erosolar-cli 2.1.295 → 2.1.297

package/dist/science/cancerResearch.d.ts

@@ -0,0 +1,59 @@
+/**
+ * Cancer Research Module
+ *
+ * This module demonstrates how TypeScript/JavaScript can be used for
+ * cancer research data analysis and machine learning pipelines.
+ *
+ * While real cancer research requires domain expertise and clinical validation,
+ * software engineering enables scalable analysis and reproducible research.
+ */
+export interface CancerDataset {
+    samples: number;
+    features: number;
+    data: number[][];
+    labels: number[];
+    featureNames: string[];
+}
+export interface CancerStatistics {
+    nSamples: number;
+    nFeatures: number;
+    classDistribution: {
+        benign: number;
+        malignant: number;
+    };
+    featureMeans: Record<string, number>;
+    featureStds: Record<string, number>;
+}
+export interface ModelMetrics {
+    accuracy: number;
+    precision: number;
+    recall: number;
+    f1Score: number;
+}
+export declare class CancerResearchPipeline {
+    private seed;
+    private dataset;
+    private results;
+    constructor(seed?: number);
+    /**
+     * Generate synthetic cancer dataset
+     */
+    generateSyntheticData(nSamples?: number, nFeatures?: number): CancerDataset;
+    /**
+     * Compute basic statistics on the dataset
+     */
+    computeStatistics(): CancerStatistics;
+    /**
+     * Simple logistic regression implementation (educational purposes only)
+     */
+    trainLogisticRegression(testSize?: number): ModelMetrics;
+    /**
+     * Run complete pipeline
+     */
+    runPipeline(): Record<string, any>;
+    /**
+     * Export results to JSON file (node.js environment)
+     */
+    exportResults(filePath?: string): Promise<void>;
+}
+//# sourceMappingURL=cancerResearch.d.ts.map

package/dist/science/cancerResearch.d.ts.map

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package/dist/science/cancerResearch.js

@@ -0,0 +1,219 @@
+/**
+ * Cancer Research Module
+ *
+ * This module demonstrates how TypeScript/JavaScript can be used for
+ * cancer research data analysis and machine learning pipelines.
+ *
+ * While real cancer research requires domain expertise and clinical validation,
+ * software engineering enables scalable analysis and reproducible research.
+ */
+export class CancerResearchPipeline {
+    seed;
+    dataset = null;
+    results = {};
+    constructor(seed = 42) {
+        this.seed = seed;
+        // Simple seed for reproducibility
+        // Note: In production, use proper seeding libraries
+    }
+    /**
+     * Generate synthetic cancer dataset
+     */
+    generateSyntheticData(nSamples = 1000, nFeatures = 30) {
+        const data = [];
+        const labels = [];
+        const featureNames = Array.from({ length: nFeatures }, (_, i) => `gene_${i + 1}`);
+        // Simple synthetic data generation
+        for (let i = 0; i < nSamples; i++) {
+            const sample = [];
+            let weightedSum = 0;
+            for (let j = 0; j < nFeatures; j++) {
+                // Generate feature with normal distribution-like values
+                const value = (Math.random() * 2 - 1) + (Math.random() * 2 - 1); // Rough normal approximation
+                sample.push(value);
+                // Simple weight for correlation with label
+                weightedSum += value * (j % 3 - 1); // Arbitrary weights
+            }
+            // Convert to probability using sigmoid
+            const probability = 1 / (1 + Math.exp(-weightedSum / nFeatures));
+            const label = probability > 0.5 ? 1 : 0;
+            // Add some noise
+            const finalLabel = Math.random() > 0.8 ? 1 - label : label;
+            labels.push(finalLabel);
+            data.push(sample);
+        }
+        this.dataset = {
+            samples: nSamples,
+            features: nFeatures,
+            data,
+            labels,
+            featureNames
+        };
+        console.log(`Generated synthetic cancer dataset with ${nSamples} samples, ${nFeatures} features`);
+        return this.dataset;
+    }
+    /**
+     * Compute basic statistics on the dataset
+     */
+    computeStatistics() {
+        if (!this.dataset) {
+            throw new Error('No dataset loaded. Call generateSyntheticData() first.');
+        }
+        const { data, labels, featureNames } = this.dataset;
+        // Class distribution
+        const benign = labels.filter(l => l === 0).length;
+        const malignant = labels.filter(l => l === 1).length;
+        // Feature means and stds
+        const featureMeans = {};
+        const featureStds = {};
+        for (let j = 0; j < this.dataset.features; j++) {
+            const values = data.map(row => row[j]);
+            const mean = values.reduce((a, b) => a + b, 0) / values.length;
+            const variance = values.reduce((sq, n) => sq + Math.pow(n - mean, 2), 0) / values.length;
+            featureMeans[featureNames[j]] = mean;
+            featureStds[featureNames[j]] = Math.sqrt(variance);
+        }
+        const stats = {
+            nSamples: this.dataset.samples,
+            nFeatures: this.dataset.features,
+            classDistribution: { benign, malignant },
+            featureMeans,
+            featureStds
+        };
+        this.results.statistics = stats;
+        return stats;
+    }
+    /**
+     * Simple logistic regression implementation (educational purposes only)
+     */
+    trainLogisticRegression(testSize = 0.2) {
+        if (!this.dataset) {
+            throw new Error('No dataset loaded.');
+        }
+        const { data, labels } = this.dataset;
+        const n = data.length;
+        const splitIdx = Math.floor(n * (1 - testSize));
+        // Simple shuffle (Fisher-Yates)
+        const indices = Array.from({ length: n }, (_, i) => i);
+        for (let i = n - 1; i > 0; i--) {
+            const j = Math.floor(Math.random() * (i + 1));
+            [indices[i], indices[j]] = [indices[j], indices[i]];
+        }
+        // Split data
+        const trainData = indices.slice(0, splitIdx).map(i => data[i]);
+        const trainLabels = indices.slice(0, splitIdx).map(i => labels[i]);
+        const testData = indices.slice(splitIdx).map(i => data[i]);
+        const testLabels = indices.slice(splitIdx).map(i => labels[i]);
+        // Simple logistic regression weights (gradient descent)
+        const nFeatures = data[0].length;
+        const weights = Array(nFeatures + 1).fill(0); // +1 for bias
+        const learningRate = 0.01;
+        const epochs = 100;
+        for (let epoch = 0; epoch < epochs; epoch++) {
+            for (let i = 0; i < trainData.length; i++) {
+                const features = [1, ...trainData[i]]; // Add bias term
+                let weightedSum = 0;
+                for (let j = 0; j < weights.length; j++) {
+                    weightedSum += weights[j] * features[j];
+                }
+                const prediction = 1 / (1 + Math.exp(-weightedSum));
+                const error = prediction - trainLabels[i];
+                // Update weights
+                for (let j = 0; j < weights.length; j++) {
+                    weights[j] -= learningRate * error * features[j];
+                }
+            }
+        }
+        // Evaluate on test set
+        let truePositives = 0;
+        let falsePositives = 0;
+        let falseNegatives = 0;
+        let correct = 0;
+        for (let i = 0; i < testData.length; i++) {
+            const features = [1, ...testData[i]];
+            let weightedSum = 0;
+            for (let j = 0; j < weights.length; j++) {
+                weightedSum += weights[j] * features[j];
+            }
+            const prediction = weightedSum > 0 ? 1 : 0;
+            const actual = testLabels[i];
+            if (prediction === actual) {
+                correct++;
+                if (prediction === 1)
+                    truePositives++;
+            }
+            else {
+                if (prediction === 1)
+                    falsePositives++;
+                else
+                    falseNegatives++;
+            }
+        }
+        const accuracy = correct / testData.length;
+        const precision = truePositives / (truePositives + falsePositives) || 0;
+        const recall = truePositives / (truePositives + falseNegatives) || 0;
+        const f1Score = 2 * (precision * recall) / (precision + recall) || 0;
+        const metrics = {
+            accuracy,
+            precision,
+            recall,
+            f1Score
+        };
+        this.results.modelMetrics = metrics;
+        return metrics;
+    }
+    /**
+     * Run complete pipeline
+     */
+    runPipeline() {
+        console.log('Starting TypeScript cancer research pipeline...');
+        // Generate data
+        this.generateSyntheticData(800, 25);
+        // Compute statistics
+        const stats = this.computeStatistics();
+        console.log('Statistics:', JSON.stringify(stats, null, 2));
+        // Train model
+        const metrics = this.trainLogisticRegression();
+        console.log('Model metrics:', JSON.stringify(metrics, null, 2));
+        // Generate report
+        const report = {
+            pipelineVersion: '1.0.0',
+            timestamp: new Date().toISOString(),
+            dataset: {
+                samples: this.dataset.samples,
+                features: this.dataset.features
+            },
+            statistics: stats,
+            modelMetrics: metrics,
+            interpretation: 'This TypeScript implementation demonstrates basic ML for cancer research. Real applications require domain expertise, validated datasets, and clinical trials.'
+        };
+        this.results.report = report;
+        return report;
+    }
+    /**
+     * Export results to JSON file (node.js environment)
+     */
+    async exportResults(filePath = 'cancer_research_typescript.json') {
+        if (typeof window !== 'undefined') {
+            console.warn('Browser environment: cannot write to file system');
+            return;
+        }
+        const fs = await import('fs/promises');
+        await fs.writeFile(filePath, JSON.stringify(this.results, null, 2));
+        console.log(`Results exported to ${filePath}`);
+    }
+}
+// Example usage (if run directly)
+if (require.main === module) {
+    const pipeline = new CancerResearchPipeline();
+    const report = pipeline.runPipeline();
+    console.log('\n=== TypeScript Cancer Research Pipeline Complete ===');
+    console.log('This demonstrates how Node.js/TypeScript can be used for biomedical research.');
+    console.log('Key advantages:');
+    console.log('- Strong typing for data integrity');
+    console.log('- Async/await for large-scale data processing');
+    console.log('- Integration with web technologies for visualization');
+    console.log('- Cross-platform deployment (server, browser, mobile)');
+    pipeline.exportResults().catch(console.error);
+}
+//# sourceMappingURL=cancerResearch.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "erosolar-cli",
-  "version": "2.1.295",
+  "version": "2.1.297",
   "description": "Unified AI agent framework for the command line - Multi-provider support with schema-driven tools, code intelligence, and transparent reasoning",
   "main": "dist/bin/erosolar.js",
   "type": "module",
@@ -53,8 +53,6 @@
     "quality-gate": "npm run complexity-check && npm run health-check && npm run type-check",
     "quality-dashboard": "node scripts/code-quality-dashboard.js",
     "full-flow": "node scripts/full-flow-human.mjs",
-    "agi:verify": "node scripts/verify-agi.mjs",
-    "agi:real-flow": "node scripts/real-agi-flow-test.mjs",
     "ai-code-review": "node scripts/ai-code-reviewer.mjs",
     "code-intelligence": "node scripts/code-intelligence-enhancer.mjs",
     "dev-productivity": "node scripts/dev-productivity-booster.mjs",
@@ -129,7 +127,6 @@
     "boxen": "^5.1.2",
     "chalk": "^4.1.2",
     "cli-spinners": "^2.9.2",
-    "erosolar-cli": "^2.1.248",
     "gradient-string": "^2.0.2",
     "nanospinner": "^1.1.0",
     "nodemailer": "^7.0.10",

package/dist/core/realAGI.d.ts

@@ -1,121 +0,0 @@
-/**
- * Real AGI Core - Pure Tool-Based Autonomous Intelligence
- *
- * NO INTENTS - Only tools
- * NO SIMULATIONS - Everything executes for real
- * NO CATEGORIES - Just understanding and execution
- *
- * This mirrors how Claude Code works:
- * 1. Understand the prompt
- * 2. Think about what tools to use
- * 3. Execute tools in sequence
- * 4. Display results in Claude Code style
- *
- * Handles ANY prompt: software, research, legal, finance, defense, or anything else
- */
-import { type ToolMatch } from './toolEmbeddings.js';
-/** A real tool that can be executed */
-export interface RealTool {
-    name: string;
-    execute: (args: Record<string, unknown>) => Promise<ToolResult>;
-}
-/** Result from executing a tool */
-export interface ToolResult {
-    success: boolean;
-    output: string;
-    error?: string;
-    duration: number;
-    artifacts?: string[];
-}
-/** A step in execution - just tool + args */
-export interface ExecutionStep {
-    id: string;
-    tool: string;
-    args: Record<string, unknown>;
-    description: string;
-    dependsOn: string[];
-    status: 'pending' | 'running' | 'completed' | 'failed';
-    result?: ToolResult;
-}
-/** Full execution plan */
-export interface ExecutionPlan {
-    prompt: string;
-    thinking: string[];
-    steps: ExecutionStep[];
-    startTime: number;
-    endTime?: number;
-}
-/** Memory for learning */
-export interface AGIMemory {
-    successfulApproaches: Array<{
-        prompt: string;
-        tools: string[];
-        success: boolean;
-        timestamp: number;
-    }>;
-    projectInfo: {
-        type: string;
-        buildCmd: string | null;
-        testCmd: string | null;
-        lintCmd: string | null;
-    };
-}
-/** Callback for streaming output through the UI */
-export type DisplayCallback = (message: string, type?: 'thinking' | 'step' | 'result' | 'complete' | 'error') => void;
-export declare class RealAGI {
-    private workingDir;
-    private memory;
-    private memoryPath;
-    private tools;
-    private embeddings;
-    private displayCallback;
-    constructor(workingDir?: string);
-    /** Set callback for streaming output through the shell UI */
-    setDisplayCallback(callback: DisplayCallback | null): void;
-    /** Stream a message through the UI if callback is set */
-    private streamToUI;
-    private loadMemory;
-    private saveMemory;
-    private detectProject;
-    private createRealTools;
-    /**
-     * Search for relevant tools using embeddings (dot product similarity)
-     */
-    searchTools(prompt: string, topK?: number): Promise<ToolMatch[]>;
-    /**
-     * Get recommended tools for a prompt using embeddings
-     */
-    getRecommendedTools(prompt: string): Promise<string[]>;
-    /**
-     * Format tool search results
-     */
-    formatToolSearch(prompt: string): Promise<string>;
-    /**
-     * Understand any prompt and figure out what tools to run
-     * This is the core AGI function - no intents, just tool planning
-     */
-    understand(prompt: string): ExecutionPlan;
-    /**
-     * Execute a plan - runs each tool for real
-     */
-    execute(plan: ExecutionPlan): Promise<ExecutionPlan>;
-    private executeStep;
-    /**
-     * Format execution plan in Claude Code style
-     */
-    formatPlan(plan: ExecutionPlan): string;
-    /**
-     * Format execution results in Claude Code style
-     */
-    formatResults(plan: ExecutionPlan): string;
-    private formatArgs;
-    /**
-     * Process any prompt - understand, plan, execute, display
-     * Streams output through the UI callback if set
-     */
-    process(prompt: string, dryRun?: boolean): Promise<string>;
-    getMemory(): AGIMemory;
-}
-export declare function getRealAGI(workingDir?: string): RealAGI;
-export declare function resetRealAGI(): void;
-//# sourceMappingURL=realAGI.d.ts.map

package/dist/core/realAGI.d.ts.map

@@ -1 +0,0 @@
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