feat: predictions

.github/workflows/docker-publish.yml

@@ -0,0 +1,92 @@
+name: Docker
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+on:
+  push:
+    tags: [ 'v*.*.*' ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: ${{ github.repository }}
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@59acb6260d9c0ba8f4a2f9d9b48431a222b68e20 #v3.5.0
+        with:
+          cosign-release: 'v2.2.4'
+
+      # Set up BuildKit Docker container builder to be able to build
+      # multi-platform images and export cache
+      # https://github.com/docker/setup-buildx-action
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      # Sign the resulting Docker image digest except on PRs.
+      # This will only write to the public Rekor transparency log when the Docker
+      # repository is public to avoid leaking data.  If you would like to publish
+      # transparency data even for private images, pass --force to cosign below.
+      # https://github.com/sigstore/cosign
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        # This step uses the identity token to provision an ephemeral certificate
+        # against the sigstore community Fulcio instance.
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

.github/workflows/lint.yml

@@ -18,6 +18,6 @@ jobs:
           go-version-file: go.mod
 
       - name: Run linter
-        uses: golangci/golangci-lint-action@v6
+        uses: golangci/golangci-lint-action@v7
         with:
-          version: v1.63.4
+          version: v2.1.5

.golangci.yml

@@ -1,33 +1,15 @@
+version: "2"
 run:
-  timeout: 5m
   allow-parallel-runners: true
-
-issues:
-  # don't skip warning about doc comments
-  # don't exclude the default set of lint
-  exclude-use-default: false
-  # restore some of the defaults
-  # (fill in the rest as needed)
-  exclude-rules:
-    - path: "api/*"
-      linters:
-        - lll
-    - path: "internal/*"
-      linters:
-        - dupl
-        - lll
 linters:
-  disable-all: true
+  default: none
   enable:
+    - copyloopvar
     - dupl
     - errcheck
-    - copyloopvar
     - ginkgolinter
     - goconst
     - gocyclo
-    - gofmt
-    - goimports
-    - gosimple
     - govet
     - ineffassign
     - lll
@@ -36,12 +18,34 @@ linters:
     - prealloc
     - revive
     - staticcheck
-    - typecheck
     - unconvert
     - unparam
     - unused
-
-linters-settings:
-  revive:
+  settings:
+    revive:
+      rules:
+        - name: comment-spacings
+  exclusions:
+    generated: lax
     rules:
-      - name: comment-spacings
+      - linters:
+          - lll
+        path: api/*
+      - linters:
+          - dupl
+          - lll
+        path: internal/*
+    paths:
+      - third_party$
+      - builtin$
+      - examples$
+formatters:
+  enable:
+    - gofmt
+    - goimports
+  exclusions:
+    generated: lax
+    paths:
+      - third_party$
+      - builtin$
+      - examples$

Dockerfile

@@ -1,5 +1,5 @@
 # Build the manager binary
-FROM docker.io/golang:1.23 AS builder
+FROM docker.io/golang:1.24.2 AS builder
 ARG TARGETOS
 ARG TARGETARCH
 

PROJECT

@@ -17,4 +17,13 @@ resources:
   kind: ProteinDatabase
   path: github.com/kubefold/operator/api/v1
   version: v1
+- api:
+    crdVersion: v1
+    namespaced: true
+  controller: true
+  domain: kubefold.io
+  group: data
+  kind: ProteinConformationPrediction
+  path: github.com/kubefold/operator/api/v1
+  version: v1
 version: "3"

api/v1/proteinconformationprediction_types.go

@@ -0,0 +1,105 @@
+package v1
+
+import (
+	v1 "k8s.io/api/core/v1"
+	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
+)
+
+type ProteinConformationPredictionProtein struct {
+	// +kubebuilder:validation:XValidation:rule="self == oldSelf",message="Value is immutable"
+	Sequence string `json:"sequence"`
+	// +kubebuilder:validation:XValidation:rule="self == oldSelf",message="Value is immutable"
+	ID []string `json:"id"`
+}
+
+type ProteinConformationPredictionModelWeights struct {
+	HTTP string `json:"http"`
+}
+
+type ProteinConformationPredictionModelVolume struct {
+	// +optional
+	StorageClassName *string `json:"storageClassName,omitempty" protobuf:"bytes,5,opt,name=storageClassName"`
+	// +optional
+	Selector *metav1.LabelSelector `json:"selector,omitempty" protobuf:"bytes,4,opt,name=selector"`
+}
+
+type ProteinConformationPredictionModel struct {
+	// +kubebuilder:validation:XValidation:rule="self == oldSelf",message="Value is immutable"
+	Seeds   []int                                     `json:"seeds,omitempty"`
+	Weights ProteinConformationPredictionModelWeights `json:"weights"`
+	Volume  ProteinConformationPredictionModelVolume  `json:"volume,omitempty"`
+}
+
+type ProteinConformationPredictionDestinationS3 struct {
+	Bucket string `json:"bucket"`
+	Region string `json:"region"`
+}
+
+type ProteinConformationPredictionDestination struct {
+	S3 ProteinConformationPredictionDestinationS3 `json:"s3"`
+}
+
+type ProteinConformationPredictionNotifications struct {
+	SMS    []string `json:"sms,omitempty"`
+	Region string   `json:"region"`
+}
+
+type ProteinConformationPredictionJob struct {
+	SearchNodeSelector     v1.NodeSelector `json:"searchNodeSelector,omitempty"`
+	PredictionNodeSelector v1.NodeSelector `json:"predictionNodeSelector,omitempty"`
+}
+
+type ProteinConformationPredictionSpec struct {
+	// +kubebuilder:validation:XValidation:rule="self == oldSelf",message="Value is immutable"
+	Protein       ProteinConformationPredictionProtein       `json:"protein"`
+	Model         ProteinConformationPredictionModel         `json:"model,omitempty"`
+	Destination   ProteinConformationPredictionDestination   `json:"destination"`
+	Notifications ProteinConformationPredictionNotifications `json:"notify,omitempty"`
+	Job           ProteinConformationPredictionJob           `json:"job,omitempty"`
+	Database      string                                     `json:"database"`
+	StorageClass  string                                     `json:"storageClass,omitempty"`
+}
+
+type ProteinConformationPredictionStatusPhase string
+
+const (
+	ProteinConformationPredictionStatusPhaseNotStarted         ProteinConformationPredictionStatusPhase = "NotStarted"
+	ProteinConformationPredictionStatusPhaseAligning           ProteinConformationPredictionStatusPhase = "Aligning"
+	ProteinConformationPredictionStatusPhasePredicting         ProteinConformationPredictionStatusPhase = "Predicting"
+	ProteinConformationPredictionStatusPhaseUploadingArtifacts ProteinConformationPredictionStatusPhase = "UploadingArtifacts"
+	ProteinConformationPredictionStatusPhaseCompleted          ProteinConformationPredictionStatusPhase = "Completed"
+	ProteinConformationPredictionStatusPhaseFailed             ProteinConformationPredictionStatusPhase = "Failed"
+)
+
+type ProteinConformationPredictionStatus struct {
+	Phase          ProteinConformationPredictionStatusPhase `json:"phase,omitempty"`
+	SequencePrefix string                                   `json:"sequencePrefix,omitempty"`
+	Error          string                                   `json:"error,omitempty"`
+	RetryCount     int32                                    `json:"retryCount,omitempty"`
+}
+
+// +kubebuilder:object:root=true
+// +kubebuilder:subresource:status
+// +kubebuilder:printcolumn:name="Phase",type=string,JSONPath=`.status.phase`
+// +kubebuilder:printcolumn:name="Sequence",type=string,JSONPath=`.status.sequencePrefix`
+// +kubebuilder:printcolumn:name="Age",type="date",JSONPath=".metadata.creationTimestamp"
+
+type ProteinConformationPrediction struct {
+	metav1.TypeMeta   `json:",inline"`
+	metav1.ObjectMeta `json:"metadata,omitempty"`
+
+	Spec   ProteinConformationPredictionSpec   `json:"spec,omitempty"`
+	Status ProteinConformationPredictionStatus `json:"status,omitempty"`
+}
+
+// +kubebuilder:object:root=true
+
+type ProteinConformationPredictionList struct {
+	metav1.TypeMeta `json:",inline"`
+	metav1.ListMeta `json:"metadata,omitempty"`
+	Items           []ProteinConformationPrediction `json:"items"`
+}
+
+func init() {
+	SchemeBuilder.Register(&ProteinConformationPrediction{}, &ProteinConformationPredictionList{})
+}