@yibeichan/claude-skills 1.0.2

package/LICENSE

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+MIT License
+
+Copyright (c) 2025 Yibei Chen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# Claude Skills
+
+A collection of reusable Claude skills for neuroimaging research workflows and scientific writing.
+
+## Available Skills
+
+| Skill | Install | Description |
+|-------|---------|-------------|
+| [dicom2fmriprep](skills/dicom2fmriprep/SKILL.md) | `npx @yibeichen/claude-skills install dicom2fmriprep` | Full DICOM→BIDS→fMRIPrep pipeline: heudiconv heuristics, BIDS validation fixes, fMRIPrep on SLURM via BABS. |
+| [fmri-ssm](skills/fmri-ssm/SKILL.md) | `npx @yibeichen/claude-skills install fmri-ssm` | State-space models for fMRI: HMM, SLDS, rSLDS, SNLDS for resting-state, task, and naturalistic designs. |
+| [neuroimaging-qc](skills/neuroimaging-qc/SKILL.md) | `npx @yibeichen/claude-skills install neuroimaging-qc` | Evidence-based QC decisions for fMRI, EEG, fNIRS using metrics from fMRIPrep, MRIQC, FreeSurfer. |
+| [bidsapp-nidm-standards](skills/bidsapp-nidm-standards/SKILL.md) | `npx @yibeichen/claude-skills install bidsapp-nidm-standards` | Standards for creating NIDM-integrated BIDSapps that run through BABS. |
+| [scientific-writer](skills/scientific-writer/SKILL.md) | `npx @yibeichen/claude-skills install scientific-writer` | Rigorous scientific manuscripts following IMRAD, CONSORT/STROBE/PRISMA guidelines. |
+
+## Installation
+
+Skills are installed to `.claude/skills/` in your current working directory by default.
+
+### Quick Install (Recommended)
+
+Install a specific skill using npx:
+
+```bash
+npx @yibeichen/claude-skills install bidsapp-nidm-standards
+```
+
+Install all skills:
+
+```bash
+npx @yibeichen/claude-skills install-all
+```
+
+List available skills:
+
+```bash
+npx @yibeichen/claude-skills list
+```
+
+### Custom Target Directory
+
+Install to a custom directory:
+
+```bash
+npx @yibeichen/claude-skills install bidsapp-nidm-standards --target ./my-skills
+```
+
+### Overwrite Existing Skills
+
+If a skill already exists, use `--overwrite` to replace it:
+
+```bash
+npx @yibeichen/claude-skills install bidsapp-nidm-standards --overwrite
+```
+
+### Python Script (Alternative)
+
+If you don't have npm/node installed, use the Python script:
+
+```bash
+# List skills
+python install.py --list
+
+# Install a skill
+python install.py bidsapp-nidm-standards
+
+# Install all skills
+python install.py --all
+
+# Custom target
+python install.py scientific-writer --target ./skills
+```
+
+### Uninstall Skills
+
+Remove installed skills:
+
+```bash
+# Uninstall a specific skill
+npx @yibeichen/claude-skills uninstall neuroimaging-qc
+
+# Uninstall all skills
+npx @yibeichen/claude-skills uninstall-all
+```
+
+Or with Python:
+
+```bash
+python install.py --uninstall neuroimaging-qc
+python install.py --uninstall-all
+```
+
+## Development
+
+See [CLAUDE.md](CLAUDE.md) for development guidelines or [MAINTAINERS.md](MAINTAINERS.md) for adding/updating skills.
+
+## License
+
+MIT

package/cli.js

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+#!/usr/bin/env node
+
+/**
+ * Claude Skills CLI
+ * Install and manage Claude skills from this repository
+ */
+
+import fs from 'fs';
+import path from 'path';
+import { fileURLToPath } from 'url';
+import { createRequire } from 'module';
+
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = path.dirname(__filename);
+const require = createRequire(import.meta.url);
+
+// Load package.json
+const packageJson = JSON.parse(fs.readFileSync(path.join(__dirname, 'package.json'), 'utf8'));
+
+// Load skills manifest
+const manifest = JSON.parse(fs.readFileSync(path.join(__dirname, 'skills.json'), 'utf8'));
+
+// Default Claude Code skills directory (relative to current working directory)
+const DEFAULT_SKILLS_DIR = path.join(process.cwd(), '.claude', 'skills');
+
+function printHeader() {
+  console.log(`\x1b[36mClaude Skills\x1b[0m v${packageJson.version}`);
+  console.log(`Repository: ${packageJson.repository.url}\n`);
+}
+
+function listSkills() {
+  printHeader();
+  console.log('Available skills:\n');
+
+  for (const skill of manifest.skills) {
+    console.log(`\x1b[1;36m${skill.name}\x1b[0m`);
+    console.log(`  Version: ${skill.version || '1.0.0'}`);
+    console.log(`  Description: ${skill.description || 'No description'}`);
+    console.log(`  Tags: ${skill.tags?.join(', ') || 'none'}`);
+    console.log('');
+  }
+}
+
+function copyDirectory(src, dest) {
+  // Create destination directory if it doesn't exist
+  if (!fs.existsSync(dest)) {
+    fs.mkdirSync(dest, { recursive: true });
+  }
+
+  // Copy all files and subdirectories
+  const entries = fs.readdirSync(src, { withFileTypes: true });
+
+  for (const entry of entries) {
+    const srcPath = path.join(src, entry.name);
+    const destPath = path.join(dest, entry.name);
+
+    if (entry.isDirectory()) {
+      copyDirectory(srcPath, destPath);
+    } else {
+      fs.copyFileSync(srcPath, destPath);
+    }
+  }
+}
+
+function installSkill(skillName, options = {}) {
+  const targetDir = options.target || DEFAULT_SKILLS_DIR;
+  const overwrite = options.overwrite || false;
+
+  // Find the skill
+  const skill = manifest.skills.find(s => s.name === skillName);
+
+  if (!skill) {
+    console.error(`\x1b[31mError: Skill '${skillName}' not found.\x1b[0m`);
+    console.log("Run 'npx claude-skills list' to see available skills.");
+    return false;
+  }
+
+  // Source path
+  const sourcePath = path.join(__dirname, skill.path);
+  if (!fs.existsSync(sourcePath)) {
+    console.error(`\x1b[31mError: Skill directory not found at ${sourcePath}\x1b[0m`);
+    return false;
+  }
+
+  // Target path
+  const targetPath = path.join(targetDir, skillName);
+
+  // Check if already exists
+  if (fs.existsSync(targetPath)) {
+    if (!overwrite) {
+      console.error(`\x1b[31mError: Target directory already exists: ${targetPath}\x1b[0m`);
+      console.log("Use --overwrite to replace the existing skill.");
+      return false;
+    }
+    fs.rmSync(targetPath, { recursive: true, force: true });
+  }
+
+  // Create target directory
+  fs.mkdirSync(targetDir, { recursive: true });
+
+  // Copy the skill
+  console.log(`Installing ${skillName}...`);
+  console.log(`  Source: ${sourcePath}`);
+  console.log(`  Target: ${targetPath}`);
+
+  copyDirectory(sourcePath, targetPath);
+
+  console.log(`\x1b[32m✓ Successfully installed ${skillName}\x1b[0m\n`);
+  return true;
+}
+
+function installAll(options = {}) {
+  printHeader();
+  console.log('Installing all skills...\n');
+
+  let success = true;
+  for (const skill of manifest.skills) {
+    if (!installSkill(skill.name, options)) {
+      success = false;
+    }
+  }
+
+  return success;
+}
+
+function uninstallSkill(skillName, options = {}) {
+  const targetDir = options.target || DEFAULT_SKILLS_DIR;
+  const targetPath = path.join(targetDir, skillName);
+
+  if (!fs.existsSync(targetPath)) {
+    console.error(`\x1b[31mError: Skill '${skillName}' is not installed at ${targetPath}\x1b[0m`);
+    return false;
+  }
+
+  console.log(`Uninstalling ${skillName}...`);
+  console.log(`  Removing: ${targetPath}`);
+
+  fs.rmSync(targetPath, { recursive: true, force: true });
+
+  // Clean up empty parent directories
+  try {
+    fs.rmdirSync(targetDir);
+    fs.rmdirSync(path.dirname(targetDir));
+  } catch (e) {
+    // Ignore if directories are not empty
+  }
+
+  console.log(`\x1b[32m✓ Successfully uninstalled ${skillName}\x1b[0m\n`);
+  return true;
+}
+
+function uninstallAll(options = {}) {
+  printHeader();
+  console.log('Uninstalling all skills...\n');
+
+  const targetDir = options.target || DEFAULT_SKILLS_DIR;
+
+  if (!fs.existsSync(targetDir)) {
+    console.log('No skills installed.');
+    return true;
+  }
+
+  const installedSkills = fs.readdirSync(targetDir, { withFileTypes: true })
+    .filter(d => d.isDirectory())
+    .map(d => d.name);
+
+  if (installedSkills.length === 0) {
+    console.log('No skills installed.');
+    return true;
+  }
+
+  let success = true;
+  for (const skillName of installedSkills) {
+    if (!uninstallSkill(skillName, options)) {
+      success = false;
+    }
+  }
+
+  return success;
+}
+
+function printHelp() {
+  printHeader();
+  console.log(`Usage: npx @yibeichan/claude-skills [command] [options]
+
+Commands:
+  list, ls              List all available skills
+  install <skill>       Install a specific skill
+  install-all           Install all skills
+  uninstall <skill>     Uninstall a specific skill
+  uninstall-all         Uninstall all skills
+
+Options:
+  --target, -t <dir>    Target directory for skills (default: ./.claude/skills)
+  --overwrite, -o       Overwrite existing skill directory
+  --help, -h            Show this help message
+
+Examples:
+  npx @yibeichan/claude-skills list
+  npx @yibeichan/claude-skills install bidsapp-nidm-standards
+  npx @yibeichan/claude-skills install scientific-writer --target ./my-skills
+  npx @yibeichan/claude-skills install-all --overwrite
+  npx @yibeichan/claude-skills uninstall neuroimaging-qc
+  npx @yibeichan/claude-skills uninstall-all
+`);
+}
+
+// Main CLI logic
+function main() {
+  const args = process.argv.slice(2);
+  const command = args[0];
+
+  const options = {
+    target: null,
+    overwrite: false
+  };
+
+  // Parse options
+  for (let i = 1; i < args.length; i++) {
+    if (args[i] === '--target' || args[i] === '-t') {
+      options.target = args[++i];
+    } else if (args[i] === '--overwrite' || args[i] === '-o') {
+      options.overwrite = true;
+    } else if (args[i] === '--help' || args[i] === '-h') {
+      printHelp();
+      return;
+    }
+  }
+
+  switch (command) {
+    case 'list':
+    case 'ls':
+      listSkills();
+      break;
+
+    case 'install':
+      if (args[1] && !args[1].startsWith('-')) {
+        installSkill(args[1], options);
+      } else {
+        console.error('\x1b[31mError: Please specify a skill name.\x1b[0m');
+        console.log("Run 'npx @yibeichan/claude-skills list' to see available skills.");
+      }
+      break;
+
+    case 'install-all':
+      installAll(options);
+      break;
+
+    case 'uninstall':
+      if (args[1] && !args[1].startsWith('-')) {
+        uninstallSkill(args[1], options);
+      } else {
+        console.error('\x1b[31mError: Please specify a skill name.\x1b[0m');
+        console.log("Run 'npx @yibeichan/claude-skills list' to see available skills.");
+      }
+      break;
+
+    case 'uninstall-all':
+      uninstallAll(options);
+      break;
+
+    default:
+      if (!command || command.startsWith('-')) {
+        printHelp();
+      } else {
+        console.error(`\x1b[31mUnknown command: ${command}\x1b[0m`);
+        printHelp();
+      }
+  }
+}
+
+main();

package/install.py

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+#!/usr/bin/env python3
+"""
+Install Claude skills from this repository to a target directory.
+
+Usage:
+    python install.py --list                          # List available skills
+    python install.py bidsapp-nidm-standards          # Install a skill (default: ./.claude/skills/)
+    python install.py scientific-writer --target ./skills
+    python install.py --all                           # Install all skills
+    python install.py --uninstall neuroimaging-qc     # Uninstall a skill
+    python install.py --uninstall-all                 # Uninstall all skills
+"""
+
+import argparse
+import json
+import os
+import shutil
+import sys
+from pathlib import Path
+from typing import Optional
+
+
+# Default Claude Code skills directory (relative to current working directory)
+DEFAULT_SKILLS_DIR = Path.cwd() / ".claude" / "skills"
+
+# Repository root
+REPO_ROOT = Path(__file__).parent
+
+
+def load_manifest() -> dict:
+    """Load the skills manifest."""
+    manifest_path = REPO_ROOT / "skills.json"
+    if not manifest_path.exists():
+        print(f"Error: skills.json not found at {manifest_path}")
+        sys.exit(1)
+    with open(manifest_path) as f:
+        return json.load(f)
+
+
+def list_skills():
+    """List all available skills."""
+    manifest = load_manifest()
+    print("Available skills:")
+    print()
+    for skill in manifest.get("skills", []):
+        print(f"  {skill['name']}")
+        print(f"    Version: {skill.get('version', '1.0.0')}")
+        print(f"    Description: {skill.get('description', 'No description')}")
+        print(f"    Tags: {', '.join(skill.get('tags', []))}")
+        print()
+
+
+def install_skill(skill_name: str, target_dir: Path, overwrite: bool = False) -> bool:
+    """Install a skill to the target directory."""
+    manifest = load_manifest()
+
+    # Find the skill
+    skill = next((s for s in manifest.get("skills", []) if s["name"] == skill_name), None)
+    if not skill:
+        print(f"Error: Skill '{skill_name}' not found.")
+        print("Run 'python install.py --list' to see available skills.")
+        return False
+
+    # Source path
+    source_path = REPO_ROOT / skill["path"]
+    if not source_path.exists():
+        print(f"Error: Skill directory not found at {source_path}")
+        return False
+
+    # Target path
+    target_path = target_dir / skill_name
+
+    # Check if already exists
+    if target_path.exists():
+        if not overwrite:
+            print(f"Error: Target directory already exists: {target_path}")
+            print("Use --overwrite to replace the existing skill.")
+            return False
+        shutil.rmtree(target_path)
+
+    # Create target directory
+    target_dir.mkdir(parents=True, exist_ok=True)
+
+    # Copy the skill
+    print(f"Installing {skill_name}...")
+    print(f"  Source: {source_path}")
+    print(f"  Target: {target_path}")
+
+    shutil.copytree(source_path, target_path)
+
+    print(f"✓ Successfully installed {skill_name}")
+    return True
+
+
+def install_all_skills(target_dir: Path, overwrite: bool = False) -> bool:
+    """Install all skills."""
+    manifest = load_manifest()
+    success = True
+
+    for skill in manifest.get("skills", []):
+        if not install_skill(skill["name"], target_dir, overwrite):
+            success = False
+
+    return success
+
+
+def uninstall_skill(skill_name: str, target_dir: Path) -> bool:
+    """Uninstall a skill from the target directory."""
+    target_path = target_dir / skill_name
+
+    if not target_path.exists():
+        print(f"Error: Skill '{skill_name}' is not installed at {target_path}")
+        return False
+
+    print(f"Uninstalling {skill_name}...")
+    print(f"  Removing: {target_path}")
+
+    shutil.rmtree(target_path)
+
+    # Clean up empty parent directories
+    try:
+        target_dir.rmdir()
+        target_dir.parent.rmdir()
+    except OSError:
+        # Ignore if directories are not empty
+        pass
+
+    print(f"✓ Successfully uninstalled {skill_name}")
+    return True
+
+
+def uninstall_all_skills(target_dir: Path) -> bool:
+    """Uninstall all skills."""
+    if not target_dir.exists():
+        print("No skills installed.")
+        return True
+
+    installed_skills = [d for d in target_dir.iterdir() if d.is_dir()]
+
+    if not installed_skills:
+        print("No skills installed.")
+        return True
+
+    success = True
+    for skill_dir in installed_skills:
+        if not uninstall_skill(skill_dir.name, target_dir):
+            success = False
+
+    return success
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Install Claude skills from this repository",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  python install.py --list
+  python install.py bidsapp-nidm-standards
+  python install.py scientific-writer --target ./my-skills
+  python install.py --all --overwrite
+  python install.py --uninstall neuroimaging-qc
+  python install.py --uninstall-all
+        """
+    )
+
+    parser.add_argument(
+        "skill",
+        nargs="?",
+        help="Name of the skill to install/uninstall (use --list to see available)"
+    )
+    parser.add_argument(
+        "--target", "-t",
+        type=Path,
+        default=DEFAULT_SKILLS_DIR,
+        help=f"Target directory for skills (default: ./.claude/skills)"
+    )
+    parser.add_argument(
+        "--list", "-l",
+        action="store_true",
+        help="List available skills"
+    )
+    parser.add_argument(
+        "--all",
+        action="store_true",
+        help="Install all available skills"
+    )
+    parser.add_argument(
+        "--overwrite", "-o",
+        action="store_true",
+        help="Overwrite existing skill directory"
+    )
+    parser.add_argument(
+        "--uninstall",
+        action="store_true",
+        help="Uninstall the specified skill"
+    )
+    parser.add_argument(
+        "--uninstall-all",
+        action="store_true",
+        help="Uninstall all skills"
+    )
+
+    args = parser.parse_args()
+
+    # List mode
+    if args.list:
+        list_skills()
+        return 0
+
+    # Uninstall all mode
+    if args.uninstall_all:
+        success = uninstall_all_skills(args.target)
+        return 0 if success else 1
+
+    # Uninstall mode
+    if args.uninstall:
+        if not args.skill:
+            print("Error: Please specify a skill name to uninstall.")
+            print("Run 'python install.py --list' to see available skills.")
+            return 1
+        success = uninstall_skill(args.skill, args.target)
+        return 0 if success else 1
+
+    # Install all mode
+    if args.all:
+        success = install_all_skills(args.target, args.overwrite)
+        return 0 if success else 1
+
+    # Install specific skill
+    if not args.skill:
+        parser.print_help()
+        return 1
+
+    success = install_skill(args.skill, args.target, args.overwrite)
+    return 0 if success else 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())

package/package.json

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+{
+  "name": "@yibeichan/claude-skills",
+  "version": "1.0.2",
+  "description": "Claude skills for neuroimaging research workflows and scientific writing",
+  "type": "module",
+  "bin": {
+    "claude-skills": "./cli.js"
+  },
+  "scripts": {
+    "list": "node cli.js list",
+    "add": "node scripts/add-skill.js"
+  },
+  "keywords": [
+    "claude",
+    "claude-code",
+    "skills",
+    "neuroimaging",
+    "bids",
+    "nidm",
+    "scientific-writing"
+  ],
+  "author": "Yibei Chen",
+  "license": "MIT",
+  "publishConfig": {
+    "access": "public"
+  },
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/yibeichen/claude-skills.git"
+  },
+  "bugs": {
+    "url": "https://github.com/yibeichen/claude-skills/issues"
+  },
+  "homepage": "https://github.com/yibeichen/claude-skills#readme",
+  "engines": {
+    "node": ">=18.0.0"
+  },
+  "files": [
+    "cli.js",
+    "install.py",
+    "skills.json",
+    "skills/**/*"
+  ]
+}