[R] Upgrade dependencies 2024-01-08 (#5831, PR #5855)

Author: achave11-ucsc

environment.py

@@ -241,14 +241,14 @@ def env() -> Mapping[str, Optional[str]]:
 
         # The tag of the Elasticsearch image that we use to run test cases.
         #
-        'azul_docker_elasticsearch_version': '7.17.16-8',
+        'azul_docker_elasticsearch_version': '7.17.16-9',
 
         # The tag of the PyCharm image that we use to format the source code in
         # continuous integration. We specify it here instead of directly in the
         # Makefile so that a change to the version does not require updating
         # requirements.
         #
-        'azul_docker_pycharm_version': '2023.3.2-8',
+        'azul_docker_pycharm_version': '2023.3.2-10',
 
         # The version of Terraform used throughout the system. This variable is
         # defined in the bootstrap environment (environment.boot) because it is

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==1.34.17
+botocore-stubs==1.34.21
 brotli==1.1.0
 cachetools==5.3.2
 certifi==2023.11.17
@@ -38,7 +38,7 @@ furl==2.1.3
 gevent==23.9.1
 geventhttpclient==2.0.11
 gitdb==4.0.11
-gitpython==3.1.37
+gitpython==3.1.41
 google-api-core==2.12.0
 google-api-python-client==2.103.0
 google-auth==2.23.3

requirements.dev.trans.txt

@@ -1,6 +1,6 @@
 blessed==1.20.0
 blinker==1.7.0
-botocore-stubs==1.34.17
+botocore-stubs==1.34.21
 brotli==1.1.0
 click==8.1.7
 colorama==0.4.4

requirements.dev.txt

@@ -5,7 +5,7 @@ coverage==6.5.0
 docker==6.1.2
 flake8==5.0.4
 gevent==23.9.1
-gitpython==3.1.37
+gitpython==3.1.41
 google-api-python-client==2.103.0
 google-cloud-storage==2.12.0
 google-cloud-bigquery-reservation==1.11.3

src/azul/__init__.py

@@ -1486,9 +1486,9 @@ def docker_images(self) -> dict[str, str]:
             bigquery_emulator='ghcr.io/goccy/bigquery-emulator:0.4.4',
             # Updating any of the four images below additionally requires
             # redeploying the `gitlab` TF component.
-            clamav='docker.io/clamav/clamav:1.2.1-24',
-            gitlab='docker.io/gitlab/gitlab-ce:16.6.2-ce.0',
-            gitlab_runner='docker.io/gitlab/gitlab-runner:ubuntu-v16.6.2',
+            clamav='docker.io/clamav/clamav:1.2.1-26',
+            gitlab='docker.io/gitlab/gitlab-ce:16.7.3-ce.0',
+            gitlab_runner='docker.io/gitlab/gitlab-runner:ubuntu-v16.7.0',
             dind=f'docker.io/library/docker:{self.docker_version}-dind',
             # The images below are not used within the security boundary:
             signing_proxy='docker.io/cllunsford/aws-signing-proxy:0.2.2',