Clean up updates

.github/workflows/nextflow.yaml

@@ -6,25 +6,8 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Set up Go 1.x
-      uses: actions/setup-go@v5
-      with:
-        go-version: 1.21
+    uses: ./.github/workflows/build.yml
 
-    - name: Check out code
-      uses: actions/checkout@v2
-
-    - name: Build Funnel (if cache does not exist)
-      run: make build
-
-    - name: Store Funnel
-      uses: actions/upload-artifact@v4
-      with:
-        name: funnelBin
-        path: funnel
-
   nextflow:
     needs: build
     runs-on: ubuntu-latest

compute/kubernetes/backend_test.go

@@ -1,62 +1,15 @@
 package kubernetes
 
 import (
-	"context"
 	"fmt"
 	"os"
 	"testing"
 
-	"path/filepath"
-
 	"github.com/ohsu-comp-bio/funnel/config"
 	"github.com/ohsu-comp-bio/funnel/logger"
 	"github.com/ohsu-comp-bio/funnel/tes"
-	"k8s.io/client-go/kubernetes"
-	"k8s.io/client-go/rest"
-	"k8s.io/client-go/tools/clientcmd"
-	"k8s.io/client-go/util/homedir"
 )
 
-// getKubernetesClient creates a Kubernetes clientset for communication with the Kubernetes API
-func getKubernetesClient() (*kubernetes.Clientset, error) {
-	var config *rest.Config
-	var err error
-	var contextName string
-
-	// Try to create an in-cluster client
-	config, err = rest.InClusterConfig()
-	if err != nil {
-		// If in-cluster config fails, fallback to kubeconfig file for out-of-cluster
-		kubeconfig := filepath.Join(homedir.HomeDir(), ".kube", "config")
-		kubeConfig, err := clientcmd.LoadFromFile(kubeconfig)
-		if err != nil {
-			return nil, fmt.Errorf("failed to load kubeconfig: %v", err)
-		}
-
-		// Get the current context name
-		contextName = kubeConfig.CurrentContext
-
-		// Build config from flags or kubeconfig
-		config, err = clientcmd.BuildConfigFromFlags("", kubeconfig)
-		if err != nil {
-			return nil, fmt.Errorf("failed to create kubernetes config: %v", err)
-		}
-	} else {
-		contextName = "in-cluster"
-	}
-
-	// Create the clientset
-	clientset, err := kubernetes.NewForConfig(config)
-	if err != nil {
-		return nil, fmt.Errorf("failed to create kubernetes clientset: %v", err)
-	}
-
-	// Log or print the current context being used
-	fmt.Printf("Using Kubernetes context: %s\n", contextName)
-
-	return clientset, nil
-}
-
 func TestCreateJobc(t *testing.T) {
 	conf := config.DefaultConfig().Kubernetes
 	content, err := os.ReadFile("../../config/kubernetes-template.yaml")
@@ -65,15 +18,8 @@ func TestCreateJobc(t *testing.T) {
 	}
 	conf.Template = string(content)
 	log := logger.NewLogger("test", logger.DefaultConfig())
-
-	// Create Kubernetes client
-	clientset, err := getKubernetesClient()
-	if err != nil {
-		t.Fatal(fmt.Errorf("creating kubernetes client: %v", err))
-	}
-
 	b := &Backend{
-		client:    clientset.BatchV1().Jobs(conf.Namespace),
+		client:    nil,
 		namespace: conf.Namespace,
 		template:  conf.Template,
 		event:     nil,
@@ -96,9 +42,4 @@ func TestCreateJobc(t *testing.T) {
 		t.Fatal(err)
 	}
 	t.Logf("%+v", job)
-
-	err = b.Submit(context.Background(), task)
-	if err != nil {
-		t.Fatal(err)
-	}
 }

compute/scheduler/testutils_test.go

@@ -3,7 +3,7 @@ package scheduler
 import (
 	"context"
 	"fmt"
-	"io/ioutil"
+	"os"
 	"testing"
 	"time"