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Auto track binary files #828

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78 changes: 74 additions & 4 deletions src/huggingface_hub/repository.py
Expand Up @@ -226,6 +226,27 @@ def is_git_ignored(filename: Union[str, Path]) -> bool:
return is_ignored


def is_binary_file(filename: Union[str, Path]) -> bool:
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Other than reading the first few bytes, I think this answer gives a more accurate way of checking if the file is binary or not: https://stackoverflow.com/a/7392391/2536294

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I implemented what you propose in 9fe6bb6, let me know if that's what you had in mind. Cc @coyotte508

"""
Check if file is a binary file.

Args:
filename (`str` or `Path`):
The filename to check.

Returns:
`bool`: `True` if the file passed is a binary file, `False` otherwise.
"""
try:
with open(filename) as f:
content = f.read()
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Suggested change
content = f.read()
content = f.read(1024) # or 512 if we want to be consistent with the backend

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This was discussed above here: #828 (comment)

Do you disagree with the conclusion?

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Didn't see that. Yeah I don't think we should ever read 11GB of data into memory. This will most certainly crash most people's systems. I'd be happy if we read like 10MB instead of 1MB to reduce the probability of a false detection, which should address those concerns. If we really do want to read a lot more, we should read in chunks. As python's docs state:

To read a file’s contents, call f.read(size), which reads some quantity of data and returns it as a string (in text mode) or bytes object (in binary mode). size is an optional numeric argument. When size is omitted or negative, the entire contents of the file will be read and returned; it’s your problem if the file is twice as large as your machine’s memory.

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The solution currently implemented loads a maximum of 10MB in memory when calling git_add: it tracks large files before tracking binary files.

When tracking binary files, it looks at files which are not yet tracked with lfs, eliminating large files.

Instead of the 1MB limit that you propose here, we could instead put a max of 10MB here, which will only be triggered when auto_track_binary_files is called independently of git_add (which is a possibility!).

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yes, but you also want to have this method public, which means people can call it before having tracked large files.

I'm happy with your suggestion of 10MB.

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Sounds good, thanks for your review. Addressed in cbfdce5


# Check for the presence of the null character in the string
return "\x00" in content
except UnicodeDecodeError:
return True


def files_to_be_staged(pattern: str, folder: Union[str, Path]) -> List[str]:
"""
Returns a list of filenames that are to be staged.
Expand Down Expand Up @@ -485,8 +506,8 @@ def __init__(
skip_lfs_files (`bool`, *optional*, defaults to `False`):
whether to skip git-LFS files or not.
client (`HfApi`, *optional*):
Instance of HfApi to use when calling the HF Hub API.
A new instance will be created if this is left to `None`.
Instance of HfApi to use when calling the HF Hub API. A new
instance will be created if this is left to `None`.
"""

os.makedirs(local_dir, exist_ok=True)
Expand Down Expand Up @@ -981,6 +1002,49 @@ def lfs_enable_largefiles(self):
except subprocess.CalledProcessError as exc:
raise EnvironmentError(exc.stderr)

def auto_track_binary_files(self, pattern: Optional[str] = ".") -> List[str]:
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"""
Automatically track binary files with git-lfs.

Args:
pattern (`str`, *optional*, defaults to "."):
The pattern with which to track files that are binary.

Returns:
`List[str]`: List of filenames that are now tracked due to being
binary files
"""
files_to_be_tracked_with_lfs = []

deleted_files = self.list_deleted_files()

for filename in files_to_be_staged(pattern, folder=self.local_dir):
if filename in deleted_files:
continue

path_to_file = os.path.join(os.getcwd(), self.local_dir, filename)

if not (is_tracked_with_lfs(path_to_file) or is_git_ignored(path_to_file)):
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size_in_mb = os.path.getsize(path_to_file) / (1024 * 1024)

if size_in_mb >= 10:
logger.warning(
"Parsing a large file to check if binary or not. Tracking large "
"files using `repository.auto_track_large_files` is recommended "
"so as to not load the full file in memory."
)

is_binary = is_binary_file(path_to_file)

if is_binary:
self.lfs_track(filename)
files_to_be_tracked_with_lfs.append(filename)

# Cleanup the .gitattributes if files were deleted
self.lfs_untrack(deleted_files)

return files_to_be_tracked_with_lfs

def auto_track_large_files(self, pattern: Optional[str] = ".") -> List[str]:
"""
Automatically track large files (files that weigh more than 10MBs) with
Expand Down Expand Up @@ -1090,11 +1154,17 @@ def git_add(
pattern (`str`, *optional*, defaults to "."):
The pattern with which to add files to staging.
auto_lfs_track (`bool`, *optional*, defaults to `False`):
Whether to automatically track large files with git-lfs. Any
file over 10MB in size will be automatically tracked.
Whether to automatically track large and binary files with
git-lfs. Any file over 10MB in size, or in binary format, will
be automatically tracked.
"""
if auto_lfs_track:
# Track files according to their size (>=10MB)
tracked_files = self.auto_track_large_files(pattern)

# Read the remaining files and track them if they're binary
tracked_files.extend(self.auto_track_binary_files(pattern))

if tracked_files:
logger.warning(
f"Adding files tracked by Git LFS: {tracked_files}. This may take a bit of time if the files are large."
Expand Down
121 changes: 121 additions & 0 deletions tests/test_repository.py
Expand Up @@ -1128,6 +1128,30 @@ def test_auto_track_large_files(self):
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "small_file.txt"))
)

def test_auto_track_binary_files(self):
repo = Repository(WORKING_REPO_DIR)

# This content is non-binary
non_binary_file = [100] * int(1e6)

# This content is binary (contains the null character)
binary_file = "\x00\x00\x00\x00"

with open(f"{WORKING_REPO_DIR}/non_binary_file.txt", "w+") as f:
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we shouldn't write on the working dir, we should work with python's temp files and folders.

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The WORKING_REPO_DIR is a folder that is created on the start of the test, and which is reset at every beginning of every test, see here:

def setUp(self):
if os.path.exists(WORKING_REPO_DIR):
shutil.rmtree(WORKING_REPO_DIR, onerror=set_write_permission_and_retry)
logger.info(
f"Does {WORKING_REPO_DIR} exist: {os.path.exists(WORKING_REPO_DIR)}"
)
self.REPO_NAME = repo_name()
self._repo_url = self._api.create_repo(
repo_id=self.REPO_NAME, token=self._token
)
self._api.upload_file(
path_or_fileobj=BytesIO(b"some initial binary data: \x00\x01"),
path_in_repo="random_file.txt",
repo_id=f"{USER}/{self.REPO_NAME}",
token=self._token,
)

This isn't the working directory in which the test is run, but a folder nested in the fixtures folder:

WORKING_REPO_DIR = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "fixtures/working_repo_2"
)

f.write(json.dumps(non_binary_file))

with open(f"{WORKING_REPO_DIR}/binary_file.txt", "w+") as f:
f.write(binary_file)

repo.auto_track_binary_files()

self.assertFalse(
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "non_binary)file.txt"))
)
self.assertTrue(
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "binary_file.txt"))
)

def test_auto_track_large_files_ignored_with_gitignore(self):
repo = Repository(WORKING_REPO_DIR)

Expand Down Expand Up @@ -1157,6 +1181,7 @@ def test_auto_track_large_files_ignored_with_gitignore(self):

repo.auto_track_large_files()

# Large files
self.assertFalse(
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "large_file.txt"))
)
Expand All @@ -1175,6 +1200,54 @@ def test_auto_track_large_files_ignored_with_gitignore(self):
)
)

def test_auto_track_binary_files_ignored_with_gitignore(self):
repo = Repository(WORKING_REPO_DIR)

# This content is binary (contains the null character)
binary_file = "\x00\x00\x00\x00"

# Test nested gitignores
os.makedirs(f"{WORKING_REPO_DIR}/directory")
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same here

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Same answer as above :)


with open(f"{WORKING_REPO_DIR}/.gitignore", "w+") as f:
f.write("binary_file.txt")

with open(f"{WORKING_REPO_DIR}/directory/.gitignore", "w+") as f:
f.write("binary_file_3.txt")

with open(f"{WORKING_REPO_DIR}/binary_file.txt", "w+") as f:
f.write(binary_file)

with open(f"{WORKING_REPO_DIR}/binary_file_2.txt", "w+") as f:
f.write(binary_file)

with open(f"{WORKING_REPO_DIR}/directory/binary_file_3.txt", "w+") as f:
f.write(binary_file)

with open(f"{WORKING_REPO_DIR}/directory/binary_file_4.txt", "w+") as f:
f.write(binary_file)

repo.auto_track_binary_files()

# Binary files
self.assertFalse(
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "binary_file.txt"))
)
self.assertTrue(
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "binary_file_2.txt"))
)

self.assertFalse(
is_tracked_with_lfs(
os.path.join(WORKING_REPO_DIR, "directory/binary_file_3.txt")
)
)
self.assertTrue(
is_tracked_with_lfs(
os.path.join(WORKING_REPO_DIR, "directory/binary_file_4.txt")
)
)

def test_auto_track_large_files_through_git_add(self):
repo = Repository(WORKING_REPO_DIR)

Expand All @@ -1199,6 +1272,30 @@ def test_auto_track_large_files_through_git_add(self):
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "small_file.txt"))
)

def test_auto_track_binary_files_through_git_add(self):
repo = Repository(WORKING_REPO_DIR)

# This content is non binary
non_binary_file = [100] * int(1e6)

# This content is binary (contains the null character)
binary_file = "\x00\x00\x00\x00"

with open(f"{WORKING_REPO_DIR}/small_file.txt", "w+") as f:
f.write(json.dumps(non_binary_file))

with open(f"{WORKING_REPO_DIR}/binary_file.txt", "w+") as f:
f.write(binary_file)

repo.git_add(auto_lfs_track=True)

self.assertFalse(
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "non_binary_file.txt"))
)
self.assertTrue(
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "binary_file.txt"))
)

def test_auto_no_track_large_files_through_git_add(self):
repo = Repository(WORKING_REPO_DIR)

Expand All @@ -1223,6 +1320,30 @@ def test_auto_no_track_large_files_through_git_add(self):
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "small_file.txt"))
)

def test_auto_no_track_binary_files_through_git_add(self):
repo = Repository(WORKING_REPO_DIR)

# This content is non-binary
non_binary_file = [100] * int(1e6)

# This content is binary (contains the null character)
binary_file = "\x00\x00\x00\x00"

with open(f"{WORKING_REPO_DIR}/small_file.txt", "w+") as f:
f.write(json.dumps(non_binary_file))

with open(f"{WORKING_REPO_DIR}/binary_file.txt", "w+") as f:
f.write(binary_file)

repo.git_add(auto_lfs_track=False)

self.assertFalse(
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "non_binary_file.txt"))
)
self.assertFalse(
is_tracked_with_lfs(os.path.join(WORKING_REPO_DIR, "binary_file.txt"))
)

def test_auto_track_updates_removed_gitattributes(self):
repo = Repository(WORKING_REPO_DIR)

Expand Down