@galaxy-tool-util/cli 0.2.0 → 1.0.0

package/dist/commands/convert.js

@@ -1,11 +1,12 @@
 /**
  * `gxwf convert` — convert between native (.ga) and format2 (.gxwf.yml) formats.
  */
-import { ToolCache } from "@galaxy-tool-util/core";
-import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, } from "@galaxy-tool-util/schema";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, checkStrictEncoding, checkStrictStructure, } from "@galaxy-tool-util/schema";
 import { dirname } from "node:path";
 import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
 import { createDefaultResolver } from "./url-resolver.js";
+import { resolveStrictOptions } from "./strict-options.js";
 import { readWorkflowFile, resolveFormat, serializeWorkflow, writeWorkflowOutput, } from "./workflow-io.js";
 export async function runConvert(filePath, opts) {
     const data = await readWorkflowFile(filePath);
@@ -13,6 +14,28 @@ export async function runConvert(filePath, opts) {
         return;
     const sourceFormat = resolveFormat(data, opts.format);
     const targetFormat = resolveTargetFormat(sourceFormat, opts.to);
+    const strict = resolveStrictOptions(opts);
+    // Pre-conversion strict checks on input
+    if (strict.strictEncoding) {
+        const encErrors = checkStrictEncoding(data, sourceFormat);
+        if (encErrors.length > 0) {
+            console.error("Encoding errors:");
+            for (const e of encErrors)
+                console.error(`  ${e}`);
+            process.exitCode = 2;
+            return;
+        }
+    }
+    if (strict.strictStructure) {
+        const structErrors = checkStrictStructure(data, sourceFormat);
+        if (structErrors.length > 0) {
+            console.error("Structure errors (strict):");
+            for (const e of structErrors)
+                console.error(`  ${e}`);
+            process.exitCode = 2;
+            return;
+        }
+    }
     if (sourceFormat === targetFormat) {
         console.error(`Source and target formats are both ${sourceFormat}. ` +
             `Use --to to specify the target format.`);
@@ -22,9 +45,9 @@ export async function runConvert(filePath, opts) {
     let result;
     let stepStatuses = null;
     if (opts.stateful) {
-        const cache = new ToolCache({ cacheDir: opts.cacheDir });
+        const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
         await cache.index.load();
-        if (cache.index.listAll().length === 0) {
+        if ((await cache.index.listAll()).length === 0) {
             console.warn("Tool cache is empty — stateful conversion will fall back for every step");
         }
         const expansionOpts = {
@@ -63,6 +86,15 @@ export async function runConvert(filePath, opts) {
     await writeWorkflowOutput(output, opts.output, "Converted workflow");
     if (stepStatuses !== null) {
         reportStepStatuses(stepStatuses);
+        // --strict-state: require all steps to convert successfully
+        if (strict.strictState) {
+            const hasFailures = stepStatuses.some((s) => !s.converted);
+            if (hasFailures) {
+                console.error("Strict state: all steps must convert successfully");
+                process.exitCode = 2;
+                return;
+            }
+        }
     }
 }
 function reportStepStatuses(statuses) {

package/dist/commands/convert.js.map

@@ -1 +1 @@
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package/dist/commands/info.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"info.d.ts","sourceRoot":"","sources":["../../src/commands/info.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,WAAW;IAC1B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,OAAO,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA+B9E"}
+{"version":3,"file":"info.d.ts","sourceRoot":"","sources":["../../src/commands/info.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,WAAW;IAC1B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,OAAO,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA+B9E"}

package/dist/commands/info.js

@@ -1,6 +1,7 @@
-import { ToolCache, cacheKey } from "@galaxy-tool-util/core";
+import { cacheKey } from "@galaxy-tool-util/core";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
 export async function runInfo(toolId, opts) {
-    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
     await cache.index.load();
     const coords = cache.resolveToolCoordinates(toolId, opts.version);
     if (coords.version === null) {
@@ -8,14 +9,14 @@ export async function runInfo(toolId, opts) {
         process.exitCode = 1;
         return;
     }
-    const key = cacheKey(coords.toolshedUrl, coords.trsToolId, coords.version);
+    const key = await cacheKey(coords.toolshedUrl, coords.trsToolId, coords.version);
     const tool = await cache.loadCached(key);
     if (tool === null) {
         console.error(`Tool not found in cache: ${toolId}`);
         process.exitCode = 1;
         return;
     }
-    const indexEntry = cache.index.listAll().find((e) => e.cache_key === key);
+    const indexEntry = (await cache.index.listAll()).find((e) => e.cache_key === key);
     console.log(`Name:        ${tool.name}`);
     console.log(`ID:          ${tool.id}`);
     console.log(`Version:     ${tool.version ?? "unknown"}`);

package/dist/commands/info.js.map

@@ -1 +1 @@
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package/dist/commands/lint-tree.d.ts

@@ -1,27 +1,11 @@
-import { type LintReport } from "./lint.js";
-import { type TreeSummary } from "./tree.js";
-export interface LintTreeOptions {
+import { type StrictOptions } from "./strict-options.js";
+import { type ReportOutputOptions } from "./report-output.js";
+export interface LintTreeOptions extends StrictOptions, ReportOutputOptions {
     format?: string;
     skipBestPractices?: boolean;
     skipStateValidation?: boolean;
     cacheDir?: string;
     json?: boolean;
 }
-export interface WorkflowLintResult {
-    relativePath: string;
-    report: LintReport;
-}
-export interface LintTreeReport {
-    root: string;
-    results: (WorkflowLintResult | {
-        relativePath: string;
-        error: string;
-    })[];
-    summary: TreeSummary & {
-        lintErrors: number;
-        lintWarnings: number;
-        stateFail: number;
-    };
-}
 export declare function runLintTree(dir: string, opts: LintTreeOptions): Promise<void>;
 //# sourceMappingURL=lint-tree.d.ts.map

package/dist/commands/lint-tree.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"lint-tree.d.ts","sourceRoot":"","sources":["../../src/commands/lint-tree.ts"],"names":[],"mappings":"AAcA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAG/E,OAAO,EAAsC,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAElG,MAAM,WAAW,eAAgB,SAAQ,aAAa,EAAE,mBAAmB;IACzE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAUD,wBAAsB,WAAW,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAyEnF"}

package/dist/commands/lint-tree.js

@@ -1,18 +1,25 @@
-/**
- * `gxwf lint-tree` — batch lint all workflows under a directory.
- */
-import { ToolCache } from "@galaxy-tool-util/core";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { buildLintWorkflowResult, buildLintTreeReport as schemaBuildLintTreeReport, } from "@galaxy-tool-util/schema";
 import { resolveFormat } from "./workflow-io.js";
+import { resolveStrictOptions } from "./strict-options.js";
 import { lintWorkflowReport } from "./lint.js";
-import { collectTree, summarizeOutcomes } from "./tree.js";
+import { collectTree } from "./tree.js";
+import { writeReportOutput, writeReportHtml } from "./report-output.js";
+/** Map internal LintReport to schema's flat LintWorkflowResult fields. */
+function toLintWorkflowResult(relativePath, lr) {
+    const lint_errors = lr.structural.error_count + (lr.bestPractices?.error_count ?? 0);
+    const lint_warnings = lr.structural.warn_count + (lr.bestPractices?.warn_count ?? 0);
+    const stepResults = lr.stateValidation ?? [];
+    return buildLintWorkflowResult(relativePath, lint_errors, lint_warnings, stepResults);
+}
 export async function runLintTree(dir, opts) {
     // Load tool cache once for all files
     let cache;
     if (!opts.skipStateValidation) {
         try {
-            cache = new ToolCache({ cacheDir: opts.cacheDir });
+            cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
             await cache.index.load();
-            if (cache.index.listAll().length === 0) {
+            if ((await cache.index.listAll()).length === 0) {
                 console.warn("Tool cache is empty — skipping tool state validation for all files");
                 cache = undefined;
             }
@@ -22,94 +29,75 @@ export async function runLintTree(dir, opts) {
             console.warn(`Failed to load tool cache: ${msg}`);
         }
     }
+    const strict = resolveStrictOptions(opts);
     const treeResult = await collectTree(dir, async (info, data) => {
         const format = resolveFormat(data, opts.format);
-        const report = await lintWorkflowReport(info.path, data, format, {
+        const lr = await lintWorkflowReport(info.path, data, format, {
             skipBestPractices: opts.skipBestPractices,
             skipStateValidation: opts.skipStateValidation,
             cache,
+            strict,
         });
-        return { relativePath: info.relativePath, report };
+        return toLintWorkflowResult(info.relativePath, lr);
     });
-    const report = buildLintTreeReport(treeResult);
+    const report = buildReport(treeResult);
+    await writeReportOutput("lint_tree.md.j2", report, { reportMarkdown: opts.reportMarkdown });
+    await writeReportHtml("lint-tree", report, opts.reportHtml);
     if (opts.json) {
         console.log(JSON.stringify(report, null, 2));
         process.exitCode = computeLintExitCode(report);
         return;
     }
     // Text output
-    for (const outcome of treeResult.outcomes) {
-        if (outcome.error) {
-            console.error(`  ${outcome.info.relativePath}: ERROR (${outcome.error})`);
+    for (const wf of report.workflows) {
+        if (wf.error) {
+            console.error(`  ${wf.path}: ERROR (${wf.error})`);
             continue;
         }
-        if (outcome.skipped) {
-            console.warn(`  ${outcome.info.relativePath}: SKIPPED (${outcome.skipReason})`);
+        if (wf.skipped_reason) {
+            console.warn(`  ${wf.path}: SKIPPED (${wf.skipped_reason})`);
             continue;
         }
-        const r = outcome.result;
-        const lr = r.report;
-        const errors = lr.structural.error_count + (lr.bestPractices?.error_count ?? 0);
-        const warnings = lr.structural.warn_count + (lr.bestPractices?.warn_count ?? 0);
-        const stateFails = lr.stateValidation?.filter((s) => s.status === "fail").length ?? 0;
-        if (errors > 0 || stateFails > 0) {
-            console.error(`  ${r.relativePath}: ${errors} errors, ${warnings} warnings, ${stateFails} state failures`);
-            for (const e of lr.structural.errors)
-                console.error(`    [structural] ${e}`);
-            if (lr.bestPractices) {
-                for (const e of lr.bestPractices.errors)
-                    console.error(`    [best-practices] ${e}`);
-            }
-            if (lr.stateValidation) {
-                for (const s of lr.stateValidation.filter((s) => s.status === "fail")) {
-                    for (const err of s.errors)
-                        console.error(`    [state] Step ${s.stepLabel} (${s.toolId}): ${err}`);
-                }
-            }
+        const stateFails = wf.results.filter((s) => s.status === "fail").length;
+        if (wf.lint_errors > 0 || stateFails > 0) {
+            console.error(`  ${wf.path}: ${wf.lint_errors} errors, ${wf.lint_warnings} warnings, ${stateFails} state failures`);
+            // Detailed error output would require the internal LintReport;
+            // for tree output we show the summary counts per workflow.
         }
-        else if (warnings > 0) {
-            console.warn(`  ${r.relativePath}: ${warnings} warnings`);
+        else if (wf.lint_warnings > 0) {
+            console.warn(`  ${wf.path}: ${wf.lint_warnings} warnings`);
         }
         else {
-            console.log(`  ${r.relativePath}: OK`);
+            console.log(`  ${wf.path}: OK`);
         }
     }
     const s = report.summary;
-    console.log(`\nSummary: ${s.total} workflows | ${s.lintErrors} errors, ${s.lintWarnings} warnings, ${s.stateFail} state failures`);
+    const total = report.workflows.length;
+    console.log(`\nSummary: ${total} workflows | ${s.lint_errors} errors, ${s.lint_warnings} warnings, ${s.state_fail} state failures`);
     process.exitCode = computeLintExitCode(report);
 }
-function buildLintTreeReport(treeResult) {
-    const results = [];
-    let lintErrors = 0;
-    let lintWarnings = 0;
-    let stateFail = 0;
+function buildReport(treeResult) {
+    const workflows = [];
     for (const o of treeResult.outcomes) {
         if (o.error) {
-            results.push({ relativePath: o.info.relativePath, error: o.error });
+            workflows.push(buildLintWorkflowResult(o.info.relativePath, 0, 0, [], { error: o.error }));
             continue;
         }
         if (o.skipped) {
-            results.push({ relativePath: o.info.relativePath, error: `SKIPPED: ${o.skipReason}` });
+            workflows.push(buildLintWorkflowResult(o.info.relativePath, 0, 0, [], {
+                skipped_reason: o.skipReason ?? null,
+            }));
             continue;
         }
-        const r = o.result;
-        results.push(r);
-        lintErrors += r.report.structural.error_count + (r.report.bestPractices?.error_count ?? 0);
-        lintWarnings += r.report.structural.warn_count + (r.report.bestPractices?.warn_count ?? 0);
-        stateFail += r.report.stateValidation?.filter((s) => s.status === "fail").length ?? 0;
+        workflows.push(o.result);
     }
-    const wfSummary = summarizeOutcomes(treeResult.outcomes, (r) => r.report.exitCode >= 2);
-    return {
-        root: treeResult.root,
-        results,
-        summary: { ...wfSummary, lintErrors, lintWarnings, stateFail },
-    };
+    return schemaBuildLintTreeReport(treeResult.root, workflows);
 }
 function computeLintExitCode(report) {
     const s = report.summary;
-    if (s.lintErrors > 0 || s.stateFail > 0 || s.error > 0)
+    if (s.lint_errors > 0 || s.state_fail > 0 || s.errors > 0)
         return 2;
-    if (s.lintWarnings > 0)
+    if (s.lint_warnings > 0)
         return 1;
     return 0;
 }

package/dist/commands/lint-tree.js.map

@@ -1 +1 @@
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package/dist/commands/lint.d.ts

@@ -2,26 +2,30 @@
  * `gxwf lint` — unified lint combining structural checks, best practices,
  * and tool state validation.
  */
-import { ToolCache } from "@galaxy-tool-util/core";
-import { type LintResult } from "@galaxy-tool-util/schema";
-import { type StepValidationResult } from "./validate-workflow.js";
-export interface LintOptions {
+import type { ToolCache } from "@galaxy-tool-util/core";
+import { type LintResult, type ValidationStepResult as StepValidationResult } from "@galaxy-tool-util/schema";
+import { type StrictOptions, type ResolvedStrictOptions } from "./strict-options.js";
+export interface LintOptions extends StrictOptions {
     format?: string;
     skipBestPractices?: boolean;
     skipStateValidation?: boolean;
     cacheDir?: string;
     json?: boolean;
+    reportHtml?: string | boolean;
 }
 export interface LintReportOptions {
     skipBestPractices?: boolean;
     skipStateValidation?: boolean;
     cache?: ToolCache;
+    strict?: ResolvedStrictOptions;
 }
 export interface LintReport {
     structural: LintResult;
     bestPractices: LintResult | null;
     stateValidation: StepValidationResult[] | null;
     stateSkipped: boolean;
+    encodingErrors: string[];
+    structureErrors: string[];
     exitCode: number;
 }
 export declare function runLint(filePath: string, opts: LintOptions): Promise<void>;

package/dist/commands/lint.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"lint.d.ts","sourceRoot":"","sources":["../../src/commands/lint.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAExD,OAAO,EAQL,KAAK,UAAU,EAGf,KAAK,oBAAoB,IAAI,oBAAoB,EAClD,MAAM,0BAA0B,CAAC;AAKlC,OAAO,EAEL,KAAK,aAAa,EAClB,KAAK,qBAAqB,EAC3B,MAAM,qBAAqB,CAAC;AAS7B,MAAM,WAAW,WAAY,SAAQ,aAAa;IAChD,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC/B;AAED,MAAM,WAAW,iBAAiB;IAChC,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,KAAK,CAAC,EAAE,SAAS,CAAC;IAClB,MAAM,CAAC,EAAE,qBAAqB,CAAC;CAChC;AAED,MAAM,WAAW,UAAU;IACzB,UAAU,EAAE,UAAU,CAAC;IACvB,aAAa,EAAE,UAAU,GAAG,IAAI,CAAC;IACjC,eAAe,EAAE,oBAAoB,EAAE,GAAG,IAAI,CAAC;IAC/C,YAAY,EAAE,OAAO,CAAC;IACtB,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,QAAQ,EAAE,MAAM,CAAC;CAClB;AAaD,wBAAsB,OAAO,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA4GhF;AAED,+EAA+E;AAC/E,wBAAsB,kBAAkB,CACtC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,iBAAiB,GACtB,OAAO,CAAC,UAAU,CAAC,CA8ErB"}

package/dist/commands/lint.js

@@ -1,14 +1,12 @@
-/**
- * `gxwf lint` — unified lint combining structural checks, best practices,
- * and tool state validation.
- */
-import { ToolCache } from "@galaxy-tool-util/core";
-import { lintWorkflow, lintBestPracticesNative, lintBestPracticesFormat2, } from "@galaxy-tool-util/schema";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { lintWorkflow, lintBestPracticesNative, lintBestPracticesFormat2, checkStrictEncoding, checkStrictStructure, buildSingleLintReport, } from "@galaxy-tool-util/schema";
 import { dirname } from "node:path";
 import { renderStepResults } from "./render-results.js";
 import { readWorkflowFile, resolveFormat } from "./workflow-io.js";
 import { createDefaultResolver } from "./url-resolver.js";
-import { validateNativeSteps, validateFormat2Steps, } from "./validate-workflow.js";
+import { resolveStrictOptions, } from "./strict-options.js";
+import { validateNativeSteps, validateFormat2Steps, decodeStructureErrors, detectEncodingErrors, } from "./validate-workflow.js";
+import { writeReportHtml } from "./report-output.js";
 function mergeLintResults(...results) {
     const errors = [];
     const warnings = [];
@@ -29,7 +27,7 @@ export async function runLint(filePath, opts) {
     let cache;
     if (!opts.skipStateValidation) {
         try {
-            cache = new ToolCache({ cacheDir: opts.cacheDir });
+            cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
             await cache.index.load();
         }
         catch (e) {
@@ -37,16 +35,45 @@ export async function runLint(filePath, opts) {
             console.warn(`Failed to load tool cache: ${msg}`);
         }
     }
+    const strict = resolveStrictOptions(opts);
     const report = await lintWorkflowReport(filePath, data, format, {
         skipBestPractices: opts.skipBestPractices,
         skipStateValidation: opts.skipStateValidation,
         cache,
+        strict,
     });
-    if (opts.json) {
-        console.log(JSON.stringify(report, null, 2));
+    if (opts.json || opts.reportHtml) {
+        const lintErrors = report.structural.error_count + (report.bestPractices?.error_count ?? 0);
+        const lintWarnings = report.structural.warn_count + (report.bestPractices?.warn_count ?? 0);
+        // Effect Schema decode for structure_errors
+        const structureErrors = decodeStructureErrors(data, format);
+        // Legacy encoding detection for encoding_errors
+        let encodingErrors = [];
+        if (cache && !opts.skipStateValidation) {
+            const expansionOpts = {
+                resolver: createDefaultResolver({ workflowDirectory: dirname(filePath) }),
+            };
+            encodingErrors = await detectEncodingErrors(data, cache, format, expansionOpts);
+        }
+        const singleReport = buildSingleLintReport(filePath, lintErrors, lintWarnings, report.stateValidation ?? [], { structure_errors: structureErrors, encoding_errors: encodingErrors });
+        if (opts.json) {
+            console.log(JSON.stringify(singleReport, null, 2));
+        }
+        await writeReportHtml("lint", singleReport, opts.reportHtml);
         process.exitCode = report.exitCode;
         return;
     }
+    // Strict checks
+    if (report.encodingErrors.length > 0) {
+        console.error("Encoding errors:");
+        for (const e of report.encodingErrors)
+            console.error(`  ${e}`);
+    }
+    if (report.structureErrors.length > 0) {
+        console.error("Structure errors (strict):");
+        for (const e of report.structureErrors)
+            console.error(`  ${e}`);
+    }
     // Structural lint
     const { structural } = report;
     if (structural.error_count > 0) {
@@ -93,6 +120,16 @@ export async function runLint(filePath, opts) {
 }
 /** Lint a workflow, returning a structured report. Pure logic — no CLI I/O. */
 export async function lintWorkflowReport(filePath, data, format, opts) {
+    const strict = opts.strict ?? {
+        strictStructure: false,
+        strictEncoding: false,
+        strictState: false,
+    };
+    const fmt = format;
+    // Strict encoding check
+    const encodingErrors = strict.strictEncoding ? checkStrictEncoding(data, fmt) : [];
+    // Strict structure check
+    const structureErrors = strict.strictStructure ? checkStrictStructure(data, fmt) : [];
     // Phase 1: Structural lint (always runs)
     const structural = lintWorkflow(data);
     // Phase 2: Best practices
@@ -111,7 +148,7 @@ export async function lintWorkflowReport(filePath, data, format, opts) {
         }
         else {
             try {
-                const isEmpty = cache.index.listAll().length === 0;
+                const isEmpty = (await cache.index.listAll()).length === 0;
                 if (isEmpty) {
                     console.warn("Tool cache is empty — skipping tool state validation");
                     stateSkipped = true;
@@ -139,9 +176,20 @@ export async function lintWorkflowReport(filePath, data, format, opts) {
     // Compute exit code: 0 = clean, 1 = warnings only, 2 = errors
     const merged = mergeLintResults(structural, bestPractices);
     const hasStateErrors = stateValidation?.some((r) => r.status === "fail") ?? false;
-    const hasErrors = merged.error_count > 0 || hasStateErrors;
+    const hasStrictErrors = encodingErrors.length > 0 || structureErrors.length > 0;
+    const hasStrictStateSkips = strict.strictState &&
+        (stateValidation?.some((r) => r.status !== "ok" && r.status !== "fail") ?? false);
+    const hasErrors = merged.error_count > 0 || hasStateErrors || hasStrictErrors || hasStrictStateSkips;
     const hasWarnings = merged.warn_count > 0;
     const exitCode = hasErrors ? 2 : hasWarnings ? 1 : 0;
-    return { structural, bestPractices, stateValidation, stateSkipped, exitCode };
+    return {
+        structural,
+        bestPractices,
+        stateValidation,
+        stateSkipped,
+        encodingErrors,
+        structureErrors,
+        exitCode,
+    };
 }
 //# sourceMappingURL=lint.js.map

package/dist/commands/lint.js.map

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package/dist/commands/list.js

@@ -1,8 +1,8 @@
-import { ToolCache } from "@galaxy-tool-util/core";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
 export async function runList(opts) {
-    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
     await cache.index.load();
-    const entries = cache.listCached();
+    const entries = await cache.listCached();
     if (entries.length === 0) {
         console.log("Cache is empty.");
         return;

package/dist/commands/list.js.map

@@ -1 +1 @@
-{"version":3,"file":"list.js","sourceRoot":"","sources":["../../src/commands/list.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAOnD,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,IAAiB;IAC7C,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IACzD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,OAAO,GAAG,KAAK,CAAC,UAAU,EAAE,CAAC;IAEnC,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzB,OAAO,CAAC,GAAG,CAAC,iBAAiB,CAAC,CAAC;QAC/B,OAAO;IACT,CAAC;IAED,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC9C,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,CAAC,SAAS,EAAE,SAAS,EAAE,QAAQ,EAAE,WAAW,CAAC,CAAC;IAC7D,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC;IAEpF,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;IACzF,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAExD,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;IAClE,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;IACjB,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;IACjE,CAAC;AACH,CAAC"}
+{"version":3,"file":"list.js","sourceRoot":"","sources":["../../src/commands/list.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAOhE,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,IAAiB;IAC7C,MAAM,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC7D,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,OAAO,GAAG,MAAM,KAAK,CAAC,UAAU,EAAE,CAAC;IAEzC,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzB,OAAO,CAAC,GAAG,CAAC,iBAAiB,CAAC,CAAC;QAC/B,OAAO;IACT,CAAC;IAED,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC9C,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,CAAC,SAAS,EAAE,SAAS,EAAE,QAAQ,EAAE,WAAW,CAAC,CAAC;IAC7D,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC;IAEpF,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;IACzF,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAExD,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;IAClE,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;IACjB,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;IACjE,CAAC;AACH,CAAC"}

package/dist/commands/mermaid.d.ts

@@ -0,0 +1,6 @@
+export interface MermaidCommandOptions {
+    output?: string;
+    comments?: boolean;
+}
+export declare function runMermaid(filePath: string, opts: MermaidCommandOptions): Promise<void>;
+//# sourceMappingURL=mermaid.d.ts.map

package/dist/commands/mermaid.d.ts.map

@@ -0,0 +1 @@
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