Merge pull request #12 from amun-ai/dev

Dev

.github/workflows/helm-lint-test.yml

@@ -0,0 +1,45 @@
+# See https://github.com/helm/chart-testing-action
+name: Lint and Test Charts
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+  workflow_dispatch:
+
+jobs:
+  lint-test:
+    runs-on: ubuntu-latest
+    # strategy:
+      # matrix:
+        # k8s: ["1.19.16", "1.21.14", "1.22.9", "1.23.12", "1.24.7", "1.25.2"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Install Helm
+        uses: azure/[email protected]
+        # as of 2022/12 the set-output still not fixed in this action
+        # https://github.com/Azure/setup-helm/issues/103
+        with:
+          version: v3.7.0
+
+      - name: Install chart-testing
+        uses: helm/[email protected]
+
+      - name: Run chart-testing (lint)
+        run: ct lint --config ct.yaml
+
+      - name: Create kind cluster
+        uses: helm/[email protected]
+
+      # See https://github.com/helm/chart-testing/blob/main/doc/ct_install.md
+      - name: Run chart-testing (install)
+        run: ct install --config ct.yaml --debug

.github/workflows/helm-release.yml

@@ -4,19 +4,18 @@ on:
   push:
     branches:
       - main
+      - dev
 
 jobs:
   release:
-    # depending on default permission settings for your org (contents being read-only or read-write for workloads), you will have to add permissions
-    # see: https://docs.github.com/en/actions/security-guides/automatic-token-authentication#modifying-the-permissions-for-the-github_token
     permissions:
       contents: write
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v2
         with:
-          fetch-depth: 0
+          fetch-depth: 0  # Ensure tags are fetched too
 
       - name: Configure Git
         run: |
@@ -27,10 +26,7 @@ jobs:
         uses: azure/setup-helm@v1
         with:
           version: v3.9.3
-      # https://hoetker.engineer/post/helm-github-workflow-dependency/
-      # This is bad practise, but it works for now. Chart-releaser 
-      #  should add the helm repos but doesn't
-      #TODO fix hard coding
+
       - name: Add Helm dependency repos
         run: |
           helm repo add docker-registry https://helm.twun.io
@@ -41,7 +37,22 @@ jobs:
         run: |
           helm dependency update charts/hypha
           helm dependency build charts/hypha
+
+      - name: Get semantic version
+        id: semver
+        uses: mathieudutour/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+
+      # - name: Update Chart.yaml version
+      #   uses: fjogeleit/[email protected]
+      #   with:
+      #     valueFile: 'charts/hypha/Chart.yaml'
+      #     propertyPath: 'version'
+      #     value: ${{ steps.semver.outputs.new_tag }}
+
       - name: Run chart-releaser
         uses: helm/[email protected]
         env:
-          CR_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+          CR_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+          VERSION: "${{ steps.semver.outputs.new_tag }}"

.gitignore

@@ -1,2 +1,8 @@
-secrets.yaml
-.history
+/*
+!.gitignore
+!Makefile
+!README.md
+# !helmsman.yaml
+!charts
+!.github
+!ct.yaml

Makefile

@@ -1,9 +1,14 @@
+.PHONY: minikube.setup
+
 minikube.setup:
 	minikube config set memory 16384
 	minikube config set cpus 4
-	minikube start
-
+	minikube config set disk-size 32GB
+	minikube start --addons=gpu,ingress,nvidia-driver-installer,nvidia-gpu-device-plugin 
 
+helm.package:
+	helm package charts/hypha --dependency-update --destination helm-chart
+	helm package charts/tritoninferenceserver-hypha --dependency-update --destination helm-chart
 # VERSION=$(shell grep -Eo '[0-9]\.[0-9]\.[0-9]+' helm-chart/hypha/Chart.yaml | head -1)
 
 VERSION=$(shell grep -Po "(?<=version: )([0-9]|\.)*(?=\s|$$)" charts/hypha/Chart.yaml | head -1)
@@ -16,5 +21,14 @@ tag.release:
 	version=${VERSION}
 	echo "Tagging release ${VERSION}"
 	git tag -a "v${VERSION}" -m "v${VERSION}" -f
-	git push origin "v${
-
+	git push origin
+
+install:
+	helm upgrade hypha charts/hypha --install --timeout 20m
+
+test:
+	helm test hypha
+
+install.and.test: install test
+
+

charts/hypha/Chart.lock

@@ -7,9 +7,9 @@ dependencies:
   version: 3.3.0
 - name: tritoninferenceserver-hypha
   repository: file://../tritoninferenceserver-hypha
-  version: 1.0.4
+  version: 1.0.5
 - name: redis
   repository: https://charts.bitnami.com/bitnami
   version: 17.11.6
-digest: sha256:54badeeee47a31d44c715b931fca25801036bfebd773806eb31d74d5fa4feeb3
-generated: "2023-07-03T12:44:14.147747653+01:00"
+digest: sha256:f513dba8f9978281f7d8e496c3341cdcabb07389f08fe168e52869b186acc852
+generated: "2023-09-19T10:41:56.049018409+01:00"

charts/hypha/Chart.yaml

@@ -1,7 +1,6 @@
 apiVersion: v2
 name: hypha
 description: A Helm chart for deploying Hypha to Kubernetes
-
 # A chart can be either an 'application' or a 'library' chart.
 #
 # Application charts are a collection of templates that can be packaged into versioned archives
@@ -11,18 +10,15 @@ description: A Helm chart for deploying Hypha to Kubernetes
 # a dependency of application charts to inject those utilities and functions into the rendering
 # pipeline. Library charts do not define any templates and therefore cannot be deployed.
 type: application
-
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 0.15.25
-
+version: 0.16.1
 # This is the version number of the application being deployed. This version number should be
 # 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: 0.15.25
-
 dependencies:
   - name: docker-registry
     # condition: docker-registry-mirror.enabled
@@ -47,9 +43,12 @@ dependencies:
   #   condition: ingress-nginx.enabled
   - name: tritoninferenceserver-hypha
     repository: "file://../tritoninferenceserver-hypha"
-    version: 1.0.4
+    version: 1.0.5
     condition: tritoninferenceserver-hypha.enabled
   - name: redis
     repository: "https://charts.bitnami.com/bitnami"
     version: 17.11.6
-    condition: redis.enabled
+    condition: redis.enabled
+maintainers:
+  - name: ctr26
+  - name: oeway

charts/hypha/templates/deployment.yaml

@@ -1,4 +1,3 @@
-
 {{- $S3_ENDPOINT_URL := .Values.s3_endpoint_url -}}
 {{- $S3_ENDPOINT_URL_PUBLIC := .Values.s3_endpoint_url_public -}}
 {{- $S3_ACCESS_KEY := .Values.s3_access_key -}}
@@ -43,6 +42,10 @@ spec:
       labels:
         {{- include "hypha.selectorLabels" . | nindent 8 }}
     spec:
+      {{- if .Values.nodeSelector }}
+      nodeSelector:
+{{ toYaml .Values.nodeSelector | indent 8 }}
+      {{- end }}
       containers:
       - name:  {{ .Chart.Name }}
         command: ["/bin/sh", "-c"]

charts/hypha/templates/tests/cellpose-test-configmap.yaml

@@ -0,0 +1,33 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ .Release.Name }}-test-script
+data:
+  test-hypha.py: |
+
+    import subprocess
+    subprocess.call(["pip", "install", "pyotritonclient", "kaibu-utils","numpy","Pillow"])
+
+    import io
+    from PIL import Image
+    # import matplotlib.pyplot as plt
+    # import numpy as np
+    from pyotritonclient import execute
+    from kaibu_utils import fetch_image
+    import asyncio
+    async def main():
+      image = await fetch_image("https://static.imjoy.io/img/img02.png")
+      image = image.astype("float32")
+      print("example image downloaded: ", image.shape)
+
+      param = {"diameter": 30, "model_type": "cyto"}
+      # run inference
+      results = await execute([image.transpose(2, 0, 1), param],
+                              server_url="http://{{ include "hypha.fullname" . }}/triton",
+                              model_name="cellpose-python",
+                              decode_bytes=True)
+      mask = results["mask"]
+      print("cellpose prediction: ", mask.shape)
+
+    if __name__ == "__main__":
+      asyncio.run(main())

charts/hypha/templates/tests/test-hypha-connection.yaml

@@ -0,0 +1,23 @@
+apiVersion: batch/v1
+kind: Job
+metadata:
+  name: "{{ .Release.Name }}-hypha-test"
+  labels:
+    app.kubernetes.io/managed-by: {{ .Release.Service | quote }}
+  annotations:
+    "helm.sh/hook": test-success
+spec:
+  template:
+    spec:
+      containers:
+      - name: hypha-test
+        image: python:3.8-slim
+        command: ["python", "/scripts/test-hypha.py"]
+        volumeMounts:
+        - name: test-script
+          mountPath: /scripts
+      restartPolicy: Never
+      volumes:
+      - name: test-script
+        configMap:
+          name: {{ .Release.Name }}-test-script