[R] Upgrade dependencies 2024-09-16 (#6570, PR #6578)

DataBiosphere · Sep 21, 2024 · 74c4894 · 74c4894
2 parents 34a12fb + 735bfa8
commit 74c4894
Show file tree

Hide file tree

Showing 17 changed files with 75 additions and 68 deletions.
diff --git a/UPGRADING.rst b/UPGRADING.rst
@@ -20,6 +20,13 @@ reverted. This is all fairly informal and loosely defined. Hopefully we won't
 have too many entries in this file.
 
 
+#6570 Upgrade dependencies 2024-09-16
+=====================================
+
+Update Python on your developer machines to version 3.11.10. In your working
+copy, run ``make virtualenv`` and ``make requirements envhook``.
+
+
 #6355 Explicitly configure source type in environment files
 ===========================================================
 

diff --git a/bin/wheels/runtime/idna-3.10-py3-none-any.whl b/bin/wheels/runtime/idna-3.10-py3-none-any.whl
diff --git a/bin/wheels/runtime/idna-3.8-py3-none-any.whl b/bin/wheels/runtime/idna-3.8-py3-none-any.whl
diff --git a/bin/wheels/runtime/protobuf-4.25.4-cp37-abi3-manylinux2014_x86_64.whl b/bin/wheels/runtime/protobuf-4.25.4-cp37-abi3-manylinux2014_x86_64.whl
diff --git a/bin/wheels/runtime/protobuf-4.25.5-cp37-abi3-manylinux2014_x86_64.whl b/bin/wheels/runtime/protobuf-4.25.5-cp37-abi3-manylinux2014_x86_64.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/bin/wheels/runtime/pyasn1-0.6.1-py3-none-any.whl b/bin/wheels/runtime/pyasn1-0.6.1-py3-none-any.whl
diff --git a/bin/wheels/runtime/pyasn1_modules-0.4.0-py3-none-any.whl b/bin/wheels/runtime/pyasn1_modules-0.4.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/pyasn1_modules-0.4.1-py3-none-any.whl b/bin/wheels/runtime/pyasn1_modules-0.4.1-py3-none-any.whl
diff --git a/bin/wheels/runtime/pytz-2024.1-py2.py3-none-any.whl b/bin/wheels/runtime/pytz-2024.1-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/pytz-2024.2-py2.py3-none-any.whl b/bin/wheels/runtime/pytz-2024.2-py2.py3-none-any.whl
diff --git a/docker_images.json b/docker_images.json
@@ -1,81 +1,81 @@
 {
-    "docker.io/library/docker:27.2.0": {
-        "digest": "sha256:d1d6d5265119696d8fa9b883f813953c560c5d87ea128a57681239b576f62997",
-        "mirror_digest": "sha256:e24ae425c729df0334e55d78389fc8f7fefe3debab1fb8995c1bd92fa59d4281",
+    "docker.io/library/docker:27.2.1": {
+        "digest": "sha256:ecfcb834c5047a751833f089e3a9a3e97ecec4a4dca8e9f13ff03694fd002443",
+        "mirror_digest": "sha256:9cd6203137a161ba6dbb0aa555074786238459958145cbfa9282947f61978085",
         "parts": {
             "linux/amd64": {
-                "digest": "sha256:dedb8ca94ea4fb6ebe843474b2bd4a83fcc62e0e0eb627f26c01b4c59f1b2a4e",
-                "id": "sha256:5a47c0fa2c99dc639ba53d1f4672320311666aef94ef754a85154cb34643e160",
+                "digest": "sha256:a0b423a19e3500f3a4c4598b9edb040fc2226327f32337b08898b1d60733618c",
+                "id": "sha256:14b13eefe14549a36d3ac6b111f61f66597afcc6458d1f8a369260d7704358a5",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:7600dc8fc3557d7ee7a19921a4d8fbe28f56aed480a936dfd9d51592560a330f",
-                "id": "sha256:1d9d41861c64112cb8a31a202d69e0803e0adbd65012ac57b637f37645cbec8f",
+                "digest": "sha256:168a2757d6d76c692f63c7e09ef856f070d14b217b1b13cfb47f1f2a26bedb97",
+                "id": "sha256:6ed4f1338b0acfa09f5fd99ed35ee6694b83b0f38a55f1ac875dc04444ca3ee9",
                 "platform": "linux/arm64"
             }
         }
     },
-    "docker.io/library/python:3.11.9-slim-bullseye": {
-        "digest": "sha256:fe8df05de0fe659668a0b6fa204c652092e3e96832a9c7d6f8cc1e0e03e663d8",
-        "mirror_digest": "sha256:d199928824a2b982a40097d2c219807ed11ce178936774152473a577c1480fe7",
+    "docker.io/library/python:3.11.10-slim-bullseye": {
+        "digest": "sha256:21e2cc29feabc9fa1335feb5efd98ebaf323a5963b8670a2212289b1db74cf73",
+        "mirror_digest": "sha256:ccb0c6383303002a6d15d2f52a24eb240f46a16f38984b04012a46c6a3b81560",
         "parts": {
             "linux/amd64": {
-                "digest": "sha256:8983cb8c63f49ecf9313146b0ea09ab7e8ae19fe30712bd08f0d26c45db1fcb3",
-                "id": "sha256:93f632478576cc591489aa70b52c5f47132bcb50ccc13b0c65d3ade8577006e2",
+                "digest": "sha256:654e637c2166468582a55f3cd6e0a7f424376ca234a1548872bcf275b7ac0da3",
+                "id": "sha256:50aba0dbbd8dc58f036908d46b48720b067a1b983a8fe9ef94743d731533296a",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:1c07092e76dbdc4dbc46101a0144b59c9397971be4f87fb6760f38dd06a24429",
-                "id": "sha256:28553d309dd279163937c15279e6a9d34dde44de12c3253bfde569b68b4a2943",
+                "digest": "sha256:35e15060ff683085ff1cb53efe6ca298807736da05b0972d098c990a76448b9a",
+                "id": "sha256:1a6f347c514a94a24970cf1be6d8379dce200dffd1929d4246db78118b54c9ba",
                 "platform": "linux/arm64"
             }
         }
     },
-    "docker.io/ucscgi/azul-pycharm:2024.2.1-32": {
-        "digest": "sha256:b415a4f3c4b0b1ddf3093d61584d59d23db80d392cbd5a29f92eab5e5855995a",
-        "mirror_digest": "sha256:f78cd14adfed72221cb1f65262ca99fedc5fe6b4b709a483f3fa636fc27f142c",
+    "docker.io/ucscgi/azul-pycharm:2024.2.1-33": {
+        "digest": "sha256:0e070d2e887c27566f8050ada4b55cf07da40e1a2e3cd0cc03427895d1c0cd48",
+        "mirror_digest": "sha256:9ec3b5d31c7b6f5168d1ed675d53a4b36eab19806c3a0eeef836b9e8e2f3f433",
         "parts": {
             "linux/amd64": {
-                "digest": "sha256:725fc63a68bd63340444441f557b4aa972bd6e6130af8183929e9113fe40b6d7",
-                "id": "sha256:050a2d63ba7a2db7f3ec9a9412f412911b2db9e6e23886850dfa79a9918e9d9c",
+                "digest": "sha256:66cadedd5ce726648a6c8d5fac5dbbf5264ec94baca2607a075ac5715431c095",
+                "id": "sha256:4866a88c7767960fdf74b2a788baad5467fe7555d27673058d0d4fde08a606c5",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:259a1cdba7e576819f8e1e8b33c195668cc9d3a269bdcae6eedc54fc13d7f257",
-                "id": "sha256:66bb13ae7547df51269d30e6bfd55a090049e034716e5e339ecef31d20fccbb5",
+                "digest": "sha256:f21799f827eb526166c417c10526d29ee30fc34ff48f354cdd6957c4c3296940",
+                "id": "sha256:cc7d6fda770ae623e69daa8c1fb856c67b88aadbc497025666998b7da3371fe6",
                 "platform": "linux/arm64"
             }
         }
     },
-    "docker.io/ucscgi/azul-elasticsearch:7.17.23-26": {
-        "digest": "sha256:6c453c2b0d6f6a816612bfb0616d153995c9e8dbc6fd8136dcff790fde955019",
-        "mirror_digest": "sha256:f5a003a702006e55d7d81589759b4317ddfb6e04d2c34fed59551930028e4207",
+    "docker.io/ucscgi/azul-elasticsearch:7.17.24-27": {
+        "digest": "sha256:c38462f9f8d632116635d869b02e3c4b23b0ca246a803e24fc42b3d893ab0690",
+        "mirror_digest": "sha256:f8c78b3f91faf59197a544792d14fb24180e5000ee6442466551b64e539f1430",
         "parts": {
             "linux/amd64": {
-                "digest": "sha256:c00b732d99f7f31619b138f9f2e8975dfb1e8d4b629e9422f3c0ed0877f57c95",
-                "id": "sha256:8305f8f10cd7284e16863c5249df91491ab67627d5f663e75958b20bcccd50d0",
+                "digest": "sha256:0e0c1d767950608777489140e56eac83163d6718ebd1b0a707aeb2313a93c1a8",
+                "id": "sha256:6f04aeb0998b5ee2d6db0a3cb5063921b78a1d9156a085e730825f89f7991333",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:2a877123a2d6452330f58932ee43050b26a5b1109a3a6c320c7e3ca32521a881",
-                "id": "sha256:dbacedc2237f1f011c186d5468018c9bb2619e33fa3eb26c4acc2d01d2567ea9",
+                "digest": "sha256:5c7191bac77a6a12f6cba2cb125ed67a3f0960a6a48855fe0d6c8dec88d3bb6d",
+                "id": "sha256:55785c7f500a8aa49f5de55526ce1afb46816f2bc76ee14b6532981fca6fecf3",
                 "platform": "linux/arm64"
             }
         }
     },
-    "docker.io/ucscgi/azul-bigquery-emulator:0.4.4-11": {
-        "digest": "sha256:6ac04e59c348492f011daea741150a45a5748b08f735a5f8b694a4f6ebc00eec",
-        "id": "sha256:c5cdaeeed9e3b88ebf3a7f45af82b37093907071eecde3e1d05b355d0fac423e",
+    "docker.io/ucscgi/azul-bigquery-emulator:0.4.4-12": {
+        "digest": "sha256:d4e072251a7fb277b6dfc389502fc4a68083c766991e6b3dd4df179243adcf50",
+        "id": "sha256:930b511738bf092007f4627197dc7ae4cd325246c197856475f63d1f817bb581",
         "platform": "linux/amd64"
     },
-    "docker.io/clamav/clamav:1.4.1-4": {
-        "digest": "sha256:e8543b5cf5bd2d4bea49f00473707f4ffdd7704ed2d4b98b75c6f9b7e26efa05",
-        "id": "sha256:5269a125399d5f8957fd3deba01f5aa69f1f02e1025bdbbc01f88c7298ac56a3",
+    "docker.io/clamav/clamav:1.4.1-5": {
+        "digest": "sha256:09ed837cb10f1f3e3175ccd6c749861c76fbf5ca3de45ec91711c8e75fe80bea",
+        "id": "sha256:e15968788d10f750f4d7486900c4e9f5ba24eb9cd0920d1f09bfa3981ce00517",
         "platform": "linux/amd64"
     },
-    "docker.io/gitlab/gitlab-ce:17.3.1-ce.0": {
-        "digest": "sha256:6f2ab9c42cef6b8058ef45042ce33a4505a0a9ac1a8d9ed85016ceca743dd01d",
-        "id": "sha256:b3c3467dc55c9e34380e6802d7c6c0b5af0088a738795553b1ba7ec5d78f0f79",
+    "docker.io/gitlab/gitlab-ce:17.3.3-ce.0": {
+        "digest": "sha256:bef394818ac85471965400e6a86b5c5de3994ba6400f32b20b16eec266c5f3b3",
+        "id": "sha256:2eac78f2ca2670530a6c965269b68167058c09b33a5a3f64ccc1013d016795f7",
         "platform": "linux/amd64"
     },
     "docker.io/gitlab/gitlab-runner:ubuntu-v17.3.1": {
@@ -94,18 +94,18 @@
             }
         }
     },
-    "docker.io/library/docker:27.2.0-dind": {
-        "digest": "sha256:d1d6d5265119696d8fa9b883f813953c560c5d87ea128a57681239b576f62997",
-        "mirror_digest": "sha256:e24ae425c729df0334e55d78389fc8f7fefe3debab1fb8995c1bd92fa59d4281",
+    "docker.io/library/docker:27.2.1-dind": {
+        "digest": "sha256:ecfcb834c5047a751833f089e3a9a3e97ecec4a4dca8e9f13ff03694fd002443",
+        "mirror_digest": "sha256:9cd6203137a161ba6dbb0aa555074786238459958145cbfa9282947f61978085",
         "parts": {
             "linux/amd64": {
-                "digest": "sha256:dedb8ca94ea4fb6ebe843474b2bd4a83fcc62e0e0eb627f26c01b4c59f1b2a4e",
-                "id": "sha256:5a47c0fa2c99dc639ba53d1f4672320311666aef94ef754a85154cb34643e160",
+                "digest": "sha256:a0b423a19e3500f3a4c4598b9edb040fc2226327f32337b08898b1d60733618c",
+                "id": "sha256:14b13eefe14549a36d3ac6b111f61f66597afcc6458d1f8a369260d7704358a5",
                 "platform": "linux/amd64"
             },
             "linux/arm64": {
-                "digest": "sha256:7600dc8fc3557d7ee7a19921a4d8fbe28f56aed480a936dfd9d51592560a330f",
-                "id": "sha256:1d9d41861c64112cb8a31a202d69e0803e0adbd65012ac57b637f37645cbec8f",
+                "digest": "sha256:168a2757d6d76c692f63c7e09ef856f070d14b217b1b13cfb47f1f2a26bedb97",
+                "id": "sha256:6ed4f1338b0acfa09f5fd99ed35ee6694b83b0f38a55f1ac875dc04444ca3ee9",
                 "platform": "linux/arm64"
             }
         }

diff --git a/environment.boot b/environment.boot
@@ -1,4 +1,4 @@
-azul_python_version=3.11.9
-azul_python_image=docker.io/library/python@sha256:d199928824a2b982a40097d2c219807ed11ce178936774152473a577c1480fe7
-azul_docker_version=27.2.0
+azul_python_version=3.11.10
+azul_python_image=docker.io/library/python@sha256:ccb0c6383303002a6d15d2f52a24eb240f46a16f38984b04012a46c6a3b81560
+azul_docker_version=27.2.1
 azul_terraform_version=1.9.5
diff --git a/environment.py b/environment.py
@@ -234,7 +234,7 @@ def env() -> Mapping[str, Optional[str]]:
         # `gitlab` components, as well as building and pushing the executor
         # image (see terraform/gitlab/runner/Dockerfile for how).
         #
-        'azul_docker_version': '27.2.0',
+        'azul_docker_version': '27.2.1',
 
         # The version of Python used throughout the system.
         #
@@ -248,7 +248,7 @@ def env() -> Mapping[str, Optional[str]]:
         # and committing the resulting changes. It also requires redeploying the
         # `shared` component.
         #
-        'azul_python_version': '3.11.9',
+        'azul_python_version': '3.11.10',
 
         # The version of Terraform used throughout the system.
         #
@@ -282,28 +282,28 @@ def env() -> Mapping[str, Optional[str]]:
                 'url': 'https://hub.docker.com/_/python',
             },
             'pycharm': {
-                'ref': 'docker.io/ucscgi/azul-pycharm:2024.2.1-32',
+                'ref': 'docker.io/ucscgi/azul-pycharm:2024.2.1-33',
                 'url': 'https://hub.docker.com/repository/docker/ucscgi/azul-pycharm',
                 'is_custom': True
             },
             'elasticsearch': {
-                'ref': 'docker.io/ucscgi/azul-elasticsearch:7.17.23-26',
+                'ref': 'docker.io/ucscgi/azul-elasticsearch:7.17.24-27',
                 'url': 'https://hub.docker.com/repository/docker/ucscgi/azul-elasticsearch',
                 'is_custom': True
             },
             'bigquery_emulator': {
-                'ref': 'docker.io/ucscgi/azul-bigquery-emulator:0.4.4-11',
+                'ref': 'docker.io/ucscgi/azul-bigquery-emulator:0.4.4-12',
                 '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:1.4.1-4',
+                'ref': 'docker.io/clamav/clamav:1.4.1-5',
                 'url': 'https://hub.docker.com/r/clamav/clamav'
             },
             'gitlab': {
-                'ref': 'docker.io/gitlab/gitlab-ce:17.3.1-ce.0',
+                'ref': 'docker.io/gitlab/gitlab-ce:17.3.3-ce.0',
                 'url': 'https://hub.docker.com/r/gitlab/gitlab-ce'
             },
             'gitlab_runner': {

diff --git a/requirements.all.txt b/requirements.all.txt
@@ -10,7 +10,7 @@ blinker==1.8.2
 boto3==1.28.63
 boto3-stubs==1.28.63
 botocore==1.31.63
-botocore-stubs==1.35.15
+botocore-stubs==1.35.24
 brotli==1.1.0
 cachetools==5.5.0
 certifi==2024.8.30
@@ -50,13 +50,13 @@ google-cloud-storage==2.12.0
 google-crc32c==1.6.0
 google-resumable-media==2.7.2
 googleapis-common-protos==1.65.0
-greenlet==3.0.3
+greenlet==3.1.1
 grpcio==1.66.1
 grpcio-status==1.62.3
 http-message-signatures==0.4.4
 http_sfv==0.9.9
 httplib2==0.22.0
-idna==3.8
+idna==3.10
 importlib-resources==5.13.0
 inquirer==2.10.1
 itsdangerous==2.2.0
@@ -91,11 +91,11 @@ pathable==0.4.3
 pip==23.3.2
 posix_ipc==1.1.1
 proto-plus==1.24.0
-protobuf==4.25.4
+protobuf==4.25.5
 psutil==6.0.0
 py-partiql-parser==0.3.3
-pyasn1==0.6.0
-pyasn1_modules==0.4.0
+pyasn1==0.6.1
+pyasn1_modules==0.4.1
 pycodestyle==2.9.1
 pycparser==2.22
 pyflakes==2.5.0
@@ -109,7 +109,7 @@ python-dateutil==2.9.0.post0
 python-dxf==11.4.0
 python-editor==1.0.4
 python-gitlab==3.13.0
-pytz==2024.1
+pytz==2024.2
 pyyaml==6.0.1
 pyzmq==26.2.0
 readchar==4.2.0

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==1.35.15
+botocore-stubs==1.35.24
 brotli==1.1.0
 click==8.1.7
 colorama==0.4.4
@@ -13,7 +13,7 @@ flask-cors==5.0.0
 geventhttpclient==2.3.1
 gitdb==4.0.11
 google-auth-httplib2==0.2.0
-greenlet==3.0.3
+greenlet==3.1.1
 httplib2==0.22.0
 importlib-resources==5.13.0
 inquirer==2.10.1

diff --git a/requirements.trans.txt b/requirements.trans.txt
@@ -12,18 +12,18 @@ googleapis-common-protos==1.65.0
 grpcio==1.66.1
 grpcio-status==1.62.3
 http_sfv==0.9.9
-idna==3.8
+idna==3.10
 markupsafe==2.1.5
 orderedmultidict==1.0.1
 packaging==24.1
 proto-plus==1.24.0
-protobuf==4.25.4
-pyasn1==0.6.0
-pyasn1_modules==0.4.0
+protobuf==4.25.5
+pyasn1==0.6.1
+pyasn1_modules==0.4.1
 pycparser==2.22
 pyopenssl==24.2.1
 python-dateutil==2.9.0.post0
-pytz==2024.1
+pytz==2024.2
 s3transfer==0.7.0
 setuptools-scm==5.0.2
 six==1.16.0