A missing python function to copy directory tree and overwrite existing files.

copydir.py

import os
import random
import shutil


def copydir(source, dest, indent = 0):
    """Copy a directory structure overwriting existing files"""
    for root, dirs, files in os.walk(source):
        if not os.path.isdir(root):
            os.makedirs(root)
        for each_file in files:
            rel_path = root.replace(source, '').lstrip(os.sep)
            dest_path = os.path.join(dest, rel_path, each_file)
            shutil.copyfile(os.path.join(root, each_file), dest_path)


# Tests

src_path = 'test-source'
dest_path = 'test-dest'

source_files = [
        '1.txt',
        '2.txt',
        '3.txt',
        'subdir/4.txt',
        'subdir/5.txt',
        'subdir/subsubdir/6.txt',
        'subdir/subsubdir/7.txt',
    ]

dest_files = [
        '1.txt',
        '4.txt',
        '5.txt',
        'subdir/4.txt',
        'subdir/6.txt',
        'subdir/subsubdir/6.txt',
        'subdir/subsubdir/9.txt',
    ]

result_files = [
        '1.txt',
        '2.txt',
        '3.txt',
        '4.txt',
        '5.txt',
        'subdir/4.txt',
        'subdir/5.txt',
        'subdir/6.txt',
        'subdir/subsubdir/6.txt',
        'subdir/subsubdir/7.txt',
        'subdir/subsubdir/9.txt',
    ]


def test():
    """Use nosetests (http://nose.readthedocs.org/en/latest/usage.html)"""
    _create_samples(src_path, dest_path)
    copydir(src_path, dest_path)
    result = []
    for root, dirs, files in os.walk(dest_path):
        for each_file in files:
            each_file = os.path.join(root, each_file).replace(dest_path, '')
            each_file = each_file.lstrip(os.sep).replace(os.sep, '/')
            result.append(each_file)
    assert set(result) == set(result_files)
    shutil.rmtree(src_path)
    shutil.rmtree(dest_path)


def _create_samples(src_path, dest_path):
    _create_files(src_path, source_files)
    _create_files(dest_path, dest_files)


def _create_files(root_path, files):
    for each in files:
        each = os.path.join(root_path, each)
        dirpath = os.path.dirname(each)
        if not os.path.isdir(dirpath):
            os.makedirs(dirpath)
        open(each, 'w').write(_random_contents())


def _random_contents(length = 100):
    return ' '.join([str(random.randint(0, 100)) for i in range(0, length)])

Use nosetests copydir.py for testing.

This function copies files only. Does not include folders. I also added folders here.

def copydir(source, dest):
    """Copy a directory structure overwriting existing files"""
    for root, dirs, files in os.walk(source):
        if not os.path.isdir(root):
            os.makedirs(root)

        for file in files:
            rel_path = root.replace(source, '').lstrip(os.sep)
            dest_path = os.path.join(dest, rel_path)

            if not os.path.isdir(dest_path):
                os.makedirs(dest_path)

            shutil.copyfile(os.path.join(root, file), os.path.join(dest_path, file))

From Python 3.8 you can just use

import shutil
shutil.copytree("src", "dst", dirs_exist_ok=True)