docrev 0.8.1 → 0.8.5

package/dist/lib/rate-limiter.js

@@ -0,0 +1,79 @@
+/**
+ * Rate Limiter - Prevents API abuse with exponential backoff
+ */
+export class RateLimiter {
+    minDelay;
+    maxDelay;
+    maxRetries;
+    backoffFactor;
+    lastRequestTime;
+    currentDelay;
+    consecutiveErrors;
+    constructor(options = {}) {
+        this.minDelay = options.minDelay || 100; // Min delay between requests (ms)
+        this.maxDelay = options.maxDelay || 30000; // Max delay after backoff (ms)
+        this.maxRetries = options.maxRetries || 3; // Max retry attempts
+        this.backoffFactor = options.backoffFactor || 2;
+        this.lastRequestTime = 0;
+        this.currentDelay = this.minDelay;
+        this.consecutiveErrors = 0;
+    }
+    async wait() {
+        const now = Date.now();
+        const elapsed = now - this.lastRequestTime;
+        if (elapsed < this.currentDelay) {
+            await new Promise(r => setTimeout(r, this.currentDelay - elapsed));
+        }
+        this.lastRequestTime = Date.now();
+    }
+    onSuccess() {
+        // Gradually reduce delay on success
+        this.consecutiveErrors = 0;
+        this.currentDelay = Math.max(this.minDelay, this.currentDelay / this.backoffFactor);
+    }
+    onError(statusCode) {
+        this.consecutiveErrors++;
+        // Exponential backoff
+        if (statusCode === 429 || statusCode >= 500) {
+            this.currentDelay = Math.min(this.maxDelay, this.currentDelay * this.backoffFactor);
+        }
+        return this.consecutiveErrors <= this.maxRetries;
+    }
+    async fetchWithRetry(url, options = {}) {
+        let lastError;
+        for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
+            await this.wait();
+            try {
+                const response = await fetch(url, options);
+                if (response.status === 429) {
+                    // Rate limited - back off
+                    const retryAfter = response.headers.get('Retry-After');
+                    const delay = retryAfter ? parseInt(retryAfter, 10) * 1000 : this.currentDelay * 2;
+                    this.currentDelay = Math.min(this.maxDelay, delay);
+                    if (!this.onError(429))
+                        break;
+                    continue;
+                }
+                if (response.status >= 500 && attempt < this.maxRetries) {
+                    // Server error - retry with backoff
+                    if (!this.onError(response.status))
+                        break;
+                    continue;
+                }
+                this.onSuccess();
+                return response;
+            }
+            catch (err) {
+                lastError = err;
+                if (!this.onError(0))
+                    break;
+            }
+        }
+        throw lastError || new Error('Max retries exceeded');
+    }
+}
+// Shared rate limiters for different APIs
+export const crossrefLimiter = new RateLimiter({ minDelay: 100, maxDelay: 10000 });
+export const dataciteLimiter = new RateLimiter({ minDelay: 100, maxDelay: 10000 });
+export const doiOrgLimiter = new RateLimiter({ minDelay: 200, maxDelay: 15000 });
+//# sourceMappingURL=rate-limiter.js.map

package/dist/lib/rate-limiter.js.map

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package/dist/lib/response.d.ts

@@ -0,0 +1,41 @@
+/**
+ * Response letter generator
+ * Extract comments and replies from markdown files for journal resubmission
+ */
+interface Reply {
+    author: string;
+    text: string;
+}
+interface CommentWithReplies {
+    author: string;
+    text: string;
+    replies: Reply[];
+    context: string;
+    file: string;
+    line: number;
+}
+interface ResponseOptions {
+    title?: string;
+    authorName?: string;
+    includeContext?: boolean;
+    includeLocation?: boolean;
+}
+/**
+ * Parse a comment with potential replies
+ * Format: {>>Author: comment<<} {>>Reply Author: reply<<}
+ */
+export declare function parseCommentsWithReplies(text: string, file?: string): CommentWithReplies[];
+/**
+ * Group comments by reviewer
+ */
+export declare function groupByReviewer(comments: CommentWithReplies[]): Map<string, CommentWithReplies[]>;
+/**
+ * Generate response letter in Markdown format
+ */
+export declare function generateResponseLetter(comments: CommentWithReplies[], options?: ResponseOptions): string;
+/**
+ * Collect comments from multiple files
+ */
+export declare function collectComments(files: string[]): CommentWithReplies[];
+export {};
+//# sourceMappingURL=response.d.ts.map

package/dist/lib/response.d.ts.map

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package/dist/lib/response.js

@@ -0,0 +1,150 @@
+/**
+ * Response letter generator
+ * Extract comments and replies from markdown files for journal resubmission
+ */
+import * as fs from 'fs';
+import * as path from 'path';
+/**
+ * Parse a comment with potential replies
+ * Format: {>>Author: comment<<} {>>Reply Author: reply<<}
+ */
+export function parseCommentsWithReplies(text, file = '') {
+    const comments = [];
+    const lines = text.split('\n');
+    // Pattern for comments: {>>Author: text<<}
+    const commentPattern = /\{>>([^:]+):\s*([^<]+)<<\}/g;
+    for (let lineNum = 0; lineNum < lines.length; lineNum++) {
+        const line = lines[lineNum];
+        if (!line)
+            continue;
+        const matches = [...line.matchAll(commentPattern)];
+        if (matches.length === 0)
+            continue;
+        // Get context (surrounding text without comments)
+        const contextLine = line.replace(/\{>>[^<]+<<\}/g, '').trim();
+        const context = contextLine.slice(0, 100) + (contextLine.length > 100 ? '...' : '');
+        // First match is the original comment, rest are replies
+        const [first, ...rest] = matches;
+        if (!first || !first[1] || !first[2])
+            continue;
+        comments.push({
+            author: first[1].trim(),
+            text: first[2].trim(),
+            replies: rest.map(m => ({
+                author: m[1]?.trim() || '',
+                text: m[2]?.trim() || '',
+            })),
+            context,
+            file,
+            line: lineNum + 1,
+        });
+    }
+    return comments;
+}
+/**
+ * Group comments by reviewer
+ */
+export function groupByReviewer(comments) {
+    const grouped = new Map();
+    for (const comment of comments) {
+        const reviewer = comment.author;
+        if (!grouped.has(reviewer)) {
+            grouped.set(reviewer, []);
+        }
+        grouped.get(reviewer).push(comment);
+    }
+    return grouped;
+}
+/**
+ * Generate response letter in Markdown format
+ */
+export function generateResponseLetter(comments, options = {}) {
+    const { title = 'Response to Reviewers', authorName = 'Author', includeContext = true, includeLocation = true, } = options;
+    const lines = [];
+    lines.push(`# ${title}`);
+    lines.push('');
+    lines.push(`We thank the reviewers for their constructive feedback. Below we address each comment.`);
+    lines.push('');
+    // Group by reviewer
+    const grouped = groupByReviewer(comments);
+    // Sort reviewers (put known reviewer names first, then others)
+    const reviewers = [...grouped.keys()].sort((a, b) => {
+        // "Reviewer" names first, then alphabetical
+        const aIsReviewer = a.toLowerCase().includes('reviewer');
+        const bIsReviewer = b.toLowerCase().includes('reviewer');
+        if (aIsReviewer && !bIsReviewer)
+            return -1;
+        if (!aIsReviewer && bIsReviewer)
+            return 1;
+        return a.localeCompare(b);
+    });
+    for (const reviewer of reviewers) {
+        // Skip if this is the author's own comments (replies)
+        if (reviewer.toLowerCase() === authorName.toLowerCase())
+            continue;
+        if (reviewer.toLowerCase() === 'claude')
+            continue;
+        const reviewerComments = grouped.get(reviewer);
+        lines.push(`## ${reviewer}`);
+        lines.push('');
+        for (let i = 0; i < reviewerComments.length; i++) {
+            const c = reviewerComments[i];
+            if (!c)
+                continue;
+            lines.push(`### Comment ${i + 1}`);
+            if (includeLocation) {
+                lines.push(`*${c.file}:${c.line}*`);
+            }
+            lines.push('');
+            // Original comment
+            lines.push(`> **${c.author}:** ${c.text}`);
+            lines.push('');
+            // Context if available
+            if (includeContext && c.context) {
+                lines.push(`*Context:* "${c.context}"`);
+                lines.push('');
+            }
+            // Replies
+            if (c.replies.length > 0) {
+                lines.push('**Response:**');
+                lines.push('');
+                for (const reply of c.replies) {
+                    lines.push(`${reply.text}`);
+                }
+            }
+            else {
+                lines.push('**Response:**');
+                lines.push('');
+                lines.push('*[TODO: Add response]*');
+            }
+            lines.push('');
+            lines.push('---');
+            lines.push('');
+        }
+    }
+    // Summary stats
+    const totalComments = comments.filter(c => !c.author.toLowerCase().includes('claude') &&
+        c.author.toLowerCase() !== authorName.toLowerCase()).length;
+    const answered = comments.filter(c => c.replies.length > 0).length;
+    lines.push('## Summary');
+    lines.push('');
+    lines.push(`- Total comments: ${totalComments}`);
+    lines.push(`- Addressed: ${answered}`);
+    lines.push(`- Pending: ${totalComments - answered}`);
+    return lines.join('\n');
+}
+/**
+ * Collect comments from multiple files
+ */
+export function collectComments(files) {
+    const allComments = [];
+    for (const file of files) {
+        if (!fs.existsSync(file))
+            continue;
+        const text = fs.readFileSync(file, 'utf-8');
+        const comments = parseCommentsWithReplies(text, path.basename(file));
+        allComments.push(...comments);
+    }
+    return allComments;
+}
+//# sourceMappingURL=response.js.map

package/dist/lib/response.js.map

@@ -0,0 +1 @@
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package/dist/lib/review.d.ts

@@ -0,0 +1,35 @@
+/**
+ * Interactive review TUI for track changes
+ */
+import type { Comment } from './types.js';
+interface ReviewResult {
+    text: string;
+    accepted: number;
+    rejected: number;
+    skipped: number;
+}
+interface CommentReviewOptions {
+    author?: string;
+    addReply?: (text: string, comment: Comment, author: string, replyText: string) => string;
+    setCommentStatus?: (text: string, comment: Comment, resolved: boolean) => string;
+}
+interface CommentReviewResult {
+    text: string;
+    resolved: number;
+    replied: number;
+    skipped: number;
+}
+/**
+ * Run interactive review session
+ */
+export declare function interactiveReview(text: string): Promise<ReviewResult>;
+/**
+ * List all comments
+ */
+export declare function listComments(text: string): void;
+/**
+ * Run interactive comment review session
+ */
+export declare function interactiveCommentReview(text: string, options?: CommentReviewOptions): Promise<CommentReviewResult>;
+export {};
+//# sourceMappingURL=review.d.ts.map

package/dist/lib/review.d.ts.map

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package/dist/lib/review.js

@@ -0,0 +1,263 @@
+/**
+ * Interactive review TUI for track changes
+ */
+import * as readline from 'readline';
+import chalk from 'chalk';
+import { getTrackChanges, getComments, applyDecision } from './annotations.js';
+/**
+ * Format an annotation for display
+ */
+function formatAnnotation(annotation, index, total) {
+    const header = chalk.dim(`─── Change ${index + 1}/${total} (line ${annotation.line}) ───`);
+    let action;
+    let display;
+    switch (annotation.type) {
+        case 'insert':
+            action = chalk.green(`+ Insert: "${annotation.content}"`);
+            display =
+                chalk.dim(annotation.before || '') +
+                    chalk.green.bold(`[${annotation.content}]`) +
+                    chalk.dim(annotation.after || '');
+            break;
+        case 'delete':
+            action = chalk.red(`- Delete: "${annotation.content}"`);
+            display =
+                chalk.dim(annotation.before || '') +
+                    chalk.red.strikethrough(`[${annotation.content}]`) +
+                    chalk.dim(annotation.after || '');
+            break;
+        case 'substitute':
+            action = chalk.yellow(`~ Change: "${annotation.content}" → "${annotation.replacement}"`);
+            display =
+                chalk.dim(annotation.before || '') +
+                    chalk.red.strikethrough(`[${annotation.content}]`) +
+                    chalk.dim(' → ') +
+                    chalk.green.bold(`[${annotation.replacement}]`) +
+                    chalk.dim(annotation.after || '');
+            break;
+        default:
+            action = chalk.gray(`? Unknown: "${annotation.content}"`);
+            display = chalk.dim(annotation.before || '') + chalk.gray(`[${annotation.content}]`) + chalk.dim(annotation.after || '');
+    }
+    return `\n${header}\n\n  ${action}\n\n  ${display}\n`;
+}
+/**
+ * Prompt for a single keypress
+ */
+function promptKey(prompt, validKeys) {
+    return new Promise((resolve) => {
+        const rl = readline.createInterface({
+            input: process.stdin,
+            output: process.stdout,
+        });
+        // Enable raw mode for single keypress
+        if (process.stdin.isTTY) {
+            process.stdin.setRawMode(true);
+        }
+        process.stdin.resume();
+        process.stdout.write(prompt);
+        process.stdin.once('data', (key) => {
+            const char = key.toString().toLowerCase();
+            if (process.stdin.isTTY) {
+                process.stdin.setRawMode(false);
+            }
+            rl.close();
+            if (char === '\u0003') {
+                // Ctrl+C
+                process.exit(0);
+            }
+            if (validKeys.includes(char)) {
+                console.log(char);
+                resolve(char);
+            }
+            else {
+                console.log();
+                resolve(promptKey(prompt, validKeys));
+            }
+        });
+    });
+}
+/**
+ * Run interactive review session
+ */
+export async function interactiveReview(text) {
+    const changes = getTrackChanges(text);
+    const comments = getComments(text);
+    if (changes.length === 0) {
+        console.log(chalk.green('No track changes found.'));
+        if (comments.length > 0) {
+            console.log(chalk.yellow(`${comments.length} comment(s) remain in the document.`));
+        }
+        return { text, accepted: 0, rejected: 0, skipped: 0 };
+    }
+    console.log(chalk.cyan(`\nFound ${changes.length} track change(s)\n`));
+    let accepted = 0;
+    let rejected = 0;
+    let skipped = 0;
+    let currentText = text;
+    for (let i = 0; i < changes.length; i++) {
+        const change = changes[i];
+        if (!change)
+            continue;
+        console.log(formatAnnotation(change, i, changes.length));
+        const prompt = chalk.dim('[a]ccept [r]eject [s]kip | accept [A]ll reject a[L]l [q]uit: ');
+        const choice = await promptKey(prompt, ['a', 'r', 's', 'A', 'L', 'q']);
+        switch (choice) {
+            case 'q':
+                console.log(chalk.yellow('\nAborted. No changes saved.'));
+                return { text, accepted: 0, rejected: 0, skipped: changes.length };
+            case 'A':
+                // Accept all remaining
+                for (let j = i; j < changes.length; j++) {
+                    const ch = changes[j];
+                    if (ch)
+                        currentText = applyDecision(currentText, ch, true);
+                }
+                accepted += changes.length - i;
+                console.log(chalk.green(`\nAccepted all ${changes.length - i} remaining changes.`));
+                i = changes.length; // Exit loop
+                break;
+            case 'L':
+                // Reject all remaining
+                for (let j = i; j < changes.length; j++) {
+                    const ch = changes[j];
+                    if (ch)
+                        currentText = applyDecision(currentText, ch, false);
+                }
+                rejected += changes.length - i;
+                console.log(chalk.red(`\nRejected all ${changes.length - i} remaining changes.`));
+                i = changes.length; // Exit loop
+                break;
+            case 'a':
+                currentText = applyDecision(currentText, change, true);
+                accepted++;
+                break;
+            case 'r':
+                currentText = applyDecision(currentText, change, false);
+                rejected++;
+                break;
+            case 's':
+                skipped++;
+                break;
+        }
+    }
+    console.log(chalk.cyan('\n─── Summary ───'));
+    console.log(chalk.green(`Accepted: ${accepted}`));
+    console.log(chalk.red(`Rejected: ${rejected}`));
+    console.log(chalk.yellow(`Skipped: ${skipped}`));
+    if (comments.length > 0) {
+        console.log(chalk.blue(`\n${comments.length} comment(s) preserved.`));
+    }
+    return { text: currentText, accepted, rejected, skipped };
+}
+/**
+ * List all comments
+ */
+export function listComments(text) {
+    const comments = getComments(text);
+    if (comments.length === 0) {
+        console.log(chalk.green('No comments found.'));
+        return;
+    }
+    console.log(chalk.cyan(`\nFound ${comments.length} comment(s):\n`));
+    for (let i = 0; i < comments.length; i++) {
+        const c = comments[i];
+        if (!c)
+            continue;
+        const author = c.author || 'Anonymous';
+        const header = chalk.blue(`[${i + 1}] ${author}`) + chalk.dim(` (line ${c.line})`);
+        console.log(header);
+        console.log(`  ${c.content}`);
+        console.log(chalk.dim(`  Context: ...${(c.before || '').slice(-25)}`) +
+            chalk.yellow('*') +
+            chalk.dim(`${(c.after || '').slice(0, 25)}...`));
+        console.log();
+    }
+}
+/**
+ * Format a comment for interactive display
+ */
+function formatComment(comment, index, total) {
+    const statusIcon = comment.resolved ? chalk.green('✓') : chalk.yellow('○');
+    const author = comment.author || 'Anonymous';
+    const header = chalk.dim(`─── Comment ${index + 1}/${total} (line ${comment.line}) ───`);
+    const authorLine = chalk.blue(`${author}`) + ` ${statusIcon}`;
+    const context = chalk.dim(`Context: "...${(comment.before || '').slice(-40)}"`);
+    return `\n${header}\n\n  ${authorLine}\n  ${comment.content}\n\n  ${context}\n`;
+}
+/**
+ * Run interactive comment review session
+ */
+export async function interactiveCommentReview(text, options = {}) {
+    const { author = 'Author', addReply, setCommentStatus } = options;
+    const comments = getComments(text, { pendingOnly: true });
+    if (comments.length === 0) {
+        console.log(chalk.green('No pending comments found.'));
+        return { text, resolved: 0, replied: 0, skipped: 0 };
+    }
+    console.log(chalk.cyan(`\nReviewing ${comments.length} pending comment(s) as ${chalk.bold(author)}\n`));
+    let resolved = 0;
+    let replied = 0;
+    let skipped = 0;
+    let currentText = text;
+    for (let i = 0; i < comments.length; i++) {
+        const comment = comments[i];
+        if (!comment)
+            continue;
+        console.log(formatComment(comment, i, comments.length));
+        const prompt = chalk.dim('[r]eply [m]ark resolved [s]kip | resolve [A]ll [q]uit: ');
+        const choice = await promptKey(prompt, ['r', 'm', 's', 'A', 'q']);
+        switch (choice) {
+            case 'q':
+                console.log(chalk.yellow('\nAborted.'));
+                return { text: currentText, resolved, replied, skipped: comments.length - i };
+            case 'A':
+                // Resolve all remaining
+                for (let j = i; j < comments.length; j++) {
+                    const c = comments[j];
+                    if (setCommentStatus && c) {
+                        currentText = setCommentStatus(currentText, c, true);
+                    }
+                }
+                resolved += comments.length - i;
+                console.log(chalk.green(`\nResolved all ${comments.length - i} remaining comments.`));
+                i = comments.length;
+                break;
+            case 'm':
+                if (setCommentStatus) {
+                    currentText = setCommentStatus(currentText, comment, true);
+                }
+                resolved++;
+                console.log(chalk.green('  Marked as resolved'));
+                break;
+            case 'r':
+                // Get reply text
+                const rl = readline.createInterface({
+                    input: process.stdin,
+                    output: process.stdout,
+                });
+                const replyText = await new Promise((resolve) => {
+                    rl.question(chalk.cyan('  Reply: '), resolve);
+                });
+                rl.close();
+                if (replyText.trim() && addReply) {
+                    currentText = addReply(currentText, comment, author, replyText.trim());
+                    replied++;
+                    console.log(chalk.green('  Reply added'));
+                }
+                else {
+                    console.log(chalk.dim('  No reply added'));
+                }
+                break;
+            case 's':
+                skipped++;
+                break;
+        }
+    }
+    console.log(chalk.cyan('\n─── Summary ───'));
+    console.log(chalk.green(`Resolved: ${resolved}`));
+    console.log(chalk.blue(`Replied: ${replied}`));
+    console.log(chalk.yellow(`Skipped: ${skipped}`));
+    return { text: currentText, resolved, replied, skipped };
+}
+//# sourceMappingURL=review.js.map

package/dist/lib/review.js.map

@@ -0,0 +1 @@
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