@inflexa-ai/harness 0.41.0 → 0.41.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/contracts/report-blocks.d.ts +10 -10
- package/dist/contracts/report-reference.d.ts +4 -4
- package/dist/memory/message-backfill.d.ts +8 -2
- package/dist/prompts/briefing.d.ts +28 -1
- package/dist/prompts/briefing.js +44 -1
- package/dist/prompts/compaction.d.ts +2 -2
- package/dist/prompts/compaction.js +9 -5
- package/dist/prompts/conversation.d.ts +1 -1
- package/dist/prompts/conversation.js +12 -0
- package/dist/prompts/sandbox-standards.d.ts +1 -1
- package/dist/prompts/sandbox-standards.js +4 -0
- package/dist/report-model/authoring-grammar.d.ts +4 -4
- package/dist/runtime/assemble.d.ts +4 -2
- package/dist/runtime/assemble.js +8 -1
- package/dist/runtime/boot.d.ts +2 -2
- package/dist/runtime/boot.js +3 -3
- package/dist/schemas/file-metadata.js +9 -9
- package/dist/schemas/plan-schemas.d.ts +3 -3
- package/dist/state/init.d.ts +7 -6
- package/dist/state/init.js +51 -672
- package/dist/state/migrations/20260927120000_baseline.d.ts +11 -0
- package/dist/state/migrations/20260927120000_baseline.js +675 -0
- package/dist/state/migrations/index.d.ts +10 -0
- package/dist/state/migrations/index.js +13 -0
- package/dist/tools/ad-hoc-router.js +9 -4
- package/dist/tools/bio/chembl.js +8 -5
- package/dist/tools/bio/comptox.js +4 -4
- package/dist/tools/bio/drug-gene-interactions.js +5 -4
- package/dist/tools/bio/gene-disease-evidence.js +4 -4
- package/dist/tools/bio/lookup-annotation.js +7 -3
- package/dist/tools/bio/opentargets.js +8 -6
- package/dist/tools/bio/pubchem.js +4 -2
- package/dist/tools/bio/pubmed.d.ts +1 -1
- package/dist/tools/bio/pubmed.js +10 -6
- package/dist/tools/bio/search-clinical-trials.js +2 -1
- package/dist/tools/bio/search-gene.js +2 -1
- package/dist/tools/bio/search-interactions.js +8 -4
- package/dist/tools/bio/target-safety.js +2 -1
- package/dist/tools/display/show-user.js +7 -5
- package/dist/tools/execute-analysis.js +14 -4
- package/dist/tools/lib/opentargets-client.d.ts +8 -3
- package/dist/tools/lib/opentargets-client.js +12 -3
- package/dist/tools/read-tool-output.js +7 -4
- package/dist/tools/report-authoring/authoring-tools.js +22 -15
- package/dist/tools/report-session/derive-table.js +5 -1
- package/dist/tools/report-session/examine-page.js +5 -4
- package/dist/tools/report-session/preview-report.js +6 -1
- package/dist/tools/report-session/record-version.js +2 -1
- package/dist/tools/research/context7-docs.js +8 -2
- package/dist/tools/research/generate-analogy-report.js +15 -15
- package/dist/tools/research/generate-plan.js +12 -7
- package/dist/tools/research/inspect-data-profile.js +7 -5
- package/dist/tools/research/inspect-run.js +6 -2
- package/dist/tools/research/literature-reviewer.js +11 -6
- package/dist/tools/research/search-arxiv.js +2 -1
- package/dist/tools/research/search-github-repos.js +9 -3
- package/dist/tools/sandbox/list-available-refs.js +3 -2
- package/dist/tools/sandbox/report-blocker.js +6 -1
- package/dist/tools/sandbox/skills.js +4 -2
- package/dist/tools/start-report-session.js +4 -1
- package/dist/tools/workspace/edit-file.js +4 -3
- package/dist/tools/workspace/execute-command.js +6 -5
- package/dist/tools/workspace/grep.js +9 -7
- package/dist/tools/workspace/list-files.js +1 -1
- package/dist/tools/workspace/read-file.js +2 -1
- package/dist/tools/workspace/scan-inputs.js +3 -1
- package/dist/tools/workspace/show-file.js +6 -3
- package/dist/tools/workspace/workspace-search.js +3 -1
- package/dist/tools/workspace/write-file.js +5 -3
- package/dist/workflows/execute-analysis.d.ts +28 -5
- package/dist/workflows/execute-analysis.js +34 -10
- package/package.json +2 -1
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@@ -24,16 +24,16 @@ export const FileMetadataSchema = z
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*/
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export const SubmittedFileDescriptionSchema = z.object({
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/** Exact path of the file being described, copied from the prompt's list. */
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path: z.string(),
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description: z.string(),
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dataType: z.string(),
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format: z.string(),
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rows: z.number().nullish(),
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cols: z.number().nullish(),
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tags: z.array(z.string()).optional(),
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warnings: z.array(z.string()).optional(),
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path: z.string().describe("The path of the file, copied exactly from the list of files that the harness gave."),
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description: z.string().describe("One sentence that says what the file contains. A semantic search of the workspace later finds the file by this text."),
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dataType: z.string().describe('The semantic type of the data, for example "count matrix" or "QC report".'),
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format: z.string().describe('The file format, for example "csv", "tsv", "h5ad", or "png".'),
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rows: z.number().nullish().describe("The count of rows, when you know it."),
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cols: z.number().nullish().describe("The count of columns, when you know it."),
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tags: z.array(z.string()).optional().describe("Short labels that help a search find the file."),
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warnings: z.array(z.string()).optional().describe("Known problems of the file that a reader must know before use."),
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});
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/** Input contract for the `submit_file_metadata` tool. */
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export const SubmitFileMetadataInputSchema = z.object({
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files: z.array(SubmittedFileDescriptionSchema),
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files: z.array(SubmittedFileDescriptionSchema).describe("One entry per output file. You can cover the files in one call or in several."),
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});
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@@ -11,10 +11,10 @@ export declare const PlanStepSchema: z.ZodObject<{
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context: z.ZodOptional<z.ZodString>;
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description: z.ZodOptional<z.ZodString>;
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id: z.ZodString;
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constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
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track: z.ZodString;
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step_type: z.ZodString;
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question: z.ZodString;
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constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
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acceptance_criteria: z.ZodArray<z.ZodString>;
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caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
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packages: z.ZodNonOptional<z.ZodOptional<z.ZodArray<z.ZodString>>>;
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@@ -44,10 +44,10 @@ export declare const PlannerPlanSchema: z.ZodObject<{
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context: z.ZodOptional<z.ZodString>;
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description: z.ZodOptional<z.ZodString>;
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id: z.ZodString;
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constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
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track: z.ZodString;
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step_type: z.ZodString;
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question: z.ZodString;
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constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
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acceptance_criteria: z.ZodArray<z.ZodString>;
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caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
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packages: z.ZodNonOptional<z.ZodOptional<z.ZodArray<z.ZodString>>>;
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context: z.ZodOptional<z.ZodString>;
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description: z.ZodOptional<z.ZodString>;
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id: z.ZodString;
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constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
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track: z.ZodString;
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step_type: z.ZodString;
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question: z.ZodString;
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constraints: z.ZodOptional<z.ZodArray<z.ZodString>>;
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acceptance_criteria: z.ZodArray<z.ZodString>;
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caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
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packages: z.ZodNonOptional<z.ZodOptional<z.ZodArray<z.ZodString>>>;
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package/dist/state/init.d.ts
CHANGED
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/**
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* Cortex state table initialization.
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*
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*
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*
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*
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*
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* The schema of the `cortex_*` tables is a list of versioned migrations
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* (`./migrations`), which the Kysely migrator applies. It records each applied
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* migration in `cortex_migration`, and it serializes concurrent runs with a
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* Postgres advisory lock. A run with no pending migration runs no DDL, thus it
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* takes no lock on a Cortex table.
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*/
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import type { Pool } from "pg";
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import type { Logger } from "../lib/logger.js";
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/**
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*
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*
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* Apply the pending migrations of the Cortex state tables. Safe to call on every
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* startup and across concurrent replicas.
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*/
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export declare function initCortexState(pool: Pool, injected?: Logger): Promise<void>;
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