[R] Upgrade dependencies 2024-09-30 (#6598, PR #6628)

DataBiosphere · Oct 14, 2024 · 16ec5f9 · 16ec5f9
2 parents 54e12dd + 1f35104
commit 16ec5f9
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diff --git a/...heels/runtime/MarkupSafe-2.1.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/...heels/runtime/MarkupSafe-2.1.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/...heels/runtime/MarkupSafe-3.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/...heels/runtime/MarkupSafe-3.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/...ntime/charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/...ntime/charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/...ntime/charset_normalizer-3.4.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/...ntime/charset_normalizer-3.4.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/bin/wheels/runtime/grpcio-1.66.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/bin/wheels/runtime/grpcio-1.66.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/bin/wheels/runtime/grpcio-1.66.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/bin/wheels/runtime/grpcio-1.66.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/docker_images.json b/docker_images.json
@@ -1,111 +1,111 @@
 {
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+    "docker.io/ucscgi/azul-bigquery-emulator:0.4.4-14": {
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-    "docker.io/gitlab/gitlab-ce:17.3.3-ce.0": {
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-        "id": "sha256:2eac78f2ca2670530a6c965269b68167058c09b33a5a3f64ccc1013d016795f7",
+    "docker.io/gitlab/gitlab-ce:17.4.2-ce.0": {
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         "platform": "linux/amd64"
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-        "mirror_digest": "sha256:9cd6203137a161ba6dbb0aa555074786238459958145cbfa9282947f61978085",
+        "digest": "sha256:db7c4d6d0321c8f674c78a8d1186c8bdfc2f42909d28542a54358a426d34b25c",
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-                "id": "sha256:14b13eefe14549a36d3ac6b111f61f66597afcc6458d1f8a369260d7704358a5",
+                "digest": "sha256:c11cff2ed9b991b0ff231f3cc803e40511c7e1f2a54522fb84ba2856756e18c7",
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-                "id": "sha256:6ed4f1338b0acfa09f5fd99ed35ee6694b83b0f38a55f1ac875dc04444ca3ee9",
+                "digest": "sha256:d358a0fdb1993bec9c1a81842100d4a242d1c872f7556b8e0d537b00ea4c4926",
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                 "platform": "linux/arm64"
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diff --git a/environment.boot b/environment.boot
@@ -1,4 +1,4 @@
 azul_python_version=3.11.10
-azul_python_image=docker.io/library/python@sha256:ccb0c6383303002a6d15d2f52a24eb240f46a16f38984b04012a46c6a3b81560
+azul_python_image=docker.io/library/python@sha256:13b5591078b6450547762ed1faec89f9934d69d5cffc746f8cdbc1d2ee5b44d4
 azul_docker_version=27.2.1
-azul_terraform_version=1.9.5
+azul_terraform_version=1.9.7
diff --git a/environment.py b/environment.py
@@ -261,7 +261,7 @@ def env() -> Mapping[str, Optional[str]]:
         # Modifying this variable requires running `make environment.boot` and
         # committing the resulting changes.
         #
-        'azul_terraform_version': '1.9.5',
+        'azul_terraform_version': '1.9.7',
 
         # A dictionary mapping the short name of each Docker image used in Azul
         # to its fully qualified name. Note that a change to any of the image
@@ -282,32 +282,32 @@ def env() -> Mapping[str, Optional[str]]:
                 'url': 'https://hub.docker.com/_/python',
             },
             'pycharm': {
-                'ref': 'docker.io/ucscgi/azul-pycharm:2024.2.1-34',
+                'ref': 'docker.io/ucscgi/azul-pycharm:2024.2.3-35',
                 'url': 'https://hub.docker.com/repository/docker/ucscgi/azul-pycharm',
                 'is_custom': True
             },
             'elasticsearch': {
-                'ref': 'docker.io/ucscgi/azul-elasticsearch:7.17.24-27',
+                'ref': 'docker.io/ucscgi/azul-elasticsearch:7.17.24-28',
                 'url': 'https://hub.docker.com/repository/docker/ucscgi/azul-elasticsearch',
                 'is_custom': True
             },
             'bigquery_emulator': {
-                'ref': 'docker.io/ucscgi/azul-bigquery-emulator:0.4.4-12',
+                'ref': 'docker.io/ucscgi/azul-bigquery-emulator:0.4.4-14',
                 '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:1.4.1-5',
+                'ref': 'docker.io/clamav/clamav:1.4.1-7',
                 'url': 'https://hub.docker.com/r/clamav/clamav'
             },
             'gitlab': {
-                'ref': 'docker.io/gitlab/gitlab-ce:17.3.3-ce.0',
+                'ref': 'docker.io/gitlab/gitlab-ce:17.4.2-ce.0',
                 'url': 'https://hub.docker.com/r/gitlab/gitlab-ce'
             },
             'gitlab_runner': {
-                'ref': 'docker.io/gitlab/gitlab-runner:ubuntu-v17.3.1',
+                'ref': 'docker.io/gitlab/gitlab-runner:ubuntu-v17.4.0',
                 'url': 'https://hub.docker.com/r/gitlab/gitlab-runner'
             },
             'dind': {

diff --git a/requirements.all.txt b/requirements.all.txt
@@ -10,13 +10,13 @@ blinker==1.8.2
 boto3==1.28.63
 boto3-stubs==1.28.63
 botocore==1.31.63
-botocore-stubs==1.35.24
+botocore-stubs==1.35.39
 brotli==1.1.0
 cachetools==5.5.0
 certifi==2024.8.30
 cffi==1.17.1
 chalice==1.30.0+12
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
 chevron==0.14.0
 click==8.1.7
 colorama==0.4.4
@@ -51,7 +51,7 @@ google-crc32c==1.6.0
 google-resumable-media==2.7.2
 googleapis-common-protos==1.65.0
 greenlet==3.1.1
-grpcio==1.66.1
+grpcio==1.66.2
 grpcio-status==1.62.3
 http-message-signatures==0.4.4
 http_sfv==0.9.9
@@ -69,7 +69,7 @@ jsonschema-spec==0.1.6
 jwcrypto==1.5.6
 lazy-object-proxy==1.10.0
 locust==2.12.2
-markupsafe==2.1.5
+markupsafe==3.0.1
 mccabe==0.7.0
 more-itertools==9.0.0
 moto==4.1.13
@@ -103,7 +103,7 @@ pygithub==1.56
 pyjwt==2.9.0
 pynacl==1.5.0
 pyopenssl==24.2.1
-pyparsing==3.1.4
+pyparsing==3.2.0
 pyrsistent==0.20.0
 python-dateutil==2.9.0.post0
 python-dxf==11.4.0
@@ -127,8 +127,8 @@ smmap==5.0.1
 strict-rfc3339==0.7
 toml==0.10.2
 tqdm==4.66.5
-types-awscrt==0.21.5
-types-s3transfer==0.10.2
+types-awscrt==0.22.0
+types-s3transfer==0.10.3
 types-toml==0.10.8.20240310
 typing_extensions==4.12.2
 tzlocal==2.1
@@ -140,6 +140,6 @@ werkzeug==3.0.3
 wheel==0.38.4
 wrapt==1.16.0
 www-authenticate==0.9.2
-xmltodict==0.13.0
+xmltodict==0.14.1
 zope.event==5.0
-zope.interface==7.0.3
+zope.interface==7.1.0
diff --git a/requirements.dev.trans.txt b/requirements.dev.trans.txt
@@ -1,6 +1,6 @@
 blessed==1.20.0
 blinker==1.8.2
-botocore-stubs==1.35.24
+botocore-stubs==1.35.39
 brotli==1.1.0
 click==8.1.7
 colorama==0.4.4
@@ -41,7 +41,7 @@ pycodestyle==2.9.1
 pyflakes==2.5.0
 pyjwt==2.9.0
 pynacl==1.5.0
-pyparsing==3.1.4
+pyparsing==3.2.0
 pyrsistent==0.20.0
 python-editor==1.0.4
 pyzmq==26.2.0
@@ -51,12 +51,12 @@ roundrobin==0.0.4
 smmap==5.0.1
 toml==0.10.2
 tqdm==4.66.5
-types-awscrt==0.21.5
-types-s3transfer==0.10.2
+types-awscrt==0.22.0
+types-s3transfer==0.10.3
 types-toml==0.10.8.20240310
 uritemplate==4.1.1
 wcwidth==0.2.13
 www-authenticate==0.9.2
-xmltodict==0.13.0
+xmltodict==0.14.1
 zope.event==5.0
-zope.interface==7.0.3
+zope.interface==7.1.0
diff --git a/requirements.trans.txt b/requirements.trans.txt
@@ -3,17 +3,17 @@ bagit-profile==1.3.1
 cachetools==5.5.0
 certifi==2024.8.30
 cffi==1.17.1
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
 cryptography==43.0.1
 google-cloud-core==2.4.1
 google-crc32c==1.6.0
 google-resumable-media==2.7.2
 googleapis-common-protos==1.65.0
-grpcio==1.66.1
+grpcio==1.66.2
 grpcio-status==1.62.3
 http_sfv==0.9.9
 idna==3.10
-markupsafe==2.1.5
+markupsafe==3.0.1
 orderedmultidict==1.0.1
 packaging==24.1
 proto-plus==1.24.0

diff --git a/terraform/_schema.json.gz b/terraform/_schema.json.gz
diff --git a/terraform/gitlab/gitlab.tf.json.template.py b/terraform/gitlab/gitlab.tf.json.template.py
@@ -244,10 +244,10 @@
 # For instructions on finding the latest CIS-hardened AMI, see
 # OPERATOR.rst#upgrading-linux-ami
 #
-# CIS Amazon Linux 2 Kernel 4.14 Benchmark - Level 1 - v08 -4c096026-c6b0-440c-bd2f-6d34904e4fc6
+# CIS Amazon Linux 2 Kernel 4.14 Benchmark - Level 1 - v09 -4c096026-c6b0-440c-bd2f-6d34904e4fc6
 #
 ami_id = {
-    'us-east-1': 'ami-0cdfc773f3f462447'
+    'us-east-1': 'ami-080cfaeb213b9f981'
 }
 
 gitlab_mount = '/mnt/gitlab'