@platforma-open/milaboratories.3d-structure-prediction.workflow 1.1.1 → 1.1.2

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/3d-structure-prediction/3d-structure-prediction/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.3d-structure-prediction.workflow@1.1.1 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/workflow
+> @platforma-open/milaboratories.3d-structure-prediction.workflow@1.1.2 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/workflow
 > shx rm -rf dist && pl-tengo check && pl-tengo build
 
   info: Skipping unknown file type: wf.test.ts

package/CHANGELOG.md

@@ -1,5 +1,13 @@
 # @platforma-open/milaboratories.3d-structure-prediction.workflow
 
+## 1.1.2
+
+### Patch Changes
+
+- 8aeaff0: Load ImmuneBuilder model weights from a published Platforma asset (`immunebuilder-weights-assets`) instead of downloading them from Zenodo at runtime. The matching per-mode asset is mounted into each batch workdir and passed to ImmuneBuilder via `--weights-dir`. Removes the pre-warmup step, the per-batch warmup sentinel wiring, and the Docker image weight bake.
+- Updated dependencies [8aeaff0]
+  - @platforma-open/milaboratories.3d-structure-prediction.software@1.0.7
+
 ## 1.1.1
 
 ### Patch Changes

package/package.json

@@ -1,13 +1,14 @@
 {
   "name": "@platforma-open/milaboratories.3d-structure-prediction.workflow",
-  "version": "1.1.1",
+  "version": "1.1.2",
   "description": "Block Workflow",
   "type": "module",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "6.2.0",
-    "@platforma-open/milaboratories.3d-structure-prediction.software": "1.0.6"
+    "@platforma-open/milaboratories.3d-structure-prediction.software": "1.0.7"
   },
   "devDependencies": {
+    "@platforma-open/milaboratories.immunebuilder-weights-assets": "^1.1.0",
     "@platforma-sdk/tengo-builder": "4.0.2",
     "@platforma-sdk/test": "1.77.19"
   },

package/src/main.tpl.tengo

@@ -5,14 +5,11 @@ xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
 pSpec := import("@platforma-sdk/workflow-tengo:pframes.spec")
 pt := import("@platforma-sdk/workflow-tengo:pt")
 smart := import("@platforma-sdk/workflow-tengo:smart")
-exec := import("@platforma-sdk/workflow-tengo:exec")
-units := import("@platforma-sdk/workflow-tengo:units")
 times := import("times")
 
 structureColsConv := import(":structure-cols-conv")
 
 predictBatchTpl := assets.importTemplate(":predict-batch")
-immuneBuilderSw := assets.importSoftware("@platforma-open/milaboratories.3d-structure-prediction.software:immunebuilder-predict")
 
 wf.setPreRun(assets.importTemplate(":prerun"))
 
@@ -98,36 +95,17 @@ wf.body(func(args) {
 
 	confidenceXsvColumns := structureColsConv.getConfidenceColumns(isPaired)
 
-	// Pre-download model weights once, before the batch fan-out. ImmuneBuilder
-	// fetches weights on first predictor construction into a shared on-disk
-	// cache; without this step, N parallel batch containers race to write the
-	// same files and produce partial/corrupt caches that fail with no retry.
-	// The sentinel file is forwarded as a body input — each batch awaits it
-	// (via addFile in predict-batch.tpl.tengo) before its own exec runs, so
-	// every batch starts against an already-warm cache.
-	warmupRun := exec.builder().
-		software(immuneBuilderSw).
-		cpu(1).mem(2 * units.GiB).
-		env("BLOCK_VERSION", blockId).
-		arg("--warmup").
-		arg("--mode").arg(args.mode).
-		arg("--sentinel").arg("warmup.done").
-		saveFile("warmup.done").
-		printErrStreamToStdout().
-		saveStdoutStream().
-		run()
-	warmupSentinel := warmupRun.getFile("warmup.done")
-
-	// Per-batch scalar settings forwarded to predict-batch as `inputs.<key>`.
 	bodyExtra := {
 		mode: smart.createJsonResource(args.mode),
 		seed: smart.createJsonResource(seed),
-		cpu: smart.createJsonResource(cpu),
-		memGiB: smart.createJsonResource(memGiB),
 		confidenceMetric: smart.createJsonResource(confidenceMetric),
 		threshold: smart.createJsonResource(threshold),
-		blockId: smart.createJsonResource(blockId),
-		warmupSentinel: warmupSentinel
+		blockId: smart.createJsonResource(blockId)
+	}
+
+	bodyMeta := {
+		cpu: smart.createJsonResource(cpu),
+		memGiB: smart.createJsonResource(memGiB)
 	}
 
 	processResult := pframes.processColumn(
@@ -162,6 +140,7 @@ wf.body(func(args) {
 				passContent: false
 			},
 			extra: bodyExtra,
+			metaExtra: bodyMeta,
 			stepCache: 30 * times.minute
 		}
 	)

package/src/predict-batch.tpl.tengo

@@ -35,24 +35,34 @@ self.body(func(inputs) {
 
 	mode := inputs.mode
 	seed := inputs.seed
-	cpu := inputs.cpu
-	memGiB := inputs.memGiB
+	cpu := is_undefined(inputs.cpu) ? 4 : inputs.cpu
+	memGiB := is_undefined(inputs.memGiB) ? 4 : inputs.memGiB
 	confidenceMetric := inputs.confidenceMetric
 	threshold := inputs.threshold
 	blockId := inputs.blockId
-	// Sentinel produced by the workflow's pre-warmup step. We don't consume
-	// the file content — adding it as a workdir input is what wires this batch
-	// to await the warmup resource, so every batch only starts after the
-	// shared model cache is populated.
-	warmupSentinel := inputs.warmupSentinel
+
+	// Model weights ship as a published Platforma asset (one per predictor),
+	// mounted into `models/` in the workdir. ImmuneBuilder is pointed at it via
+	// `--weights-dir`, so it never downloads from Zenodo at runtime. `mode` is a
+	// plain build-time value here (processColumn `extra`), so we pick the
+	// matching asset directly.
+	weightsAsset := undefined
+	if mode == "ABodyBuilder2" {
+		weightsAsset = assets.importAsset("@platforma-open/milaboratories.immunebuilder-weights-assets:abodybuilder2")
+	} else if mode == "NanoBodyBuilder2" {
+		weightsAsset = assets.importAsset("@platforma-open/milaboratories.immunebuilder-weights-assets:nanobodybuilder2")
+	} else {
+		ll.panic("predict-batch: unknown mode %v", mode)
+	}
 
 	predictRun := exec.builder().
 		software(immuneBuilderSw).
 		cpu(cpu).mem(memGiB * units.GiB).
 		env("BLOCK_VERSION", blockId).
-		addFile("warmup.done", warmupSentinel).
+		addAsset(weightsAsset, "models").
 		addFile("batch.tsv", batchFile).
 		arg("--mode").arg(mode).
+		arg("--weights-dir").arg("models").
 		arg("--input").arg("batch.tsv").
 		arg("--output-dir").arg("pdbs").
 		arg("--manifest").arg("manifest.tsv").