Pylint skipping similarly named project directory.

[cinnion]

Bug description

In working on my project, I found that there was a discrepancy between the number of files being checked and how many files I had in my project, which includes both a `applications` and a `applications_api` module. In single stepping through `PyLinter._discover_files()`, I found that it would first walk over `applications`, add it to the `skip_subtrees` list, then when it hit the `applications_api` module, it would falsely skip it as having already been discovered.

Given that both of these are directories which include an `__init__.py` file, the solution is to append the OS directory separator to the name when appending the directory to the `skip_subtrees` list on line 688. I will be following this up with a PR with that fix.

The URL for my project is https://github.com/cinnion/job-application-tracker and I am running tests against the version tagged v1.99.1.

Configuration

[tool.pylint.main]
django-settings-module="job_application_tracker.settings"
load-plugins = [
    "pylint_django",
    "pylint_per_file_ignores",
]
max-line-length = 120
ignore = [
    ".git",
    ".venv",
    "__pycache__",
    "manage.py",
    "node_modules"
]
jobs = 0
recursive = true
source-roots = "."

Command used

pylint --verbose --recursive=y .

or

pylint --verbose --recursive=y $(git ls-files '*.py')

Pylint output

For the command `pylint --verbose --recursive=y .`, the output is as follows (less the fixmes):


(.venv) [cinnion@wing-1 job-application-tracker]$ pylint --verbose --recursive=y .
Using config file /home/cinnion/git.github/job-application-tracker/pyproject.toml

-----------------------------------------------------------------------------------------------------------------------
Your code has been rated at 9.98/10 (previous run: 9.98/10, +0.00)
Checked 43 files/modules (), skipped 0 files/modules



With the command `pylint --verbose --recursive=y $(git ls-files '*.py')`, the output is as follows:


(.venv) [cinnion@wing-1 job-application-tracker]$ pylint --verbose --recursive=y $(git ls-files '*.py')
Using config file /home/cinnion/git.github/job-application-tracker/pyproject.toml

-----------------------------------------------------------------------------------------------------------------------
Your code has been rated at 9.98/10 (previous run: 9.98/10, +0.00)
Checked 58 files/modules (), skipped 3 files/modules

Expected behavior

I would have expected more than 43 files to have been checked in the first case. In debugging, I tracked down 6 files as being "legitimately" skipped, due to an undocumented behaviour of pylint-django adding "migrations" to the ignore list, but that still leaves 9 files being missed, which is directly attributable to it skipping applications_api in the walk of the tree in _discover_files(). This has been verified after I added my fix for issue #10968 to the code.

Pylint version

pylint 4.0.5
astroid 4.0.4
Python 3.13.12 (main, Feb  4 2026, 00:00:00) [GCC 11.5.0 20240719 (Red Hat 11.5.0-11)]

OS / Environment

RHEL 9.7 and Rocky 9.7

Additional dependencies

Please see my project at https://github.com/cinnion/job-application-tracker

[Pierre-Sassoulas]

Thank you for opening the issue and for the detailed report !

[cinnion]

Thank you for opening the issue and for the detailed report !

Sure thing Pierre! I have multiple decades of experience knowing what a pain it is to not have sufficient information for reproducing a bug, and how nice it is when someone can tell you exactly how to do it. After a night of thinking about it, this may very well involve the order in which the directories are created.

Please feel free to reach out to me on Discord. Among other things, I have a question about 10968, and am wondering if there is perhaps a fix to that in the pipeline from something I am seeing in my testing.