Ruff configuration from pyproject.toml is ignored

Hi,

I'm trying to use the pre-commit hook for Ruff, but it ignores my settings from the pyproject.toml. I want Ruff to ignore the line-length but if I commit a file with lines that exceed this limit it is complaining about it. If I use a ruff.toml to configure Ruff it works as expected.

I use version 0.0.292.

My settings in .pre-commit-config.yaml:

# See https://pre-commit.com for more information
# See https://pre-commit.com/hooks.html for more hooks
repos:
-   repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v3.2.0
    hooks:
    -   id: end-of-file-fixer
    -   id: check-added-large-files
-   repo: https://github.com/charliermarsh/ruff-pre-commit
    rev: v0.0.292
    hooks:
    -   id: ruff

Ruff configuration part in my pyproject.toml (same is used in the ruff.toml)

[tool.ruff]
select = ["E"]

# Never enforce `E501` (line length violations).
ignore = ["E501"]

Hmm, a bit of a tough one to debug. When you switch between pyproject.toml and ruff.toml, are the files located in the same directory?

Yes they are in the same directory.

I tried it on another laptop with a small example project and this problem did not occur. I try to find a way to reproduce the problem and give you an update.

I could reproduce the problem and find a solution. If I use a project with already added code and a pyproject.toml to the git repo and then

add pre-commit to the virtual environment,
create a .pre-commit-config.yaml,
install the git hooks with pre-commit install
add the ruff configuration (ignore line length) to the pyproject.toml
try to only commit the python file that contains too long lines -> ruff complains about too long lines

When I first commit the .pre-commit-config.yaml and the pyproject.toml and after that commit the file with the long line then ruff ignores it as expected. Is this behavior expected?

same issue with v0.1.0 but committing the config doesn't change anything

found the issue : the configuration needs to be added in the toml and we need to select the rule to use even for line-length

repos:
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.1.0
    hooks:
      - id: ruff
        args: [--select=C901, --select=E501]

by default line-length is not checked, seems strange no ?

@klow68

@klow68 - We removed E501 from the default configuration in v0.1.0 (https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md#breaking-changes), so I think that's working as intended.

@beajifu

@beajifu I'm unable to reproduce with the steps mentioned although I'm using F401 as an example rule.

Gist: https://gist.github.com/dhruvmanila/8c796087330cb22699f3b20e929fde45

.
├── .pre-commit-config.yaml
├── pyproject.toml
└── test.py

Steps

Install pre-commit and hooks
Comment out the ignore in config file

$ pre-commit run
ruff.....................................................................Failed
- hook id: ruff
- exit code: 1

test.py:1:8: F401 [*] `os` imported but unused
Found 1 error.
[*] 1 potentially fixable with the --fix option.

Uncomment the ignore in config file

$ pre-commit run
ruff.....................................................................Passed

My configuration in pyproject.toml also seems to be having an issue.

Running ruff without any config: 3 errors

Running ruff with 3 select = ["ALL"] in pyproject.toml: 389 errors

Running ruff through pre-commit: 89 errors.

It seems like running ruff through pre-commit is using more rules than default but ignoring the rules in pyproject.toml

Chiming in just in case it may help someone. In my case, clearing the precommit cache ($HOME/.cache/pre-commit/) fixed a similarly sounding issue some time ago. Alas, I didn't keep the cache so I couldn't debug it further.

This still seems to be an issue; using v0.1.7

Would really appreciate if you could share some more information -- we weren't able to reproduce it above and it doesn't seem to be a common issue, so we need some help. What behavior are you seeing? What commands are you running? How is your project structured? Have you tried clearing the cache, as above? Thank you in advance!

@charliermarsh

It seems I have more than one project reliably producing this bug (even after clearing caches), and I constructed a new project as a minimal example for @charliermarsh to reproduce the bug reliably. The new project I made ended up reading the pyproject.toml correctly, and I checked by causing N999: Invalid module name and then ignoring the rule: ignore = ["N999"] on a separate run. The bugged and new project that I compared both use ruff-pre-commit v0.1.7 and were invoked the same way. I don't think it's related to the version, but if I spend some more time I can isolate the issue.

[tool.ruff]
select = ["E"]

# Never enforce `E501` (line length violations).
ignore = ["E501"]

don't these go in tool.ruff.lint?

@rafalkrupinski

@rafalkrupinski I double checked docs, and you're right. I have been busy with other tasks, but I saved this thread for later. I'll retest, and repost.

@caerulescens - Both are accepted right now -- putting ignore under [tool.ruff] and [tool.ruff.lint] are interchangeable. (We're moving towards the latter, but they both work as-is.)

I realized the same thing just now; I'll retest

I have the same problem that ruff-pre-commit does not load ruff config from pyproject.toml.

I resolved it by adding the config in the args.

  - repo: https://github.com/astral-sh/ruff-pre-commit
    # Ruff version.
    rev: v0.4.3
    hooks:
      # Run the linter.
      - id: ruff
        args: ["--select", "E,W,F,I,C,B,UP", "--ignore", "E203,B008,C901"]
      # Run the formatter.
      - id: ruff-format

Same here, but more explicitly for the --exclude config which is not accounted for

I had the same problem and I fixed it with this config, passing the config file to the args explicitly.

repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
  # Ruff version.
  rev: v0.4.5
  hooks:
    # Run the linter.
    - id: ruff
      args: [ --fix, --config=pyproject.toml ]
    # Run the formatter.
    - id: ruff-format

If you think your config is ignored. Add --verbose to the pre-commit hook.

- repo: https://github.com/astral-sh/ruff-pre-commit
  # Ruff: Formatter and Linter.
  rev: v0.5.1
  hooks:
    - id: ruff-format
      args: [--verbose, ]
    - id: ruff
      args: [--verbose, --fix,]

Then you can run pre-commit run --verbose --all-files

The output for me is:

ruff-format..............................................................Passed
- hook id: ruff-format
- duration: 0.08s

[ruff::resolve][DEBUG] Using configuration file (via parent) at: SOMEPATH/pyproject_template\pyproject.toml

I upgraded from 0.4.5 to 0.5.1, and Ruff detects pyproject.toml automatically.

# See https://pre-commit.com for more information
default_language_version:
  python: python3.12
repos:
  - repo: https://github.com/astral-sh/ruff-pre-commit
    # Ruff version.
    rev: v0.5.1
    hooks:
      # Run the linter.
      - id: ruff
        args: [--fix]
      # Run the formatter.
      - id: ruff-format

It works now for me too, but one thing I stumbled upon was when updating some ruff rules or exceptions and not commiting them with the python files (for whatever reason), the hook uses the last commited version of pyproject.toml, which does not have the new rule (or exclusion) and thus produces other results when calling ruff check from console.

@Blumenkind111

It works now for me too, but one thing I stumbled upon was when updating some ruff rules or exceptions and not commiting them with the python files (for whatever reason), the hook uses the last commited version of pyproject.toml, which does not have the new rule (or exclusion) and thus produces other results when calling ruff check from console.

@Blumenkind111 This is expected behavior of pre-commit. Pre-Commit Issue #818

I'm currently also running into this.

My issue was that the exclude setting to ignore some folders was under the [tool.ruff.lint] section. Following the comment below made me think that was the correct location:

@caerulescens - Both are accepted right now -- putting ignore under [tool.ruff] and [tool.ruff.lint] are interchangeable. (We're moving towards the latter, but they both work as-is.)

Moving it back to [tool.ruff] fixed it.

In case that might help someone. In my case I noticed that the pyproject.toml was read (syntax errors there were found by ruff) but that ignore directives were... ignored. I found that was because I was using a --select directive in the .pre-commit-config.yaml file. For some reason this seems to reset the options put in the pyproject.toml. (This might be a feature so as to enforce some checks but I am unaware of a documentation supporting that.)

In order to be able to have ignore rules defined in one or multiple pyproject.toml I had to move select directives from the .pre-commit-config.yaml to those files.

@tazr

@tazr For that, I believe you should use --extend-select instead of --select

I'm still having this issue. This bug was also present in pydocstring (now deprecated). Is there a relation?

I'm running into this issue as well.

In pyproject.toml I specify that the alembic folder should be exluded:

[tool.ruff]
line-length = 120
extend-exclude = ["alembic"]

[tool.ruff.lint]
select=["E4", "E7", "E9", "F", "INP001", "I"]

[tool.ruff.format]
quote-style = "preserve"

This works as it should when invoking ruff 0.11.5 directly.

But when trying to commit with this pre-commit 4.2.0 config:

repos:
  - repo: local
    hooks:
      - id: ruff-check
        name: ruff-check
        entry: uv run ruff check --fix
        language: system
        types: [python]
        stages: [pre-commit]
      - id: ruff-format
        name: ruff-format
        entry: uv run ruff format
        language: system
        types: [python]
        stages: [pre-commit]

the pyproject.toml setting extend-exclude is ignored and ruff starts to mess with the alembic folder:

(backend-fastapi) (base) cdeil@Kryvoff-MBP backend_fastapi_5 % git status
On branch alembic-update-autogenerate
Your branch is up to date with 'origin/alembic-update-autogenerate'.

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
        modified:   alembic/versions/2024_04_29_1554-822ce1de1694_add_transport_task.py
        modified:   alembic/versions/2024_05_07_1151-c59bcfee52df_add_default_address_to_groups.py
        modified:   alembic/versions/2024_05_08_1313-92fe12293446_move_container_to_transaction_list.py
        modified:   alembic/versions/2024_06_23_1305-a7f232338b89_introduce_virtual_containers.py

(backend-fastapi) (base) cdeil@Kryvoff-MBP backend_fastapi_5 % git commit -m 'Fix declarative_base imports in alembic'         
ruff-check...............................................................Failed
- hook id: ruff-check
- exit code: 1
- files were modified by this hook

alembic/versions/2024_04_29_1554-822ce1de1694_add_transport_task.py:1:1: INP001 File `alembic/versions/2024_04_29_1554-822ce1de1694_add_transport_task.py` is part of an implicit namespace package. Add an `__init__.py`.
alembic/versions/2024_05_07_1151-c59bcfee52df_add_default_address_to_groups.py:1:1: INP001 File `alembic/versions/2024_05_07_1151-c59bcfee52df_add_default_address_to_groups.py` is part of an implicit namespace package. Add an `__init__.py`.
alembic/versions/2024_05_08_1313-92fe12293446_move_container_to_transaction_list.py:1:1: INP001 File `alembic/versions/2024_05_08_1313-92fe12293446_move_container_to_transaction_list.py` is part of an implicit namespace package. Add an `__init__.py`.
alembic/versions/2024_06_23_1305-a7f232338b89_introduce_virtual_containers.py:1:1: INP001 File `alembic/versions/2024_06_23_1305-a7f232338b89_introduce_virtual_containers.py` is part of an implicit namespace package. Add an `__init__.py`.
Found 5 errors (1 fixed, 4 remaining).

ruff-format..............................................................Failed
- hook id: ruff-format
- files were modified by this hook

2 files reformatted, 2 files left unchanged

Can one of the ruff maintainers reproduce?

OK, so adding pass_filenames: false in .pre-commit-config.yaml fixed the issue and the commit worked. I had missed that suggestion in a comment above.

Suggestion: at https://docs.astral.sh/ruff/integrations/#pre-commit please also document how to work with the repo: local option. I would prefer to use the existing ruff I already have installed with uv add --dev ruff and then installed and locked to given version by uv. I think the recommended repo: https://github.com/astral-sh/ruff-pre-commit way will create yet another venv and install and will make it harder to maintain consistent version local & CI because it doesn't use uv.lock?

The solution for me was git adding the updated .pre-commit-config.yaml. Someone told me that a cached (outdated) version of the file might be used before adding it. This solved the issue for me.

I ran into this same problem on a new project. Turns out that I just needed to git add (stage) all the relevant files. The hooks don't seem to be aware of files that are unstaged.

I was getting ruff check...............................................................Passed, but after staging all my files it worked as expected.

git add .
git commit -m 'build: testing hooks'
# commit failed due to my configured rules in .ruff.toml

I tied staging just my pyproject.toml file, and that didn't help.

Next, I broke my config out into a separate .ruff.toml file, but that didn't help (note, i never tried staging that file).

Finally I just tried git add . and then things worked as expected. So I'm not sure if it was staging the .ruff.toml file, or some other files. This was a brand new project.

Hope this helps someone!

I am having a similar issue, where the pre-commit ignores the

[tool.ruff]
fix = true

configuration in my pyproject.toml file. Using the CLI, it works fine, but pre-commit seems to ignore it.

Navigation Menu

Repository navigation

Ruff configuration from pyproject.toml is ignored #54

Steps

15 remaining items

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Ruff configuration from pyproject.toml is ignored #54

Description

Activity

charliermarsh commented on Oct 13, 2023

beajifu commented on Oct 14, 2023

beajifu commented on Oct 15, 2023

klow68 commented on Oct 19, 2023

charliermarsh commented on Oct 19, 2023

dhruvmanila commented on Oct 30, 2023

Steps

rpop0 commented on Nov 21, 2023

rytilahti commented on Nov 21, 2023

andylinzie commented on Jan 12, 2024

charliermarsh commented on Jan 12, 2024

andylinzie commented on Jan 12, 2024

rafalkrupinski commented on Jan 26, 2024

andylinzie commented on Jan 27, 2024

charliermarsh commented on Jan 27, 2024

andylinzie commented on Jan 27, 2024

15 remaining items

mazzma12 commented on May 7, 2024

artefactop commented on Jun 23, 2024

NIvo172 commented on Jul 12, 2024

ezeparziale commented on Jul 14, 2024

Blumenkind111 commented on Jul 31, 2024

NIvo172 commented on Aug 1, 2024

exhuma commented on Oct 10, 2024

tazr commented on Oct 22, 2024

denes44 commented on Nov 9, 2024

MatthijsdeJ commented on Apr 15, 2025

cdeil commented on Apr 30, 2025

cdeil commented on Apr 30, 2025

MatthijsdeJ commented on May 1, 2025

craigulliott commented on Aug 26, 2025

samcorky commented on Dec 14, 2025

Metadata

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Issue actions