@inflexa-ai/harness 0.14.1 → 0.15.0

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Files changed (120) hide show
  1. package/README.md +2 -1
  2. package/dist/agents/conversation-agent.d.ts +7 -0
  3. package/dist/agents/conversation-agent.js +5 -3
  4. package/dist/app/synthesize-run.d.ts +3 -0
  5. package/dist/app/synthesize-run.js +2 -1
  6. package/dist/billing/noop-usage-recorder.d.ts +7 -0
  7. package/dist/billing/noop-usage-recorder.js +10 -0
  8. package/dist/billing/usage-recorder.d.ts +63 -0
  9. package/dist/billing/usage-recorder.js +15 -0
  10. package/dist/contracts/chat-events.d.ts +44 -3
  11. package/dist/contracts/chat-parts.d.ts +38 -2
  12. package/dist/contracts/chat-parts.js +1 -1
  13. package/dist/contracts/data-profile.d.ts +26 -0
  14. package/dist/contracts/data-profile.js +26 -0
  15. package/dist/contracts/index.d.ts +3 -1
  16. package/dist/contracts/index.js +1 -0
  17. package/dist/contracts/message.d.ts +21 -1
  18. package/dist/contracts/part-registry.js +1 -0
  19. package/dist/contracts/schemas/chat-events.d.ts +48 -2
  20. package/dist/contracts/schemas/chat-events.js +8 -1
  21. package/dist/contracts/schemas/chat-parts.d.ts +46 -3
  22. package/dist/contracts/schemas/chat-parts.js +13 -0
  23. package/dist/contracts/schemas/index.d.ts +2 -1
  24. package/dist/contracts/schemas/index.js +2 -1
  25. package/dist/contracts/schemas/usage.d.ts +11 -0
  26. package/dist/contracts/schemas/usage.js +18 -0
  27. package/dist/contracts/usage.d.ts +51 -0
  28. package/dist/contracts/usage.js +41 -0
  29. package/dist/execution/artifact-metadata.d.ts +3 -0
  30. package/dist/execution/artifact-metadata.js +1 -0
  31. package/dist/execution/dbos-workflow-purger.d.ts +30 -0
  32. package/dist/execution/dbos-workflow-purger.js +193 -0
  33. package/dist/execution/post-step-pipeline.d.ts +3 -0
  34. package/dist/execution/post-step-pipeline.js +2 -0
  35. package/dist/execution/reconcile-manifest.js +28 -15
  36. package/dist/execution/report-runner.d.ts +16 -0
  37. package/dist/execution/report-runner.js +4 -0
  38. package/dist/execution/run-synthesis.d.ts +3 -0
  39. package/dist/execution/run-synthesis.js +2 -0
  40. package/dist/execution/step-summary.d.ts +3 -0
  41. package/dist/execution/step-summary.js +1 -0
  42. package/dist/execution/workflow-purger.d.ts +38 -0
  43. package/dist/execution/workflow-purger.js +24 -0
  44. package/dist/index.d.ts +25 -3
  45. package/dist/index.js +28 -1
  46. package/dist/lib/metrics.js +2 -1
  47. package/dist/loop/metrics.d.ts +18 -0
  48. package/dist/loop/metrics.js +18 -1
  49. package/dist/loop/run-agent.d.ts +35 -0
  50. package/dist/loop/run-agent.js +149 -23
  51. package/dist/loop/run-to-terminal.d.ts +5 -2
  52. package/dist/loop/run-to-terminal.js +36 -2
  53. package/dist/loop/tool-detail.d.ts +54 -0
  54. package/dist/loop/tool-detail.js +105 -0
  55. package/dist/loop/tool-outcome.d.ts +21 -0
  56. package/dist/loop/tool-outcome.js +25 -0
  57. package/dist/loop/types.d.ts +15 -1
  58. package/dist/memory/content-to-cortex.d.ts +28 -4
  59. package/dist/memory/content-to-cortex.js +70 -14
  60. package/dist/memory/thread-history.d.ts +21 -1
  61. package/dist/memory/thread-history.js +29 -7
  62. package/dist/memory/thread-store.d.ts +65 -8
  63. package/dist/memory/thread-store.js +81 -17
  64. package/dist/provenance/collector.d.ts +5 -3
  65. package/dist/provenance/collector.js +5 -3
  66. package/dist/providers/ai-sdk.d.ts +18 -0
  67. package/dist/providers/ai-sdk.js +129 -16
  68. package/dist/providers/anthropic.d.ts +2 -0
  69. package/dist/providers/anthropic.js +1 -0
  70. package/dist/providers/streaming-chat.js +5 -0
  71. package/dist/providers/types.d.ts +23 -0
  72. package/dist/providers/types.js +1 -0
  73. package/dist/runtime/assemble.d.ts +25 -8
  74. package/dist/runtime/assemble.js +7 -4
  75. package/dist/sandbox/sandbox-step-translate.d.ts +22 -1
  76. package/dist/sandbox/sandbox-step-translate.js +23 -36
  77. package/dist/schemas/run-synthesis.d.ts +2 -2
  78. package/dist/state/index.d.ts +2 -0
  79. package/dist/state/index.js +3 -0
  80. package/dist/state/init.js +28 -0
  81. package/dist/state/purge-analysis.d.ts +74 -0
  82. package/dist/state/purge-analysis.js +205 -0
  83. package/dist/state/vector-store.d.ts +6 -0
  84. package/dist/state/vector-store.js +22 -2
  85. package/dist/tasks/data-profile-activity.d.ts +14 -2
  86. package/dist/tasks/data-profile-activity.js +1 -1
  87. package/dist/tasks/data-profile.d.ts +3 -0
  88. package/dist/tasks/data-profile.js +9 -3
  89. package/dist/tools/bio/pubmed.js +15 -0
  90. package/dist/tools/bio/search-gene.js +12 -0
  91. package/dist/tools/define-tool.d.ts +41 -3
  92. package/dist/tools/define-tool.js +4 -1
  93. package/dist/tools/detail-resolver.d.ts +35 -0
  94. package/dist/tools/detail-resolver.js +39 -0
  95. package/dist/tools/execute-analysis.js +3 -0
  96. package/dist/tools/iterate-report.d.ts +3 -0
  97. package/dist/tools/iterate-report.js +3 -0
  98. package/dist/tools/memory/update-working-memory.js +8 -0
  99. package/dist/tools/research/generate-analogy-report.d.ts +3 -0
  100. package/dist/tools/research/generate-analogy-report.js +6 -0
  101. package/dist/tools/research/generate-plan.d.ts +3 -0
  102. package/dist/tools/research/generate-plan.js +6 -0
  103. package/dist/tools/research/inspect-run.js +4 -0
  104. package/dist/tools/research/literature-reviewer.d.ts +3 -0
  105. package/dist/tools/research/literature-reviewer.js +6 -0
  106. package/dist/tools/workspace/edit-file.js +2 -0
  107. package/dist/tools/workspace/execute-command.js +25 -0
  108. package/dist/tools/workspace/grep.js +3 -0
  109. package/dist/tools/workspace/list-files.js +2 -0
  110. package/dist/tools/workspace/read-file.js +7 -0
  111. package/dist/tools/workspace/workspace-search.js +1 -0
  112. package/dist/tools/workspace/write-file.js +3 -0
  113. package/dist/workflows/execute-analysis.d.ts +7 -0
  114. package/dist/workflows/execute-analysis.js +31 -2
  115. package/dist/workflows/execute-target-assessment.d.ts +3 -0
  116. package/dist/workflows/sandbox-step.d.ts +23 -0
  117. package/dist/workflows/sandbox-step.js +33 -2
  118. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.d.ts +3 -0
  119. package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js +1 -0
  120. package/package.json +2 -2
package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.d.ts CHANGED
@@ -19,6 +19,7 @@ import { z } from "zod";
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  import type { Pool } from "pg";
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  import type { AgentSession } from "../../../auth/types.js";
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  import type { ChatProvider } from "../../../providers/types.js";
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+ import type { UsageRecorder } from "../../../billing/usage-recorder.js";
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  export declare const OffTargetAnnotationSchema: z.ZodObject<{
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  clinical_consequence: z.ZodString;
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  provenance: z.ZodString;
@@ -28,6 +29,8 @@ export interface ClinicalConsequenceAnnotatorDeps {
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  readonly provider: ChatProvider;
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  readonly session: AgentSession;
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  readonly model: string;
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+ /** LLM usage-accounting seam for the annotator loop; omitted falls back to the no-op recorder. */
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+ readonly usageRecorder?: UsageRecorder;
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  }
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  export interface AnnotationInput {
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  primaryTargetGene: string;
package/dist/workflows/target-assessment/lib/clinical-consequence-annotator.js CHANGED
@@ -126,6 +126,7 @@ export async function annotateClinicalConsequence(pool, input, deps) {
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  signal: controller.signal,
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  emit: () => { },
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  runStep: passthroughStep,
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+ usageRecorder: deps.usageRecorder,
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  });
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  const raw = extractJsonObject(finalText(messages));
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  if (raw === null)
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@inflexa-ai/harness",
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- "version": "0.14.1",
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+ "version": "0.15.0",
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  "description": "Host-agnostic bioinformatics agent harness \u2014 hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
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  "license": "Apache-2.0",
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  "type": "module",
@@ -44,7 +44,7 @@
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  "typecheck": "tsc --noEmit"
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  },
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  "dependencies": {
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- "@ai-sdk/anthropic": "^4.0.15",
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+ "@ai-sdk/anthropic": "^4.0.20",
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  "@ai-sdk/openai-compatible": "^3.0.10",
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  "@ai-sdk/provider": "^4.0.3",
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  "@ai-sdk/provider-utils": "5.0.10",