dulwich/dulwich/porcelain.py

# porcelain.py -- Porcelain-like layer on top of Dulwich
# Copyright (C) 2013 Jelmer Vernooij <jelmer@jelmer.uk>
#
# SPDX-License-Identifier: Apache-2.0 OR GPL-2.0-or-later
# Dulwich is dual-licensed under the Apache License, Version 2.0 and the GNU
# General Public License as public by the Free Software Foundation; version 2.0
# or (at your option) any later version. You can redistribute it and/or
# modify it under the terms of either of these two licenses.
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# You should have received a copy of the licenses; if not, see
# <http://www.gnu.org/licenses/> for a copy of the GNU General Public License
# and <http://www.apache.org/licenses/LICENSE-2.0> for a copy of the Apache
# License, Version 2.0.
#

"""Simple wrapper that provides porcelain-like functions on top of Dulwich.

Currently implemented:
 * archive
 * add
 * branch{_create,_delete,_list}
 * check_ignore
 * checkout
 * checkout_branch
 * clone
 * cone mode{_init, _set, _add}
 * commit
 * commit_tree
 * daemon
 * describe
 * diff_tree
 * fetch
 * for_each_ref
 * init
 * ls_files
 * ls_remote
 * ls_tree
 * merge
 * merge_tree
 * pull
 * push
 * rm
 * remote{_add}
 * receive_pack
 * reset
 * sparse_checkout
 * submodule_add
 * submodule_init
 * submodule_list
 * rev_list
 * tag{_create,_delete,_list}
 * upload_pack
 * update_server_info
 * status
 * symbolic_ref

These functions are meant to behave similarly to the git subcommands.
Differences in behaviour are considered bugs.

Note: one of the consequences of this is that paths tend to be
interpreted relative to the current working directory rather than relative
to the repository root.

Functions should generally accept both unicode strings and bytestrings
"""

import datetime
import fnmatch
import os
import posixpath
import stat
import sys
import time
from collections import namedtuple
from contextlib import closing, contextmanager
from dataclasses import dataclass
from io import BytesIO, RawIOBase
from pathlib import Path
from typing import Optional, Union

from . import replace_me
from .archive import tar_stream
from .client import get_transport_and_path
from .config import Config, ConfigFile, StackedConfig, read_submodules
from .diff_tree import (
    CHANGE_ADD,
    CHANGE_COPY,
    CHANGE_DELETE,
    CHANGE_MODIFY,
    CHANGE_RENAME,
    RENAME_CHANGE_TYPES,
)
from .errors import SendPackError
from .graph import can_fast_forward
from .ignore import IgnoreFilterManager
from .index import (
    _fs_to_tree_path,
    blob_from_path_and_stat,
    build_file_from_blob,
    get_unstaged_changes,
    update_working_tree,
)
from .object_store import tree_lookup_path
from .objects import (
    Commit,
    Tag,
    format_timezone,
    parse_timezone,
    pretty_format_tree_entry,
)
from .objectspec import (
    parse_commit,
    parse_object,
    parse_ref,
    parse_reftuples,
    parse_tree,
)
from .pack import write_pack_from_container, write_pack_index
from .patch import write_tree_diff
from .protocol import ZERO_SHA, Protocol
from .refs import (
    LOCAL_BRANCH_PREFIX,
    LOCAL_NOTES_PREFIX,
    LOCAL_TAG_PREFIX,
    Ref,
    _import_remote_refs,
)
from .repo import BaseRepo, Repo, get_user_identity
from .server import (
    FileSystemBackend,
    ReceivePackHandler,
    TCPGitServer,
    UploadPackHandler,
)
from .server import update_server_info as server_update_server_info
from .sparse_patterns import (
    SparseCheckoutConflictError,
    apply_included_paths,
    determine_included_paths,
)

# Module level tuple definition for status output
GitStatus = namedtuple("GitStatus", "staged unstaged untracked")


@dataclass
class CountObjectsResult:
    """Result of counting objects in a repository.

    Attributes:
      count: Number of loose objects
      size: Total size of loose objects in bytes
      in_pack: Number of objects in pack files
      packs: Number of pack files
      size_pack: Total size of pack files in bytes
    """

    count: int
    size: int
    in_pack: Optional[int] = None
    packs: Optional[int] = None
    size_pack: Optional[int] = None


class NoneStream(RawIOBase):
    """Fallback if stdout or stderr are unavailable, does nothing."""

    def read(self, size=-1) -> None:
        return None

    def readall(self) -> bytes:
        return b""

    def readinto(self, b) -> None:
        return None

    def write(self, b) -> None:
        return None


default_bytes_out_stream = getattr(sys.stdout, "buffer", None) or NoneStream()
default_bytes_err_stream = getattr(sys.stderr, "buffer", None) or NoneStream()


DEFAULT_ENCODING = "utf-8"


class Error(Exception):
    """Porcelain-based error."""

    def __init__(self, msg) -> None:
        super().__init__(msg)


class RemoteExists(Error):
    """Raised when the remote already exists."""


class TimezoneFormatError(Error):
    """Raised when the timezone cannot be determined from a given string."""


class CheckoutError(Error):
    """Indicates that a checkout cannot be performed."""


def parse_timezone_format(tz_str):
    """Parse given string and attempt to return a timezone offset.

    Different formats are considered in the following order:

     - Git internal format: <unix timestamp> <timezone offset>
     - RFC 2822: e.g. Mon, 20 Nov 1995 19:12:08 -0500
     - ISO 8601: e.g. 1995-11-20T19:12:08-0500

    Args:
      tz_str: datetime string
    Returns: Timezone offset as integer
    Raises:
      TimezoneFormatError: if timezone information cannot be extracted
    """
    import re

    # Git internal format
    internal_format_pattern = re.compile("^[0-9]+ [+-][0-9]{,4}$")
    if re.match(internal_format_pattern, tz_str):
        try:
            tz_internal = parse_timezone(tz_str.split(" ")[1].encode(DEFAULT_ENCODING))
            return tz_internal[0]
        except ValueError:
            pass

    # RFC 2822
    import email.utils

    rfc_2822 = email.utils.parsedate_tz(tz_str)
    if rfc_2822:
        return rfc_2822[9]

    # ISO 8601

    # Supported offsets:
    # sHHMM, sHH:MM, sHH
    iso_8601_pattern = re.compile(
        "[0-9] ?([+-])([0-9]{2})(?::(?=[0-9]{2}))?([0-9]{2})?$"
    )
    match = re.search(iso_8601_pattern, tz_str)
    total_secs = 0
    if match:
        sign, hours, minutes = match.groups()
        total_secs += int(hours) * 3600
        if minutes:
            total_secs += int(minutes) * 60
        total_secs = -total_secs if sign == "-" else total_secs
        return total_secs

    # YYYY.MM.DD, MM/DD/YYYY, DD.MM.YYYY contain no timezone information

    raise TimezoneFormatError(tz_str)


def get_user_timezones():
    """Retrieve local timezone as described in
    https://raw.githubusercontent.com/git/git/v2.3.0/Documentation/date-formats.txt
    Returns: A tuple containing author timezone, committer timezone.
    """
    local_timezone = time.localtime().tm_gmtoff

    if os.environ.get("GIT_AUTHOR_DATE"):
        author_timezone = parse_timezone_format(os.environ["GIT_AUTHOR_DATE"])
    else:
        author_timezone = local_timezone
    if os.environ.get("GIT_COMMITTER_DATE"):
        commit_timezone = parse_timezone_format(os.environ["GIT_COMMITTER_DATE"])
    else:
        commit_timezone = local_timezone

    return author_timezone, commit_timezone


def open_repo(path_or_repo: Union[str, os.PathLike, BaseRepo]):
    """Open an argument that can be a repository or a path for a repository."""
    if isinstance(path_or_repo, BaseRepo):
        return path_or_repo
    return Repo(path_or_repo)


@contextmanager
def _noop_context_manager(obj):
    """Context manager that has the same api as closing but does nothing."""
    yield obj


def open_repo_closing(path_or_repo: Union[str, os.PathLike, BaseRepo]):
    """Open an argument that can be a repository or a path for a repository.
    returns a context manager that will close the repo on exit if the argument
    is a path, else does nothing if the argument is a repo.
    """
    if isinstance(path_or_repo, BaseRepo):
        return _noop_context_manager(path_or_repo)
    return closing(Repo(path_or_repo))


def path_to_tree_path(repopath, path, tree_encoding=DEFAULT_ENCODING):
    """Convert a path to a path usable in an index, e.g. bytes and relative to
    the repository root.

    Args:
      repopath: Repository path, absolute or relative to the cwd
      path: A path, absolute or relative to the cwd
    Returns: A path formatted for use in e.g. an index
    """
    # Resolve might returns a relative path on Windows
    # https://bugs.python.org/issue38671
    if sys.platform == "win32":
        path = os.path.abspath(path)

    path = Path(path)
    resolved_path = path.resolve()

    # Resolve and abspath seems to behave differently regarding symlinks,
    # as we are doing abspath on the file path, we need to do the same on
    # the repo path or they might not match
    if sys.platform == "win32":
        repopath = os.path.abspath(repopath)

    repopath = Path(repopath).resolve()

    try:
        relpath = resolved_path.relative_to(repopath)
    except ValueError:
        # If path is a symlink that points to a file outside the repo, we
        # want the relpath for the link itself, not the resolved target
        if path.is_symlink():
            parent = path.parent.resolve()
            relpath = (parent / path.name).relative_to(repopath)
        else:
            raise
    if sys.platform == "win32":
        return str(relpath).replace(os.path.sep, "/").encode(tree_encoding)
    else:
        return bytes(relpath)


class DivergedBranches(Error):
    """Branches have diverged and fast-forward is not possible."""

    def __init__(self, current_sha, new_sha) -> None:
        self.current_sha = current_sha
        self.new_sha = new_sha


def check_diverged(repo, current_sha, new_sha) -> None:
    """Check if updating to a sha can be done with fast forwarding.

    Args:
      repo: Repository object
      current_sha: Current head sha
      new_sha: New head sha
    """
    try:
        can = can_fast_forward(repo, current_sha, new_sha)
    except KeyError:
        can = False
    if not can:
        raise DivergedBranches(current_sha, new_sha)


def archive(
    repo,
    committish=None,
    outstream=default_bytes_out_stream,
    errstream=default_bytes_err_stream,
) -> None:
    """Create an archive.

    Args:
      repo: Path of repository for which to generate an archive.
      committish: Commit SHA1 or ref to use
      outstream: Output stream (defaults to stdout)
      errstream: Error stream (defaults to stderr)
    """
    if committish is None:
        committish = "HEAD"
    with open_repo_closing(repo) as repo_obj:
        c = parse_commit(repo_obj, committish)
        for chunk in tar_stream(
            repo_obj.object_store, repo_obj.object_store[c.tree], c.commit_time
        ):
            outstream.write(chunk)


def update_server_info(repo=".") -> None:
    """Update server info files for a repository.

    Args:
      repo: path to the repository
    """
    with open_repo_closing(repo) as r:
        server_update_server_info(r)


def symbolic_ref(repo, ref_name, force=False) -> None:
    """Set git symbolic ref into HEAD.

    Args:
      repo: path to the repository
      ref_name: short name of the new ref
      force: force settings without checking if it exists in refs/heads
    """
    with open_repo_closing(repo) as repo_obj:
        ref_path = _make_branch_ref(ref_name)
        if not force and ref_path not in repo_obj.refs.keys():
            raise Error(f"fatal: ref `{ref_name}` is not a ref")
        repo_obj.refs.set_symbolic_ref(b"HEAD", ref_path)


def pack_refs(repo, all=False) -> None:
    with open_repo_closing(repo) as repo_obj:
        repo_obj.refs.pack_refs(all=all)


def commit(
    repo=".",
    message=None,
    author=None,
    author_timezone=None,
    committer=None,
    commit_timezone=None,
    encoding=None,
    no_verify=False,
    signoff=False,
):
    """Create a new commit.

    Args:
      repo: Path to repository
      message: Optional commit message
      author: Optional author name and email
      author_timezone: Author timestamp timezone
      committer: Optional committer name and email
      commit_timezone: Commit timestamp timezone
      no_verify: Skip pre-commit and commit-msg hooks
      signoff: GPG Sign the commit (bool, defaults to False,
        pass True to use default GPG key,
        pass a str containing Key ID to use a specific GPG key)
    Returns: SHA1 of the new commit
    """
    # FIXME: Support --all argument
    if getattr(message, "encode", None):
        message = message.encode(encoding or DEFAULT_ENCODING)
    if getattr(author, "encode", None):
        author = author.encode(encoding or DEFAULT_ENCODING)
    if getattr(committer, "encode", None):
        committer = committer.encode(encoding or DEFAULT_ENCODING)
    local_timezone = get_user_timezones()
    if author_timezone is None:
        author_timezone = local_timezone[0]
    if commit_timezone is None:
        commit_timezone = local_timezone[1]
    with open_repo_closing(repo) as r:
        return r.do_commit(
            message=message,
            author=author,
            author_timezone=author_timezone,
            committer=committer,
            commit_timezone=commit_timezone,
            encoding=encoding,
            no_verify=no_verify,
            sign=signoff if isinstance(signoff, (str, bool)) else None,
        )


def commit_tree(repo, tree, message=None, author=None, committer=None):
    """Create a new commit object.

    Args:
      repo: Path to repository
      tree: An existing tree object
      author: Optional author name and email
      committer: Optional committer name and email
    """
    with open_repo_closing(repo) as r:
        return r.do_commit(
            message=message, tree=tree, committer=committer, author=author
        )


def init(
    path: Union[str, os.PathLike] = ".", *, bare=False, symlinks: Optional[bool] = None
):
    """Create a new git repository.

    Args:
      path: Path to repository.
      bare: Whether to create a bare repository.
      symlinks: Whether to create actual symlinks (defaults to autodetect)
    Returns: A Repo instance
    """
    if not os.path.exists(path):
        os.mkdir(path)

    if bare:
        return Repo.init_bare(path)
    else:
        return Repo.init(path, symlinks=symlinks)


def clone(
    source,
    target: Optional[Union[str, os.PathLike]] = None,
    bare=False,
    checkout=None,
    errstream=default_bytes_err_stream,
    outstream=None,
    origin: Optional[str] = "origin",
    depth: Optional[int] = None,
    branch: Optional[Union[str, bytes]] = None,
    config: Optional[Config] = None,
    filter_spec=None,
    protocol_version: Optional[int] = None,
    **kwargs,
):
    """Clone a local or remote git repository.

    Args:
      source: Path or URL for source repository
      target: Path to target repository (optional)
      bare: Whether or not to create a bare repository
      checkout: Whether or not to check-out HEAD after cloning
      errstream: Optional stream to write progress to
      outstream: Optional stream to write progress to (deprecated)
      origin: Name of remote from the repository used to clone
      depth: Depth to fetch at
      branch: Optional branch or tag to be used as HEAD in the new repository
        instead of the cloned repository's HEAD.
      config: Configuration to use
      filter_spec: A git-rev-list-style object filter spec, as an ASCII string.
        Only used if the server supports the Git protocol-v2 'filter'
        feature, and ignored otherwise.
      protocol_version: desired Git protocol version. By default the highest
        mutually supported protocol version will be used.

    Keyword Args:
      refspecs: refspecs to fetch. Can be a bytestring, a string, or a list of
        bytestring/string.

    Returns: The new repository
    """
    if outstream is not None:
        import warnings

        warnings.warn(
            "outstream= has been deprecated in favour of errstream=.",
            DeprecationWarning,
            stacklevel=3,
        )
        # TODO(jelmer): Capture logging output and stream to errstream

    if config is None:
        config = StackedConfig.default()

    if checkout is None:
        checkout = not bare
    if checkout and bare:
        raise Error("checkout and bare are incompatible")

    if target is None:
        target = source.split("/")[-1]

    if isinstance(branch, str):
        branch = branch.encode(DEFAULT_ENCODING)

    mkdir = not os.path.exists(target)

    (client, path) = get_transport_and_path(source, config=config, **kwargs)

    if filter_spec:
        filter_spec = filter_spec.encode("ascii")

    return client.clone(
        path,
        target,
        mkdir=mkdir,
        bare=bare,
        origin=origin,
        checkout=checkout,
        branch=branch,
        progress=errstream.write,
        depth=depth,
        filter_spec=filter_spec,
        protocol_version=protocol_version,
    )


def add(repo: Union[str, os.PathLike, BaseRepo] = ".", paths=None):
    """Add files to the staging area.

    Args:
      repo: Repository for the files
      paths: Paths to add. If None, stages all untracked and modified files from the
        current working directory (mimicking 'git add .' behavior).
    Returns: Tuple with set of added files and ignored files

    If the repository contains ignored directories, the returned set will
    contain the path to an ignored directory (with trailing slash). Individual
    files within ignored directories will not be returned.

    Note: When paths=None, this function adds all untracked and modified files
    from the entire repository, mimicking 'git add -A' behavior.
    """
    ignored = set()
    with open_repo_closing(repo) as r:
        repo_path = Path(r.path).resolve()
        ignore_manager = IgnoreFilterManager.from_repo(r)

        # Get unstaged changes once for the entire operation
        index = r.open_index()
        normalizer = r.get_blob_normalizer()
        filter_callback = normalizer.checkin_normalize
        all_unstaged_paths = list(get_unstaged_changes(index, r.path, filter_callback))

        if not paths:
            # When no paths specified, add all untracked and modified files from repo root
            paths = [str(repo_path)]
        relpaths = []
        if not isinstance(paths, list):
            paths = [paths]
        for p in paths:
            path = Path(p)
            if not path.is_absolute():
                # Make relative paths relative to the repo directory
                path = repo_path / path

            # Don't resolve symlinks completely - only resolve the parent directory
            # to avoid issues when symlinks point outside the repository
            if path.is_symlink():
                # For symlinks, resolve only the parent directory
                parent_resolved = path.parent.resolve()
                resolved_path = parent_resolved / path.name
            else:
                # For regular files/dirs, resolve normally
                resolved_path = path.resolve()

            try:
                relpath = str(resolved_path.relative_to(repo_path)).replace(os.sep, "/")
            except ValueError:
                # Path is not within the repository
                raise ValueError(f"Path {p} is not within repository {repo_path}")

            # Handle directories by scanning their contents
            if resolved_path.is_dir():
                # Check if the directory itself is ignored
                dir_relpath = posixpath.join(relpath, "") if relpath != "." else ""
                if dir_relpath and ignore_manager.is_ignored(dir_relpath):
                    ignored.add(dir_relpath)
                    continue

                # When adding a directory, add all untracked files within it
                current_untracked = list(
                    get_untracked_paths(
                        str(resolved_path),
                        str(repo_path),
                        index,
                    )
                )
                for untracked_path in current_untracked:
                    # If we're scanning a subdirectory, adjust the path
                    if relpath != ".":
                        untracked_path = posixpath.join(relpath, untracked_path)

                    if not ignore_manager.is_ignored(untracked_path):
                        relpaths.append(untracked_path)
                    else:
                        ignored.add(untracked_path)

                # Also add unstaged (modified) files within this directory
                for unstaged_path in all_unstaged_paths:
                    if isinstance(unstaged_path, bytes):
                        unstaged_path = unstaged_path.decode("utf-8")

                    # Check if this unstaged file is within the directory we're processing
                    unstaged_full_path = repo_path / unstaged_path
                    try:
                        unstaged_full_path.relative_to(resolved_path)
                        # File is within this directory, add it
                        if not ignore_manager.is_ignored(unstaged_path):
                            relpaths.append(unstaged_path)
                        else:
                            ignored.add(unstaged_path)
                    except ValueError:
                        # File is not within this directory, skip it
                        continue
                continue

            # FIXME: Support patterns
            if ignore_manager.is_ignored(relpath):
                ignored.add(relpath)
                continue
            relpaths.append(relpath)
        r.stage(relpaths)
    return (relpaths, ignored)


def _is_subdir(subdir, parentdir):
    """Check whether subdir is parentdir or a subdir of parentdir.

    If parentdir or subdir is a relative path, it will be disamgibuated
    relative to the pwd.
    """
    parentdir_abs = os.path.realpath(parentdir) + os.path.sep
    subdir_abs = os.path.realpath(subdir) + os.path.sep
    return subdir_abs.startswith(parentdir_abs)


# TODO: option to remove ignored files also, in line with `git clean -fdx`
def clean(repo=".", target_dir=None) -> None:
    """Remove any untracked files from the target directory recursively.

    Equivalent to running ``git clean -fd`` in target_dir.

    Args:
      repo: Repository where the files may be tracked
      target_dir: Directory to clean - current directory if None
    """
    if target_dir is None:
        target_dir = os.getcwd()

    with open_repo_closing(repo) as r:
        if not _is_subdir(target_dir, r.path):
            raise Error("target_dir must be in the repo's working dir")

        config = r.get_config_stack()
        config.get_boolean((b"clean",), b"requireForce", True)

        # TODO(jelmer): if require_force is set, then make sure that -f, -i or
        # -n is specified.

        index = r.open_index()
        ignore_manager = IgnoreFilterManager.from_repo(r)

        paths_in_wd = _walk_working_dir_paths(target_dir, r.path)
        # Reverse file visit order, so that files and subdirectories are
        # removed before containing directory
        for ap, is_dir in reversed(list(paths_in_wd)):
            if is_dir:
                # All subdirectories and files have been removed if untracked,
                # so dir contains no tracked files iff it is empty.
                is_empty = len(os.listdir(ap)) == 0
                if is_empty:
                    os.rmdir(ap)
            else:
                ip = path_to_tree_path(r.path, ap)
                is_tracked = ip in index

                rp = os.path.relpath(ap, r.path)
                is_ignored = ignore_manager.is_ignored(rp)

                if not is_tracked and not is_ignored:
                    os.remove(ap)


def remove(repo=".", paths=None, cached=False) -> None:
    """Remove files from the staging area.

    Args:
      repo: Repository for the files
      paths: Paths to remove
    """
    with open_repo_closing(repo) as r:
        index = r.open_index()
        for p in paths:
            full_path = os.fsencode(os.path.abspath(p))
            tree_path = path_to_tree_path(r.path, p)
            try:
                index_sha = index[tree_path].sha
            except KeyError as exc:
                raise Error(f"{p} did not match any files") from exc

            if not cached:
                try:
                    st = os.lstat(full_path)
                except OSError:
                    pass
                else:
                    try:
                        blob = blob_from_path_and_stat(full_path, st)
                    except OSError:
                        pass
                    else:
                        try:
                            committed_sha = tree_lookup_path(
                                r.__getitem__, r[r.head()].tree, tree_path
                            )[1]
                        except KeyError:
                            committed_sha = None

                        if blob.id != index_sha and index_sha != committed_sha:
                            raise Error(
                                "file has staged content differing "
                                f"from both the file and head: {p}"
                            )

                        if index_sha != committed_sha:
                            raise Error(f"file has staged changes: {p}")
                        os.remove(full_path)
            del index[tree_path]
        index.write()


rm = remove


def commit_decode(commit, contents, default_encoding=DEFAULT_ENCODING):
    if commit.encoding:
        encoding = commit.encoding.decode("ascii")
    else:
        encoding = default_encoding
    return contents.decode(encoding, "replace")


def commit_encode(commit, contents, default_encoding=DEFAULT_ENCODING):
    if commit.encoding:
        encoding = commit.encoding.decode("ascii")
    else:
        encoding = default_encoding
    return contents.encode(encoding)


def print_commit(commit, decode, outstream=sys.stdout) -> None:
    """Write a human-readable commit log entry.

    Args:
      commit: A `Commit` object
      outstream: A stream file to write to
    """
    outstream.write("-" * 50 + "\n")
    outstream.write("commit: " + commit.id.decode("ascii") + "\n")
    if len(commit.parents) > 1:
        outstream.write(
            "merge: "
            + "...".join([c.decode("ascii") for c in commit.parents[1:]])
            + "\n"
        )
    outstream.write("Author: " + decode(commit.author) + "\n")
    if commit.author != commit.committer:
        outstream.write("Committer: " + decode(commit.committer) + "\n")

    time_tuple = time.gmtime(commit.author_time + commit.author_timezone)
    time_str = time.strftime("%a %b %d %Y %H:%M:%S", time_tuple)
    timezone_str = format_timezone(commit.author_timezone).decode("ascii")
    outstream.write("Date:   " + time_str + " " + timezone_str + "\n")
    if commit.message:
        outstream.write("\n")
        outstream.write(decode(commit.message) + "\n")
        outstream.write("\n")


def print_tag(tag, decode, outstream=sys.stdout) -> None:
    """Write a human-readable tag.

    Args:
      tag: A `Tag` object
      decode: Function for decoding bytes to unicode string
      outstream: A stream to write to
    """
    outstream.write("Tagger: " + decode(tag.tagger) + "\n")
    time_tuple = time.gmtime(tag.tag_time + tag.tag_timezone)
    time_str = time.strftime("%a %b %d %Y %H:%M:%S", time_tuple)
    timezone_str = format_timezone(tag.tag_timezone).decode("ascii")
    outstream.write("Date:   " + time_str + " " + timezone_str + "\n")
    outstream.write("\n")
    outstream.write(decode(tag.message))
    outstream.write("\n")


def show_blob(repo, blob, decode, outstream=sys.stdout) -> None:
    """Write a blob to a stream.

    Args:
      repo: A `Repo` object
      blob: A `Blob` object
      decode: Function for decoding bytes to unicode string
      outstream: A stream file to write to
    """
    outstream.write(decode(blob.data))


def show_commit(repo, commit, decode, outstream=sys.stdout) -> None:
    """Show a commit to a stream.

    Args:
      repo: A `Repo` object
      commit: A `Commit` object
      decode: Function for decoding bytes to unicode string
      outstream: Stream to write to
    """
    print_commit(commit, decode=decode, outstream=outstream)
    if commit.parents:
        parent_commit = repo[commit.parents[0]]
        base_tree = parent_commit.tree
    else:
        base_tree = None
    diffstream = BytesIO()
    write_tree_diff(diffstream, repo.object_store, base_tree, commit.tree)
    diffstream.seek(0)
    outstream.write(commit_decode(commit, diffstream.getvalue()))


def show_tree(repo, tree, decode, outstream=sys.stdout) -> None:
    """Print a tree to a stream.

    Args:
      repo: A `Repo` object
      tree: A `Tree` object
      decode: Function for decoding bytes to unicode string
      outstream: Stream to write to
    """
    for n in tree:
        outstream.write(decode(n) + "\n")


def show_tag(repo, tag, decode, outstream=sys.stdout) -> None:
    """Print a tag to a stream.

    Args:
      repo: A `Repo` object
      tag: A `Tag` object
      decode: Function for decoding bytes to unicode string
      outstream: Stream to write to
    """
    print_tag(tag, decode, outstream)
    show_object(repo, repo[tag.object[1]], decode, outstream)


def show_object(repo, obj, decode, outstream):
    return {
        b"tree": show_tree,
        b"blob": show_blob,
        b"commit": show_commit,
        b"tag": show_tag,
    }[obj.type_name](repo, obj, decode, outstream)


def print_name_status(changes):
    """Print a simple status summary, listing changed files."""
    for change in changes:
        if not change:
            continue
        if isinstance(change, list):
            change = change[0]
        if change.type == CHANGE_ADD:
            path1 = change.new.path
            path2 = ""
            kind = "A"
        elif change.type == CHANGE_DELETE:
            path1 = change.old.path
            path2 = ""
            kind = "D"
        elif change.type == CHANGE_MODIFY:
            path1 = change.new.path
            path2 = ""
            kind = "M"
        elif change.type in RENAME_CHANGE_TYPES:
            path1 = change.old.path
            path2 = change.new.path
            if change.type == CHANGE_RENAME:
                kind = "R"
            elif change.type == CHANGE_COPY:
                kind = "C"
        yield "%-8s%-20s%-20s" % (kind, path1, path2)  # noqa: UP031


def log(
    repo=".",
    paths=None,
    outstream=sys.stdout,
    max_entries=None,
    reverse=False,
    name_status=False,
) -> None:
    """Write commit logs.

    Args:
      repo: Path to repository
      paths: Optional set of specific paths to print entries for
      outstream: Stream to write log output to
      reverse: Reverse order in which entries are printed
      name_status: Print name status
      max_entries: Optional maximum number of entries to display
    """
    with open_repo_closing(repo) as r:
        try:
            include = [r.head()]
        except KeyError:
            include = []
        walker = r.get_walker(
            include=include, max_entries=max_entries, paths=paths, reverse=reverse
        )
        for entry in walker:

            def decode(x):
                return commit_decode(entry.commit, x)

            print_commit(entry.commit, decode, outstream)
            if name_status:
                outstream.writelines(
                    [line + "\n" for line in print_name_status(entry.changes())]
                )


# TODO(jelmer): better default for encoding?
def show(
    repo=".",
    objects=None,
    outstream=sys.stdout,
    default_encoding=DEFAULT_ENCODING,
) -> None:
    """Print the changes in a commit.

    Args:
      repo: Path to repository
      objects: Objects to show (defaults to [HEAD])
      outstream: Stream to write to
      default_encoding: Default encoding to use if none is set in the
        commit
    """
    if objects is None:
        objects = ["HEAD"]
    if not isinstance(objects, list):
        objects = [objects]
    with open_repo_closing(repo) as r:
        for objectish in objects:
            o = parse_object(r, objectish)
            if isinstance(o, Commit):

                def decode(x):
                    return commit_decode(o, x, default_encoding)

            else:

                def decode(x):
                    return x.decode(default_encoding)

            show_object(r, o, decode, outstream)


def diff_tree(repo, old_tree, new_tree, outstream=default_bytes_out_stream) -> None:
    """Compares the content and mode of blobs found via two tree objects.

    Args:
      repo: Path to repository
      old_tree: Id of old tree
      new_tree: Id of new tree
      outstream: Stream to write to
    """
    with open_repo_closing(repo) as r:
        write_tree_diff(outstream, r.object_store, old_tree, new_tree)


def rev_list(repo, commits, outstream=sys.stdout) -> None:
    """Lists commit objects in reverse chronological order.

    Args:
      repo: Path to repository
      commits: Commits over which to iterate
      outstream: Stream to write to
    """
    with open_repo_closing(repo) as r:
        for entry in r.get_walker(include=[r[c].id for c in commits]):
            outstream.write(entry.commit.id + b"\n")


def _canonical_part(url: str) -> str:
    name = url.rsplit("/", 1)[-1]
    if name.endswith(".git"):
        name = name[:-4]
    return name


def submodule_add(repo, url, path=None, name=None) -> None:
    """Add a new submodule.

    Args:
      repo: Path to repository
      url: URL of repository to add as submodule
      path: Path where submodule should live
    """
    with open_repo_closing(repo) as r:
        if path is None:
            path = os.path.relpath(_canonical_part(url), r.path)
        if name is None:
            name = path

        # TODO(jelmer): Move this logic to dulwich.submodule
        gitmodules_path = os.path.join(r.path, ".gitmodules")
        try:
            config = ConfigFile.from_path(gitmodules_path)
        except FileNotFoundError:
            config = ConfigFile()
            config.path = gitmodules_path
        config.set(("submodule", name), "url", url)
        config.set(("submodule", name), "path", path)
        config.write_to_path()


def submodule_init(repo) -> None:
    """Initialize submodules.

    Args:
      repo: Path to repository
    """
    with open_repo_closing(repo) as r:
        config = r.get_config()
        gitmodules_path = os.path.join(r.path, ".gitmodules")
        for path, url, name in read_submodules(gitmodules_path):
            config.set((b"submodule", name), b"active", True)
            config.set((b"submodule", name), b"url", url)
        config.write_to_path()


def submodule_list(repo):
    """List submodules.

    Args:
      repo: Path to repository
    """
    from .submodule import iter_cached_submodules

    with open_repo_closing(repo) as r:
        for path, sha in iter_cached_submodules(r.object_store, r[r.head()].tree):
            yield path, sha.decode(DEFAULT_ENCODING)


def tag_create(
    repo,
    tag: Union[str, bytes],
    author: Optional[Union[str, bytes]] = None,
    message: Optional[Union[str, bytes]] = None,
    annotated=False,
    objectish: Union[str, bytes] = "HEAD",
    tag_time=None,
    tag_timezone=None,
    sign: bool = False,
    encoding: str = DEFAULT_ENCODING,
) -> None:
    """Creates a tag in git via dulwich calls.

    Args:
      repo: Path to repository
      tag: tag string
      author: tag author (optional, if annotated is set)
      message: tag message (optional)
      annotated: whether to create an annotated tag
      objectish: object the tag should point at, defaults to HEAD
      tag_time: Optional time for annotated tag
      tag_timezone: Optional timezone for annotated tag
      sign: GPG Sign the tag (bool, defaults to False,
        pass True to use default GPG key,
        pass a str containing Key ID to use a specific GPG key)
    """
    with open_repo_closing(repo) as r:
        object = parse_object(r, objectish)

        if isinstance(tag, str):
            tag = tag.encode(encoding)

        if annotated:
            # Create the tag object
            tag_obj = Tag()
            if author is None:
                author = get_user_identity(r.get_config_stack())
            elif isinstance(author, str):
                author = author.encode(encoding)
            else:
                assert isinstance(author, bytes)
            tag_obj.tagger = author
            if isinstance(message, str):
                message = message.encode(encoding)
            elif isinstance(message, bytes):
                pass
            else:
                message = b""
            tag_obj.message = message + "\n".encode(encoding)
            tag_obj.name = tag
            tag_obj.object = (type(object), object.id)
            if tag_time is None:
                tag_time = int(time.time())
            tag_obj.tag_time = tag_time
            if tag_timezone is None:
                tag_timezone = get_user_timezones()[1]
            elif isinstance(tag_timezone, str):
                tag_timezone = parse_timezone(tag_timezone)
            tag_obj.tag_timezone = tag_timezone
            if sign:
                tag_obj.sign(sign if isinstance(sign, str) else None)

            r.object_store.add_object(tag_obj)
            tag_id = tag_obj.id
        else:
            tag_id = object.id

        r.refs[_make_tag_ref(tag)] = tag_id


def tag_list(repo, outstream=sys.stdout):
    """List all tags.

    Args:
      repo: Path to repository
      outstream: Stream to write tags to
    """
    with open_repo_closing(repo) as r:
        tags = sorted(r.refs.as_dict(b"refs/tags"))
        return tags


def tag_delete(repo, name) -> None:
    """Remove a tag.

    Args:
      repo: Path to repository
      name: Name of tag to remove
    """
    with open_repo_closing(repo) as r:
        if isinstance(name, bytes):
            names = [name]
        elif isinstance(name, list):
            names = name
        else:
            raise Error(f"Unexpected tag name type {name!r}")
        for name in names:
            del r.refs[_make_tag_ref(name)]


def _make_notes_ref(name: bytes) -> bytes:
    """Make a notes ref name."""
    if name.startswith(b"refs/notes/"):
        return name
    return LOCAL_NOTES_PREFIX + name


def notes_add(
    repo, object_sha, note, ref=b"commits", author=None, committer=None, message=None
):
    """Add or update a note for an object.

    Args:
      repo: Path to repository
      object_sha: SHA of the object to annotate
      note: Note content
      ref: Notes ref to use (defaults to "commits" for refs/notes/commits)
      author: Author identity (defaults to committer)
      committer: Committer identity (defaults to config)
      message: Commit message for the notes update

    Returns:
      SHA of the new notes commit
    """
    with open_repo_closing(repo) as r:
        # Parse the object to get its SHA
        obj = parse_object(r, object_sha)
        object_sha = obj.id

        if isinstance(note, str):
            note = note.encode(DEFAULT_ENCODING)
        if isinstance(ref, str):
            ref = ref.encode(DEFAULT_ENCODING)

        notes_ref = _make_notes_ref(ref)
        config = r.get_config_stack()

        return r.notes.set_note(
            object_sha,
            note,
            notes_ref,
            author=author,
            committer=committer,
            message=message,
            config=config,
        )


def notes_remove(
    repo, object_sha, ref=b"commits", author=None, committer=None, message=None
):
    """Remove a note for an object.

    Args:
      repo: Path to repository
      object_sha: SHA of the object to remove notes from
      ref: Notes ref to use (defaults to "commits" for refs/notes/commits)
      author: Author identity (defaults to committer)
      committer: Committer identity (defaults to config)
      message: Commit message for the notes removal

    Returns:
      SHA of the new notes commit, or None if no note existed
    """
    with open_repo_closing(repo) as r:
        # Parse the object to get its SHA
        obj = parse_object(r, object_sha)
        object_sha = obj.id

        if isinstance(ref, str):
            ref = ref.encode(DEFAULT_ENCODING)

        notes_ref = _make_notes_ref(ref)
        config = r.get_config_stack()

        return r.notes.remove_note(
            object_sha,
            notes_ref,
            author=author,
            committer=committer,
            message=message,
            config=config,
        )


def notes_show(repo, object_sha, ref=b"commits"):
    """Show the note for an object.

    Args:
      repo: Path to repository
      object_sha: SHA of the object
      ref: Notes ref to use (defaults to "commits" for refs/notes/commits)

    Returns:
      Note content as bytes, or None if no note exists
    """
    with open_repo_closing(repo) as r:
        # Parse the object to get its SHA
        obj = parse_object(r, object_sha)
        object_sha = obj.id

        if isinstance(ref, str):
            ref = ref.encode(DEFAULT_ENCODING)

        notes_ref = _make_notes_ref(ref)
        config = r.get_config_stack()

        return r.notes.get_note(object_sha, notes_ref, config=config)


def notes_list(repo, ref=b"commits"):
    """List all notes in a notes ref.

    Args:
      repo: Path to repository
      ref: Notes ref to use (defaults to "commits" for refs/notes/commits)

    Returns:
      List of tuples of (object_sha, note_content)
    """
    with open_repo_closing(repo) as r:
        if isinstance(ref, str):
            ref = ref.encode(DEFAULT_ENCODING)

        notes_ref = _make_notes_ref(ref)
        config = r.get_config_stack()

        return r.notes.list_notes(notes_ref, config=config)


def reset(repo, mode, treeish="HEAD") -> None:
    """Reset current HEAD to the specified state.

    Args:
      repo: Path to repository
      mode: Mode ("hard", "soft", "mixed")
      treeish: Treeish to reset to
    """
    if mode != "hard":
        raise Error("hard is the only mode currently supported")

    with open_repo_closing(repo) as r:
        tree = parse_tree(r, treeish)

        # Get current HEAD tree for comparison
        try:
            current_head = r.refs[b"HEAD"]
            current_tree = r[current_head].tree
        except KeyError:
            current_tree = None

        # Get configuration for working directory update
        config = r.get_config()
        honor_filemode = config.get_boolean(b"core", b"filemode", os.name != "nt")

        # Import validation functions
        from .index import validate_path_element_default, validate_path_element_ntfs

        if config.get_boolean(b"core", b"core.protectNTFS", os.name == "nt"):
            validate_path_element = validate_path_element_ntfs
        else:
            validate_path_element = validate_path_element_default

        if config.get_boolean(b"core", b"symlinks", True):
            # Import symlink function
            from .index import symlink

            symlink_fn = symlink
        else:

            def symlink_fn(  # type: ignore
                source, target, target_is_directory=False, *, dir_fd=None
            ) -> None:
                mode = "w" + ("b" if isinstance(source, bytes) else "")
                with open(target, mode) as f:
                    f.write(source)

        # Update working tree and index
        update_working_tree(
            r,
            current_tree,
            tree.id,
            honor_filemode=honor_filemode,
            validate_path_element=validate_path_element,
            symlink_fn=symlink_fn,
            force_remove_untracked=True,
        )


def get_remote_repo(
    repo: Repo, remote_location: Optional[Union[str, bytes]] = None
) -> tuple[Optional[str], str]:
    config = repo.get_config()
    if remote_location is None:
        remote_location = get_branch_remote(repo)
    if isinstance(remote_location, str):
        encoded_location = remote_location.encode()
    else:
        encoded_location = remote_location

    section = (b"remote", encoded_location)

    remote_name: Optional[str] = None

    if config.has_section(section):
        remote_name = encoded_location.decode()
        encoded_location = config.get(section, "url")
    else:
        remote_name = None

    return (remote_name, encoded_location.decode())


def push(
    repo,
    remote_location=None,
    refspecs=None,
    outstream=default_bytes_out_stream,
    errstream=default_bytes_err_stream,
    force=False,
    **kwargs,
) -> None:
    """Remote push with dulwich via dulwich.client.

    Args:
      repo: Path to repository
      remote_location: Location of the remote
      refspecs: Refs to push to remote
      outstream: A stream file to write output
      errstream: A stream file to write errors
      force: Force overwriting refs
    """
    # Open the repo
    with open_repo_closing(repo) as r:
        if refspecs is None:
            refspecs = [active_branch(r)]
        (remote_name, remote_location) = get_remote_repo(r, remote_location)

        # Get the client and path
        client, path = get_transport_and_path(
            remote_location, config=r.get_config_stack(), **kwargs
        )

        selected_refs = []
        remote_changed_refs = {}

        def update_refs(refs):
            selected_refs.extend(parse_reftuples(r.refs, refs, refspecs, force=force))
            new_refs = {}
            # TODO: Handle selected_refs == {None: None}
            for lh, rh, force_ref in selected_refs:
                if lh is None:
                    new_refs[rh] = ZERO_SHA
                    remote_changed_refs[rh] = None
                else:
                    try:
                        localsha = r.refs[lh]
                    except KeyError as exc:
                        raise Error(f"No valid ref {lh} in local repository") from exc
                    if not force_ref and rh in refs:
                        check_diverged(r, refs[rh], localsha)
                    new_refs[rh] = localsha
                    remote_changed_refs[rh] = localsha
            return new_refs

        err_encoding = getattr(errstream, "encoding", None) or DEFAULT_ENCODING
        remote_location = client.get_url(path)
        try:
            result = client.send_pack(
                path,
                update_refs,
                generate_pack_data=r.generate_pack_data,
                progress=errstream.write,
            )
        except SendPackError as exc:
            raise Error(
                "Push to " + remote_location + " failed -> " + exc.args[0].decode(),
            ) from exc
        else:
            errstream.write(
                b"Push to " + remote_location.encode(err_encoding) + b" successful.\n"
            )

        for ref, error in (result.ref_status or {}).items():
            if error is not None:
                errstream.write(
                    b"Push of ref %s failed: %s\n" % (ref, error.encode(err_encoding))
                )
            else:
                errstream.write(b"Ref %s updated\n" % ref)

        if remote_name is not None:
            _import_remote_refs(r.refs, remote_name, remote_changed_refs)


def pull(
    repo,
    remote_location=None,
    refspecs=None,
    outstream=default_bytes_out_stream,
    errstream=default_bytes_err_stream,
    fast_forward=True,
    ff_only=False,
    force=False,
    filter_spec=None,
    protocol_version=None,
    **kwargs,
) -> None:
    """Pull from remote via dulwich.client.

    Args:
      repo: Path to repository
      remote_location: Location of the remote
      refspecs: refspecs to fetch. Can be a bytestring, a string, or a list of
        bytestring/string.
      outstream: A stream file to write to output
      errstream: A stream file to write to errors
      fast_forward: If True, raise an exception when fast-forward is not possible
      ff_only: If True, only allow fast-forward merges. Raises DivergedBranches
        when branches have diverged rather than performing a merge.
      filter_spec: A git-rev-list-style object filter spec, as an ASCII string.
        Only used if the server supports the Git protocol-v2 'filter'
        feature, and ignored otherwise.
      protocol_version: desired Git protocol version. By default the highest
        mutually supported protocol version will be used
    """
    # Open the repo
    with open_repo_closing(repo) as r:
        (remote_name, remote_location) = get_remote_repo(r, remote_location)

        selected_refs = []

        if refspecs is None:
            refspecs = [b"HEAD"]

        def determine_wants(remote_refs, *args, **kwargs):
            selected_refs.extend(
                parse_reftuples(remote_refs, r.refs, refspecs, force=force)
            )
            return [
                remote_refs[lh]
                for (lh, rh, force_ref) in selected_refs
                if remote_refs[lh] not in r.object_store
            ]

        client, path = get_transport_and_path(
            remote_location, config=r.get_config_stack(), **kwargs
        )
        if filter_spec:
            filter_spec = filter_spec.encode("ascii")
        fetch_result = client.fetch(
            path,
            r,
            progress=errstream.write,
            determine_wants=determine_wants,
            filter_spec=filter_spec,
            protocol_version=protocol_version,
        )

        # Store the old HEAD tree before making changes
        try:
            old_head = r.refs[b"HEAD"]
            old_tree_id = r[old_head].tree
        except KeyError:
            old_tree_id = None

        merged = False
        for lh, rh, force_ref in selected_refs:
            if not force_ref and rh in r.refs:
                try:
                    check_diverged(r, r.refs.follow(rh)[1], fetch_result.refs[lh])
                except DivergedBranches as exc:
                    if ff_only or fast_forward:
                        raise
                    else:
                        # Perform merge
                        merge_result, conflicts = _do_merge(r, fetch_result.refs[lh])
                        if conflicts:
                            raise Error(
                                f"Merge conflicts occurred: {conflicts}"
                            ) from exc
                        merged = True
                        # Skip updating ref since merge already updated HEAD
                        continue
            r.refs[rh] = fetch_result.refs[lh]

        # Only update HEAD if we didn't perform a merge
        if selected_refs and not merged:
            r[b"HEAD"] = fetch_result.refs[selected_refs[0][1]]

        # Update working tree to match the new HEAD
        # Skip if merge was performed as merge already updates the working tree
        if not merged and old_tree_id is not None:
            new_tree_id = r[b"HEAD"].tree
            update_working_tree(r, old_tree_id, new_tree_id)
        if remote_name is not None:
            _import_remote_refs(r.refs, remote_name, fetch_result.refs)


def status(repo=".", ignored=False, untracked_files="all"):
    """Returns staged, unstaged, and untracked changes relative to the HEAD.

    Args:
      repo: Path to repository or repository object
      ignored: Whether to include ignored files in untracked
      untracked_files: How to handle untracked files, defaults to "all":
          "no": do not return untracked files
          "all": include all files in untracked directories
        Using untracked_files="no" can be faster than "all" when the worktreee
          contains many untracked files/directories.

    Note: untracked_files="normal" (git's default) is not implemented.

    Returns: GitStatus tuple,
        staged -  dict with lists of staged paths (diff index/HEAD)
        unstaged -  list of unstaged paths (diff index/working-tree)
        untracked - list of untracked, un-ignored & non-.git paths
    """
    with open_repo_closing(repo) as r:
        # 1. Get status of staged
        tracked_changes = get_tree_changes(r)
        # 2. Get status of unstaged
        index = r.open_index()
        normalizer = r.get_blob_normalizer()
        filter_callback = normalizer.checkin_normalize
        unstaged_changes = list(get_unstaged_changes(index, r.path, filter_callback))

        untracked_paths = get_untracked_paths(
            r.path,
            r.path,
            index,
            exclude_ignored=not ignored,
            untracked_files=untracked_files,
        )
        if sys.platform == "win32":
            untracked_changes = [
                path.replace(os.path.sep, "/") for path in untracked_paths
            ]
        else:
            untracked_changes = list(untracked_paths)

        return GitStatus(tracked_changes, unstaged_changes, untracked_changes)


def _walk_working_dir_paths(frompath, basepath, prune_dirnames=None):
    """Get path, is_dir for files in working dir from frompath.

    Args:
      frompath: Path to begin walk
      basepath: Path to compare to
      prune_dirnames: Optional callback to prune dirnames during os.walk
        dirnames will be set to result of prune_dirnames(dirpath, dirnames)
    """
    for dirpath, dirnames, filenames in os.walk(frompath):
        # Skip .git and below.
        if ".git" in dirnames:
            dirnames.remove(".git")
            if dirpath != basepath:
                continue

        if ".git" in filenames:
            filenames.remove(".git")
            if dirpath != basepath:
                continue

        if dirpath != frompath:
            yield dirpath, True

        for filename in filenames:
            filepath = os.path.join(dirpath, filename)
            yield filepath, False

        if prune_dirnames:
            dirnames[:] = prune_dirnames(dirpath, dirnames)


def get_untracked_paths(
    frompath, basepath, index, exclude_ignored=False, untracked_files="all"
):
    """Get untracked paths.

    Args:
      frompath: Path to walk
      basepath: Path to compare to
      index: Index to check against
      exclude_ignored: Whether to exclude ignored paths
      untracked_files: How to handle untracked files:
        - "no": return an empty list
        - "all": return all files in untracked directories
        - "normal": Not implemented

    Note: ignored directories will never be walked for performance reasons.
      If exclude_ignored is False, only the path to an ignored directory will
      be yielded, no files inside the directory will be returned
    """
    if untracked_files == "normal":
        raise NotImplementedError("normal is not yet supported")

    if untracked_files not in ("no", "all"):
        raise ValueError("untracked_files must be one of (no, all)")

    if untracked_files == "no":
        return

    with open_repo_closing(basepath) as r:
        ignore_manager = IgnoreFilterManager.from_repo(r)

    ignored_dirs = []

    def prune_dirnames(dirpath, dirnames):
        for i in range(len(dirnames) - 1, -1, -1):
            path = os.path.join(dirpath, dirnames[i])
            ip = os.path.join(os.path.relpath(path, basepath), "")
            if ignore_manager.is_ignored(ip):
                if not exclude_ignored:
                    ignored_dirs.append(
                        os.path.join(os.path.relpath(path, frompath), "")
                    )
                del dirnames[i]
        return dirnames

    for ap, is_dir in _walk_working_dir_paths(
        frompath, basepath, prune_dirnames=prune_dirnames
    ):
        if not is_dir:
            ip = path_to_tree_path(basepath, ap)
            if ip not in index:
                if not exclude_ignored or not ignore_manager.is_ignored(
                    os.path.relpath(ap, basepath)
                ):
                    yield os.path.relpath(ap, frompath)

    yield from ignored_dirs


def get_tree_changes(repo):
    """Return add/delete/modify changes to tree by comparing index to HEAD.

    Args:
      repo: repo path or object
    Returns: dict with lists for each type of change
    """
    with open_repo_closing(repo) as r:
        index = r.open_index()

        # Compares the Index to the HEAD & determines changes
        # Iterate through the changes and report add/delete/modify
        # TODO: call out to dulwich.diff_tree somehow.
        tracked_changes = {
            "add": [],
            "delete": [],
            "modify": [],
        }
        try:
            tree_id = r[b"HEAD"].tree
        except KeyError:
            tree_id = None

        for change in index.changes_from_tree(r.object_store, tree_id):
            if not change[0][0]:
                tracked_changes["add"].append(change[0][1])
            elif not change[0][1]:
                tracked_changes["delete"].append(change[0][0])
            elif change[0][0] == change[0][1]:
                tracked_changes["modify"].append(change[0][0])
            else:
                raise NotImplementedError("git mv ops not yet supported")
        return tracked_changes


def daemon(path=".", address=None, port=None) -> None:
    """Run a daemon serving Git requests over TCP/IP.

    Args:
      path: Path to the directory to serve.
      address: Optional address to listen on (defaults to ::)
      port: Optional port to listen on (defaults to TCP_GIT_PORT)
    """
    # TODO(jelmer): Support git-daemon-export-ok and --export-all.
    backend = FileSystemBackend(path)
    server = TCPGitServer(backend, address, port)
    server.serve_forever()


def web_daemon(path=".", address=None, port=None) -> None:
    """Run a daemon serving Git requests over HTTP.

    Args:
      path: Path to the directory to serve
      address: Optional address to listen on (defaults to ::)
      port: Optional port to listen on (defaults to 80)
    """
    from .web import (
        WSGIRequestHandlerLogger,
        WSGIServerLogger,
        make_server,
        make_wsgi_chain,
    )

    backend = FileSystemBackend(path)
    app = make_wsgi_chain(backend)
    server = make_server(
        address,
        port,
        app,
        handler_class=WSGIRequestHandlerLogger,
        server_class=WSGIServerLogger,
    )
    server.serve_forever()


def upload_pack(path=".", inf=None, outf=None) -> int:
    """Upload a pack file after negotiating its contents using smart protocol.

    Args:
      path: Path to the repository
      inf: Input stream to communicate with client
      outf: Output stream to communicate with client
    """
    if outf is None:
        outf = getattr(sys.stdout, "buffer", sys.stdout)
    if inf is None:
        inf = getattr(sys.stdin, "buffer", sys.stdin)
    path = os.path.expanduser(path)
    backend = FileSystemBackend(path)

    def send_fn(data) -> None:
        outf.write(data)
        outf.flush()

    proto = Protocol(inf.read, send_fn)
    handler = UploadPackHandler(backend, [path], proto)
    # FIXME: Catch exceptions and write a single-line summary to outf.
    handler.handle()
    return 0


def receive_pack(path=".", inf=None, outf=None) -> int:
    """Receive a pack file after negotiating its contents using smart protocol.

    Args:
      path: Path to the repository
      inf: Input stream to communicate with client
      outf: Output stream to communicate with client
    """
    if outf is None:
        outf = getattr(sys.stdout, "buffer", sys.stdout)
    if inf is None:
        inf = getattr(sys.stdin, "buffer", sys.stdin)
    path = os.path.expanduser(path)
    backend = FileSystemBackend(path)

    def send_fn(data) -> None:
        outf.write(data)
        outf.flush()

    proto = Protocol(inf.read, send_fn)
    handler = ReceivePackHandler(backend, [path], proto)
    # FIXME: Catch exceptions and write a single-line summary to outf.
    handler.handle()
    return 0


def _make_branch_ref(name: Union[str, bytes]) -> Ref:
    if isinstance(name, str):
        name = name.encode(DEFAULT_ENCODING)
    return LOCAL_BRANCH_PREFIX + name


def _make_tag_ref(name: Union[str, bytes]) -> Ref:
    if isinstance(name, str):
        name = name.encode(DEFAULT_ENCODING)
    return LOCAL_TAG_PREFIX + name


def branch_delete(repo, name) -> None:
    """Delete a branch.

    Args:
      repo: Path to the repository
      name: Name of the branch
    """
    with open_repo_closing(repo) as r:
        if isinstance(name, list):
            names = name
        else:
            names = [name]
        for name in names:
            del r.refs[_make_branch_ref(name)]


def branch_create(repo, name, objectish=None, force=False) -> None:
    """Create a branch.

    Args:
      repo: Path to the repository
      name: Name of the new branch
      objectish: Target object to point new branch at (defaults to HEAD)
      force: Force creation of branch, even if it already exists
    """
    with open_repo_closing(repo) as r:
        if objectish is None:
            objectish = "HEAD"
        object = parse_object(r, objectish)
        refname = _make_branch_ref(name)
        ref_message = b"branch: Created from " + objectish.encode(DEFAULT_ENCODING)
        if force:
            r.refs.set_if_equals(refname, None, object.id, message=ref_message)
        else:
            if not r.refs.add_if_new(refname, object.id, message=ref_message):
                raise Error(f"Branch with name {name} already exists.")


def branch_list(repo):
    """List all branches.

    Args:
      repo: Path to the repository
    """
    with open_repo_closing(repo) as r:
        return r.refs.keys(base=LOCAL_BRANCH_PREFIX)


def active_branch(repo):
    """Return the active branch in the repository, if any.

    Args:
      repo: Repository to open
    Returns:
      branch name
    Raises:
      KeyError: if the repository does not have a working tree
      IndexError: if HEAD is floating
    """
    with open_repo_closing(repo) as r:
        active_ref = r.refs.follow(b"HEAD")[0][1]
        if not active_ref.startswith(LOCAL_BRANCH_PREFIX):
            raise ValueError(active_ref)
        return active_ref[len(LOCAL_BRANCH_PREFIX) :]


def get_branch_remote(repo):
    """Return the active branch's remote name, if any.

    Args:
      repo: Repository to open
    Returns:
      remote name
    Raises:
      KeyError: if the repository does not have a working tree
    """
    with open_repo_closing(repo) as r:
        branch_name = active_branch(r.path)
        config = r.get_config()
        try:
            remote_name = config.get((b"branch", branch_name), b"remote")
        except KeyError:
            remote_name = b"origin"
    return remote_name


def fetch(
    repo,
    remote_location=None,
    outstream=sys.stdout,
    errstream=default_bytes_err_stream,
    message=None,
    depth=None,
    prune=False,
    prune_tags=False,
    force=False,
    **kwargs,
):
    """Fetch objects from a remote server.

    Args:
      repo: Path to the repository
      remote_location: String identifying a remote server
      outstream: Output stream (defaults to stdout)
      errstream: Error stream (defaults to stderr)
      message: Reflog message (defaults to b"fetch: from <remote_name>")
      depth: Depth to fetch at
      prune: Prune remote removed refs
      prune_tags: Prune reomte removed tags
    Returns:
      Dictionary with refs on the remote
    """
    with open_repo_closing(repo) as r:
        (remote_name, remote_location) = get_remote_repo(r, remote_location)
        if message is None:
            message = b"fetch: from " + remote_location.encode(DEFAULT_ENCODING)
        client, path = get_transport_and_path(
            remote_location, config=r.get_config_stack(), **kwargs
        )
        fetch_result = client.fetch(path, r, progress=errstream.write, depth=depth)
        if remote_name is not None:
            _import_remote_refs(
                r.refs,
                remote_name,
                fetch_result.refs,
                message,
                prune=prune,
                prune_tags=prune_tags,
            )

    return fetch_result


def for_each_ref(
    repo: Union[Repo, str] = ".",
    pattern: Optional[Union[str, bytes]] = None,
) -> list[tuple[bytes, bytes, bytes]]:
    """Iterate over all refs that match the (optional) pattern.

    Args:
      repo: Path to the repository
      pattern: Optional glob (7) patterns to filter the refs with
    Returns: List of bytes tuples with: (sha, object_type, ref_name)
    """
    if isinstance(pattern, str):
        pattern = os.fsencode(pattern)

    with open_repo_closing(repo) as r:
        refs = r.get_refs()

    if pattern:
        matching_refs: dict[bytes, bytes] = {}
        pattern_parts = pattern.split(b"/")
        for ref, sha in refs.items():
            matches = False

            # git for-each-ref uses glob (7) style patterns, but fnmatch
            # is greedy and also matches slashes, unlike glob.glob.
            # We have to check parts of the pattern individually.
            # See https://github.com/python/cpython/issues/72904
            ref_parts = ref.split(b"/")
            if len(ref_parts) > len(pattern_parts):
                continue

            for pat, ref_part in zip(pattern_parts, ref_parts):
                matches = fnmatch.fnmatchcase(ref_part, pat)
                if not matches:
                    break

            if matches:
                matching_refs[ref] = sha

        refs = matching_refs

    ret: list[tuple[bytes, bytes, bytes]] = [
        (sha, r.get_object(sha).type_name, ref)
        for ref, sha in sorted(
            refs.items(),
            key=lambda ref_sha: ref_sha[0],
        )
        if ref != b"HEAD"
    ]

    return ret


def ls_remote(remote, config: Optional[Config] = None, **kwargs):
    """List the refs in a remote.

    Args:
      remote: Remote repository location
      config: Configuration to use
    Returns:
      Dictionary with remote refs
    """
    if config is None:
        config = StackedConfig.default()
    client, host_path = get_transport_and_path(remote, config=config, **kwargs)
    return client.get_refs(host_path)


def repack(repo) -> None:
    """Repack loose files in a repository.

    Currently this only packs loose objects.

    Args:
      repo: Path to the repository
    """
    with open_repo_closing(repo) as r:
        r.object_store.pack_loose_objects()


def pack_objects(
    repo,
    object_ids,
    packf,
    idxf,
    delta_window_size=None,
    deltify=None,
    reuse_deltas=True,
    pack_index_version=None,
) -> None:
    """Pack objects into a file.

    Args:
      repo: Path to the repository
      object_ids: List of object ids to write
      packf: File-like object to write to
      idxf: File-like object to write to (can be None)
      delta_window_size: Sliding window size for searching for deltas;
                         Set to None for default window size.
      deltify: Whether to deltify objects
      reuse_deltas: Allow reuse of existing deltas while deltifying
      pack_index_version: Pack index version to use (1, 2, or 3). If None, uses default version.
    """
    with open_repo_closing(repo) as r:
        entries, data_sum = write_pack_from_container(
            packf.write,
            r.object_store,
            [(oid, None) for oid in object_ids],
            deltify=deltify,
            delta_window_size=delta_window_size,
            reuse_deltas=reuse_deltas,
        )
    if idxf is not None:
        entries = sorted([(k, v[0], v[1]) for (k, v) in entries.items()])
        write_pack_index(idxf, entries, data_sum, version=pack_index_version)


def ls_tree(
    repo,
    treeish=b"HEAD",
    outstream=sys.stdout,
    recursive=False,
    name_only=False,
) -> None:
    """List contents of a tree.

    Args:
      repo: Path to the repository
      treeish: Tree id to list
      outstream: Output stream (defaults to stdout)
      recursive: Whether to recursively list files
      name_only: Only print item name
    """

    def list_tree(store, treeid, base) -> None:
        for name, mode, sha in store[treeid].iteritems():
            if base:
                name = posixpath.join(base, name)
            if name_only:
                outstream.write(name + b"\n")
            else:
                outstream.write(pretty_format_tree_entry(name, mode, sha))
            if stat.S_ISDIR(mode) and recursive:
                list_tree(store, sha, name)

    with open_repo_closing(repo) as r:
        tree = parse_tree(r, treeish)
        list_tree(r.object_store, tree.id, "")


def remote_add(repo, name: Union[bytes, str], url: Union[bytes, str]) -> None:
    """Add a remote.

    Args:
      repo: Path to the repository
      name: Remote name
      url: Remote URL
    """
    if not isinstance(name, bytes):
        name = name.encode(DEFAULT_ENCODING)
    if not isinstance(url, bytes):
        url = url.encode(DEFAULT_ENCODING)
    with open_repo_closing(repo) as r:
        c = r.get_config()
        section = (b"remote", name)
        if c.has_section(section):
            raise RemoteExists(section)
        c.set(section, b"url", url)
        c.write_to_path()


def remote_remove(repo: Repo, name: Union[bytes, str]) -> None:
    """Remove a remote.

    Args:
      repo: Path to the repository
      name: Remote name
    """
    if not isinstance(name, bytes):
        name = name.encode(DEFAULT_ENCODING)
    with open_repo_closing(repo) as r:
        c = r.get_config()
        section = (b"remote", name)
        del c[section]
        c.write_to_path()


def _quote_path(path: str) -> str:
    """Quote a path using C-style quoting similar to git's core.quotePath.

    Args:
        path: Path to quote

    Returns:
        Quoted path string
    """
    # Check if path needs quoting (non-ASCII or special characters)
    needs_quoting = False
    for char in path:
        if ord(char) > 127 or char in '"\\':
            needs_quoting = True
            break

    if not needs_quoting:
        return path

    # Apply C-style quoting
    quoted = '"'
    for char in path:
        if ord(char) > 127:
            # Non-ASCII character, encode as octal escape
            utf8_bytes = char.encode("utf-8")
            for byte in utf8_bytes:
                quoted += f"\\{byte:03o}"
        elif char == '"':
            quoted += '\\"'
        elif char == "\\":
            quoted += "\\\\"
        else:
            quoted += char
    quoted += '"'
    return quoted


def check_ignore(repo, paths, no_index=False, quote_path=True):
    r"""Debug gitignore files.

    Args:
      repo: Path to the repository
      paths: List of paths to check for
      no_index: Don't check index
      quote_path: If True, quote non-ASCII characters in returned paths using
                  C-style octal escapes (e.g. "тест.txt" becomes "\\321\\202\\320\\265\\321\\201\\321\\202.txt").
                  If False, return raw unicode paths.
    Returns: List of ignored files
    """
    with open_repo_closing(repo) as r:
        index = r.open_index()
        ignore_manager = IgnoreFilterManager.from_repo(r)
        for original_path in paths:
            if not no_index and path_to_tree_path(r.path, original_path) in index:
                continue

            # Preserve whether the original path had a trailing slash
            had_trailing_slash = original_path.endswith("/")

            if os.path.isabs(original_path):
                path = os.path.relpath(original_path, r.path)
            else:
                path = original_path

            # Restore trailing slash if it was in the original
            if had_trailing_slash and not path.endswith("/"):
                path = path + "/"

            # For directories, check with trailing slash to get correct ignore behavior
            test_path = path
            path_without_slash = path.rstrip("/")
            is_directory = os.path.isdir(os.path.join(r.path, path_without_slash))

            # If this is a directory path, ensure we test it correctly
            if is_directory and not path.endswith("/"):
                test_path = path + "/"

            if ignore_manager.is_ignored(test_path):
                yield _quote_path(path) if quote_path else path


def update_head(repo, target, detached=False, new_branch=None) -> None:
    """Update HEAD to point at a new branch/commit.

    Note that this does not actually update the working tree.

    Args:
      repo: Path to the repository
      detached: Create a detached head
      target: Branch or committish to switch to
      new_branch: New branch to create
    """
    with open_repo_closing(repo) as r:
        if new_branch is not None:
            to_set = _make_branch_ref(new_branch)
        else:
            to_set = b"HEAD"
        if detached:
            # TODO(jelmer): Provide some way so that the actual ref gets
            # updated rather than what it points to, so the delete isn't
            # necessary.
            del r.refs[to_set]
            r.refs[to_set] = parse_commit(r, target).id
        else:
            r.refs.set_symbolic_ref(to_set, parse_ref(r, target))
        if new_branch is not None:
            r.refs.set_symbolic_ref(b"HEAD", to_set)


def checkout(
    repo,
    target: Union[bytes, str],
    force: bool = False,
    new_branch: Optional[Union[bytes, str]] = None,
) -> None:
    """Switch to a branch or commit, updating both HEAD and the working tree.

    This is similar to 'git checkout', allowing you to switch to a branch,
    tag, or specific commit. Unlike update_head, this function also updates
    the working tree to match the target.

    Args:
      repo: Path to repository or repository object
      target: Branch name, tag, or commit SHA to checkout
      force: Force checkout even if there are local changes
      new_branch: Create a new branch at target (like git checkout -b)

    Raises:
      CheckoutError: If checkout cannot be performed due to conflicts
      KeyError: If the target reference cannot be found
    """
    with open_repo_closing(repo) as r:
        if isinstance(target, str):
            target = target.encode(DEFAULT_ENCODING)
        if isinstance(new_branch, str):
            new_branch = new_branch.encode(DEFAULT_ENCODING)

        # Parse the target to get the commit
        target_commit = parse_commit(r, target)
        target_tree_id = target_commit.tree

        # Get current HEAD tree for comparison
        try:
            current_head = r.refs[b"HEAD"]
            current_tree_id = r[current_head].tree
        except KeyError:
            # No HEAD yet (empty repo)
            current_tree_id = None

        # Check for uncommitted changes if not forcing
        if not force and current_tree_id is not None:
            status_report = status(r)
            changes = []
            # staged is a dict with 'add', 'delete', 'modify' keys
            if isinstance(status_report.staged, dict):
                changes.extend(status_report.staged.get("add", []))
                changes.extend(status_report.staged.get("delete", []))
                changes.extend(status_report.staged.get("modify", []))
            # unstaged is a list
            changes.extend(status_report.unstaged)
            if changes:
                # Check if any changes would conflict with checkout
                target_tree = r[target_tree_id]
                for change in changes:
                    if isinstance(change, str):
                        change = change.encode(DEFAULT_ENCODING)

                    try:
                        target_tree.lookup_path(r.object_store.__getitem__, change)
                        # File exists in target tree - would overwrite local changes
                        raise CheckoutError(
                            f"Your local changes to '{change.decode()}' would be "
                            "overwritten by checkout. Please commit or stash before switching."
                        )
                    except KeyError:
                        # File doesn't exist in target tree - change can be preserved
                        pass

        # Get configuration for working directory update
        config = r.get_config()
        honor_filemode = config.get_boolean(b"core", b"filemode", os.name != "nt")

        # Import validation functions
        from .index import validate_path_element_default, validate_path_element_ntfs

        if config.get_boolean(b"core", b"core.protectNTFS", os.name == "nt"):
            validate_path_element = validate_path_element_ntfs
        else:
            validate_path_element = validate_path_element_default

        if config.get_boolean(b"core", b"symlinks", True):
            # Import symlink function
            from .index import symlink

            symlink_fn = symlink
        else:

            def symlink_fn(source, target) -> None:  # type: ignore
                mode = "w" + ("b" if isinstance(source, bytes) else "")
                with open(target, mode) as f:
                    f.write(source)

        # Update working tree
        update_working_tree(
            r,
            current_tree_id,
            target_tree_id,
            honor_filemode=honor_filemode,
            validate_path_element=validate_path_element,
            symlink_fn=symlink_fn,
            force_remove_untracked=force,
        )

        # Update HEAD
        if new_branch:
            # Create new branch and switch to it
            branch_create(r, new_branch, objectish=target_commit.id.decode("ascii"))
            update_head(r, new_branch)
        else:
            # Check if target is a branch name (with or without refs/heads/ prefix)
            branch_ref = None
            if target in r.refs.keys():
                if target.startswith(LOCAL_BRANCH_PREFIX):
                    branch_ref = target
            else:
                # Try adding refs/heads/ prefix
                potential_branch = _make_branch_ref(target)
                if potential_branch in r.refs.keys():
                    branch_ref = potential_branch

            if branch_ref:
                # It's a branch - update HEAD symbolically
                update_head(r, branch_ref)
            else:
                # It's a tag, other ref, or commit SHA - detached HEAD
                update_head(r, target_commit.id.decode("ascii"), detached=True)


def reset_file(repo, file_path: str, target: bytes = b"HEAD", symlink_fn=None) -> None:
    """Reset the file to specific commit or branch.

    Args:
      repo: dulwich Repo object
      file_path: file to reset, relative to the repository path
      target: branch or commit or b'HEAD' to reset
    """
    tree = parse_tree(repo, treeish=target)
    tree_path = _fs_to_tree_path(file_path)

    file_entry = tree.lookup_path(repo.object_store.__getitem__, tree_path)
    full_path = os.path.join(os.fsencode(repo.path), tree_path)
    blob = repo.object_store[file_entry[1]]
    mode = file_entry[0]
    build_file_from_blob(blob, mode, full_path, symlink_fn=symlink_fn)


@replace_me(since="0.22.9", remove_in="0.24.0")
def checkout_branch(repo, target: Union[bytes, str], force: bool = False) -> None:
    """Switch branches or restore working tree files.

    This is now a wrapper around the general checkout() function.
    Preserved for backward compatibility.

    Args:
      repo: dulwich Repo object
      target: branch name or commit sha to checkout
      force: true or not to force checkout
    """
    # Simply delegate to the new checkout function
    return checkout(repo, target, force=force)


def sparse_checkout(
    repo, patterns=None, force: bool = False, cone: Union[bool, None] = None
):
    """Perform a sparse checkout in the repository (either 'full' or 'cone mode').

    Perform sparse checkout in either 'cone' (directory-based) mode or
    'full pattern' (.gitignore) mode, depending on the ``cone`` parameter.

    If ``cone`` is ``None``, the mode is inferred from the repository's
    ``core.sparseCheckoutCone`` config setting.

    Steps:
      1) If ``patterns`` is provided, write them to ``.git/info/sparse-checkout``.
      2) Determine which paths in the index are included vs. excluded.
         - If ``cone=True``, use "cone-compatible" directory-based logic.
         - If ``cone=False``, use standard .gitignore-style matching.
      3) Update the index's skip-worktree bits and add/remove files in
         the working tree accordingly.
      4) If ``force=False``, refuse to remove files that have local modifications.

    Args:
      repo: Path to the repository or a Repo object.
      patterns: Optional list of sparse-checkout patterns to write.
      force: Whether to force removal of locally modified files (default False).
      cone: Boolean indicating cone mode (True/False). If None, read from config.

    Returns:
      None
    """
    with open_repo_closing(repo) as repo_obj:
        # --- 0) Possibly infer 'cone' from config ---
        if cone is None:
            cone = repo_obj.infer_cone_mode()

        # --- 1) Read or write patterns ---
        if patterns is None:
            lines = repo_obj.get_sparse_checkout_patterns()
            if lines is None:
                raise Error("No sparse checkout patterns found.")
        else:
            lines = patterns
            repo_obj.set_sparse_checkout_patterns(patterns)

        # --- 2) Determine the set of included paths ---
        included_paths = determine_included_paths(repo_obj, lines, cone)

        # --- 3) Apply those results to the index & working tree ---
        try:
            apply_included_paths(repo_obj, included_paths, force=force)
        except SparseCheckoutConflictError as exc:
            raise CheckoutError(*exc.args) from exc


def cone_mode_init(repo):
    """Initialize a repository to use sparse checkout in 'cone' mode.

    Sets ``core.sparseCheckout`` and ``core.sparseCheckoutCone`` in the config.
    Writes an initial ``.git/info/sparse-checkout`` file that includes only
    top-level files (and excludes all subdirectories), e.g. ``["/*", "!/*/"]``.
    Then performs a sparse checkout to update the working tree accordingly.

    If no directories are specified, then only top-level files are included:
    https://git-scm.com/docs/git-sparse-checkout#_internalscone_mode_handling

    Args:
      repo: Path to the repository or a Repo object.

    Returns:
      None
    """
    with open_repo_closing(repo) as repo_obj:
        repo_obj.configure_for_cone_mode()
        patterns = ["/*", "!/*/"]  # root-level files only
        sparse_checkout(repo_obj, patterns, force=True, cone=True)


def cone_mode_set(repo, dirs, force=False):
    """Overwrite the existing 'cone-mode' sparse patterns with a new set of directories.

    Ensures ``core.sparseCheckout`` and ``core.sparseCheckoutCone`` are enabled.
    Writes new patterns so that only the specified directories (and top-level files)
    remain in the working tree, and applies the sparse checkout update.

    Args:
      repo: Path to the repository or a Repo object.
      dirs: List of directory names to include.
      force: Whether to forcibly discard local modifications (default False).

    Returns:
      None
    """
    with open_repo_closing(repo) as repo_obj:
        repo_obj.configure_for_cone_mode()
        repo_obj.set_cone_mode_patterns(dirs=dirs)
        new_patterns = repo_obj.get_sparse_checkout_patterns()
        # Finally, apply the patterns and update the working tree
        sparse_checkout(repo_obj, new_patterns, force=force, cone=True)


def cone_mode_add(repo, dirs, force=False):
    """Add new directories to the existing 'cone-mode' sparse-checkout patterns.

    Reads the current patterns from ``.git/info/sparse-checkout``, adds pattern
    lines to include the specified directories, and then performs a sparse
    checkout to update the working tree accordingly.

    Args:
      repo: Path to the repository or a Repo object.
      dirs: List of directory names to add to the sparse-checkout.
      force: Whether to forcibly discard local modifications (default False).

    Returns:
      None
    """
    with open_repo_closing(repo) as repo_obj:
        repo_obj.configure_for_cone_mode()
        # Do not pass base patterns as dirs
        base_patterns = ["/*", "!/*/"]
        existing_dirs = [
            pat.strip("/")
            for pat in repo_obj.get_sparse_checkout_patterns()
            if pat not in base_patterns
        ]
        added_dirs = existing_dirs + (dirs or [])
        repo_obj.set_cone_mode_patterns(dirs=added_dirs)
        new_patterns = repo_obj.get_sparse_checkout_patterns()
        sparse_checkout(repo_obj, patterns=new_patterns, force=force, cone=True)


def check_mailmap(repo, contact):
    """Check canonical name and email of contact.

    Args:
      repo: Path to the repository
      contact: Contact name and/or email
    Returns: Canonical contact data
    """
    with open_repo_closing(repo) as r:
        from .mailmap import Mailmap

        try:
            mailmap = Mailmap.from_path(os.path.join(r.path, ".mailmap"))
        except FileNotFoundError:
            mailmap = Mailmap()
        return mailmap.lookup(contact)


def fsck(repo):
    """Check a repository.

    Args:
      repo: A path to the repository
    Returns: Iterator over errors/warnings
    """
    with open_repo_closing(repo) as r:
        # TODO(jelmer): check pack files
        # TODO(jelmer): check graph
        # TODO(jelmer): check refs
        for sha in r.object_store:
            o = r.object_store[sha]
            try:
                o.check()
            except Exception as e:
                yield (sha, e)


def stash_list(repo):
    """List all stashes in a repository."""
    with open_repo_closing(repo) as r:
        from .stash import Stash

        stash = Stash.from_repo(r)
        return enumerate(list(stash.stashes()))


def stash_push(repo) -> None:
    """Push a new stash onto the stack."""
    with open_repo_closing(repo) as r:
        from .stash import Stash

        stash = Stash.from_repo(r)
        stash.push()


def stash_pop(repo) -> None:
    """Pop a stash from the stack."""
    with open_repo_closing(repo) as r:
        from .stash import Stash

        stash = Stash.from_repo(r)
        stash.pop(0)


def stash_drop(repo, index) -> None:
    """Drop a stash from the stack."""
    with open_repo_closing(repo) as r:
        from .stash import Stash

        stash = Stash.from_repo(r)
        stash.drop(index)


def ls_files(repo):
    """List all files in an index."""
    with open_repo_closing(repo) as r:
        return sorted(r.open_index())


def find_unique_abbrev(object_store, object_id):
    """For now, just return 7 characters."""
    # TODO(jelmer): Add some logic here to return a number of characters that
    # scales relative with the size of the repository
    return object_id.decode("ascii")[:7]


def describe(repo, abbrev=None):
    """Describe the repository version.

    Args:
      repo: git repository
      abbrev: number of characters of commit to take, default is 7
    Returns: a string description of the current git revision

    Examples: "gabcdefh", "v0.1" or "v0.1-5-gabcdefh".
    """
    abbrev_slice = slice(0, abbrev if abbrev is not None else 7)
    # Get the repository
    with open_repo_closing(repo) as r:
        # Get a list of all tags
        refs = r.get_refs()
        tags = {}
        for key, value in refs.items():
            key = key.decode()
            obj = r.get_object(value)
            if "tags" not in key:
                continue

            _, tag = key.rsplit("/", 1)

            try:
                # Annotated tag case
                commit = obj.object
                commit = r.get_object(commit[1])
            except AttributeError:
                # Lightweight tag case - obj is already the commit
                commit = obj
            tags[tag] = [
                datetime.datetime(*time.gmtime(commit.commit_time)[:6]),
                commit.id.decode("ascii"),
            ]

        sorted_tags = sorted(tags.items(), key=lambda tag: tag[1][0], reverse=True)

        # Get the latest commit
        latest_commit = r[r.head()]

        # If there are no tags, return the latest commit
        if len(sorted_tags) == 0:
            if abbrev is not None:
                return "g{}".format(latest_commit.id.decode("ascii")[abbrev_slice])
            return f"g{find_unique_abbrev(r.object_store, latest_commit.id)}"

        # We're now 0 commits from the top
        commit_count = 0

        # Walk through all commits
        walker = r.get_walker()
        for entry in walker:
            # Check if tag
            commit_id = entry.commit.id.decode("ascii")
            for tag in sorted_tags:
                tag_name = tag[0]
                tag_commit = tag[1][1]
                if commit_id == tag_commit:
                    if commit_count == 0:
                        return tag_name
                    else:
                        return "{}-{}-g{}".format(
                            tag_name,
                            commit_count,
                            latest_commit.id.decode("ascii")[abbrev_slice],
                        )

            commit_count += 1

        # Return plain commit if no parent tag can be found
        return "g{}".format(latest_commit.id.decode("ascii")[abbrev_slice])


def get_object_by_path(repo, path, committish=None):
    """Get an object by path.

    Args:
      repo: A path to the repository
      path: Path to look up
      committish: Commit to look up path in
    Returns: A `ShaFile` object
    """
    if committish is None:
        committish = "HEAD"
    # Get the repository
    with open_repo_closing(repo) as r:
        commit = parse_commit(r, committish)
        base_tree = commit.tree
        if not isinstance(path, bytes):
            path = commit_encode(commit, path)
        (mode, sha) = tree_lookup_path(r.object_store.__getitem__, base_tree, path)
        return r[sha]


def write_tree(repo):
    """Write a tree object from the index.

    Args:
      repo: Repository for which to write tree
    Returns: tree id for the tree that was written
    """
    with open_repo_closing(repo) as r:
        return r.open_index().commit(r.object_store)


def _do_merge(
    r,
    merge_commit_id,
    no_commit=False,
    no_ff=False,
    message=None,
    author=None,
    committer=None,
):
    """Internal merge implementation that operates on an open repository.

    Args:
      r: Open repository object
      merge_commit_id: SHA of commit to merge
      no_commit: If True, do not create a merge commit
      no_ff: If True, force creation of a merge commit
      message: Optional merge commit message
      author: Optional author for merge commit
      committer: Optional committer for merge commit

    Returns:
      Tuple of (merge_commit_sha, conflicts) where merge_commit_sha is None
      if no_commit=True or there were conflicts
    """
    from .graph import find_merge_base
    from .merge import three_way_merge

    # Get HEAD commit
    try:
        head_commit_id = r.refs[b"HEAD"]
    except KeyError:
        raise Error("No HEAD reference found")

    head_commit = r[head_commit_id]
    merge_commit = r[merge_commit_id]

    # Check if fast-forward is possible
    merge_bases = find_merge_base(r, [head_commit_id, merge_commit_id])

    if not merge_bases:
        raise Error("No common ancestor found")

    # Use the first merge base
    base_commit_id = merge_bases[0]

    # Check if we're trying to merge the same commit
    if head_commit_id == merge_commit_id:
        # Already up to date
        return (None, [])

    # Check for fast-forward
    if base_commit_id == head_commit_id and not no_ff:
        # Fast-forward merge
        r.refs[b"HEAD"] = merge_commit_id
        # Update the working directory
        update_working_tree(r, head_commit.tree, merge_commit.tree)
        return (merge_commit_id, [])

    if base_commit_id == merge_commit_id:
        # Already up to date
        return (None, [])

    # Perform three-way merge
    base_commit = r[base_commit_id]
    merged_tree, conflicts = three_way_merge(
        r.object_store, base_commit, head_commit, merge_commit
    )

    # Add merged tree to object store
    r.object_store.add_object(merged_tree)

    # Update index and working directory
    update_working_tree(r, head_commit.tree, merged_tree.id)

    if conflicts or no_commit:
        # Don't create a commit if there are conflicts or no_commit is True
        return (None, conflicts)

    # Create merge commit
    merge_commit_obj = Commit()
    merge_commit_obj.tree = merged_tree.id
    merge_commit_obj.parents = [head_commit_id, merge_commit_id]

    # Set author/committer
    if author is None:
        author = get_user_identity(r.get_config_stack())
    if committer is None:
        committer = author

    merge_commit_obj.author = author
    merge_commit_obj.committer = committer

    # Set timestamps
    timestamp = int(time.time())
    timezone = 0  # UTC
    merge_commit_obj.author_time = timestamp
    merge_commit_obj.author_timezone = timezone
    merge_commit_obj.commit_time = timestamp
    merge_commit_obj.commit_timezone = timezone

    # Set commit message
    if message is None:
        message = f"Merge commit '{merge_commit_id.decode()[:7]}'\n"
    merge_commit_obj.message = message.encode() if isinstance(message, str) else message

    # Add commit to object store
    r.object_store.add_object(merge_commit_obj)

    # Update HEAD
    r.refs[b"HEAD"] = merge_commit_obj.id

    return (merge_commit_obj.id, [])


def merge(
    repo,
    committish,
    no_commit=False,
    no_ff=False,
    message=None,
    author=None,
    committer=None,
):
    """Merge a commit into the current branch.

    Args:
      repo: Repository to merge into
      committish: Commit to merge
      no_commit: If True, do not create a merge commit
      no_ff: If True, force creation of a merge commit
      message: Optional merge commit message
      author: Optional author for merge commit
      committer: Optional committer for merge commit

    Returns:
      Tuple of (merge_commit_sha, conflicts) where merge_commit_sha is None
      if no_commit=True or there were conflicts

    Raises:
      Error: If there is no HEAD reference or commit cannot be found
    """
    with open_repo_closing(repo) as r:
        # Parse the commit to merge
        try:
            merge_commit_id = parse_commit(r, committish).id
        except KeyError:
            raise Error(f"Cannot find commit '{committish}'")

        return _do_merge(
            r, merge_commit_id, no_commit, no_ff, message, author, committer
        )


def unpack_objects(pack_path, target="."):
    """Unpack objects from a pack file into the repository.

    Args:
      pack_path: Path to the pack file to unpack
      target: Path to the repository to unpack into

    Returns:
      Number of objects unpacked
    """
    from .pack import Pack

    with open_repo_closing(target) as r:
        pack_basename = os.path.splitext(pack_path)[0]
        with Pack(pack_basename) as pack:
            count = 0
            for unpacked in pack.iter_unpacked():
                obj = unpacked.sha_file()
                r.object_store.add_object(obj)
                count += 1
            return count


def merge_tree(repo, base_tree, our_tree, their_tree):
    """Perform a three-way tree merge without touching the working directory.

    This is similar to git merge-tree, performing a merge at the tree level
    without creating commits or updating any references.

    Args:
      repo: Repository containing the trees
      base_tree: Tree-ish of the common ancestor (or None for no common ancestor)
      our_tree: Tree-ish of our side of the merge
      their_tree: Tree-ish of their side of the merge

    Returns:
      Tuple of (merged_tree_id, conflicts) where:
        - merged_tree_id is the SHA-1 of the merged tree
        - conflicts is a list of paths (as bytes) that had conflicts

    Raises:
      KeyError: If any of the tree-ish arguments cannot be resolved
    """
    from .merge import Merger

    with open_repo_closing(repo) as r:
        # Resolve tree-ish arguments to actual trees
        base = parse_tree(r, base_tree) if base_tree else None
        ours = parse_tree(r, our_tree)
        theirs = parse_tree(r, their_tree)

        # Perform the merge
        merger = Merger(r.object_store)
        merged_tree, conflicts = merger.merge_trees(base, ours, theirs)

        # Add the merged tree to the object store
        r.object_store.add_object(merged_tree)

        return merged_tree.id, conflicts


def gc(
    repo,
    auto: bool = False,
    aggressive: bool = False,
    prune: bool = True,
    grace_period: Optional[int] = 1209600,  # 2 weeks default
    dry_run: bool = False,
    progress=None,
):
    """Run garbage collection on a repository.

    Args:
      repo: Path to the repository or a Repo object
      auto: If True, only run gc if needed
      aggressive: If True, use more aggressive settings
      prune: If True, prune unreachable objects
      grace_period: Grace period in seconds for pruning (default 2 weeks)
      dry_run: If True, only report what would be done
      progress: Optional progress callback

    Returns:
      GCStats object with garbage collection statistics
    """
    from .gc import garbage_collect

    with open_repo_closing(repo) as r:
        return garbage_collect(
            r,
            auto=auto,
            aggressive=aggressive,
            prune=prune,
            grace_period=grace_period,
            dry_run=dry_run,
            progress=progress,
        )


def count_objects(repo=".", verbose=False) -> CountObjectsResult:
    """Count unpacked objects and their disk usage.

    Args:
      repo: Path to repository or repository object
      verbose: Whether to return verbose information

    Returns:
      CountObjectsResult object with detailed statistics
    """
    with open_repo_closing(repo) as r:
        object_store = r.object_store

        # Count loose objects
        loose_count = 0
        loose_size = 0
        for sha in object_store._iter_loose_objects():
            loose_count += 1
            path = object_store._get_shafile_path(sha)
            try:
                stat_info = os.stat(path)
                # Git uses disk usage, not file size. st_blocks is always in
                # 512-byte blocks per POSIX standard
                if hasattr(stat_info, "st_blocks"):
                    # Available on Linux and macOS
                    loose_size += stat_info.st_blocks * 512  # type: ignore
                else:
                    # Fallback for Windows
                    loose_size += stat_info.st_size
            except FileNotFoundError:
                # Object may have been removed between iteration and stat
                pass

        if not verbose:
            return CountObjectsResult(count=loose_count, size=loose_size)

        # Count pack information
        pack_count = len(object_store.packs)
        in_pack_count = 0
        pack_size = 0

        for pack in object_store.packs:
            in_pack_count += len(pack)
            # Get pack file size
            pack_path = pack._data_path
            try:
                pack_size += os.path.getsize(pack_path)
            except FileNotFoundError:
                pass
            # Get index file size
            idx_path = pack._idx_path
            try:
                pack_size += os.path.getsize(idx_path)
            except FileNotFoundError:
                pass

        return CountObjectsResult(
            count=loose_count,
            size=loose_size,
            in_pack=in_pack_count,
            packs=pack_count,
            size_pack=pack_size,
        )


def rebase(
    repo: Union[Repo, str],
    upstream: Union[bytes, str],
    onto: Optional[Union[bytes, str]] = None,
    branch: Optional[Union[bytes, str]] = None,
    abort: bool = False,
    continue_rebase: bool = False,
    skip: bool = False,
) -> list[bytes]:
    """Rebase commits onto another branch.

    Args:
      repo: Repository to rebase in
      upstream: Upstream branch/commit to rebase onto
      onto: Specific commit to rebase onto (defaults to upstream)
      branch: Branch to rebase (defaults to current branch)
      abort: Abort an in-progress rebase
      continue_rebase: Continue an in-progress rebase
      skip: Skip current commit and continue rebase

    Returns:
      List of new commit SHAs created by rebase

    Raises:
      Error: If rebase fails or conflicts occur
    """
    from .rebase import RebaseConflict, RebaseError, Rebaser

    with open_repo_closing(repo) as r:
        rebaser = Rebaser(r)

        if abort:
            try:
                rebaser.abort()
                return []
            except RebaseError as e:
                raise Error(str(e))

        if continue_rebase:
            try:
                result = rebaser.continue_()
                if result is None:
                    # Rebase complete
                    return []
                elif isinstance(result, tuple) and result[1]:
                    # Still have conflicts
                    raise Error(
                        f"Conflicts in: {', '.join(f.decode('utf-8', 'replace') for f in result[1])}"
                    )
            except RebaseError as e:
                raise Error(str(e))

        # Convert string refs to bytes
        if isinstance(upstream, str):
            upstream = upstream.encode("utf-8")
        if isinstance(onto, str):
            onto = onto.encode("utf-8") if onto else None
        if isinstance(branch, str):
            branch = branch.encode("utf-8") if branch else None

        try:
            # Start rebase
            rebaser.start(upstream, onto, branch)

            # Continue rebase automatically
            result = rebaser.continue_()
            if result is not None:
                # Conflicts
                raise RebaseConflict(result[1])

            # Return the SHAs of the rebased commits
            return [c.id for c in rebaser._done]

        except RebaseConflict as e:
            raise Error(str(e))
        except RebaseError as e:
            raise Error(str(e))