.2
-tzlocal==5.2
+tzlocal==5.3
 wrapt==1.17.2