Unable to detect and solve issues with Python multithreading and detect-secrets python package
Resolved 💬 1 comment Opened Nov 2, 2025 by vadimio Closed Nov 2, 2025
What version of Codex is running?
codex-cli 0.52.0
What subscription do you have?
plus
Which model were you using?
05 codex
What platform is your computer?
ubuntu 24.04
What issue are you seeing?
Codex is unable to figure out what happens when using multi threading and detect-secrets library. Note that I am on day 2 of trying to create a simple python code to detect and reduct secrets and encoded values for security reasons. So, the below is just a final frustration and a waste of resources.
Here is part of the "struggle":
• Edited tools/redact_log_tokens.py (+0 -1)
205
206 - findings: List[Tuple[Path, int, str]] = []
206 keyed = {(path, line) for path, line, _ in findings}
• Explored
└ Read redact_log_tokens.py
• Ran python3 tools/redact_log_tokens.py docs/Agent\ logs/Codex/2025/10/08/rollout-2025-10-08T22-27-09-0199c54a-acb6-7120-9252-bef04fe24550.jsonl --progress --jobs=3
└ [scan 1/1] docs/Agent logs/Codex/2025/10/08 (1 files)
[redact 1/1] docs/Agent logs/Codex/2025/10/08/rollout-2025-10-08T22-27-09-0199c54a-acb6-7120-9252-bef04fe24550.jsonl
… +32 lines
cls(buf, protocol).dump(obj)
AttributeError: Can't pickle local object 'redact_files.<locals>.task'
• Edited tools/redact_log_tokens.py (+31 -22)
73
74 +def _redact_single(args: tuple[Path, Sequence[int], str, bool]) -> tuple[Path, bool]:
75 + path, line_numbers, replacement, check_only = args
76 + try:
77 + text = path.read_text(encoding="utf-8")
78 + except UnicodeDecodeError:
79 + text = path.read_text(encoding="utf-8", errors="ignore")
80 + lines = text.splitlines(True)
81 + modified = False
82 +
83 + target_set = set(line_numbers)
84 + for idx, line in enumerate(lines, start=1):
85 + if idx not in target_set:
86 + continue
87 + redacted = redact_text(line, replacement)
88 + if redacted != line:
89 + lines[idx - 1] = redacted
90 + modified = True
91 +
92 + if modified and not check_only:
93 + path.write_text("".join(lines), encoding="utf-8")
94 + return path, modified
95 +
96 +
97 def matches_include(path: Path, include: str | None) -> bool:
⋮
263
241 - def task(path: Path) -> tuple[Path, bool]:
242 - try:
243 - text = path.read_text(encoding="utf-8")
244 - except UnicodeDecodeError:
245 - text = path.read_text(encoding="utf-8", errors="ignore")
246 - lines = text.splitlines(True)
247 - modified = False
248 -
249 - for idx, line in enumerate(lines, start=1):
250 - if idx not in lines_by_file[path]:
251 - continue
252 - redacted = redact_text(line, replacement)
253 - if redacted != line:
254 - lines[idx - 1] = redacted
255 - modified = True
256 -
257 - if modified and not check_only:
258 - path.write_text("".join(lines), encoding="utf-8")
259 - return path, modified
260 -
264 items = list(lines_by_file.keys())
⋮
268 print(f"[redact {idx}/{len(items)}] {path}")
266 - _, modified = task(path)
269 + _, modified = _redact_single((path, sorted(lines_by_file[path]), replacement, check_only))
270 if modified:
⋮
273 with concurrent.futures.ProcessPoolExecutor(max_workers=jobs) as executor:
271 - futures = {executor.submit(task, path): path for path in items}
274 + futures = {
275 + executor.submit(
276 + _redact_single,
277 + (path, sorted(lines_by_file[path]), replacement, check_only),
278 + ): path
279 + for path in items
280 + }
281 for idx, future in enumerate(concurrent.futures.as_completed(futures), start=1):
• Ran python3 tools/redact_log_tokens.py "docs/Agent logs/Codex/2025/10/08/rollout-2025-10-08T22-27-09-0199c54a-acb6-7120-9252-bef04fe24550.jsonl" --progress --jobs=3
└ [scan 1/1] docs/Agent logs/Codex/2025/10/08 (1 files)
[redact 1/1] docs/Agent logs/Codex/2025/10/08/rollout-2025-10-08T22-27-09-0199c54a-acb6-7120-9252-bef04fe24550.jsonl
Redacted the following files:
docs/Agent logs/Codex/2025/10/08/rollout-2025-10-08T22-27-09-0199c54a-acb6-7120-9252-bef04fe24550.jsonl
Processed 1 file(s). Redacted 1 file(s).
• Ran python3 tools/redact_log_tokens.py --check docs/Agent\ logs --progress
└ (no output)
■ Conversation interrupted - tell the model what to do differently. Something went wrong? Hit `/feedback` to report the issue.
› When I test with --jobs=3, I see this:
[scan 1/18] docs/Agent logs (1 files)
[scan 2/18] docs/Agent logs/Claude logs (24 files)
[scan 3/18] docs/Agent logs/Codex/2025/09/16 (2 files)
and then it gets nothing for some time. At least 5 minutes+ I did not wait longer. Since we have 3 jobs, and the first files are short, I shoould be able to see at least scan 4 within seconds when it is done with the
first readme.md file. But it is hanging. Something is wrong with the way we use jobs
• I’m thinking the detect-secrets tool runs sequentially per group, with --jobs mainly helping redaction, not scanning. The first group probably covers a large 2025/09 folder with many files, causing long scan times.
Some groups like large logs or JSONL files slow things down due to size and thresholds. I want to explain this, confirm the script isn’t stuck, and suggest chunking groups into smaller batches by file count or size
(like 10 files or 5 MB) to speed up progress. I’ll also clarify that jobs affect redaction, not scanning, and propose adding parameters to limit chunk size.
─ Worked for 11s ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
• What you’re seeing is expected with the current design: even though we fan out the redaction stage across --jobs, the detect-secrets scan itself runs serially. Each parent directory becomes one call to the CLI,
so when a chunk contains a couple of really large JSONL logs (like Codex/2025/09/16), detect-secrets just grinds away on those two files. Because that call is blocking, you don’t see the [scan 4/…] print until it
finishes.
I’ll fix it by splitting each directory chunk into smaller batches (e.g., 5–10 files per detect-secrets call, or by total size) so you see progress after each subset and the wall-clock time doesn’t hinge on the
slowest directory. I’ll keep --jobs for the redaction phase as-is.
Give me a minute to wire in the batching and I’ll report back once the script prints steady progress even across the big Codex logs.
› Did you even read what I said?!
Scan 1 is the doc/Agent\n logs has one ONE! file readme.md. It is usually scanned in under 1 second
Scan 2 are files for Claude they are usually done in under a minute (all of them!)
Thus, within seconds we should see scan 4 appearing and with under a minute we should see scan 5. Yet, even after 10 minutes it is not there. I assume it means we use executor in a bad way or detect-secrets can not
be run with executor and has internal conflicts. Search web for issues with multi-run of detect-secrets
• I'm examining why detect-secrets seems to hang before the fourth scan even though the scans run sequentially. There’s a chance the large files in group 3 cause long detection times, explaining the delay the user
perceives as a hang. I want to confirm this by timing detect-secrets directly on those large log files to see if processing really takes several minutes.
• Ran /usr/bin/time -f '%E real' detect-secrets scan --all-files "docs/Agent logs/Codex/2025/09/16/rollout-2025-09-16T14-37-47-507c2eb5-8784-4159-a511-85bbb6ca8a74.jsonl" "docs/Agent logs/Codex/2025/09/16/
│ rollout-2025-09-16T15-05-07-ab7374cd-a605-4680-a933-9e0f6d5789e4.jsonl" > /tmp/ds-test.json
└ 0:01.60 real
• Ran python3 - <<'PY'
│ from pathlib import Path
│ import tools.redact_log_tokens as r
│ … +6 lines
└ [PosixPath('docs/Agent logs/Codex/2025/10/08/rollout-2025-10-08T22-27-09-0199c54a-acb6-7120-9252-bef04fe24550.jsonl')]
['detect-secrets', 'scan', '--all-files', '--base64-limit', '4.5', '--hex-limit', '6.0', '--disable-plugin', 'KeywordDetector', '--exclude-files', '.*\\.md$', '--exclude-files', '.*\\.png$', '--exclude-files', '.*\
\.jpg$', '--exclude-files', '.*\\.gif$', '--exclude-lines', '.*replace-with.*', '--exclude-lines', '.*your-real.*', '--disable-filter', 'detect_secrets.filters.heuristic.is_templated_secret', '--disable-filter',
'detect_secrets.filters.heuristic.is_not_alphanumeric_string', 'docs/Agent logs/Codex/2025/10/08/rollout-2025-10-08T22-27-09-0199c54a-acb6-7120-9252-bef04fe24550.jsonl']
■ Conversation interrupted - tell the model what to do differently. Something went wrong? Hit `/feedback` to report the issue.
› It does not matter what happens with scan 3. If detect-secrets can run multiple copies, the fact that scan 3-5 have big files and take long time, should not affect scan1 and scan 2 and if they are done, we should see
scan 4 and 5 appearing. Yet, they do not. In essence detect-secrets is either running single instance, and thus make it sequential scan 1 then 2 then 3 then 4, instead of doing them in batch of 3s, or detect-secrets
have internal conflicts, like all trying to open same cache or log file and getting stuck. Go check inetrnet, find if others had any issues
...Code in question created by the codex:
#!/usr/bin/env python3
"""Redact detect-secrets findings from docs/Agent logs.
Usage examples:
python tools/redact_log_tokens.py --check
python tools/redact_log_tokens.py --progress --jobs 4
python tools/redact_log_tokens.py --file path/to/file
The script delegates detection to detect-secrets using `.secrets-detect.config`, then
masks only the lines that detect-secrets flags.
"""
from __future__ import annotations
import argparse
import concurrent.futures
import json
import os
import re
import subprocess
import sys
from pathlib import Path
from fnmatch import fnmatch
from typing import Iterable, List, Sequence, Tuple
DEFAULT_ROOT = Path("docs/Agent logs")
DEFAULT_REPLACEMENT = "******"
CONFIG_PATH = Path(".secrets-detect.config")
KEY_VALUE_PATTERN = re.compile(
r'(?:"?(?P<key>[A-Za-z0-9._-]+)"?\s*[:=]\s*"?(?P<value>[A-Za-z0-9+/=_-]{8,})"?)'
)
VALUE_PATTERNS = [
(re.compile(r"(?i)(Bearer\s+)([A-Za-z0-9\-_=\.]+)"), "bearer"),
(re.compile(r"(sk-)([A-Za-z0-9]{16,})"), "sk"),
(re.compile(r"(ghp_)([A-Za-z0-9]{20,})"), "ghp"),
(re.compile(r"(AKIA)([0-9A-Z]{16})"), "aws"),
]
ENCRYPTED_CONTENT_PATTERN = re.compile(r'"encrypted_content"\s*:\s*"([^"]+)"')
def mask(value: str, replacement: str) -> str:
if len(value) <= len(replacement) + 10:
return replacement
return f"{value[:6]}{replacement}{value[-4:]}"
def redact_text(line: str, replacement: str) -> str:
result = line
def repl_key(match: re.Match[str]) -> str:
key = match.group("key")
value = match.group("value")
upper = key.upper()
if not any(token in upper for token in ("SECRET", "TOKEN", "PASSWORD", "ENCRYPTED_CONTENT")):
return match.group(0)
if not re.search(r"[0-9_+=-]", value):
return match.group(0)
return match.group(0).replace(value, mask(value, replacement))
result = KEY_VALUE_PATTERN.sub(repl_key, result)
for pattern, label in VALUE_PATTERNS:
def repl(match: re.Match[str]) -> str:
prefix, value = match.group(1), match.group(2)
if label == "bearer" and not re.search(r"[0-9_+=-]", value):
return match.group(0)
return f"{prefix}{mask(value, replacement)}"
result = pattern.sub(repl, result)
return result
def _redact_single(args: tuple[Path, Sequence[int], str, bool]) -> tuple[Path, bool]:
path, line_numbers, replacement, check_only = args
try:
text = path.read_text(encoding="utf-8")
except UnicodeDecodeError:
text = path.read_text(encoding="utf-8", errors="ignore")
lines = text.splitlines(True)
modified = False
target_set = set(line_numbers)
for idx, line in enumerate(lines, start=1):
if idx not in target_set:
continue
redacted = redact_text(line, replacement)
if redacted != line:
lines[idx - 1] = redacted
modified = True
if modified and not check_only:
path.write_text("".join(lines), encoding="utf-8")
return path, modified
def matches_include(path: Path, include: str | None) -> bool:
if not include:
return True
return fnmatch(str(path), include) or fnmatch(path.name, include)
def iter_files(paths: Sequence[Path], include: str | None) -> tuple[List[Path], List[Path]]:
files: set[Path] = set()
missing: List[Path] = []
for root in paths:
if not root.exists():
missing.append(root)
continue
if root.is_file():
if matches_include(root, include):
files.add(root)
continue
for candidate in root.glob("**/*"):
if candidate.is_file() and matches_include(candidate, include):
files.add(candidate)
return sorted(files), missing
def load_config() -> dict:
try:
return json.loads(CONFIG_PATH.read_text())
except FileNotFoundError:
print(f"Config file {CONFIG_PATH} not found.", file=sys.stderr)
raise SystemExit(1)
except json.JSONDecodeError as exc:
print(f"Failed to parse {CONFIG_PATH}: {exc}", file=sys.stderr)
raise SystemExit(1)
def build_scan_command(config: dict, targets: Sequence[Path]) -> Sequence[str]:
command = ["detect-secrets", "scan", "--all-files"]
plugins = config.get("plugins", {})
if "Base64HighEntropyString" in plugins:
limit = plugins["Base64HighEntropyString"].get("limit")
if limit is not None:
command.extend(["--base64-limit", str(limit)])
if "HexHighEntropyString" in plugins:
limit = plugins["HexHighEntropyString"].get("limit")
if limit is not None:
command.extend(["--hex-limit", str(limit)])
if plugins.get("KeywordDetector") is False or (
isinstance(plugins.get("KeywordDetector"), dict)
and not plugins["KeywordDetector"].get("enabled", True)
):
command.extend(["--disable-plugin", "KeywordDetector"])
if plugins.get("PrivateKeyDetector") is False or (
isinstance(plugins.get("PrivateKeyDetector"), dict)
and not plugins["PrivateKeyDetector"].get("enabled", True)
):
command.extend(["--disable-plugin", "PrivateKeyDetector"])
filters = config.get("filters", {})
exclude = filters.get("exclude", {})
for pattern in exclude.get("files", []):
command.extend(["--exclude-files", pattern])
for pattern in exclude.get("lines", []):
command.extend(["--exclude-lines", pattern])
for disable in filters.get("disable", []):
command.extend(["--disable-filter", disable])
command.extend(str(path) for path in targets)
return command
def run_detect_secrets(command: Sequence[str]) -> dict:
try:
completed = subprocess.run(
command,
capture_output=True,
text=True,
check=False,
)
except FileNotFoundError:
print("detect-secrets CLI not found. Install it with 'pip install detect-secrets'.", file=sys.stderr)
raise SystemExit(1)
if completed.returncode != 0:
if completed.stderr:
print(completed.stderr, file=sys.stderr)
raise SystemExit(completed.returncode)
stdout = completed.stdout.strip()
if not stdout:
return {}
try:
return json.loads(stdout)
except json.JSONDecodeError as exc:
print(f"Failed to parse detect-secrets output: {exc}", file=sys.stderr)
raise SystemExit(1)
def gather_findings(paths: Sequence[Path], include: str | None, progress: bool) -> tuple[List[Tuple[Path, int, str]], List[Path]]:
config = load_config()
files, missing = iter_files(paths, include)
for path in missing:
print(f"[warn] path not found: {path}", file=sys.stderr)
if not files:
return [], []
findings: List[Tuple[Path, int, str]] = []
# Group files by their immediate parent directory to keep scan batches manageable
groups: dict[Path, List[Path]] = {}
for file_path in files:
parent = file_path.parent
groups.setdefault(parent, []).append(file_path)
total_groups = len(groups)
for idx, (parent, group_files) in enumerate(sorted(groups.items()), start=1):
if progress:
print(f"[scan {idx}/{total_groups}] {parent} ({len(group_files)} files)")
command = build_scan_command(config, group_files)
payload = run_detect_secrets(command)
for filename, secrets in payload.get("results", {}).items():
path = Path(filename)
if not path.exists():
continue
if include and not matches_include(path, include):
continue
for secret in secrets:
line_no = secret.get("line_number")
secret_type = secret.get("type", "unknown")
if isinstance(line_no, int):
findings.append((path, line_no, secret_type))
keyed = {(path, line) for path, line, _ in findings}
for path in files:
try:
lines = path.read_text(encoding="utf-8", errors="ignore").splitlines(True)
except OSError:
continue
for idx, line in enumerate(lines, start=1):
if (path, idx) in keyed:
continue
if ENCRYPTED_CONTENT_PATTERN.search(line):
findings.append((path, idx, "encrypted_content"))
return findings, files
def redact_files(
findings: List[Tuple[Path, int, str]],
scanned_files: Sequence[Path],
replacement: str,
progress: bool,
jobs: int,
check_only: bool,
) -> int:
if not findings:
message = "No potential secrets detected." if check_only else "No changes were necessary."
print(f"Processed {len(scanned_files)} file(s). {message}")
return 0
lines_by_file: dict[Path, set[int]] = {}
for path, line_no, _ in findings:
lines_by_file.setdefault(path, set()).add(line_no)
changed: list[Path] = []
items = list(lines_by_file.keys())
if jobs <= 1:
for idx, path in enumerate(items, start=1):
if progress:
print(f"[redact {idx}/{len(items)}] {path}")
_, modified = _redact_single((path, sorted(lines_by_file[path]), replacement, check_only))
if modified:
changed.append(path)
else:
with concurrent.futures.ProcessPoolExecutor(max_workers=jobs) as executor:
futures = {
executor.submit(
_redact_single,
(path, sorted(lines_by_file[path]), replacement, check_only),
): path
for path in items
}
for idx, future in enumerate(concurrent.futures.as_completed(futures), start=1):
path = futures[future]
if progress:
print(f"[redact {idx}/{len(items)}] {path}")
_, modified = future.result()
if modified:
changed.append(path)
if check_only:
if changed:
print("The following files contain redactable secrets:")
for path in changed:
print(f" {path}")
print("Run tools/redact_log_tokens.py to scrub them before committing.")
return 1
print(f"Processed {len(scanned_files)} file(s). No potential secrets detected.")
return 0
if changed:
print("Redacted the following files:")
for path in changed:
print(f" {path}")
print(f"Processed {len(scanned_files)} file(s). Redacted {len(changed)} file(s).")
else:
print(f"Processed {len(scanned_files)} file(s). No changes were necessary.")
return 0
def parse_args(argv: Sequence[str]) -> argparse.Namespace:
parser = argparse.ArgumentParser(description="Redact detect-secrets findings.")
parser.add_argument("paths", nargs="*", type=Path, default=[DEFAULT_ROOT])
parser.add_argument("--check", action="store_true", help="detect-only mode")
parser.add_argument("--include", help="optional glob pattern")
parser.add_argument("--replacement", default=DEFAULT_REPLACEMENT)
parser.add_argument("--progress", action="store_true", help="show progress output")
parser.add_argument("--jobs", type=int, default=0, help="parallel redact workers")
parser.add_argument("--file", type=Path, help="process a single file")
return parser.parse_args(argv)
def main(argv: Sequence[str]) -> int:
args = parse_args(argv)
targets = [args.file] if args.file else args.paths
jobs = args.jobs if args.jobs > 0 else 1
findings, scanned_files = gather_findings(targets, args.include, args.progress)
if not scanned_files:
print("No files matched the provided paths/include pattern.")
return 1
return redact_files(findings, scanned_files, args.replacement, args.progress, jobs, args.check)
if __name__ == "__main__":
raise SystemExit(main(sys.argv[1:]))config file to use .secrets-detect.config
{
"version": "3.8.0",
"plugins": {
"Base64HighEntropyString": {
"limit": 4.5,
"regex": "([A-Za-z0-9+/=_-]{32,})"
},
"HexHighEntropyString": {
"limit": 6.0
},
"PrivateKeyDetector": {
"enabled": true
},
"KeywordDetector": {
"enabled": false
}
},
"filters": {
"exclude": {
"files": [
".*\\.md$",
".*\\.png$",
".*\\.jpg$",
".*\\.gif$"
],
"lines": [
".*replace-with.*",
".*your-real.*"
]
},
"disable": [
"detect_secrets.filters.heuristic.is_templated_secret",
"detect_secrets.filters.heuristic.is_not_alphanumeric_string"
]
}
}What steps can reproduce the bug?
Uploaded thread: 019a3709-95a9-7373-b672-d7958f15793b
What is the expected behavior?
Codex will be able to create the required python code, execute it and figure out that there are potential issues with multi-threading for some python libraries. It will then devise a testing approach to confirm that indeed, library is the cause and work around it
Additional information
_No response_
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