@inflexa-ai/harness 0.45.0 → 0.46.0

package/dist/citations/types.d.ts

@@ -1,20 +1,20 @@
 import { z } from "zod";
 export declare const CitationKindSchema: z.ZodEnum<{
+    arxiv: "arxiv";
     auto: "auto";
     doi: "doi";
-    pmid: "pmid";
-    arxiv: "arxiv";
     free_text: "free_text";
+    pmid: "pmid";
 }>;
 export type CitationKind = z.infer<typeof CitationKindSchema>;
 export declare const CitationInputSchema: z.ZodObject<{
     citation: z.ZodString;
     kind: z.ZodOptional<z.ZodEnum<{
+        arxiv: "arxiv";
         auto: "auto";
         doi: "doi";
-        pmid: "pmid";
-        arxiv: "arxiv";
         free_text: "free_text";
+        pmid: "pmid";
     }>>;
     title: z.ZodOptional<z.ZodString>;
     authors: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -26,31 +26,31 @@ export declare const CitationInputSchema: z.ZodObject<{
 export type CitationInput = z.infer<typeof CitationInputSchema>;
 export declare const CitationSourceSchema: z.ZodEnum<{
     arxiv: "arxiv";
-    doi_registry: "doi_registry";
     crossref: "crossref";
+    doi_registry: "doi_registry";
     pubmed: "pubmed";
     semantic_scholar: "semantic_scholar";
 }>;
 export type CitationSource = z.infer<typeof CitationSourceSchema>;
 export declare const CitationSourceStatusSchema: z.ZodEnum<{
-    ok: "ok";
     no_data: "no_data";
-    unavailable: "unavailable";
     not_applicable: "not_applicable";
+    ok: "ok";
+    unavailable: "unavailable";
 }>;
 export type CitationSourceStatus = z.infer<typeof CitationSourceStatusSchema>;
 export declare const CitationVerdictSchema: z.ZodEnum<{
-    verified: "verified";
+    inconclusive: "inconclusive";
     metadata_mismatch: "metadata_mismatch";
     not_found: "not_found";
     unverifiable: "unverifiable";
-    inconclusive: "inconclusive";
+    verified: "verified";
 }>;
 export type CitationVerdict = z.infer<typeof CitationVerdictSchema>;
 export declare const CitationCoverageSchema: z.ZodEnum<{
-    partial: "partial";
-    none: "none";
     complete: "complete";
+    none: "none";
+    partial: "partial";
 }>;
 export type CitationCoverage = z.infer<typeof CitationCoverageSchema>;
 export declare const ComparisonStatusSchema: z.ZodEnum<{
@@ -60,12 +60,12 @@ export declare const ComparisonStatusSchema: z.ZodEnum<{
 }>;
 export type ComparisonStatus = z.infer<typeof ComparisonStatusSchema>;
 export declare const CitationFieldSchema: z.ZodEnum<{
-    title: "title";
     authors: "authors";
-    year: "year";
+    firstPage: "firstPage";
+    title: "title";
     venue: "venue";
     volume: "volume";
-    firstPage: "firstPage";
+    year: "year";
 }>;
 export type CitationField = z.infer<typeof CitationFieldSchema>;
 export declare const UnsupportedWorkKindSchema: z.ZodEnum<{
@@ -94,10 +94,10 @@ export declare const NormalizedCitationSchema: z.ZodObject<{
     citation: z.ZodString;
     query: z.ZodString;
     kind: z.ZodEnum<{
-        doi: "doi";
-        pmid: "pmid";
         arxiv: "arxiv";
+        doi: "doi";
         free_text: "free_text";
+        pmid: "pmid";
     }>;
     identifiers: z.ZodObject<{
         doi: z.ZodOptional<z.ZodString>;
@@ -123,8 +123,8 @@ export type NormalizedCitation = z.infer<typeof NormalizedCitationSchema>;
 export declare const CitationRecordSchema: z.ZodObject<{
     source: z.ZodEnum<{
         arxiv: "arxiv";
-        doi_registry: "doi_registry";
         crossref: "crossref";
+        doi_registry: "doi_registry";
         pubmed: "pubmed";
         semantic_scholar: "semantic_scholar";
     }>;
@@ -147,9 +147,9 @@ export declare const CitationRecordSchema: z.ZodObject<{
 export type CitationRecord = z.infer<typeof CitationRecordSchema>;
 export declare const IdentifierEvidenceSchema: z.ZodObject<{
     type: z.ZodEnum<{
+        arxiv: "arxiv";
         doi: "doi";
         pmid: "pmid";
-        arxiv: "arxiv";
     }>;
     identifier: z.ZodString;
     exists: z.ZodBoolean;
@@ -160,24 +160,24 @@ export type IdentifierEvidence = z.infer<typeof IdentifierEvidenceSchema>;
 export declare const CitationSourceOutcomeSchema: z.ZodObject<{
     source: z.ZodEnum<{
         arxiv: "arxiv";
-        doi_registry: "doi_registry";
         crossref: "crossref";
+        doi_registry: "doi_registry";
         pubmed: "pubmed";
         semantic_scholar: "semantic_scholar";
     }>;
     operation: z.ZodString;
     status: z.ZodEnum<{
-        ok: "ok";
         no_data: "no_data";
-        unavailable: "unavailable";
         not_applicable: "not_applicable";
+        ok: "ok";
+        unavailable: "unavailable";
     }>;
     requestCount: z.ZodNumber;
     records: z.ZodArray<z.ZodObject<{
         source: z.ZodEnum<{
             arxiv: "arxiv";
-            doi_registry: "doi_registry";
             crossref: "crossref";
+            doi_registry: "doi_registry";
             pubmed: "pubmed";
             semantic_scholar: "semantic_scholar";
         }>;
@@ -200,9 +200,9 @@ export declare const CitationSourceOutcomeSchema: z.ZodObject<{
     detail: z.ZodOptional<z.ZodString>;
     identifierEvidence: z.ZodOptional<z.ZodObject<{
         type: z.ZodEnum<{
+            arxiv: "arxiv";
             doi: "doi";
             pmid: "pmid";
-            arxiv: "arxiv";
         }>;
         identifier: z.ZodString;
         exists: z.ZodBoolean;
@@ -213,12 +213,12 @@ export declare const CitationSourceOutcomeSchema: z.ZodObject<{
 export type CitationSourceOutcome = z.infer<typeof CitationSourceOutcomeSchema>;
 export declare const CitationFieldComparisonSchema: z.ZodObject<{
     field: z.ZodEnum<{
-        title: "title";
         authors: "authors";
-        year: "year";
+        firstPage: "firstPage";
+        title: "title";
         venue: "venue";
         volume: "volume";
-        firstPage: "firstPage";
+        year: "year";
     }>;
     status: z.ZodEnum<{
         match: "match";
@@ -229,8 +229,8 @@ export declare const CitationFieldComparisonSchema: z.ZodObject<{
     sourceValues: z.ZodArray<z.ZodObject<{
         source: z.ZodEnum<{
             arxiv: "arxiv";
-            doi_registry: "doi_registry";
             crossref: "crossref";
+            doi_registry: "doi_registry";
             pubmed: "pubmed";
             semantic_scholar: "semantic_scholar";
         }>;
@@ -241,18 +241,18 @@ export declare const CitationFieldComparisonSchema: z.ZodObject<{
 export type CitationFieldComparison = z.infer<typeof CitationFieldComparisonSchema>;
 export declare const CitationConflictSchema: z.ZodObject<{
     field: z.ZodEnum<{
-        title: "title";
         authors: "authors";
-        year: "year";
+        firstPage: "firstPage";
+        title: "title";
         venue: "venue";
         volume: "volume";
-        firstPage: "firstPage";
+        year: "year";
     }>;
     values: z.ZodArray<z.ZodObject<{
         source: z.ZodEnum<{
             arxiv: "arxiv";
-            doi_registry: "doi_registry";
             crossref: "crossref";
+            doi_registry: "doi_registry";
             pubmed: "pubmed";
             semantic_scholar: "semantic_scholar";
         }>;
@@ -274,8 +274,8 @@ export declare const CitationCandidateClusterSchema: z.ZodObject<{
     records: z.ZodArray<z.ZodObject<{
         source: z.ZodEnum<{
             arxiv: "arxiv";
-            doi_registry: "doi_registry";
             crossref: "crossref";
+            doi_registry: "doi_registry";
             pubmed: "pubmed";
             semantic_scholar: "semantic_scholar";
         }>;
@@ -309,11 +309,11 @@ export declare const CitationResolutionResultSchema: z.ZodObject<{
     input: z.ZodObject<{
         citation: z.ZodString;
         kind: z.ZodOptional<z.ZodEnum<{
+            arxiv: "arxiv";
             auto: "auto";
             doi: "doi";
-            pmid: "pmid";
-            arxiv: "arxiv";
             free_text: "free_text";
+            pmid: "pmid";
         }>>;
         title: z.ZodOptional<z.ZodString>;
         authors: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -326,10 +326,10 @@ export declare const CitationResolutionResultSchema: z.ZodObject<{
         citation: z.ZodString;
         query: z.ZodString;
         kind: z.ZodEnum<{
-            doi: "doi";
-            pmid: "pmid";
             arxiv: "arxiv";
+            doi: "doi";
             free_text: "free_text";
+            pmid: "pmid";
         }>;
         identifiers: z.ZodObject<{
             doi: z.ZodOptional<z.ZodString>;
@@ -354,24 +354,24 @@ export declare const CitationResolutionResultSchema: z.ZodObject<{
     sourceOutcomes: z.ZodArray<z.ZodObject<{
         source: z.ZodEnum<{
             arxiv: "arxiv";
-            doi_registry: "doi_registry";
             crossref: "crossref";
+            doi_registry: "doi_registry";
             pubmed: "pubmed";
             semantic_scholar: "semantic_scholar";
         }>;
         operation: z.ZodString;
         status: z.ZodEnum<{
-            ok: "ok";
             no_data: "no_data";
-            unavailable: "unavailable";
             not_applicable: "not_applicable";
+            ok: "ok";
+            unavailable: "unavailable";
         }>;
         requestCount: z.ZodNumber;
         records: z.ZodArray<z.ZodObject<{
             source: z.ZodEnum<{
                 arxiv: "arxiv";
-                doi_registry: "doi_registry";
                 crossref: "crossref";
+                doi_registry: "doi_registry";
                 pubmed: "pubmed";
                 semantic_scholar: "semantic_scholar";
             }>;
@@ -394,9 +394,9 @@ export declare const CitationResolutionResultSchema: z.ZodObject<{
         detail: z.ZodOptional<z.ZodString>;
         identifierEvidence: z.ZodOptional<z.ZodObject<{
             type: z.ZodEnum<{
+                arxiv: "arxiv";
                 doi: "doi";
                 pmid: "pmid";
-                arxiv: "arxiv";
             }>;
             identifier: z.ZodString;
             exists: z.ZodBoolean;
@@ -410,8 +410,8 @@ export declare const CitationResolutionResultSchema: z.ZodObject<{
         records: z.ZodArray<z.ZodObject<{
             source: z.ZodEnum<{
                 arxiv: "arxiv";
-                doi_registry: "doi_registry";
                 crossref: "crossref";
+                doi_registry: "doi_registry";
                 pubmed: "pubmed";
                 semantic_scholar: "semantic_scholar";
             }>;
@@ -443,12 +443,12 @@ export declare const CitationResolutionResultSchema: z.ZodObject<{
     selectedClusterId: z.ZodOptional<z.ZodString>;
     comparisons: z.ZodArray<z.ZodObject<{
         field: z.ZodEnum<{
-            title: "title";
             authors: "authors";
-            year: "year";
+            firstPage: "firstPage";
+            title: "title";
             venue: "venue";
             volume: "volume";
-            firstPage: "firstPage";
+            year: "year";
         }>;
         status: z.ZodEnum<{
             match: "match";
@@ -459,8 +459,8 @@ export declare const CitationResolutionResultSchema: z.ZodObject<{
         sourceValues: z.ZodArray<z.ZodObject<{
             source: z.ZodEnum<{
                 arxiv: "arxiv";
-                doi_registry: "doi_registry";
                 crossref: "crossref";
+                doi_registry: "doi_registry";
                 pubmed: "pubmed";
                 semantic_scholar: "semantic_scholar";
             }>;
@@ -470,18 +470,18 @@ export declare const CitationResolutionResultSchema: z.ZodObject<{
     }, z.core.$strip>>;
     conflicts: z.ZodArray<z.ZodObject<{
         field: z.ZodEnum<{
-            title: "title";
             authors: "authors";
-            year: "year";
+            firstPage: "firstPage";
+            title: "title";
             venue: "venue";
             volume: "volume";
-            firstPage: "firstPage";
+            year: "year";
         }>;
         values: z.ZodArray<z.ZodObject<{
             source: z.ZodEnum<{
                 arxiv: "arxiv";
-                doi_registry: "doi_registry";
                 crossref: "crossref";
+                doi_registry: "doi_registry";
                 pubmed: "pubmed";
                 semantic_scholar: "semantic_scholar";
             }>;
@@ -489,63 +489,63 @@ export declare const CitationResolutionResultSchema: z.ZodObject<{
         }, z.core.$strip>>;
     }, z.core.$strip>>;
     verdict: z.ZodEnum<{
-        verified: "verified";
+        inconclusive: "inconclusive";
         metadata_mismatch: "metadata_mismatch";
         not_found: "not_found";
         unverifiable: "unverifiable";
-        inconclusive: "inconclusive";
+        verified: "verified";
     }>;
     coverage: z.ZodEnum<{
-        partial: "partial";
-        none: "none";
         complete: "complete";
+        none: "none";
+        partial: "partial";
     }>;
 }, z.core.$strip>;
 export type CitationResolutionResult = z.infer<typeof CitationResolutionResultSchema>;
-export interface CitationResolveOptions {
+export type CitationResolveOptions = {
     readonly signal?: AbortSignal;
-}
-export interface CitationResolver {
+};
+export type CitationResolver = {
     resolveOne(input: CitationInput, options?: CitationResolveOptions): Promise<CitationResolutionResult>;
     resolveMany(inputs: readonly CitationInput[], options?: CitationResolveOptions): Promise<CitationResolutionResult[]>;
-}
+};
 export declare const CitationSourceOperationSchema: z.ZodEnum<{
-    none: "none";
-    doi_exact: "doi_exact";
-    crossref_doi_if_owned: "crossref_doi_if_owned";
+    arxiv_bibliographic: "arxiv_bibliographic";
+    arxiv_exact: "arxiv_exact";
     crossref_bibliographic: "crossref_bibliographic";
-    pubmed_exact: "pubmed_exact";
+    crossref_doi_if_owned: "crossref_doi_if_owned";
+    doi_exact: "doi_exact";
+    none: "none";
     pubmed_doi: "pubmed_doi";
+    pubmed_exact: "pubmed_exact";
     pubmed_structured: "pubmed_structured";
     pubmed_title: "pubmed_title";
-    arxiv_exact: "arxiv_exact";
-    arxiv_bibliographic: "arxiv_bibliographic";
-    semantic_scholar_identifier: "semantic_scholar_identifier";
     semantic_scholar_bibliographic: "semantic_scholar_bibliographic";
+    semantic_scholar_identifier: "semantic_scholar_identifier";
 }>;
 export type CitationSourceOperation = z.infer<typeof CitationSourceOperationSchema>;
 export declare const CitationSourcePlanItemSchema: z.ZodObject<{
     source: z.ZodEnum<{
         arxiv: "arxiv";
-        doi_registry: "doi_registry";
         crossref: "crossref";
+        doi_registry: "doi_registry";
         pubmed: "pubmed";
         semantic_scholar: "semantic_scholar";
     }>;
     applicable: z.ZodBoolean;
     operation: z.ZodEnum<{
-        none: "none";
-        doi_exact: "doi_exact";
-        crossref_doi_if_owned: "crossref_doi_if_owned";
+        arxiv_bibliographic: "arxiv_bibliographic";
+        arxiv_exact: "arxiv_exact";
         crossref_bibliographic: "crossref_bibliographic";
-        pubmed_exact: "pubmed_exact";
+        crossref_doi_if_owned: "crossref_doi_if_owned";
+        doi_exact: "doi_exact";
+        none: "none";
         pubmed_doi: "pubmed_doi";
+        pubmed_exact: "pubmed_exact";
         pubmed_structured: "pubmed_structured";
         pubmed_title: "pubmed_title";
-        arxiv_exact: "arxiv_exact";
-        arxiv_bibliographic: "arxiv_bibliographic";
-        semantic_scholar_identifier: "semantic_scholar_identifier";
         semantic_scholar_bibliographic: "semantic_scholar_bibliographic";
+        semantic_scholar_identifier: "semantic_scholar_identifier";
     }>;
     candidateGeneration: z.ZodBoolean;
     reason: z.ZodString;
@@ -570,14 +570,14 @@ export type RegistrationAgencyEvidence = {
     readonly status: "undetermined";
     readonly detail: string;
 };
-export interface CitationSourceRequest {
+export type CitationSourceRequest = {
     readonly input: CitationInput;
     readonly normalized: NormalizedCitation;
     readonly plan: CitationSourcePlanItem;
     readonly registrationAgency: RegistrationAgencyEvidence;
-}
-export interface CitationSourceClient {
+};
+export type CitationSourceClient = {
     readonly source: CitationSource;
     resolve(request: CitationSourceRequest, signal?: AbortSignal): Promise<CitationSourceOutcome>;
     resolveMany?(requests: readonly CitationSourceRequest[], signal?: AbortSignal): Promise<CitationSourceOutcome[]>;
-}
+};

package/dist/config/environment-stores.d.ts

@@ -28,7 +28,7 @@ import type { Track } from "../sandbox/package-identity.js";
  * location the container mountpoint does not describe; absence must never be
  * reported as a failure.
  */
-export interface EnvironmentStorePaths {
+export type EnvironmentStorePaths = {
     /**
      * Host path of the reference store — the same bytes sandboxes mount at
      * `/mnt/refs`. Omit when the host's own process sees the store at that same
@@ -49,8 +49,10 @@ export interface EnvironmentStorePaths {
     readonly farmLockFile?: string | ((analysisId: string) => string);
     /**
      * Host path of the image inventory record, `image-packages.json` at the
-     * root of the package store — the image-owned tools and Node packages
-     * that `list_available_packages` merges into its report. Omit when the
+     * root of the package store — the image-owned tools, the Node packages,
+     * and the R packages that ship with the R runtime, which
+     * `list_available_packages` merges into its report and which the
+     * knowledge tools read for the environment of a step. Omit when the
      * host's own process sees the store at the container mountpoint, which
      * makes `/mnt/libs/image-packages.json` correct as-is; set it when the
      * host reads the store somewhere else. An absent or invalid record
@@ -71,7 +73,7 @@ export interface EnvironmentStorePaths {
      * transient.
      */
     readonly readPoolInventory?: () => Promise<PoolInventoryRead>;
-}
+};
 /**
  * What one pool-scope inventory read produced: the sections, or the reason
  * the pool cannot answer. There is no empty-on-error shape — an unreadable
@@ -85,7 +87,7 @@ export type PoolInventoryRead = {
     readonly reason: string;
 };
 /** One package entry of an inventory section, with the store identity where the source records it. */
-export interface PoolInventoryPackage {
+export type PoolInventoryPackage = {
     readonly name: string;
     /** The pinned version, rendered as `name==version`. Absent where the source pins none. */
     readonly version?: string;
@@ -93,9 +95,9 @@ export interface PoolInventoryPackage {
     readonly storeDir?: string;
     /** The full sha256 of the sorted store tree. */
     readonly hash?: string;
-}
+};
 /** One language-track section of an inventory, as `list_available_packages` renders it. */
-export interface PoolInventorySection {
+export type PoolInventorySection = {
     readonly title: string;
     /**
      * The ecosystem that holds the packages of this section. It carries the
@@ -107,4 +109,4 @@ export interface PoolInventorySection {
      */
     readonly track?: Track;
     readonly packages: readonly PoolInventoryPackage[];
-}
+};

package/dist/config/resource-limits.js

@@ -70,8 +70,6 @@ export function clampResources(spec, limits) {
     return {
         cpu: Math.min(spec.cpu, limits.maxCpu),
         memoryGb: Math.min(spec.memoryGb, limits.maxMemoryGb),
-        ...(spec.gpu && {
-            gpu: { count: Math.min(spec.gpu.count, limits.maxGpuCount) },
-        }),
+        gpu: spec.gpu === undefined ? undefined : { count: Math.min(spec.gpu.count, limits.maxGpuCount) },
     };
 }

package/dist/contracts/analogy-report.d.ts

@@ -11,9 +11,9 @@
 import { z } from "zod";
 export declare const AnalogyCoverageSchema: z.ZodEnum<{
     available: "available";
+    not_loaded: "not_loaded";
     queried_no_data: "queried_no_data";
     search_failed: "search_failed";
-    not_loaded: "not_loaded";
 }>;
 export type AnalogyCoverage = z.infer<typeof AnalogyCoverageSchema>;
 export declare const AnalogyReportSchema: z.ZodObject<{
@@ -36,9 +36,9 @@ export declare const AnalogyReportSchema: z.ZodObject<{
         sharedRelations: z.ZodString;
         coverage: z.ZodEnum<{
             available: "available";
+            not_loaded: "not_loaded";
             queried_no_data: "queried_no_data";
             search_failed: "search_failed";
-            not_loaded: "not_loaded";
         }>;
         solutions: z.ZodArray<z.ZodObject<{
             title: z.ZodString;
@@ -47,11 +47,11 @@ export declare const AnalogyReportSchema: z.ZodObject<{
             keyConcepts: z.ZodArray<z.ZodString>;
             relevance: z.ZodString;
             sources: z.ZodArray<z.ZodObject<{
-                url: z.ZodString;
+                url: z.ZodURL;
                 title: z.ZodString;
             }, z.core.$strip>>;
             githubRepos: z.ZodArray<z.ZodObject<{
-                url: z.ZodString;
+                url: z.ZodURL;
                 description: z.ZodOptional<z.ZodString>;
             }, z.core.$strip>>;
         }, z.core.$strip>>;
@@ -86,9 +86,9 @@ export declare const AnalogicalReasonerOutputSchema: z.ZodUnion<readonly [z.ZodO
         sharedRelations: z.ZodString;
         coverage: z.ZodEnum<{
             available: "available";
+            not_loaded: "not_loaded";
             queried_no_data: "queried_no_data";
             search_failed: "search_failed";
-            not_loaded: "not_loaded";
         }>;
         solutions: z.ZodArray<z.ZodObject<{
             title: z.ZodString;
@@ -97,11 +97,11 @@ export declare const AnalogicalReasonerOutputSchema: z.ZodUnion<readonly [z.ZodO
             keyConcepts: z.ZodArray<z.ZodString>;
             relevance: z.ZodString;
             sources: z.ZodArray<z.ZodObject<{
-                url: z.ZodString;
+                url: z.ZodURL;
                 title: z.ZodString;
             }, z.core.$strip>>;
             githubRepos: z.ZodArray<z.ZodObject<{
-                url: z.ZodString;
+                url: z.ZodURL;
                 description: z.ZodOptional<z.ZodString>;
             }, z.core.$strip>>;
         }, z.core.$strip>>;

package/dist/contracts/analogy-report.js

@@ -32,9 +32,9 @@ export const AnalogyReportSchema = z.object({
             description: z.string(),
             keyConcepts: z.array(z.string()),
             relevance: z.string(),
-            sources: z.array(z.object({ url: z.string().url(), title: z.string() })),
+            sources: z.array(z.object({ url: z.url(), title: z.string() })),
             githubRepos: z.array(z.object({
-                url: z.string().url(),
+                url: z.url(),
                 description: z.string().optional(),
             })),
         })),