@mantra-ai/core 0.7.3 → 0.8.0

package/dist/analysis/index.d.ts

@@ -1,13 +1,15 @@
 export { getBlocksByCategory } from "./block-filter";
 export type { FilteredBlock } from "./block-filter";
-export { PaperDigestSchema, HypothesisSetSchema, LandscapeSchema, DiscoveryQuerySetSchema, } from "./schemas";
+export { PaperDigestSchema, HypothesisSetSchema, HypothesisSchema, LandscapeSchema, DiscoveryQuerySetSchema, } from "./schemas";
 export type { PaperDigest, Hypothesis, HypothesisSet, PursueBy, Landscape, PaperRole, DiscoveryQuery, DiscoveryQuerySet } from "./schemas";
-export { buildExtractionPrompt, buildHypothesisPrompt, buildHypothesizePrompt, buildMapPrompt, buildDiscoveryQueryPrompt } from "./prompts";
+export { buildExtractionPrompt, buildHypothesisPrompt, buildHypothesizePrompt, buildMapPrompt, buildDiscoveryQueryPrompt, buildContestorPrompt } from "./prompts";
 export type { PreparedPaper } from "./prompts";
 export { extractFindings } from "./extract-findings";
 export type { ExtractFindingsOptions } from "./extract-findings";
 export { generateHypotheses } from "./generate-hypotheses";
 export type { GenerateHypothesesOptions } from "./generate-hypotheses";
+export { refineHypotheses } from "./refine-hypotheses";
+export type { RefineHypothesesOptions, RefineProgress, RefineResult } from "./refine-hypotheses";
 export { generateLandscape } from "./generate-landscape";
 export type { GenerateLandscapeOptions } from "./generate-landscape";
 export { generateDiscoveryQueries } from "./generate-discovery-queries";

package/dist/analysis/index.d.ts.map

@@ -1 +1 @@
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package/dist/analysis/index.js

@@ -1,8 +1,9 @@
 export { getBlocksByCategory } from "./block-filter";
-export { PaperDigestSchema, HypothesisSetSchema, LandscapeSchema, DiscoveryQuerySetSchema, } from "./schemas";
-export { buildExtractionPrompt, buildHypothesisPrompt, buildHypothesizePrompt, buildMapPrompt, buildDiscoveryQueryPrompt } from "./prompts";
+export { PaperDigestSchema, HypothesisSetSchema, HypothesisSchema, LandscapeSchema, DiscoveryQuerySetSchema, } from "./schemas";
+export { buildExtractionPrompt, buildHypothesisPrompt, buildHypothesizePrompt, buildMapPrompt, buildDiscoveryQueryPrompt, buildContestorPrompt } from "./prompts";
 export { extractFindings } from "./extract-findings";
 export { generateHypotheses } from "./generate-hypotheses";
+export { refineHypotheses } from "./refine-hypotheses";
 export { generateLandscape } from "./generate-landscape";
 export { generateDiscoveryQueries } from "./generate-discovery-queries";
 //# sourceMappingURL=index.js.map

package/dist/analysis/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/analysis/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,gBAAgB,CAAC;AAGrD,OAAO,EACL,iBAAiB,EACjB,mBAAmB,EACnB,gBAAgB,EAChB,eAAe,EACf,uBAAuB,GACxB,MAAM,WAAW,CAAC;AAGnB,OAAO,EAAE,qBAAqB,EAAE,qBAAqB,EAAE,sBAAsB,EAAE,cAAc,EAAE,yBAAyB,EAAE,oBAAoB,EAAE,MAAM,WAAW,CAAC;AAGlK,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AAGrD,OAAO,EAAE,kBAAkB,EAAE,MAAM,uBAAuB,CAAC;AAG3D,OAAO,EAAE,gBAAgB,EAAE,MAAM,qBAAqB,CAAC;AAGvD,OAAO,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AAGzD,OAAO,EAAE,wBAAwB,EAAE,MAAM,8BAA8B,CAAC"}

package/dist/analysis/prompts.d.ts

@@ -1,6 +1,6 @@
 import type { ChatMessage } from "../ai/types";
 import type { FilteredBlock } from "./block-filter";
-import type { PaperDigest, Landscape } from "./schemas";
+import type { PaperDigest, Landscape, Hypothesis } from "./schemas";
 import type { SeedContext } from "./generate-discovery-queries";
 interface PaperMetadata {
     title?: string;
@@ -21,5 +21,14 @@ export declare function buildHypothesizePrompt(papers: PreparedPaper[], landscap
     minPerType?: number;
 }): ChatMessage[];
 export declare function buildDiscoveryQueryPrompt(seeds: SeedContext[]): ChatMessage[];
+/**
+ * Build messages for a revision round: the generator sees its previous
+ * hypotheses, the contestor's critique, and is asked to revise.
+ */
+/**
+ * Build messages for the contestor: evaluate a single hypothesis against
+ * its cited papers, find weaknesses, and output an improved version.
+ */
+export declare function buildContestorPrompt(hypothesis: Hypothesis, citedPapers: PreparedPaper[]): ChatMessage[];
 export {};
 //# sourceMappingURL=prompts.d.ts.map

package/dist/analysis/prompts.d.ts.map

@@ -1 +1 @@
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package/dist/analysis/prompts.js

@@ -236,35 +236,14 @@ export function buildHypothesizePrompt(papers, landscape, opts) {
             "- The pursue_by search queries should find papers the citation graph would miss — target different angles, not just the same keywords.",
         ].join("\n"),
     };
-    // Serialize landscape as structured context
-    const landscapeParts = [
-        "# Research Landscape",
-        "",
-        `Domain: ${landscape.domain_summary}`,
-        "",
-    ];
-    if (landscape.connections.length > 0) {
-        landscapeParts.push("## Cross-Paper Connections");
-        for (const c of landscape.connections) {
-            landscapeParts.push(`- Papers ${c.papers.join(", ")} [${c.type}]: ${c.description}`);
-        }
-        landscapeParts.push("");
-    }
-    if (landscape.gaps.length > 0) {
-        landscapeParts.push("## Knowledge Gaps");
-        for (const g of landscape.gaps) {
-            landscapeParts.push(`- [${g.type}] (papers ${g.between.join(", ")}): ${g.description}`);
-        }
-        landscapeParts.push("");
-    }
+    // Serialize landscape
+    const landscapeText = serializeLandscape(landscape);
     // Full paper texts
-    const paperTexts = papers.map((p) => {
-        return `--- PAPER ${p.id} ---\n\n${p.content}`;
-    });
+    const paperTexts = papers.map((p) => `--- PAPER ${p.id} ---\n\n${p.content}`);
     const user = {
         role: "user",
         content: [
-            landscapeParts.join("\n"),
+            landscapeText,
             "",
             `# Full Paper Texts (${papers.length} papers)`,
             "",
@@ -322,4 +301,91 @@ export function buildDiscoveryQueryPrompt(seeds) {
     };
     return [system, user];
 }
+// ── Hypothesis revision prompt (generator + critique context) ────
+/**
+ * Build messages for a revision round: the generator sees its previous
+ * hypotheses, the contestor's critique, and is asked to revise.
+ */
+// ── Contestor prompt (critique + improve a single hypothesis) ────
+/**
+ * Build messages for the contestor: evaluate a single hypothesis against
+ * its cited papers, find weaknesses, and output an improved version.
+ */
+export function buildContestorPrompt(hypothesis, citedPapers) {
+    const system = {
+        role: "system",
+        content: [
+            "You are a rigorous scientific critic and improver. You are given a hypothesis and the papers it claims to be derived from.",
+            "",
+            "Your job is to find weaknesses and then FIX them, outputting an improved version of the hypothesis.",
+            "",
+            "Evaluate:",
+            "",
+            "EVIDENCE GROUNDING: Do the cited papers actually support the claim? Is the hypothesis overinterpreting or cherry-picking results?",
+            "",
+            "LOGICAL COHERENCE: Does the mechanism or connection actually follow from the evidence? Are there unjustified leaps?",
+            "",
+            "NOVELTY: Is this genuinely novel, or does it restate what one paper already concludes?",
+            "",
+            "TESTABILITY: Is the proposed test realistic and specific enough?",
+            "",
+            "PURSUE_BY QUALITY: Would the search queries actually find useful papers?",
+            "",
+            "After evaluating, output an IMPROVED version of the hypothesis that fixes what you found. Tighten the statement, strengthen the rationale with specific evidence from the papers, sharpen the testability, and improve the pursue_by queries.",
+            "",
+            "If the hypothesis is already strong, make minor improvements to precision and specificity. Every hypothesis can be made better.",
+            "",
+            "Output the full hypothesis object with all fields. Keep the same id and type. Improve everything else.",
+        ].join("\n"),
+    };
+    const paperTexts = citedPapers.map((p) => `--- PAPER ${p.id} ---\n\n${p.content}`);
+    const hypothesisText = [
+        `${hypothesis.id} [${hypothesis.type}] (${hypothesis.confidence})`,
+        `Statement: ${hypothesis.statement}`,
+        `Rationale: ${hypothesis.rationale}`,
+        `Supporting papers: ${hypothesis.supporting_papers.join(", ")}`,
+        `Supporting findings: ${hypothesis.supporting_findings.join("; ")}`,
+        `Novelty: ${hypothesis.novelty}`,
+        `Testability: ${hypothesis.testability.approach} (techniques: ${hypothesis.testability.key_techniques.join(", ")})`,
+        `Pursue by: ${hypothesis.pursue_by.look_for}`,
+        `  Queries: ${hypothesis.pursue_by.search_queries.map(q => `"${q.query}"`).join(", ")}`,
+    ].join("\n");
+    const user = {
+        role: "user",
+        content: [
+            "# Hypothesis to improve",
+            "",
+            hypothesisText,
+            "",
+            `# Cited Papers (${citedPapers.length})`,
+            "",
+            paperTexts.join("\n\n"),
+        ].join("\n"),
+    };
+    return [system, user];
+}
+// ── Shared helpers ──────────────────────────────────────────────
+function serializeLandscape(landscape) {
+    const parts = [
+        "# Research Landscape",
+        "",
+        `Domain: ${landscape.domain_summary}`,
+        "",
+    ];
+    if (landscape.connections.length > 0) {
+        parts.push("## Cross-Paper Connections");
+        for (const c of landscape.connections) {
+            parts.push(`- Papers ${c.papers.join(", ")} [${c.type}]: ${c.description}`);
+        }
+        parts.push("");
+    }
+    if (landscape.gaps.length > 0) {
+        parts.push("## Knowledge Gaps");
+        for (const g of landscape.gaps) {
+            parts.push(`- [${g.type}] (papers ${g.between.join(", ")}): ${g.description}`);
+        }
+        parts.push("");
+    }
+    return parts.join("\n");
+}
 //# sourceMappingURL=prompts.js.map

package/dist/analysis/prompts.js.map

@@ -1 +1 @@
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package/dist/analysis/refine-hypotheses.d.ts

@@ -0,0 +1,32 @@
+import type { LLMResult } from "../ai/types";
+import { type HypothesisSet, type Landscape } from "./schemas";
+import { type PreparedPaper } from "./prompts";
+export interface RefineHypothesesOptions {
+    model?: string;
+    temperature?: number;
+    maxOutputTokens?: number;
+    maxAttempts?: number;
+    minPerType?: number;
+    /** Called at each phase so the caller can update spinners/logs. */
+    onProgress?: (event: RefineProgress) => void;
+}
+export interface RefineProgress {
+    phase: "generating" | "contesting";
+    hypothesisId?: string;
+    total?: number;
+    current?: number;
+}
+export interface RefineResult {
+    hypotheses: HypothesisSet;
+}
+/**
+ * Generate hypotheses and improve each one through a contestor pass.
+ *
+ * 1. Generator produces initial hypotheses from papers + landscape
+ * 2. Each hypothesis goes through a contestor in parallel
+ * 3. Contestor reads the hypothesis + its cited papers, finds weaknesses,
+ *    and outputs an improved version
+ * 4. The improved versions are the final output
+ */
+export declare function refineHypotheses(papers: PreparedPaper[], landscape: Landscape, opts?: RefineHypothesesOptions): Promise<LLMResult<RefineResult>>;
+//# sourceMappingURL=refine-hypotheses.d.ts.map

package/dist/analysis/refine-hypotheses.d.ts.map

@@ -0,0 +1 @@
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package/dist/analysis/refine-hypotheses.js

@@ -0,0 +1,74 @@
+import { generateWithSchema } from "../ai/claude/generate";
+import { HypothesisSetSchema, HypothesisSchema, } from "./schemas";
+import { buildHypothesizePrompt, buildContestorPrompt, } from "./prompts";
+/**
+ * Contest a single hypothesis: critique it and output an improved version.
+ */
+async function contestOne(hypothesis, papers, llmOpts, retryOpts) {
+    const paperById = new Map(papers.map((p) => [p.id, p]));
+    const citedPapers = hypothesis.supporting_papers
+        .map((id) => paperById.get(id))
+        .filter((p) => p !== undefined);
+    const messages = buildContestorPrompt(hypothesis, citedPapers);
+    const result = await generateWithSchema({
+        messages,
+        schema: HypothesisSchema,
+        options: llmOpts,
+        retry: retryOpts,
+    });
+    if (!result.ok)
+        return null;
+    return result.value;
+}
+/**
+ * Generate hypotheses and improve each one through a contestor pass.
+ *
+ * 1. Generator produces initial hypotheses from papers + landscape
+ * 2. Each hypothesis goes through a contestor in parallel
+ * 3. Contestor reads the hypothesis + its cited papers, finds weaknesses,
+ *    and outputs an improved version
+ * 4. The improved versions are the final output
+ */
+export async function refineHypotheses(papers, landscape, opts) {
+    const minPerType = opts?.minPerType ?? 1;
+    const model = opts?.model ?? "sonnet";
+    const temperature = opts?.temperature ?? 0.4;
+    const maxOutputTokens = opts?.maxOutputTokens ?? 16384;
+    const maxAttempts = opts?.maxAttempts ?? 3;
+    const llmOpts = { model, temperature, maxOutputTokens };
+    const retryOpts = { maxAttempts };
+    // Step 1: Generate initial hypotheses
+    opts?.onProgress?.({ phase: "generating" });
+    const initialMessages = buildHypothesizePrompt(papers, landscape, { minPerType });
+    const initialResult = await generateWithSchema({
+        messages: initialMessages,
+        schema: HypothesisSetSchema,
+        options: llmOpts,
+        retry: retryOpts,
+    });
+    if (!initialResult.ok) {
+        return initialResult;
+    }
+    const initial = initialResult.value;
+    // Step 2: Contest each hypothesis in parallel
+    const total = initial.hypotheses.length;
+    opts?.onProgress?.({ phase: "contesting", total });
+    const improved = await Promise.all(initial.hypotheses.map(async (h, i) => {
+        opts?.onProgress?.({ phase: "contesting", hypothesisId: h.id, current: i + 1, total });
+        const result = await contestOne(h, papers, llmOpts, retryOpts);
+        // Fall back to original if contestor fails
+        return result ?? h;
+    }));
+    return {
+        ok: true,
+        value: {
+            hypotheses: {
+                paper_count: initial.paper_count,
+                hypotheses: improved,
+            },
+        },
+        rawText: "",
+        attempts: 1,
+    };
+}
+//# sourceMappingURL=refine-hypotheses.js.map

package/dist/analysis/refine-hypotheses.js.map

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package/dist/analysis/schemas.d.ts

@@ -172,7 +172,7 @@ declare const PursueBySchema: z.ZodObject<{
     expand_systems: string[];
     expand_techniques: string[];
 }>;
-declare const HypothesisSchema: z.ZodObject<{
+export declare const HypothesisSchema: z.ZodObject<{
     id: z.ZodString;
     type: z.ZodEnum<["mechanistic", "methodological", "gap"]>;
     statement: z.ZodString;

package/dist/analysis/schemas.d.ts.map

@@ -1 +1 @@
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package/dist/analysis/schemas.js

@@ -87,7 +87,7 @@ const PursueBySchema = z.object({
     expand_systems: z.array(z.string()).describe("Biological systems to explore further"),
     expand_techniques: z.array(z.string()).describe("Techniques to explore further"),
 });
-const HypothesisSchema = z.object({
+export const HypothesisSchema = z.object({
     id: z.string().describe("Hypothesis ID (H1, H2, ...)"),
     type: z.enum(["mechanistic", "methodological", "gap"]),
     statement: z.string(),
@@ -103,6 +103,7 @@ export const HypothesisSetSchema = z.object({
     paper_count: z.number().int().describe("Number of papers analysed"),
     hypotheses: z.array(HypothesisSchema),
 });
+// HypothesisSchema is exported directly (used by contestor to output improved hypotheses)
 // ── Research landscape mapping ───────────────────────────────────
 const PaperRoleSchema = z.object({
     paper_id: z.string().describe("Paper identifier matching the input (e.g. '1', '3')"),

package/dist/analysis/schemas.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -31,9 +31,11 @@ export { getReferences as cociGetReferences, getCitations as cociGetCitations, }
 export { searchPapers as s2SearchPapers, getPaperDetails as s2GetPaperDetails, getPaperReferences as s2GetPaperReferences, getPaperCitations as s2GetPaperCitations, } from "./sources/semantic-scholar/client";
 export type { S2Paper, S2Author, S2ExternalIds, S2SearchResponse, S2CitationEdge, S2CitationResponse, S2ClientOpts, } from "./sources/semantic-scholar/client";
 export type { PaperDigest, HypothesisSet, Hypothesis, PursueBy, Landscape, PaperRole, DiscoveryQuery, DiscoveryQuerySet } from "./analysis/schemas";
-export { PaperDigestSchema, HypothesisSetSchema, LandscapeSchema, DiscoveryQuerySetSchema } from "./analysis/schemas";
+export { PaperDigestSchema, HypothesisSetSchema, HypothesisSchema, LandscapeSchema, DiscoveryQuerySetSchema } from "./analysis/schemas";
 export { extractFindings } from "./analysis/extract-findings";
 export { generateHypotheses } from "./analysis/generate-hypotheses";
+export { refineHypotheses } from "./analysis/refine-hypotheses";
+export type { RefineHypothesesOptions, RefineProgress, RefineResult } from "./analysis/refine-hypotheses";
 export { generateLandscape } from "./analysis/generate-landscape";
 export type { GenerateLandscapeOptions } from "./analysis/generate-landscape";
 export { buildMapPrompt } from "./analysis/prompts";

package/dist/index.d.ts.map

@@ -1 +1 @@
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package/dist/index.js

@@ -29,9 +29,10 @@ export { OpenCitationsCitationGraphProvider } from "./sources/opencitations/cita
 export { getReferences as cociGetReferences, getCitations as cociGetCitations, } from "./sources/opencitations/client";
 // ── Sources: Semantic Scholar (legacy, retained for ingest paths) ──
 export { searchPapers as s2SearchPapers, getPaperDetails as s2GetPaperDetails, getPaperReferences as s2GetPaperReferences, getPaperCitations as s2GetPaperCitations, } from "./sources/semantic-scholar/client";
-export { PaperDigestSchema, HypothesisSetSchema, LandscapeSchema, DiscoveryQuerySetSchema } from "./analysis/schemas";
+export { PaperDigestSchema, HypothesisSetSchema, HypothesisSchema, LandscapeSchema, DiscoveryQuerySetSchema } from "./analysis/schemas";
 export { extractFindings } from "./analysis/extract-findings";
 export { generateHypotheses } from "./analysis/generate-hypotheses";
+export { refineHypotheses } from "./analysis/refine-hypotheses";
 export { generateLandscape } from "./analysis/generate-landscape";
 export { buildMapPrompt } from "./analysis/prompts";
 export { generateDiscoveryQueries } from "./analysis/generate-discovery-queries";

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,iCAAiC;AAEjC,sEAAsE;AACtE,cAAc,gBAAgB,CAAC;AAC/B,cAAc,kBAAkB,CAAC;AAEjC,sEAAsE;AACtE,OAAO,EAAE,aAAa,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAsCrE,sEAAsE;AACtE,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAC;AAIzC,OAAO,EACL,YAAY,EACZ,SAAS,EACT,aAAa,EACb,cAAc,EACd,gBAAgB,EAChB,mBAAmB,GACpB,MAAM,gCAAgC,CAAC;AACxC,OAAO,EAAE,6BAA6B,EAAE,MAAM,0BAA0B,CAAC;AACzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AAEvE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAGhE,sEAAsE;AACtE,OAAO,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AACpD,OAAO,EAAE,oBAAoB,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAC3E,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AACnE,OAAO,EACL,eAAe,EACf,mBAAmB,EACnB,mBAAmB,EACnB,4BAA4B,GAC7B,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,YAAY,EAAE,MAAM,sBAAsB,CAAC;AAEpD,sEAAsE;AACtE,OAAO,EACL,mBAAmB,EACnB,mBAAmB,GACpB,MAAM,uCAAuC,CAAC;AAe/C,OAAO,EAAE,gBAAgB,EAAE,MAAM,sBAAsB,CAAC;AACxD,OAAO,EACL,cAAc,EACd,eAAe,EACf,cAAc,GACf,MAAM,qBAAqB,CAAC;AAG7B,oEAAoE;AACpE,OAAO,EAAE,gBAAgB,EAAE,MAAM,6BAA6B,CAAC;AAC/D,OAAO,EAAE,uBAAuB,EAAE,MAAM,6BAA6B,CAAC;AACtE,OAAO,EACL,WAAW,IAAI,mBAAmB,EAClC,YAAY,IAAI,oBAAoB,EACpC,kBAAkB,IAAI,oBAAoB,GAC3C,MAAM,2BAA2B,CAAC;AAOnC,mEAAmE;AACnE,OAAO,EAAE,kCAAkC,EAAE,MAAM,iDAAiD,CAAC;AACrG,OAAO,EACL,aAAa,IAAI,iBAAiB,EAClC,YAAY,IAAI,gBAAgB,GACjC,MAAM,gCAAgC,CAAC;AAExC,sEAAsE;AACtE,OAAO,EACL,YAAY,IAAI,cAAc,EAC9B,eAAe,IAAI,iBAAiB,EACpC,kBAAkB,IAAI,oBAAoB,EAC1C,iBAAiB,IAAI,mBAAmB,GACzC,MAAM,mCAAmC,CAAC;AAa3C,OAAO,EAAE,iBAAiB,EAAE,mBAAmB,EAAE,gBAAgB,EAAE,eAAe,EAAE,uBAAuB,EAAE,MAAM,oBAAoB,CAAC;AACxI,OAAO,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AAC9D,OAAO,EAAE,kBAAkB,EAAE,MAAM,gCAAgC,CAAC;AACpE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAEhE,OAAO,EAAE,iBAAiB,EAAE,MAAM,+BAA+B,CAAC;AAElE,OAAO,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAEpD,OAAO,EAAE,wBAAwB,EAAE,MAAM,uCAAuC,CAAC;AAEjF,OAAO,EAAE,mBAAmB,EAAE,MAAM,yBAAyB,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mantra-ai/core",
-  "version": "0.7.3",
+  "version": "0.8.0",
   "private": false,
   "type": "module",
   "main": "./dist/index.js",