RHAIENG-1440: Upgrade packages for latest stable (opendatahub-io#2584)

* Upgrade packages for latest stable

* Add missing package updates, change manifests and fix tests

Author: daniellutz

codeserver/ubi9-python-3.12/pylock.toml

@@ -9,14 +9,14 @@ dependencies = [
     "setuptools~=80.9.0",
 
     # Datascience packages
-    "boto3~=1.40.27",
+    "boto3~=1.40.52",
     "kafka-python-ng~=2.2.3",
-    "matplotlib~=3.10.6",
-    "numpy~=2.3.3",
-    "pandas~=2.3.2",
-    "plotly~=6.3.0",
+    "matplotlib~=3.10.7",
+    "numpy~=2.3.4",
+    "pandas~=2.3.3",
+    "plotly~=6.3.1",
     "scikit-learn~=1.7.2",
-    "scipy~=1.16.1",
+    "scipy~=1.16.2",
     "skl2onnx~=1.19.1; platform_machine != 's390x'",
     "ipykernel~=6.30.1",
     "kubeflow-training==1.9.3",
@@ -25,9 +25,9 @@ dependencies = [
     # Some extra useful packages
     "opencensus~=0.11.4",
     "smart-open~=7.3.1",
-    "virtualenv~=20.34.0",
+    "virtualenv~=20.35.3",
     "py-spy~=0.4.1; platform_machine != 's390x'",
-    "prometheus-client~=0.22.1",
+    "prometheus-client~=0.23.1",
 ]
 
 [tool.uv]

codeserver/ubi9-python-3.12/pyproject.toml

@@ -5,32 +5,32 @@ requires-python = "==3.12.*"
 
 dependencies = [
     # Datascience and useful extensions
-    "boto3~=1.40.27",
+    "boto3~=1.40.52",
     "kafka-python-ng~=2.2.3",
-    "kfp~=2.14.3",
-    "matplotlib~=3.10.6",
-    "numpy~=2.3.3",
-    "pandas~=2.3.2",
-    "plotly~=6.3.0",
+    "kfp~=2.14.6",
+    "matplotlib~=3.10.7",
+    "numpy~=2.3.4",
+    "pandas~=2.3.3",
+    "plotly~=6.3.1",
     "scikit-learn~=1.7.2",
-    "scipy~=1.16.1",
+    "scipy~=1.16.2",
     "skl2onnx~=1.19.1",
     "onnxconverter-common~=1.13.0", # Required for skl2onnx, as upgraded version is not compatible with protobuf
     "kubeflow-training==1.9.3",
     "codeflare-sdk~=0.32.0; platform_machine != 'ppc64le' and platform_machine != 's390x'",
     "feast~=0.55.0",
 
     # DB connectors
-    "pymongo~=4.14.1",
+    "pymongo~=4.15.3",
     "psycopg~=3.2.10",
     "pyodbc~=5.2.0",
     "mysql-connector-python~=9.4.0",
 
     # JupyterLab packages
-    "odh-elyra==4.2.5",
+    "odh-elyra==4.3.1",
     "odh-jupyter-trash-cleanup==0.1.1",
 
-    "jupyterlab==4.4.7",
+    "jupyterlab==4.4.9",
     "jupyter-bokeh~=4.0.5",
     "jupyter-server~=2.17.0",
     "jupyter-server-proxy~=4.4.0",

jupyter/datascience/ubi9-python-3.12/pylock.toml

@@ -706,9 +706,9 @@ wheels = [{ url = "https://files.pythonhosted.org/packages/07/2d/2b32cdbe8d2a602
 
 [[packages]]
 name = "jupyterlab"
-version = "4.4.7"
-sdist = { url = "https://files.pythonhosted.org/packages/d0/07/b3beaeb5722d4a55e345a38884c67baebd9cec2269c5309ce494485a5858/jupyterlab-4.4.7.tar.gz", upload-time = 2025-09-03T13:26:40Z, size = 22965570, hashes = { sha256 = "8c8e225492f4513ebde9bbbc00a05b651ab9a1f5b0013015d96fabf671c37188" } }
-wheels = [{ url = "https://files.pythonhosted.org/packages/7e/01/44f35124896dd5c73b26705c25bb8af2089895b32f057a1e4a3488847333/jupyterlab-4.4.7-py3-none-any.whl", upload-time = 2025-09-03T13:26:35Z, size = 12291583, hashes = { sha256 = "808bae6136b507a4d18f04254218bfe71ed8ba399a36ef3280d5f259e69abf80" } }]
+version = "4.4.9"
+sdist = { url = "https://files.pythonhosted.org/packages/45/b2/7dad2d0049a904d17c070226a4f78f81905f93bfe09503722d210ccf9335/jupyterlab-4.4.9.tar.gz", upload-time = 2025-09-26T17:28:20Z, size = 22966654, hashes = { sha256 = "ea55aca8269909016d5fde2dc09b97128bc931230183fe7e2920ede5154ad9c2" } }
+wheels = [{ url = "https://files.pythonhosted.org/packages/1f/fd/ac0979ebd1b1975c266c99b96930b0a66609c3f6e5d76979ca6eb3073896/jupyterlab-4.4.9-py3-none-any.whl", upload-time = 2025-09-26T17:28:15Z, size = 12292552, hashes = { sha256 = "394c902827350c017430a8370b9f40c03c098773084bc53930145c146d3d2cb2" } }]
 
 [[packages]]
 name = "jupyterlab-git"

jupyter/datascience/ubi9-python-3.12/pyproject.toml

@@ -7,7 +7,7 @@ dependencies = [
     # JupyterLab packages
     "odh-jupyter-trash-cleanup==0.1.1",
 
-    "jupyterlab==4.4.7",
+    "jupyterlab==4.4.9",
     "jupyter-server~=2.17.0",
     "jupyter-server-proxy~=4.4.0",
     "jupyter-server-terminals~=0.5.3",

jupyter/minimal/ubi9-python-3.12/pylock.toml

@@ -18,35 +18,35 @@ dependencies = [
     # see https://redhat-internal.slack.com/archives/C0961HQ858Q/p1757007056725559?thread_ts=1756924127.136609&cid=C0961HQ858Q
 
     # llmcompressor packages
-    "llmcompressor~=0.7.1",
+    "llmcompressor~=0.8.1",
     "lm-eval~=0.4.9",
 
     # Datascience and useful extensions
-    "boto3~=1.40.27",
+    "boto3~=1.40.52",
     "kafka-python-ng~=2.2.3",
-    "kfp~=2.14.3",
-    "matplotlib~=3.10.6",
+    "kfp~=2.14.6",
+    "matplotlib~=3.10.7",
     "numpy~=2.2.6",
-    "pandas~=2.3.2",
-    "plotly~=6.3.0",
+    "pandas~=2.3.3",
+    "plotly~=6.3.1",
     "scikit-learn~=1.7.2",
-    "scipy~=1.16.1",
+    "scipy~=1.16.2",
     "skl2onnx~=1.19.1",
     "onnxconverter-common~=1.13.0", # Required for skl2onnx, as upgraded version is not compatible with protobuf
     "kubeflow-training==1.9.3",
     "feast~=0.55.0",
 
     # DB connectors
-    "pymongo~=4.14.1",
+    "pymongo~=4.15.3",
     "psycopg~=3.2.10",
     "pyodbc~=5.2.0",
     "mysql-connector-python~=9.4.0",
 
     # JupyterLab packages
-    "odh-elyra==4.2.5",
+    "odh-elyra==4.3.1",
     "odh-jupyter-trash-cleanup==0.1.1",
 
-    "jupyterlab==4.4.7",
+    "jupyterlab==4.4.9",
     "jupyter-bokeh~=4.0.5",
     "jupyter-server~=2.17.0",
     "jupyter-server-proxy~=4.4.0",