Upgrade dependencies 2025-02-03 (#6874)

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
 
 ::
 

docker_images.json

@@ -1,87 +1,87 @@
 {
     "docker.io/library/docker:27.5.1": {
-        "digest": "sha256:3ab005a2e4872f0b10fb9c00d4230334043f1281f29299bd3de94a8f14a05e69",
-        "mirror_digest": "sha256:501efe65bf84c7f49bece11906638c033361e027d87ea8f14014e976dccd2db6",
+        "digest": "sha256:ba55987d5a560d321a148e9e33b9d465b9badf0400c5e3fa06b38c0048062294",
+        "mirror_digest": "sha256:ce4c9b281dd8d2f7c021edc2312490ac85e2c60458ace1fb381641c192497dda",
         "parts": {
             "linux/amd64": {
-                "digest": "sha256:28ffbb951b2d8d4c66eba1099644e2d0aad179751c28c64b01ba5baf1c39ae6b",
-                "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"
             }
         }
     },
     "docker.io/library/python:3.12.8-slim-bookworm": {
-        "digest": "sha256:69ce3aed05675d284bee807e7c45e560e98db21fb1e4c670252b4ee0f2496b6d",
-        "mirror_digest": "sha256:2666f95b070d02be2689a2ec66adbac8b2df7d3e6f2b5f8205bd1a6d1c113c44",
+        "digest": "sha256:2199a62885a12290dc9c5be3ca0681d367576ab7bf037da120e564723292a2f0",
+        "mirror_digest": "sha256:556871eba0de3018f8cd267ee10f4ebf2fdf09cbbc7102eaf474296ecfe906ae",
         "parts": {
             "linux/amd64": {
-                "digest": "sha256:d8a24235b9434ee37c5c1959b3c7ed5fcc3ddf524e314482c8db75db28f25a72",
-                "id": "sha256:e5aa526a5748bf31960d9087db8e69078f324ce2d0c2901ab6d050c1c7cda982",
+                "digest": "sha256:8859bd6ca943079262c27e38b7119cdacede77c463139a15651dd340087a6cc9",
+                "id": "sha256:9868da1de9f4ed56f66f6f501440e23c230ea163f0636ef0e24564dcbcc1ef27",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:bcba9fdc0685393a140e206cdea14cad03ea8a55db0a07a273cc9a6139446b73",
-                "id": "sha256:ebebaaca0e0b1628f9464369acc9f7b51629ad8c038bbdc8e6daedd2ded1d0d3",
+                "digest": "sha256:608e6ed31df49009fa6c242fb61b5386a1c002e40c2b9cb1958e0f1041aaf06a",
+                "id": "sha256:70a416d0c62354c379ea7f473f5affd19f23c917adeb3a9c9b7ce39e6f97f3c9",
                 "platform": "linux/arm64"
             }
         }
     },
-    "docker.io/ucscgi/azul-pycharm:2024.3.1.1-43": {
-        "digest": "sha256:d91ac5bdb26f830bc94526be1a8c22838d1fc8e2a0fcb987ba49f3d906b73dcf",
-        "mirror_digest": "sha256:74f63a48a2fb2a5135fe73a3fcb3217a56766abedb420f9642b60805dad05d21",
+    "docker.io/ucscgi/azul-pycharm:2024.3.2-44": {
+        "digest": "sha256:a514d2fe09085180f1ffdc180d2aeb1d2002caf47f9915ef09c902e690e0156f",
+        "mirror_digest": "sha256:3930827f54e50332a26ae7755f94eef18ec194b527d2d2af251ade37654c0c14",
         "parts": {
             "linux/amd64": {
-                "digest": "sha256:2cefdd4f91fe311d207f79633570bfb85226a17f863a6ac0f89a8af97a7b42e6",
-                "id": "sha256:b96cf0253db607424c5efd42d07a67bc3fc2260f78f5fe8ed1cf1ea557a2d38c",
+                "digest": "sha256:c28280eadd96369f2d20d477586c54750912e363658aa1cac6a852cfeab6c759",
+                "id": "sha256:14d5c2fd9a94285ccf46c1fe4e5a79879cde90324c4bf6268c0beeeb2be37183",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:7d88c1a33a0b026129ed3d6c768a9f554cb62d940c2d43a432b3d5ddb556042d",
-                "id": "sha256:38069b57b2f83cd369f51c9cf3231199ac309c94faaae8194116ebe0892fa5cc",
+                "digest": "sha256:2db9fd8936380853e5eed06b5db4166d705401ec522c4161df6e2e86c15eb80f",
+                "id": "sha256:0970b7192337298f661ab8cf1f90149b91b6873ff8b7efb2c9ec26d5ff7fa6fe",
                 "platform": "linux/arm64"
             }
         }
     },
-    "docker.io/ucscgi/azul-elasticsearch:7.17.27-36": {
-        "digest": "sha256:fb8c6fc60ce4d2c1ac7ac83f56857f5043ab3d7006ad0c66bc2aa67f369c7990",
-        "mirror_digest": "sha256:e8a43e73b61bf85165720ae14bfb2784e71310b6607067f551661f422ccccab2",
+    "docker.io/ucscgi/azul-elasticsearch:7.17.27-37": {
+        "digest": "sha256:083faa11dc1135851033e68b4a2421d7c0b89006a073dc5bbfb75222308d6bfa",
+        "mirror_digest": "sha256:9b5ec01d3d51541d72c1e176f162664b6cf001809afb05b0bd60a649dcbb92f3",
         "parts": {
             "linux/amd64": {
-                "digest": "sha256:e7ff06b1e26eb13bce50ea397610ea57bc43a386aae61653ab0d667d90ef3ed1",
-                "id": "sha256:012266a6d35e7f3fc12902ca9c990141df7f19a7f189fdea84fe3799c77a1f59",
+                "digest": "sha256:430fed6247771a51a8fd4b9d1fd11ee5ee59a07dda6aeb5e6c82468e0d721f4f",
+                "id": "sha256:e12f00e92a732c449d4667285971f3a3bf46d608c0b884ad0f78b721b301c152",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:262647729c768175addf4ad9617a36555e3c95f0cf63b3602bedb93c7d099288",
-                "id": "sha256:dabc42a7142ccabd0e352ed720fae015857fc733cc04f9d716f109bb1cd92873",
+                "digest": "sha256:aa8e544220dce85f302d7e0d549f85f40215abf6d11365c25f07152f49729644",
+                "id": "sha256:acbf25ac75ddc314dffcc9951f8f1ea1e207f389ece17d49e2270eff0499ed60",
                 "platform": "linux/arm64"
             }
         }
     },
-    "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",
+        "id": "sha256:0ad0f5ef87496801a8885b2c6b561d1f1f6f670e18b1cf4abaa1b384dbf704c2",
         "platform": "linux/amd64"
     },
-    "docker.io/clamav/clamav:1.4.2-23": {
-        "digest": "sha256:52cdfe3a7028880d4516f5820ea0f673f343d3bb05e0c0492e99dfaeb8ae325a",
-        "mirror_digest": "sha256:fc06903f721674437eb0cc61e38535c37f2825daddb82126a689c7fbef7401fa",
+    "docker.io/clamav/clamav:1.4.2-25": {
+        "digest": "sha256:cb9aed55ec997eacd768af9e9d4a6194f2dad2eba4d63e32128739b2bc0d2bbd",
+        "mirror_digest": "sha256:5e62c5e652a9d39006a892e594c35b96bcccbf573c7e11c931463d553f6fa6a5",
         "parts": {
             "linux/amd64": {
-                "digest": "sha256:3f28b5d86eca3b4988d517cf2cbe428920d3af2fd55075412d4858aa8da25752",
-                "id": "sha256:5b705f901c094d55af17f46fa29799b5df1f6280e28d3d75519f5ba5c314fe3a",
+                "digest": "sha256:03ad591c6be3b8ea3dc35ea9fed7d9971f4c28fbd7ad9eedee2492c1929b5fe3",
+                "id": "sha256:90c65ee471d4982d9e8e93a41bbb7c2868b8962e70fdab833020fddd57d981a4",
                 "platform": "linux/amd64"
             }
         }
     },
-    "docker.io/gitlab/gitlab-ce:17.8.1-ce.0": {
-        "digest": "sha256:23e1afcbb1b0a16bbbd646c412d23dd41f3301da7ae87ea44ecff10cd8c980e8",
-        "id": "sha256:3f90d34496bc70ec361f1c784125fa114c3eafc0d3e933d8485d0f43c59a9984",
+    "docker.io/gitlab/gitlab-ce:17.8.2-ce.0": {
+        "digest": "sha256:dfab80df4284a1cd3a7effc7b43f56f20494bc1927932c587d16e99b04acc0b3",
+        "id": "sha256:7511aea849236e5301bb4144bb09d1453be0fd2a17207770bfc10b24f49ca0bc",
         "platform": "linux/amd64"
     },
     "docker.io/gitlab/gitlab-runner:ubuntu-v17.8.3": {
@@ -101,17 +101,17 @@
         }
     },
     "docker.io/library/docker:27.5.1-dind": {
-        "digest": "sha256:3ab005a2e4872f0b10fb9c00d4230334043f1281f29299bd3de94a8f14a05e69",
-        "mirror_digest": "sha256:501efe65bf84c7f49bece11906638c033361e027d87ea8f14014e976dccd2db6",
+        "digest": "sha256:ba55987d5a560d321a148e9e33b9d465b9badf0400c5e3fa06b38c0048062294",
+        "mirror_digest": "sha256:ce4c9b281dd8d2f7c021edc2312490ac85e2c60458ace1fb381641c192497dda",
         "parts": {
             "linux/amd64": {
-                "digest": "sha256:28ffbb951b2d8d4c66eba1099644e2d0aad179751c28c64b01ba5baf1c39ae6b",
-                "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"
             }
         }

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

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': {

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
@@ -137,7 +137,7 @@ 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

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

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/azul-chalice@1.31.3+16#egg=chalice
 git+https://github.com/hannes-ucsc/requirements-parser@v0.2.0+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

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