RHOAIENG-11679: kustomize 5 warnings removal

This updates our manifests to get rid of the following kustomize 5
warnings:
```
Warning: 'vars' is deprecated. Please use 'replacements' instead. [EXPERIMENTAL] Run 'kustomize edit fix' to update your Kustomization automatically.
Warning: 'commonLabels' is deprecated. Please use 'labels' instead. Run 'kustomize edit fix' to update your Kustomization automatically
```

The first warning is printed by kustomize 5.0.3. The second warning by
kustomize 5.6.0.

The resulting manifests are still valid to be used with the kustomize
5.0.3 version and the results match what was the generated output before
this change.

Following commands were used to ease the manual work:
```
kustomize edit fix
kustomize edit fix --vars
```

With this update we don't need the commit.yaml and params.yaml files
anymore as all is now defined in the kustomization.yaml directly.

Also, I kept the original variable values with the additional
`_PLACEHOLDER` suffix - reason for keeping the original value is to keep
them easily searchable by grep, but truth is that the value doesn't
really matter after this change.

https://issues.redhat.com/browse/RHOAIENG-11679

Author: jstourac

ci/check-software-versions.py

@@ -14,7 +14,6 @@
 import json
 import logging
 import os
-import re
 import subprocess
 import sys
 import uuid
@@ -65,10 +64,9 @@ def load_yaml(filepath):
 
 
 def extract_variable(reference):
-    """Extracts a variable name from a string (e.g.: '$(odh-rstudio-notebook-image-commit-n-1)') using regex."""
+    """Extracts a variable name from a string (e.g.: 'odh-rstudio-notebook-image-commit-n-1_PLACEHOLDER') using regex."""
 
-    match = re.search(r"\((.*?)\)", reference)
-    return match.group(1) if match else None
+    return reference.replace("_PLACEHOLDER", "")
 
 
 def get_variable_value(variable_name, params_file_path=PARAMS_ENV_PATH):

ci/package_versions_selftestdata.py

@@ -30,7 +30,7 @@
         openshift.io/imported-from: quay.io/opendatahub/workbench-images
         opendatahub.io/workbench-image-recommended: 'true'
         opendatahub.io/default-image: "true"
-        opendatahub.io/notebook-build-commit: $(odh-minimal-notebook-image-commit-n)
+        opendatahub.io/notebook-build-commit: odh-minimal-notebook-image-commit-n_PLACEHOLDER
       from:
         kind: DockerImage
         name: $(odh-minimal-notebook-image-n)
@@ -53,7 +53,7 @@
         openshift.io/imported-from: quay.io/opendatahub/workbench-images
         opendatahub.io/workbench-image-recommended: 'false'
         opendatahub.io/default-image: "true"
-        opendatahub.io/notebook-build-commit: $(odh-minimal-notebook-image-commit-n-1)
+        opendatahub.io/notebook-build-commit: odh-minimal-notebook-image-commit-n-1_PLACEHOLDER
       from:
         kind: DockerImage
         name: $(odh-minimal-notebook-image-n-1)

jupyter/datascience/ubi9-python-3.11/kustomize/base/kustomization.yaml

@@ -2,12 +2,14 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namePrefix: jupyter-datascience-ubi9-python-3-11-
-commonLabels:
-  app: jupyter-datascience-ubi9-python-3-11
 resources:
   - service.yaml
   - statefulset.yaml
 images:
   - name: quay.io/opendatahub/workbench-images
     newName: quay.io/opendatahub/workbench-images
     newTag: jupyter-datascience-ubi9-python-3.11
+labels:
+  - includeSelectors: true
+    pairs:
+      app: jupyter-datascience-ubi9-python-3-11

jupyter/minimal/ubi9-python-3.11/kustomize/base/kustomization.yaml

@@ -2,12 +2,14 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namePrefix: jupyter-minimal-ubi9-python-3-11-
-commonLabels:
-  app: jupyter-minimal-ubi9-python-3-11
 resources:
   - service.yaml
   - statefulset.yaml
 images:
   - name: quay.io/opendatahub/workbench-images
     newName: quay.io/opendatahub/workbench-images
     newTag: jupyter-minimal-ubi9-python-3.11
+labels:
+  - includeSelectors: true
+    pairs:
+      app: jupyter-minimal-ubi9-python-3-11

jupyter/pytorch/ubi9-python-3.11/kustomize/base/kustomization.yaml

@@ -2,12 +2,14 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namePrefix: jupyter-pytorch-ubi9-python-3-11-
-commonLabels:
-  app: jupyter-pytorch-ubi9-python-3-11
 resources:
   - service.yaml
   - statefulset.yaml
 images:
   - name: quay.io/opendatahub/workbench-images
     newName: quay.io/opendatahub/workbench-images
     newTag: jupyter-pytorch-ubi9-python-3.11
+labels:
+  - includeSelectors: true
+    pairs:
+      app: jupyter-pytorch-ubi9-python-3-11

jupyter/pytorch/ubi9-python-3.11/kustomize/overlays/accelerator/cuda/kustomization.yaml

@@ -1,4 +1,6 @@
 ---
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
 resources:
   - ../../../base
 

jupyter/rocm/pytorch/ubi9-python-3.11/kustomize/base/kustomization.yaml

@@ -2,12 +2,14 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namePrefix: jupyter-rocm-pytorch-ubi9-python-3-11-
-commonLabels:
-  app: jupyter-rocm-pytorch-ubi9-python-3-11
 resources:
   - service.yaml
   - statefulset.yaml
 images:
   - name: quay.io/opendatahub/workbench-images
     newName: quay.io/opendatahub/workbench-images
     newTag: rocm-jupyter-pytorch-ubi9-python-3.11
+labels:
+  - includeSelectors: true
+    pairs:
+      app: jupyter-rocm-pytorch-ubi9-python-3-11

jupyter/rocm/tensorflow/ubi9-python-3.11/kustomize/base/kustomization.yaml

@@ -2,12 +2,14 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namePrefix: jupyter-rocm-tensorflow-ubi9-python-3-11-
-commonLabels:
-  app: jupyter-rocm-tensorflow-ubi9-python-3-11
 resources:
   - service.yaml
   - statefulset.yaml
 images:
   - name: quay.io/opendatahub/workbench-images
     newName: quay.io/opendatahub/workbench-images
     newTag: jupyter-pytorch-ubi9-python-3.11-2023a-20231002-4e9bbb3
+labels:
+  - includeSelectors: true
+    pairs:
+      app: jupyter-rocm-tensorflow-ubi9-python-3-11

jupyter/tensorflow/ubi9-python-3.11/kustomize/base/kustomization.yaml

@@ -2,12 +2,14 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namePrefix: jupyter-tensorflow-ubi9-python-3-11-
-commonLabels:
-  app: jupyter-tensorflow-ubi9-python-3-11
 resources:
   - service.yaml
   - statefulset.yaml
 images:
   - name: quay.io/opendatahub/workbench-images
     newName: quay.io/opendatahub/workbench-images
     newTag: cuda-jupyter-tensorflow-ubi9-python-3.11
+labels:
+  - includeSelectors: true
+    pairs:
+      app: jupyter-tensorflow-ubi9-python-3-11

jupyter/trustyai/ubi9-python-3.11/kustomize/base/kustomization.yaml

@@ -2,12 +2,14 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namePrefix: jupyter-trustyai-ubi9-python-3-11-
-commonLabels:
-  app: jupyter-trustyai-ubi9-python-3-11
 resources:
   - service.yaml
   - statefulset.yaml
 images:
   - name: quay.io/opendatahub/workbench-images
     newName: quay.io/opendatahub/workbench-images
     newTag: cuda-jupyter-trustyai-ubi9-python-3.11
+labels:
+  - includeSelectors: true
+    pairs:
+      app: jupyter-trustyai-ubi9-python-3-11