From e3bf310ca10d3496b1b357f56e7ab9322707ac33 Mon Sep 17 00:00:00 2001
From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.>
Date: Tue, 24 Feb 2026 16:37:28 +0000
Subject: [PATCH 1/8] build(helm): Fix helm chart testing list-changed. Bump
 trainer version

---
 .github/workflows/kubernetes-charts-build.yaml        | 11 +++++++----
 .../kubernetes/charts/medcat-trainer-helm/Chart.yaml  |  2 +-
 .../kubernetes/charts/medcat-trainer-helm/values.yaml |  2 +-
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/kubernetes-charts-build.yaml b/.github/workflows/kubernetes-charts-build.yaml
index 7c64764..821e1db 100644
--- a/.github/workflows/kubernetes-charts-build.yaml
+++ b/.github/workflows/kubernetes-charts-build.yaml
@@ -39,15 +39,17 @@ jobs:
 
       - name: Run chart-testing (list-changed)
         id: list-changed
+        working-directory: .
         run: |
-          changed=$(ct list-changed --target-branch ${{ github.event.repository.default_branch}})
+          changed=$(ct list-changed --target-branch ${{ github.event.repository.default_branch }} --chart-dirs deployment/kubernetes/charts)
           if [[ -n "$changed" ]]; then
-            echo "changed=true" >> "$GITHUB_UTPUT"
+            echo "changed=true" >> "$GITHUB_OUTPUT"
           fi
 
       - name: Run chart-testing (lint)
         if: steps.list-changed.outputs.changed == 'true'
-        run: ct lint --target-branch ${{ github.event.repository.default_branch }}
+        working-directory: .
+        run: ct lint --target-branch ${{ github.event.repository.default_branch }} --chart-dirs deployment/kubernetes/charts
 
       - name: Create kind cluster
         if: steps.list-changed.outputs.changed == 'true'
@@ -55,7 +57,8 @@ jobs:
 
       - name: Run chart-testing (install)
         if: steps.list-changed.outputs.changed == 'true'
-        run: ct install --target-branch ${{ github.event.repository.default_branch }}
+        working-directory: .
+        run: ct install --target-branch ${{ github.event.repository.default_branch }} --chart-dirs deployment/kubernetes/charts
 
   helm-publish:
     runs-on: ubuntu-latest
diff --git a/deployment/kubernetes/charts/medcat-trainer-helm/Chart.yaml b/deployment/kubernetes/charts/medcat-trainer-helm/Chart.yaml
index 9a74ccd..e77569a 100644
--- a/deployment/kubernetes/charts/medcat-trainer-helm/Chart.yaml
+++ b/deployment/kubernetes/charts/medcat-trainer-helm/Chart.yaml
@@ -21,7 +21,7 @@ version: 0.0.1
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "latest"
+appVersion: "3.5.1"
 
 # Chart.yaml
 dependencies:
diff --git a/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml b/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml
index c2d9f4e..2429111 100644
--- a/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml
+++ b/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml
@@ -11,7 +11,7 @@ image:
   # This sets the pull policy for images.
   pullPolicy: Always
   # Overrides the image tag whose default is the chart appVersion.
-  tag: "latest"
+  # tag: "latest"
 nginxImage:
   repository: nginx
   pullPolicy: IfNotPresent

From 4527fec475f5cbaf557b2d94eb0ad879e11c685a Mon Sep 17 00:00:00 2001
From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.>
Date: Tue, 24 Feb 2026 16:49:28 +0000
Subject: [PATCH 2/8] build(helm): Ignore version reuse

---
 .github/workflows/kubernetes-charts-build.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/kubernetes-charts-build.yaml b/.github/workflows/kubernetes-charts-build.yaml
index 821e1db..f50b674 100644
--- a/.github/workflows/kubernetes-charts-build.yaml
+++ b/.github/workflows/kubernetes-charts-build.yaml
@@ -49,6 +49,8 @@ jobs:
       - name: Run chart-testing (lint)
         if: steps.list-changed.outputs.changed == 'true'
         working-directory: .
+        env:
+          CT_CHECK_VERSION_INCREMENT: "false"
         run: ct lint --target-branch ${{ github.event.repository.default_branch }} --chart-dirs deployment/kubernetes/charts
 
       - name: Create kind cluster

From 8ac4d42101e74e11d47e42807a1cb8f46008b2b2 Mon Sep 17 00:00:00 2001
From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.>
Date: Tue, 24 Feb 2026 16:54:52 +0000
Subject: [PATCH 3/8] build(helm): Update helm action versions

---
 .github/workflows/kubernetes-charts-build.yaml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/kubernetes-charts-build.yaml b/.github/workflows/kubernetes-charts-build.yaml
index f50b674..a5f811b 100644
--- a/.github/workflows/kubernetes-charts-build.yaml
+++ b/.github/workflows/kubernetes-charts-build.yaml
@@ -20,22 +20,20 @@ jobs:
     if: github.event.pull_request.user.login != 'dependabot[bot]' && github.repository == 'CogStack/cogstack-platform-toolkit'
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5.0.0
         with:
           fetch-depth: 0
 
       - name: Set up Helm
-        uses: azure/setup-helm@v4.3.0
-        with:
-          version: v3.18.3
+        uses: azure/setup-helm@v4.3.1
 
-      - uses: actions/setup-python@v5.3.0
+      - uses: actions/setup-python@v6.0.0
         with:
           python-version: '3.x'
           check-latest: true
 
       - name: Set up chart-testing
-        uses: helm/chart-testing-action@v2.7.0
+        uses: helm/chart-testing-action@v2.8.0
 
       - name: Run chart-testing (list-changed)
         id: list-changed

From 1afc6823b234736607df994a6930e6d74a50bcd1 Mon Sep 17 00:00:00 2001
From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.>
Date: Tue, 24 Feb 2026 17:09:41 +0000
Subject: [PATCH 4/8] build(helm): Fix lint errors and format yaml

---
 .../charts/medcat-trainer-helm/Chart.yaml     | 18 +++++---
 .../charts/medcat-trainer-helm/values.yaml    | 46 +++++++++----------
 2 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/deployment/kubernetes/charts/medcat-trainer-helm/Chart.yaml b/deployment/kubernetes/charts/medcat-trainer-helm/Chart.yaml
index e77569a..1f75d14 100644
--- a/deployment/kubernetes/charts/medcat-trainer-helm/Chart.yaml
+++ b/deployment/kubernetes/charts/medcat-trainer-helm/Chart.yaml
@@ -23,12 +23,16 @@ version: 0.0.1
 # It is recommended to use it with quotes.
 appVersion: "3.5.1"
 
+maintainers:
+  - name: alhendrickson
+    email: alistair@cogstack.org
+
 # Chart.yaml
 dependencies:
-- name: solr
-  version: "9.6.10"
-  repository: "oci://registry-1.docker.io/bitnamicharts"
-- name: postgresql
-  version: 16.7.27
-  repository: "oci://registry-1.docker.io/bitnamicharts"
-  condition: postgresql.enabled
+  - name: solr
+    version: "9.6.10"
+    repository: "oci://registry-1.docker.io/bitnamicharts"
+  - name: postgresql
+    version: 16.7.27
+    repository: "oci://registry-1.docker.io/bitnamicharts"
+    condition: postgresql.enabled
diff --git a/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml b/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml
index 2429111..10a0dde 100644
--- a/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml
+++ b/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml
@@ -55,7 +55,7 @@ postgresql:
     repository: bitnamilegacy/postgresql
     # Pin legacy version of postgresql following bitnami change to remove free images. Match prefect version
     tag: 17.6.0-debian-12-r4
-    
+
 persistence:
   media:
     # Size of PVC for files like model packs and other media downloaded by medcat trainer
@@ -64,7 +64,7 @@ persistence:
     # Size of the PVC for the static HTML site
     size: 100Mi
   sqlite:
-    # Size of the PVC for the Sqlite database 
+    # Size of the PVC for the Sqlite database
     size: 100Mi
     # Size of the PVC for the Sqlite backups
     backupDbSize: 300Mi
@@ -72,20 +72,20 @@ persistence:
 
 # MedCAT config as described here: https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/medcat/config/config.py
 medcatConfig: |
-    cat.linking.optim = {'type': 'standard', 'lr': 0.1}
-    cat.linking.filter_before_disamb = True
-    # 20 - INFO; 10 - DEBUG
-    cat.general.log_level = 20
-    # Recommended is to have this one negative
-    cat.linking.similarity_threshold = -5
-    # And this one to be used as the real th
-    cat.linking.similarity_threshold_trainer = -5
-    # Used for limiting the number of occ of a concept in a project
-    cat.general.cui_count_limit = 100000000
-    # Is unlink full
-    cat.general.full_unlink = False
-    # use this spacy model
-    cat.general.spacy_model = 'en_core_web_md'
+  cat.linking.optim = {'type': 'standard', 'lr': 0.1}
+  cat.linking.filter_before_disamb = True
+  # 20 - INFO; 10 - DEBUG
+  cat.general.log_level = 20
+  # Recommended is to have this one negative
+  cat.linking.similarity_threshold = -5
+  # And this one to be used as the real th
+  cat.linking.similarity_threshold_trainer = -5
+  # Used for limiting the number of occ of a concept in a project
+  cat.general.cui_count_limit = 100000000
+  # Is unlink full
+  cat.general.full_unlink = False
+  # use this spacy model
+  cat.general.spacy_model = 'en_core_web_md'
 
 solr:
   replicaCount: 1
@@ -109,10 +109,10 @@ solr:
     image:
       repository: bitnamilegacy/zookeeper
       tag: 3.9.3-debian-12-r22
-    replicaCount: 1 #
+    replicaCount: 1
     persistence:
-      size: 1Gi   # Default is 8Gi
-
+      # Set size of the PVC for zookeper. Default is 8Gi
+      size: 1Gi
 
 # This is for the secrets for pulling an image from a private repository more information can be found here: https://kubernetes.io/docs/tasks/configure-pod-container/pull-image-private-registry/
 imagePullSecrets: []
@@ -164,9 +164,10 @@ service:
   type: ClusterIP
   # This sets the ports more information can be found here: https://kubernetes.io/docs/concepts/services-networking/service/#field-spec-ports
   port: 8001
-  apiPort: 8000 # Note medcat-trainer API is currently hardcoded on 8000 in the run.sh script
+  # Note medcat-trainer API is currently hardcoded on 8000 in the run.sh script
+  apiPort: 8000
   # nodePort: 30001
- 
+
 # This block is for setting up the ingress for more information can be found here: https://kubernetes.io/docs/concepts/services-networking/ingress/
 ingress:
   enabled: false
@@ -224,7 +225,6 @@ nginx:
       path: /nginx/health/live
       port: http
 
-
 # This section is for setting up autoscaling more information can be found here: https://kubernetes.io/docs/concepts/workloads/autoscaling/
 autoscaling:
   enabled: false
@@ -253,4 +253,4 @@ tolerations: []
 affinity: {}
 
 # Runtime class name for the pod (e.g., "nvidia" for GPU workloads)
-runtimeClassName: ""
\ No newline at end of file
+runtimeClassName: ""

From 3d2f30ad5ba2890cee0794b6d180133d1fc33188 Mon Sep 17 00:00:00 2001
From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.>
Date: Tue, 24 Feb 2026 17:14:30 +0000
Subject: [PATCH 5/8] build(helm): Trainer - disable example download by
 default

---
 deployment/kubernetes/charts/medcat-trainer-helm/values.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml b/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml
index 10a0dde..610ca43 100644
--- a/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml
+++ b/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml
@@ -26,7 +26,7 @@ env:
   EMAIL_PORT: "465"
   EMAIL_USER: "example@cogstack.org"
   ENV: "non-prod"
-  LOAD_EXAMPLES: "1"
+  LOAD_EXAMPLES: "0"
   LOAD_NUM_DOC_PAGES: "10"
   MAX_DATASET_SIZE: "10000"
   MAX_MEDCAT_MODELS: "2"

From 8b4e17565c996e07f6ae96853bec19e78d28ae87 Mon Sep 17 00:00:00 2001
From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.>
Date: Tue, 24 Feb 2026 17:16:33 +0000
Subject: [PATCH 6/8] build(helm): Trainer - fix helm test

---
 .../medcat-trainer-helm/templates/tests/test-connection.yaml    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml b/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml
index 8a9f4cb..44cee28 100644
--- a/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml
+++ b/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml
@@ -11,5 +11,5 @@ spec:
     - name: wget
       image: busybox
       command: ['wget']
-      args: ['{{ include "medcat-trainer-helm.fullname" . }}-nginx:{{ .Values.service.port }}/nginx/health/live', '-U helm-test {{ .Chart.Name }}-v{{ .Chart.Version }}']
+      args: ['{{ include "medcat-trainer-helm.fullname" . }}:{{ .Values.service.port }}/nginx/health/live', '-U helm-test {{ .Chart.Name }}-v{{ .Chart.Version }}']
   restartPolicy: Never

From 8a9163f9863ef383c0b61a1a2a9bab2b1f3e165f Mon Sep 17 00:00:00 2001
From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.>
Date: Tue, 24 Feb 2026 17:26:41 +0000
Subject: [PATCH 7/8] build(helm): Fix test

---
 .../templates/tests/test-connection.yaml                   | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml b/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml
index 44cee28..d82f0b1 100644
--- a/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml
+++ b/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml
@@ -10,6 +10,9 @@ spec:
   containers:
     - name: wget
       image: busybox
-      command: ['wget']
-      args: ['{{ include "medcat-trainer-helm.fullname" . }}:{{ .Values.service.port }}/nginx/health/live', '-U helm-test {{ .Chart.Name }}-v{{ .Chart.Version }}']
+      command: ['wget', '-q', '--spider']
+      args:
+        - 'http://{{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer:{{ .Values.service.port }}/nginx/health/live'
+        - '-U'
+        - 'helm-test {{ .Chart.Name }}-v{{ .Chart.Version }}'
   restartPolicy: Never

From d1417662e2dc04fc3051ebbecdfe98d701ec7331 Mon Sep 17 00:00:00 2001
From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.>
Date: Tue, 24 Feb 2026 17:28:43 +0000
Subject: [PATCH 8/8] build(helm): Trainer - fix helm test

---
 .../templates/tests/test-connection.yaml                   | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml b/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml
index d82f0b1..d03f3b1 100644
--- a/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml
+++ b/deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml
@@ -10,9 +10,6 @@ spec:
   containers:
     - name: wget
       image: busybox
-      command: ['wget', '-q', '--spider']
-      args:
-        - 'http://{{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer:{{ .Values.service.port }}/nginx/health/live'
-        - '-U'
-        - 'helm-test {{ .Chart.Name }}-v{{ .Chart.Version }}'
+      command: ['wget']
+      args: ['{{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer:{{ .Values.service.port }}/nginx/health/live', '-U helm-test {{ .Chart.Name }}-v{{ .Chart.Version }}']
   restartPolicy: Never