Bump version to 0.0.94

.github/workflows/ci.yaml

@@ -27,7 +27,7 @@ jobs:
             ${{ runner.os }}-build-${{ env.cache-name }}-
             ${{ runner.os }}-build-
             ${{ runner.os }}-
-      - run: cargo build --release
+      - run: cargo build --all --release
 
   cargo_fmt:
     name: "cargo fmt"
@@ -49,7 +49,7 @@ jobs:
             ${{ runner.os }}-build-${{ env.cache-name }}-
             ${{ runner.os }}-build-
             ${{ runner.os }}-
-      - run: cargo fmt --check
+      - run: cargo fmt --all --check
 
   cargo_clippy:
     name: "cargo clippy"
@@ -71,7 +71,7 @@ jobs:
             ${{ runner.os }}-build-${{ env.cache-name }}-
             ${{ runner.os }}-build-
             ${{ runner.os }}-
-      - run: cargo clippy -- -D warnings
+      - run: cargo clippy --all -- -D warnings
 
   cargo_test:
     name: "cargo test"
@@ -93,7 +93,7 @@ jobs:
             ${{ runner.os }}-build-${{ env.cache-name }}-
             ${{ runner.os }}-build-
             ${{ runner.os }}-
-      - run: cargo test
+      - run: cargo test --all
 
   maturin_build:
     name: "maturin build"

.github/workflows/flake8-to-ruff.yaml

@@ -0,0 +1,298 @@
+name: "[flake8-to-ruff] Release"
+
+on: workflow_dispatch
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  PACKAGE_NAME: flake8-to-ruff
+  CRATE_NAME: flake8_to_ruff
+  PYTHON_VERSION: "3.7" # to build abi3 wheels
+
+jobs:
+  macos-x86_64:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          architecture: x64
+      - name: Install Rust toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          profile: minimal
+          default: true
+      - name: Build wheels - x86_64
+        uses: messense/maturin-action@v1
+        with:
+          target: x86_64
+          args: --release --out dist --sdist -m ./crates/${{ env.CRATE_NAME }}/Cargo.toml
+          maturin-version: "v0.13.0"
+      - name: Install built wheel - x86_64
+        run: |
+          pip install dist/${{ env.CRATE_NAME }}-*.whl --force-reinstall
+      - name: Upload wheels
+        uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: dist
+  macos-universal:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          architecture: x64
+      - name: Install Rust toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          profile: minimal
+          default: true
+      - name: Build wheels - universal2
+        uses: messense/maturin-action@v1
+        with:
+          args: --release --universal2 --out dist -m ./crates/${{ env.CRATE_NAME }}/Cargo.toml
+          maturin-version: "v0.13.0"
+      - name: Install built wheel - universal2
+        run: |
+          pip install dist/${{ env.CRATE_NAME }}-*universal2.whl --force-reinstall
+      - name: Upload wheels
+        uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: dist
+
+  windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        target: [x64, x86]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          architecture: ${{ matrix.target }}
+      - name: Install Rust toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          profile: minimal
+          default: true
+      - name: Build wheels
+        uses: messense/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist -m ./crates/${{ env.CRATE_NAME }}/Cargo.toml
+          maturin-version: "v0.13.0"
+      - name: Install built wheel
+        shell: bash
+        run: |
+          python -m pip install dist/${{ env.CRATE_NAME }}-*.whl --force-reinstall
+      - name: Upload wheels
+        uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: dist
+
+  linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        target: [x86_64, i686]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          architecture: x64
+      - name: Build wheels
+        uses: messense/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          manylinux: auto
+          args: --release --out dist -m ./crates/${{ env.CRATE_NAME }}/Cargo.toml
+          maturin-version: "v0.13.0"
+      - name: Install built wheel
+        if: matrix.target == 'x86_64'
+        run: |
+          pip install dist/${{ env.CRATE_NAME }}-*.whl --force-reinstall
+      - name: Upload wheels
+        uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: dist
+
+  linux-cross:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        target: [aarch64, armv7, s390x, ppc64le, ppc64]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Build wheels
+        uses: messense/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          manylinux: auto
+          args: --no-default-features --release --out dist -m ./crates/${{ env.CRATE_NAME }}/Cargo.toml
+          maturin-version: "v0.13.0"
+      - uses: uraimo/run-on-arch-action@v2.0.5
+        if: matrix.target != 'ppc64'
+        name: Install built wheel
+        with:
+          arch: ${{ matrix.target }}
+          distro: ubuntu20.04
+          githubToken: ${{ github.token }}
+          install: |
+            apt-get update
+            apt-get install -y --no-install-recommends python3 python3-pip
+            pip3 install -U pip
+          run: |
+            pip3 install ${{ env.PACKAGE_NAME }} --no-index --find-links dist/ --force-reinstall
+      - name: Upload wheels
+        uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: dist
+
+  musllinux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        target:
+          - x86_64-unknown-linux-musl
+          - i686-unknown-linux-musl
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          architecture: x64
+      - name: Build wheels
+        uses: messense/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          manylinux: musllinux_1_2
+          args: --release --out dist -m ./crates/${{ env.CRATE_NAME }}/Cargo.toml
+          maturin-version: "v0.13.0"
+      - name: Install built wheel
+        if: matrix.target == 'x86_64-unknown-linux-musl'
+        uses: addnab/docker-run-action@v3
+        with:
+          image: alpine:latest
+          options: -v ${{ github.workspace }}:/io -w /io
+          run: |
+            apk add py3-pip
+            pip3 install ${{ env.PACKAGE_NAME }} --no-index --find-links /io/dist/ --force-reinstall
+      - name: Upload wheels
+        uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: dist
+
+  musllinux-cross:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        platform:
+          - target: aarch64-unknown-linux-musl
+            arch: aarch64
+          - target: armv7-unknown-linux-musleabihf
+            arch: armv7
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Build wheels
+        uses: messense/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          manylinux: musllinux_1_2
+          args: --release --out dist -m ./crates/${{ env.CRATE_NAME }}/Cargo.toml
+          maturin-version: "v0.13.0"
+      - uses: uraimo/run-on-arch-action@master
+        name: Install built wheel
+        with:
+          arch: ${{ matrix.platform.arch }}
+          distro: alpine_latest
+          githubToken: ${{ github.token }}
+          install: |
+            apk add py3-pip
+          run: |
+            pip3 install ${{ env.PACKAGE_NAME }} --no-index --find-links dist/ --force-reinstall
+      - name: Upload wheels
+        uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: dist
+
+  pypy:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        target: [x86_64, aarch64]
+        python-version:
+          - "3.7"
+          - "3.8"
+          - "3.9"
+        exclude:
+          - os: macos-latest
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: pypy${{ matrix.python-version }}
+      - name: Build wheels
+        uses: messense/maturin-action@v1
+        with:
+          maturin-version: "v0.13.0"
+          target: ${{ matrix.target }}
+          manylinux: auto
+          args: --release --out dist -i pypy${{ matrix.python-version }} -m ./crates/${{ env.CRATE_NAME }}/Cargo.toml
+      - name: Install built wheel
+        if: matrix.target == 'x86_64'
+        run: |
+          pip install dist/${{ env.CRATE_NAME }}-*.whl --force-reinstall
+      - name: Upload wheels
+        uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    needs:
+      - macos-universal
+      - macos-x86_64
+      - windows
+      - linux
+      - linux-cross
+      - musllinux
+      - musllinux-cross
+      - pypy
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: wheels
+      - uses: actions/setup-python@v4
+      - name: Publish to PyPi
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.FLAKE8_TO_RUFF_TOKEN }}
+        run: |
+          pip install --upgrade twine
+          twine upload --skip-existing *

.github/workflows/ruff.yaml

@@ -1,8 +1,6 @@
-name: Release
+name: "[ruff] Release"
 
 on:
-  pull_request:
-    branches: [main]
   create:
     tags:
       - v*
@@ -297,7 +295,7 @@ jobs:
       - name: Publish to PyPi
         env:
           TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+          TWINE_PASSWORD: ${{ secrets.RUFF_TOKEN }}
         run: |
           pip install --upgrade twine
           twine upload --skip-existing *

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.93
+    rev: v0.0.94
     hooks:
       - id: ruff
 

Cargo.lock

@@ -571,6 +571,12 @@ dependencies = [
  "cache-padded",
 ]
 
+[[package]]
+name = "configparser"
+version = "3.0.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5458d9d1a587efaf5091602c59d299696a3877a439c8f6d461a2d3cce11df87a"
+
 [[package]]
 name = "console"
 version = "0.15.2"
@@ -912,6 +918,21 @@ version = "0.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80"
 
+[[package]]
+name = "flake8-to-ruff"
+version = "0.0.94-dev.0"
+dependencies = [
+ "anyhow",
+ "clap 4.0.15",
+ "configparser",
+ "once_cell",
+ "regex",
+ "ruff",
+ "serde",
+ "serde_json",
+ "toml",
+]
+
 [[package]]
 name = "flate2"
 version = "1.0.24"
@@ -2190,7 +2211,7 @@ dependencies = [
 
 [[package]]
 name = "ruff"
-version = "0.0.93"
+version = "0.0.94"
 dependencies = [
  "anyhow",
  "assert_cmd",

Cargo.toml

@@ -1,6 +1,11 @@
+[workspace]
+members = [
+  "crates/flake8_to_ruff",
+]
+
 [package]
 name = "ruff"
-version = "0.0.93"
+version = "0.0.94"
 edition = "2021"
 
 [lib]

README.md

@@ -89,7 +89,7 @@ Ruff also works with [pre-commit](https://pre-commit.com):
 ```yaml
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.93
+    rev: v0.0.94
     hooks:
       - id: ruff
 ```

crates/flake8_to_ruff/Cargo.toml

@@ -0,0 +1,22 @@
+[package]
+name = "flake8-to-ruff"
+version = "0.0.94-dev.0"
+edition = "2021"
+
+[lib]
+name = "flake8_to_ruff"
+
+[dependencies]
+anyhow = { version = "1.0.60" }
+clap = { version = "4.0.1", features = ["derive"] }
+configparser = { version = "3.0.2" }
+once_cell = { version = "1.13.1" }
+regex = { version = "1.6.0" }
+ruff = { path = "../..", default-features = false }
+serde = { version = "1.0.143", features = ["derive"] }
+serde_json = { version = "1.0.83" }
+toml = { version = "0.5.9" }
+
+[dev-dependencies]
+
+[features]

crates/flake8_to_ruff/README.md

@@ -0,0 +1,47 @@
+# flake8-to-ruff
+
+Convert existing Flake8 configuration files (`setup.cfg`, `tox.ini`, or `.flake8`) for use with
+[Ruff](https://github.com/charliermarsh/ruff).
+
+Generates a Ruff-compatible `pyproject.toml` section.
+
+## Installation and Usage
+
+### Installation
+
+Available as [`flake8-to-ruff`](https://pypi.org/project/flake8-to-ruff/) on PyPI:
+
+```shell
+pip install flake8-to-ruff
+```
+
+### Usage
+
+To run Ruff, try any of the following:
+
+```shell
+flake8-to-ruff path/to/setup.cfg
+flake8-to-ruff path/to/tox.ini
+flake8-to-ruff path/to/.flake8
+```
+
+## Limitations
+
+1. Ruff only supports a subset of the Flake configuration options. `flake8-to-ruff` will warn on and
+   ignore unsupported options in the `.flake8` file (or equivalent). (Similarly, Ruff has a few
+   configuration options that don't exist in Flake8.)
+2. Ruff will omit any error codes that are unimplemented or unsupported by Ruff, including error
+   codes from unsupported plugins. (See the [Ruff README](https://github.com/charliermarsh/ruff#user-content-how-does-ruff-compare-to-flake8)
+   for the complete list of supported plugins.)
+3. `flake8-to-ruff` does not auto-detect your Flake8 plugins, so any reliance on Flake8 plugins that
+   implicitly enable third-party checks will be ignored. Instead, add those error codes to your
+   `select` or `extend-select` fields, so that `flake8-to-ruff` can pick them up.
+
+## License
+
+MIT
+
+## Contributing
+
+Contributions are welcome and hugely appreciated. To get started, check out the
+[contributing guidelines](https://github.com/charliermarsh/ruff/blob/main/CONTRIBUTING.md).

crates/flake8_to_ruff/pyproject.toml

@@ -0,0 +1,33 @@
+[project]
+name = "flake8-to-ruff"
+keywords = ["automation", "flake8", "pycodestyle", "pyflakes", "pylint", "clippy"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Software Development :: Quality Assurance",
+]
+author = "Charlie Marsh"
+author_email = "charlie.r.marsh@gmail.com"
+description = "Convert existing Flake8 configuration to Ruff."
+requires-python = ">=3.7"
+
+[project.urls]
+repository = "https://github.com/charliermarsh/ruff#subdirectory=crates/flake8_to_ruff"
+
+[build-system]
+requires = ["maturin>=0.13,<0.14"]
+build-backend = "maturin"
+
+[tool.maturin]
+bindings = "bin"
+strip = true

crates/flake8_to_ruff/src/converter.rs

@@ -0,0 +1,59 @@
+use std::collections::HashMap;
+
+use anyhow::Result;
+
+use ruff::settings::options::Options;
+use ruff::settings::pyproject::Pyproject;
+
+use crate::parser;
+
+pub fn convert(config: HashMap<String, HashMap<String, Option<String>>>) -> Result<Pyproject> {
+    // Extract the Flake8 section.
+    let flake8 = config
+        .get("flake8")
+        .expect("Unable to find flake8 section in INI file.");
+
+    // Parse each supported option.
+    let mut options: Options = Default::default();
+    for (key, value) in flake8 {
+        if let Some(value) = value {
+            match key.as_str() {
+                "line-length" | "line_length" => match value.clone().parse::<usize>() {
+                    Ok(line_length) => options.line_length = Some(line_length),
+                    Err(e) => eprintln!("Unable to parse '{key}' property: {e}"),
+                },
+                "select" => {
+                    options.select = Some(parser::parse_prefix_codes(value.as_ref()));
+                }
+                "extend-select" | "extend_select" => {
+                    options.extend_select = Some(parser::parse_prefix_codes(value.as_ref()));
+                }
+                "ignore" => {
+                    options.ignore = Some(parser::parse_prefix_codes(value.as_ref()));
+                }
+                "extend-ignore" | "extend_ignore" => {
+                    options.extend_ignore = Some(parser::parse_prefix_codes(value.as_ref()));
+                }
+                "exclude" => {
+                    options.exclude = Some(parser::parse_strings(value.as_ref()));
+                }
+                "extend-exclude" | "extend_exclude" => {
+                    options.extend_exclude = Some(parser::parse_strings(value.as_ref()));
+                }
+                "per-file-ignores" | "per_file_ignores" => {
+                    match parser::parse_files_to_codes_mapping(value.as_ref()) {
+                        Ok(per_file_ignores) => {
+                            options.per_file_ignores =
+                                Some(parser::collect_per_file_ignores(per_file_ignores))
+                        }
+                        Err(e) => eprintln!("Unable to parse '{key}' property: {e}"),
+                    }
+                }
+                _ => eprintln!("Skipping unsupported property: {key}"),
+            }
+        }
+    }
+
+    // Create the pyproject.toml.
+    Ok(Pyproject::new(options))
+}

crates/flake8_to_ruff/src/lib.rs

@@ -0,0 +1,4 @@
+#![allow(clippy::collapsible_if, clippy::collapsible_else_if)]
+
+pub mod converter;
+mod parser;

crates/flake8_to_ruff/src/main.rs

@@ -0,0 +1,35 @@
+//! Utility to generate Ruff's pyproject.toml section from a Flake8 INI file.
+
+use std::path::PathBuf;
+
+use anyhow::Result;
+use clap::Parser;
+use configparser::ini::Ini;
+
+use flake8_to_ruff::converter;
+
+#[derive(Parser)]
+#[command(
+    about = "Convert existing Flake8 configuration to Ruff.",
+    long_about = None
+)]
+struct Cli {
+    /// Path to the Flake8 configuration file (e.g., 'setup.cfg', 'tox.ini', or '.flake8').
+    #[arg(required = true)]
+    file: PathBuf,
+}
+
+fn main() -> Result<()> {
+    let cli = Cli::parse();
+
+    // Read the INI file.
+    let mut ini = Ini::new_cs();
+    ini.set_multiline(true);
+    let config = ini.load(cli.file).map_err(|msg| anyhow::anyhow!(msg))?;
+
+    // Create the pyproject.toml.
+    let pyproject = converter::convert(config)?;
+    println!("{}", toml::to_string_pretty(&pyproject)?);
+
+    Ok(())
+}

crates/flake8_to_ruff/src/parser.rs

@@ -0,0 +1,374 @@
+use std::collections::BTreeMap;
+use std::str::FromStr;
+
+use anyhow::Result;
+use once_cell::sync::Lazy;
+use regex::Regex;
+
+use ruff::checks_gen::CheckCodePrefix;
+use ruff::settings::types::PatternPrefixPair;
+
+static COMMA_SEPARATED_LIST_RE: Lazy<Regex> = Lazy::new(|| Regex::new(r"[,\s]").unwrap());
+
+/// Parse a comma-separated list of `CheckCodePrefix` values (e.g., "F401,E501").
+pub fn parse_prefix_codes(value: &str) -> Vec<CheckCodePrefix> {
+    let mut codes: Vec<CheckCodePrefix> = vec![];
+    for code in COMMA_SEPARATED_LIST_RE.split(value) {
+        let code = code.trim();
+        if code.is_empty() {
+            continue;
+        }
+        if let Ok(code) = CheckCodePrefix::from_str(code) {
+            codes.push(code);
+        } else {
+            eprintln!("Unsupported prefix code: {code}");
+        }
+    }
+    codes
+}
+
+/// Parse a comma-separated list of strings (e.g., "__init__.py,__main__.py").
+pub fn parse_strings(value: &str) -> Vec<String> {
+    COMMA_SEPARATED_LIST_RE
+        .split(value)
+        .map(|part| part.trim())
+        .filter(|part| !part.is_empty())
+        .map(String::from)
+        .collect()
+}
+
+#[derive(Debug)]
+struct Token {
+    token_name: TokenType,
+    src: String,
+}
+
+#[derive(Debug)]
+enum TokenType {
+    Code,
+    File,
+    Colon,
+    Comma,
+    Ws,
+    Eof,
+}
+
+struct State {
+    seen_sep: bool,
+    seen_colon: bool,
+    filenames: Vec<String>,
+    codes: Vec<String>,
+}
+
+impl State {
+    fn new() -> Self {
+        Self {
+            seen_sep: true,
+            seen_colon: false,
+            filenames: vec![],
+            codes: vec![],
+        }
+    }
+
+    /// Generate the list of `StrCheckCodePair` pairs for the current state.
+    fn parse(&self) -> Vec<PatternPrefixPair> {
+        let mut codes: Vec<PatternPrefixPair> = vec![];
+        for code in &self.codes {
+            match CheckCodePrefix::from_str(code) {
+                Ok(code) => {
+                    for filename in &self.filenames {
+                        codes.push(PatternPrefixPair {
+                            pattern: filename.clone(),
+                            prefix: code.clone(),
+                        });
+                    }
+                }
+                Err(_) => eprintln!("Skipping unrecognized prefix: {}", code),
+            }
+        }
+        codes
+    }
+}
+
+/// Tokenize the raw 'files-to-codes' mapping.
+fn tokenize_files_to_codes_mapping(value: &str) -> Vec<Token> {
+    let mut tokens = vec![];
+    let mut i = 0;
+    while i < value.len() {
+        for (token_re, token_name) in [
+            (
+                Regex::new(r"([A-Z]+[0-9]*)(?:$|\s|,)").unwrap(),
+                TokenType::Code,
+            ),
+            (Regex::new(r"([^\s:,]+)").unwrap(), TokenType::File),
+            (Regex::new(r"(\s*:\s*)").unwrap(), TokenType::Colon),
+            (Regex::new(r"(\s*,\s*)").unwrap(), TokenType::Comma),
+            (Regex::new(r"(\s+)").unwrap(), TokenType::Ws),
+        ] {
+            if let Some(cap) = token_re.captures(&value[i..]) {
+                let mat = cap.get(1).unwrap();
+                if mat.start() == 0 {
+                    tokens.push(Token {
+                        token_name,
+                        src: mat.as_str().to_string().trim().to_string(),
+                    });
+                    i += mat.end();
+                    break;
+                }
+            }
+        }
+    }
+    tokens.push(Token {
+        token_name: TokenType::Eof,
+        src: "".to_string(),
+    });
+    tokens
+}
+
+/// Parse a 'files-to-codes' mapping, mimicking Flake8's internal logic.
+///
+/// See: https://github.com/PyCQA/flake8/blob/7dfe99616fc2f07c0017df2ba5fa884158f3ea8a/src/flake8/utils.py#L45
+pub fn parse_files_to_codes_mapping(value: &str) -> Result<Vec<PatternPrefixPair>> {
+    if value.trim().is_empty() {
+        return Ok(vec![]);
+    }
+    let mut codes: Vec<PatternPrefixPair> = vec![];
+    let mut state = State::new();
+    for token in tokenize_files_to_codes_mapping(value) {
+        if matches!(token.token_name, TokenType::Comma | TokenType::Ws) {
+            state.seen_sep = true;
+        } else if !state.seen_colon {
+            if matches!(token.token_name, TokenType::Colon) {
+                state.seen_colon = true;
+                state.seen_sep = true;
+            } else if state.seen_sep && matches!(token.token_name, TokenType::File) {
+                state.filenames.push(token.src);
+                state.seen_sep = false;
+            } else {
+                return Err(anyhow::anyhow!("Unexpected token: {:?}", token.token_name));
+            }
+        } else {
+            if matches!(token.token_name, TokenType::Eof) {
+                codes.extend(state.parse());
+                state = State::new();
+            } else if state.seen_sep && matches!(token.token_name, TokenType::Code) {
+                state.codes.push(token.src);
+                state.seen_sep = false;
+            } else if state.seen_sep && matches!(token.token_name, TokenType::File) {
+                codes.extend(state.parse());
+                state = State::new();
+                state.filenames.push(token.src);
+                state.seen_sep = false;
+            } else {
+                return Err(anyhow::anyhow!("Unexpected token: {:?}", token.token_name));
+            }
+        }
+    }
+    Ok(codes)
+}
+
+/// Collect a list of `PatternPrefixPair` structs as a `BTreeMap`.
+pub fn collect_per_file_ignores(
+    pairs: Vec<PatternPrefixPair>,
+) -> BTreeMap<String, Vec<CheckCodePrefix>> {
+    let mut per_file_ignores: BTreeMap<String, Vec<CheckCodePrefix>> = BTreeMap::new();
+    for pair in pairs {
+        per_file_ignores
+            .entry(pair.pattern)
+            .or_insert_with(Vec::new)
+            .push(pair.prefix);
+    }
+    per_file_ignores
+}
+
+#[cfg(test)]
+mod tests {
+    use anyhow::Result;
+
+    use ruff::checks_gen::CheckCodePrefix;
+    use ruff::settings::types::PatternPrefixPair;
+
+    use crate::parser::{parse_files_to_codes_mapping, parse_prefix_codes, parse_strings};
+
+    #[test]
+    fn it_parses_prefix_codes() {
+        let actual = parse_prefix_codes("");
+        let expected: Vec<CheckCodePrefix> = vec![];
+        assert_eq!(actual, expected);
+
+        let actual = parse_prefix_codes(" ");
+        let expected: Vec<CheckCodePrefix> = vec![];
+        assert_eq!(actual, expected);
+
+        let actual = parse_prefix_codes("F401");
+        let expected = vec![CheckCodePrefix::F401];
+        assert_eq!(actual, expected);
+
+        let actual = parse_prefix_codes("F401,");
+        let expected = vec![CheckCodePrefix::F401];
+        assert_eq!(actual, expected);
+
+        let actual = parse_prefix_codes("F401,E501");
+        let expected = vec![CheckCodePrefix::F401, CheckCodePrefix::E501];
+        assert_eq!(actual, expected);
+
+        let actual = parse_prefix_codes("F401, E501");
+        let expected = vec![CheckCodePrefix::F401, CheckCodePrefix::E501];
+        assert_eq!(actual, expected);
+    }
+
+    #[test]
+    fn it_parses_strings() {
+        let actual = parse_strings("");
+        let expected: Vec<String> = vec![];
+        assert_eq!(actual, expected);
+
+        let actual = parse_strings(" ");
+        let expected: Vec<String> = vec![];
+        assert_eq!(actual, expected);
+
+        let actual = parse_strings("__init__.py");
+        let expected = vec!["__init__.py".to_string()];
+        assert_eq!(actual, expected);
+
+        let actual = parse_strings("__init__.py,");
+        let expected = vec!["__init__.py".to_string()];
+        assert_eq!(actual, expected);
+
+        let actual = parse_strings("__init__.py,__main__.py");
+        let expected = vec!["__init__.py".to_string(), "__main__.py".to_string()];
+        assert_eq!(actual, expected);
+
+        let actual = parse_strings("__init__.py, __main__.py");
+        let expected = vec!["__init__.py".to_string(), "__main__.py".to_string()];
+        assert_eq!(actual, expected);
+    }
+
+    #[test]
+    fn it_parse_files_to_codes_mapping() -> Result<()> {
+        let actual = parse_files_to_codes_mapping("")?;
+        let expected: Vec<PatternPrefixPair> = vec![];
+        assert_eq!(actual, expected);
+
+        let actual = parse_files_to_codes_mapping(" ")?;
+        let expected: Vec<PatternPrefixPair> = vec![];
+        assert_eq!(actual, expected);
+
+        // Ex) locust
+        let actual = parse_files_to_codes_mapping(
+            "per-file-ignores =
+    locust/test/*: F841
+    examples/*: F841
+    *.pyi: E302,E704"
+                .strip_prefix("per-file-ignores =")
+                .unwrap(),
+        )?;
+        let expected: Vec<PatternPrefixPair> = vec![
+            PatternPrefixPair {
+                pattern: "locust/test/*".to_string(),
+                prefix: CheckCodePrefix::F841,
+            },
+            PatternPrefixPair {
+                pattern: "examples/*".to_string(),
+                prefix: CheckCodePrefix::F841,
+            },
+        ];
+        assert_eq!(actual, expected);
+
+        // Ex) celery
+        let actual = parse_files_to_codes_mapping(
+            "per-file-ignores =
+   t/*,setup.py,examples/*,docs/*,extra/*:
+       D,"
+            .strip_prefix("per-file-ignores =")
+            .unwrap(),
+        )?;
+        let expected: Vec<PatternPrefixPair> = vec![
+            PatternPrefixPair {
+                pattern: "t/*".to_string(),
+                prefix: CheckCodePrefix::D,
+            },
+            PatternPrefixPair {
+                pattern: "setup.py".to_string(),
+                prefix: CheckCodePrefix::D,
+            },
+            PatternPrefixPair {
+                pattern: "examples/*".to_string(),
+                prefix: CheckCodePrefix::D,
+            },
+            PatternPrefixPair {
+                pattern: "docs/*".to_string(),
+                prefix: CheckCodePrefix::D,
+            },
+            PatternPrefixPair {
+                pattern: "extra/*".to_string(),
+                prefix: CheckCodePrefix::D,
+            },
+        ];
+        assert_eq!(actual, expected);
+
+        // Ex) scrapy
+        let actual = parse_files_to_codes_mapping(
+            "per-file-ignores =
+    scrapy/__init__.py:E402
+    scrapy/core/downloader/handlers/http.py:F401
+    scrapy/http/__init__.py:F401
+    scrapy/linkextractors/__init__.py:E402,F401
+    scrapy/selector/__init__.py:F401
+    scrapy/spiders/__init__.py:E402,F401
+    scrapy/utils/url.py:F403,F405
+    tests/test_loader.py:E741"
+                .strip_prefix("per-file-ignores =")
+                .unwrap(),
+        )?;
+        let expected: Vec<PatternPrefixPair> = vec![
+            PatternPrefixPair {
+                pattern: "scrapy/__init__.py".to_string(),
+                prefix: CheckCodePrefix::E402,
+            },
+            PatternPrefixPair {
+                pattern: "scrapy/core/downloader/handlers/http.py".to_string(),
+                prefix: CheckCodePrefix::F401,
+            },
+            PatternPrefixPair {
+                pattern: "scrapy/http/__init__.py".to_string(),
+                prefix: CheckCodePrefix::F401,
+            },
+            PatternPrefixPair {
+                pattern: "scrapy/linkextractors/__init__.py".to_string(),
+                prefix: CheckCodePrefix::E402,
+            },
+            PatternPrefixPair {
+                pattern: "scrapy/linkextractors/__init__.py".to_string(),
+                prefix: CheckCodePrefix::F401,
+            },
+            PatternPrefixPair {
+                pattern: "scrapy/selector/__init__.py".to_string(),
+                prefix: CheckCodePrefix::F401,
+            },
+            PatternPrefixPair {
+                pattern: "scrapy/spiders/__init__.py".to_string(),
+                prefix: CheckCodePrefix::E402,
+            },
+            PatternPrefixPair {
+                pattern: "scrapy/spiders/__init__.py".to_string(),
+                prefix: CheckCodePrefix::F401,
+            },
+            PatternPrefixPair {
+                pattern: "scrapy/utils/url.py".to_string(),
+                prefix: CheckCodePrefix::F403,
+            },
+            PatternPrefixPair {
+                pattern: "scrapy/utils/url.py".to_string(),
+                prefix: CheckCodePrefix::F405,
+            },
+            PatternPrefixPair {
+                pattern: "tests/test_loader.py".to_string(),
+                prefix: CheckCodePrefix::E741,
+            },
+        ];
+        assert_eq!(actual, expected);
+
+        Ok(())
+    }
+}

examples/generate_check_code_prefix.rs

@@ -96,7 +96,7 @@ fn main() {
 
     println!("//! File automatically generated by examples/generate_check_code_prefix.rs.");
     println!();
-    println!("use serde::{{Deserialize, Serialize}};");
+    println!("use serde::{{Serialize, Deserialize}};");
     println!("use strum_macros::EnumString;");
     println!();
     println!("use crate::checks::CheckCode;");

resources/test/fixtures/F821_1.py

@@ -0,0 +1,30 @@
+"""Test: typing module imports."""
+from foo import cast
+
+# OK
+x = cast("Model")
+
+from typing import cast
+
+
+# F821 Undefined name `Model`
+x = cast("Model", x)
+
+
+import typing
+
+
+# F821 Undefined name `Model`
+x = typing.cast("Model", x)
+
+
+from typing import Pattern
+
+# F821 Undefined name `Model`
+x = Pattern["Model"]
+
+
+from typing.re import Match
+
+# F821 Undefined name `Model`
+x = Match["Model"]

resources/test/fixtures/pyproject.toml

@@ -1,13 +1,11 @@
 [tool.ruff]
 line-length = 88
 extend-exclude = [
-    "excluded.py",
-    "migrations",
-    "directory/also_excluded.py",
-]
-per-file-ignores = [
-    "__init__.py:F401",
+  "excluded.py",
+  "migrations",
+  "directory/also_excluded.py",
 ]
+per-file-ignores = { "__init__.py" = ["F401"] }
 
 [tool.ruff.flake8-quotes]
 inline-quotes = "single"
@@ -17,22 +15,22 @@ avoid-escape = true
 
 [tool.ruff.pep8-naming]
 ignore-names = [
-    "setUp",
-    "tearDown",
-    "setUpClass",
-    "tearDownClass",
-    "setUpModule",
-    "tearDownModule",
-    "asyncSetUp",
-    "asyncTearDown",
-    "setUpTestData",
-    "failureException",
-    "longMessage",
-    "maxDiff",
+  "setUp",
+  "tearDown",
+  "setUpClass",
+  "tearDownClass",
+  "setUpModule",
+  "tearDownModule",
+  "asyncSetUp",
+  "asyncTearDown",
+  "setUpTestData",
+  "failureException",
+  "longMessage",
+  "maxDiff",
 ]
 classmethod-decorators = [
-    "classmethod",
+  "classmethod",
 ]
 staticmethod-decorators = [
-    "staticmethod",
+  "staticmethod",
 ]

src/ast/helpers.rs

@@ -1,9 +1,9 @@
+use std::collections::BTreeSet;
+
 use once_cell::sync::Lazy;
 use regex::Regex;
 use rustpython_ast::{Excepthandler, ExcepthandlerKind, Expr, ExprKind, Location, StmtKind};
 
-use crate::python::typing;
-
 fn compose_call_path_inner<'a>(expr: &'a Expr, parts: &mut Vec<&'a str>) {
     match &expr.node {
         ExprKind::Call { func, .. } => {
@@ -30,6 +30,7 @@ pub fn compose_call_path(expr: &Expr) -> Option<String> {
     }
 }
 
+/// Return `true` if the `Expr` is a name or attribute reference to `${target}`.
 pub fn match_name_or_attr(expr: &Expr, target: &str) -> bool {
     match &expr.node {
         ExprKind::Attribute { attr, .. } => target == attr,
@@ -38,32 +39,27 @@ pub fn match_name_or_attr(expr: &Expr, target: &str) -> bool {
     }
 }
 
-pub enum SubscriptKind {
-    AnnotatedSubscript,
-    PEP593AnnotatedSubscript,
-}
-
-pub fn match_annotated_subscript(expr: &Expr) -> Option<SubscriptKind> {
+/// Return `true` if the `Expr` is a reference to `${module}.${target}`.
+///
+/// Useful for, e.g., ensuring that a `Union` reference represents `typing.Union`.
+pub fn match_name_or_attr_from_module(
+    expr: &Expr,
+    target: &str,
+    module: &str,
+    imports: Option<&BTreeSet<&str>>,
+) -> bool {
     match &expr.node {
-        ExprKind::Attribute { attr, .. } => {
-            if typing::is_annotated_subscript(attr) {
-                Some(SubscriptKind::AnnotatedSubscript)
-            } else if typing::is_pep593_annotated_subscript(attr) {
-                Some(SubscriptKind::PEP593AnnotatedSubscript)
-            } else {
-                None
-            }
-        }
+        ExprKind::Attribute { value, attr, .. } => match &value.node {
+            ExprKind::Name { id, .. } => id == module && target == attr,
+            _ => false,
+        },
         ExprKind::Name { id, .. } => {
-            if typing::is_annotated_subscript(id) {
-                Some(SubscriptKind::AnnotatedSubscript)
-            } else if typing::is_pep593_annotated_subscript(id) {
-                Some(SubscriptKind::PEP593AnnotatedSubscript)
-            } else {
-                None
-            }
+            target == id
+                && imports
+                    .map(|imports| imports.contains(&id.as_str()))
+                    .unwrap_or_default()
         }
-        _ => None,
+        _ => false,
     }
 }
 

src/check_ast.rs

@@ -11,7 +11,7 @@ use rustpython_parser::ast::{
 };
 use rustpython_parser::parser;
 
-use crate::ast::helpers::{extract_handler_names, match_name_or_attr, SubscriptKind};
+use crate::ast::helpers::{extract_handler_names, match_name_or_attr_from_module};
 use crate::ast::operations::extract_all_names;
 use crate::ast::relocate::relocate_expr;
 use crate::ast::types::{
@@ -25,6 +25,8 @@ use crate::checks::{Check, CheckCode, CheckKind};
 use crate::docstrings::definition::{Definition, DefinitionKind, Documentable};
 use crate::python::builtins::{BUILTINS, MAGIC_GLOBALS};
 use crate::python::future::ALL_FEATURE_NAMES;
+use crate::python::typing;
+use crate::python::typing::SubscriptKind;
 use crate::settings::types::PythonVersion;
 use crate::settings::Settings;
 use crate::source_code_locator::SourceCodeLocator;
@@ -34,7 +36,15 @@ use crate::{
     pycodestyle, pydocstyle, pyflakes, pyupgrade,
 };
 
-pub const GLOBAL_SCOPE_INDEX: usize = 0;
+const GLOBAL_SCOPE_INDEX: usize = 0;
+const TRACK_FROM_IMPORTS: [&str; 6] = [
+    "collections",
+    "collections.abc",
+    "contextlib",
+    "re",
+    "typing",
+    "typing.re",
+];
 
 pub struct Checker<'a> {
     // Input data.
@@ -70,6 +80,7 @@ pub struct Checker<'a> {
     futures_allowed: bool,
     annotations_future_enabled: bool,
     except_handlers: Vec<Vec<String>>,
+    from_imports: BTreeMap<&'a str, BTreeSet<&'a str>>,
 }
 
 impl<'a> Checker<'a> {
@@ -101,13 +112,14 @@ impl<'a> Checker<'a> {
                 modifier: Modifier::Module,
                 visibility: module_visibility(path),
             },
-            in_f_string: None,
+            in_f_string: Default::default(),
             in_annotation: Default::default(),
             in_literal: Default::default(),
             seen_import_boundary: Default::default(),
             futures_allowed: true,
             annotations_future_enabled: Default::default(),
             except_handlers: Default::default(),
+            from_imports: Default::default(),
         }
     }
 
@@ -115,6 +127,11 @@ impl<'a> Checker<'a> {
     pub fn patch(&self) -> bool {
         self.autofix.patch()
     }
+
+    /// Return `true` if the `Expr` is a reference to `typing.${target}`.
+    pub fn match_typing_module(&self, expr: &Expr, target: &str) -> bool {
+        match_name_or_attr_from_module(expr, target, "typing", self.from_imports.get("typing"))
+    }
 }
 
 impl<'a, 'b> Visitor<'b> for Checker<'a>
@@ -492,6 +509,24 @@ where
                 module,
                 level,
             } => {
+                // Track `import from` statements, to ensure that we can correctly attribute
+                // references like `from typing import Union`.
+                if level.map(|level| level == 0).unwrap_or(true) {
+                    if let Some(module) = module {
+                        if TRACK_FROM_IMPORTS.contains(&module.as_str()) {
+                            self.from_imports
+                                .entry(module)
+                                .or_insert_with(BTreeSet::new)
+                                .extend(
+                                    names
+                                        .iter()
+                                        .filter(|alias| alias.node.asname.is_none())
+                                        .map(|alias| alias.node.name.as_str()),
+                                )
+                        }
+                    }
+                }
+
                 if self.settings.enabled.contains(&CheckCode::E402) {
                     if self.seen_import_boundary && stmt.location.column() == 0 {
                         self.checks.push(Check::new(
@@ -861,7 +896,7 @@ where
                     pyupgrade::plugins::use_pep604_annotation(self, expr, value, slice);
                 }
 
-                if match_name_or_attr(value, "Literal") {
+                if self.match_typing_module(value, "Literal") {
                     self.in_literal = true;
                 }
             }
@@ -886,6 +921,7 @@ where
                     // Ex) List[...]
                     if self.settings.enabled.contains(&CheckCode::U006)
                         && self.settings.target_version >= PythonVersion::Py39
+                        && typing::is_pep585_builtin(expr, self.from_imports.get("typing"))
                     {
                         pyupgrade::plugins::use_pep585_annotation(self, expr, id);
                     }
@@ -908,16 +944,13 @@ where
                 }
                 ExprContext::Del => self.handle_node_delete(expr),
             },
-            ExprKind::Attribute { value, attr, .. } => {
+            ExprKind::Attribute { attr, .. } => {
                 // Ex) typing.List[...]
                 if self.settings.enabled.contains(&CheckCode::U006)
                     && self.settings.target_version >= PythonVersion::Py39
+                    && typing::is_pep585_builtin(expr, self.from_imports.get("typing"))
                 {
-                    if let ExprKind::Name { id, .. } = &value.node {
-                        if id == "typing" {
-                            pyupgrade::plugins::use_pep585_annotation(self, expr, attr);
-                        }
-                    }
+                    pyupgrade::plugins::use_pep585_annotation(self, expr, attr);
                 }
             }
             ExprKind::Call {
@@ -1276,12 +1309,12 @@ where
                 args,
                 keywords,
             } => {
-                if match_name_or_attr(func, "ForwardRef") {
+                if self.match_typing_module(func, "ForwardRef") {
                     self.visit_expr(func);
                     for expr in args {
                         self.visit_annotation(expr);
                     }
-                } else if match_name_or_attr(func, "cast") {
+                } else if self.match_typing_module(func, "cast") {
                     self.visit_expr(func);
                     if !args.is_empty() {
                         self.visit_annotation(&args[0]);
@@ -1289,12 +1322,12 @@ where
                     for expr in args.iter().skip(1) {
                         self.visit_expr(expr);
                     }
-                } else if match_name_or_attr(func, "NewType") {
+                } else if self.match_typing_module(func, "NewType") {
                     self.visit_expr(func);
                     for expr in args.iter().skip(1) {
                         self.visit_annotation(expr);
                     }
-                } else if match_name_or_attr(func, "TypeVar") {
+                } else if self.match_typing_module(func, "TypeVar") {
                     self.visit_expr(func);
                     for expr in args.iter().skip(1) {
                         self.visit_annotation(expr);
@@ -1311,7 +1344,7 @@ where
                             }
                         }
                     }
-                } else if match_name_or_attr(func, "NamedTuple") {
+                } else if self.match_typing_module(func, "NamedTuple") {
                     self.visit_expr(func);
 
                     // Ex) NamedTuple("a", [("a", int)])
@@ -1343,7 +1376,7 @@ where
                         let KeywordData { value, .. } = &keyword.node;
                         self.visit_annotation(value);
                     }
-                } else if match_name_or_attr(func, "TypedDict") {
+                } else if self.match_typing_module(func, "TypedDict") {
                     self.visit_expr(func);
 
                     // Ex) TypedDict("a", {"a": int})
@@ -1370,7 +1403,7 @@ where
                 }
             }
             ExprKind::Subscript { value, slice, ctx } => {
-                match helpers::match_annotated_subscript(value) {
+                match typing::match_annotated_subscript(value, &self.from_imports) {
                     Some(subscript) => match subscript {
                         // Ex) Optional[int]
                         SubscriptKind::AnnotatedSubscript => {

src/checks_gen.rs

@@ -1,11 +1,11 @@
 //! File automatically generated by examples/generate_check_code_prefix.rs.
 
 use serde::{Deserialize, Serialize};
-use strum_macros::EnumString;
+use strum_macros::{AsRefStr, EnumString};
 
 use crate::checks::CheckCode;
 
-#[derive(EnumString, Debug, PartialEq, Eq, Clone, Serialize, Deserialize)]
+#[derive(AsRefStr, EnumString, Debug, PartialEq, Eq, Clone, Serialize, Deserialize)]
 pub enum CheckCodePrefix {
     A,
     A0,

src/cli.rs

@@ -1,3 +1,4 @@
+use std::collections::BTreeMap;
 use std::fmt;
 use std::path::PathBuf;
 
@@ -8,8 +9,8 @@ use regex::Regex;
 use crate::checks_gen::CheckCodePrefix;
 use crate::printer::SerializationFormat;
 use crate::settings::configuration::Configuration;
+use crate::settings::types::PatternPrefixPair;
 use crate::settings::types::PythonVersion;
-use crate::settings::types::StrCheckCodePair;
 
 #[derive(Debug, Parser)]
 #[command(author, about = "ruff: An extremely fast Python linter.")]
@@ -61,7 +62,7 @@ pub struct Cli {
     pub extend_exclude: Vec<String>,
     /// List of mappings from file pattern to code to exclude
     #[arg(long, value_delimiter = ',')]
-    pub per_file_ignores: Vec<StrCheckCodePair>,
+    pub per_file_ignores: Vec<PatternPrefixPair>,
     /// Output serialization format for error messages.
     #[arg(long, value_enum, default_value_t=SerializationFormat::Text)]
     pub format: SerializationFormat,
@@ -143,3 +144,17 @@ pub fn warn_on(
         }
     }
 }
+
+/// Collect a list of `PatternPrefixPair` structs as a `BTreeMap`.
+pub fn collect_per_file_ignores(
+    pairs: Vec<PatternPrefixPair>,
+) -> BTreeMap<String, Vec<CheckCodePrefix>> {
+    let mut per_file_ignores: BTreeMap<String, Vec<CheckCodePrefix>> = BTreeMap::new();
+    for pair in pairs {
+        per_file_ignores
+            .entry(pair.pattern)
+            .or_insert_with(Vec::new)
+            .push(pair.prefix);
+    }
+    per_file_ignores
+}

src/flake8_quotes/settings.rs

@@ -2,14 +2,14 @@
 
 use serde::{Deserialize, Serialize};
 
-#[derive(Debug, Clone, PartialEq, Eq, Deserialize, Serialize)]
+#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 pub enum Quote {
     Single,
     Double,
 }
 
-#[derive(Debug, PartialEq, Eq, Deserialize)]
+#[derive(Debug, PartialEq, Eq, Serialize, Deserialize)]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 pub struct Options {
     pub inline_quotes: Option<Quote>,

src/lib.rs

@@ -21,7 +21,7 @@ pub mod check_ast;
 mod check_lines;
 mod check_tokens;
 pub mod checks;
-mod checks_gen;
+pub mod checks_gen;
 pub mod cli;
 pub mod code_gen;
 mod cst;

src/linter.rs

@@ -377,7 +377,8 @@ mod tests {
     #[test_case(CheckCode::F706, Path::new("F706.py"); "F706")]
     #[test_case(CheckCode::F707, Path::new("F707.py"); "F707")]
     #[test_case(CheckCode::F722, Path::new("F722.py"); "F722")]
-    #[test_case(CheckCode::F821, Path::new("F821.py"); "F821")]
+    #[test_case(CheckCode::F821, Path::new("F821_0.py"); "F821_0")]
+    #[test_case(CheckCode::F821, Path::new("F821_1.py"); "F821_1")]
     #[test_case(CheckCode::F822, Path::new("F822.py"); "F822")]
     #[test_case(CheckCode::F823, Path::new("F823.py"); "F823")]
     #[test_case(CheckCode::F831, Path::new("F831.py"); "F831")]

src/main.rs

@@ -1,3 +1,4 @@
+use std::collections::BTreeMap;
 use std::io::{self, Read};
 use std::path::{Path, PathBuf};
 use std::process::ExitCode;
@@ -17,7 +18,8 @@ use walkdir::DirEntry;
 use ruff::cache;
 use ruff::checks::CheckCode;
 use ruff::checks::CheckKind;
-use ruff::cli::{warn_on, Cli, Warnable};
+use ruff::checks_gen::CheckCodePrefix;
+use ruff::cli::{collect_per_file_ignores, warn_on, Cli, Warnable};
 use ruff::fs::iter_python_files;
 use ruff::linter::add_noqa_to_path;
 use ruff::linter::autoformat_path;
@@ -27,7 +29,7 @@ use ruff::message::Message;
 use ruff::printer::{Printer, SerializationFormat};
 use ruff::settings::configuration::Configuration;
 use ruff::settings::pyproject;
-use ruff::settings::types::{FilePattern, PerFileIgnore};
+use ruff::settings::types::FilePattern;
 use ruff::settings::user::UserConfiguration;
 use ruff::settings::Settings;
 use ruff::tell_user;
@@ -255,11 +257,8 @@ fn inner_main() -> Result<ExitCode> {
         .iter()
         .map(|path| FilePattern::from_user(path, &project_root))
         .collect();
-    let per_file_ignores: Vec<PerFileIgnore> = cli
-        .per_file_ignores
-        .into_iter()
-        .map(|pair| PerFileIgnore::new(pair, &project_root))
-        .collect();
+    let per_file_ignores: BTreeMap<String, Vec<CheckCodePrefix>> =
+        collect_per_file_ignores(cli.per_file_ignores);
 
     let mut configuration = Configuration::from_pyproject(&pyproject, &project_root)?;
     if !exclude.is_empty() {

src/pep8_naming/settings.rs

@@ -1,6 +1,6 @@
 //! Settings for the `pep8-naming` plugin.
 
-use serde::Deserialize;
+use serde::{Deserialize, Serialize};
 
 const IGNORE_NAMES: [&str; 12] = [
     "setUp",
@@ -21,7 +21,7 @@ const CLASSMETHOD_DECORATORS: [&str; 1] = ["classmethod"];
 
 const STATICMETHOD_DECORATORS: [&str; 1] = ["staticmethod"];
 
-#[derive(Debug, PartialEq, Eq, Deserialize)]
+#[derive(Debug, PartialEq, Eq, Serialize, Deserialize)]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 pub struct Options {
     pub ignore_names: Option<Vec<String>>,

src/python/typing.rs

@@ -1,101 +1,207 @@
-use std::collections::BTreeSet;
+use std::collections::{BTreeMap, BTreeSet};
 
 use once_cell::sync::Lazy;
+use rustpython_ast::{Expr, ExprKind};
 
-static ANNOTATED_SUBSCRIPTS: Lazy<BTreeSet<&'static str>> = Lazy::new(|| {
-    BTreeSet::from([
-        "AbstractAsyncContextManager",
-        "AbstractContextManager",
-        "AbstractSet",
-        // "Annotated",
-        "AsyncContextManager",
-        "AsyncGenerator",
-        "AsyncIterable",
-        "AsyncIterator",
-        "Awaitable",
-        "BinaryIO",
-        "BsdDbShelf",
-        "ByteString",
-        "Callable",
-        "ChainMap",
-        "ClassVar",
-        "Collection",
-        "Concatenate",
-        "Container",
-        "ContextManager",
-        "Coroutine",
-        "Counter",
-        "Counter",
-        "DbfilenameShelf",
-        "DefaultDict",
-        "Deque",
-        "Dict",
-        "Field",
-        "Final",
-        "FrozenSet",
-        "Generator",
-        "Iterator",
-        "Generic",
-        "IO",
-        "ItemsView",
-        "Iterable",
-        "Iterator",
-        "KeysView",
-        "LifoQueue",
-        "List",
-        "Mapping",
-        "MappingProxyType",
-        "MappingView",
-        "Match",
-        "MutableMapping",
-        "MutableSequence",
-        "MutableSet",
-        "Optional",
-        "OrderedDict",
-        "PathLike",
-        "Pattern",
-        "PriorityQueue",
-        "Protocol",
-        "Queue",
-        "Reversible",
-        "Sequence",
-        "Set",
-        "Shelf",
-        "SimpleQueue",
-        "TextIO",
-        "Tuple",
-        "Type",
-        "TypeGuard",
-        "Union",
-        "ValuesView",
-        "WeakKeyDictionary",
-        "WeakMethod",
-        "WeakSet",
-        "WeakValueDictionary",
-        "cached_property",
-        "defaultdict",
-        "deque",
-        "dict",
-        "frozenset",
-        "list",
-        "partialmethod",
-        "set",
-        "tuple",
-        "type",
-    ])
-});
+// See: https://docs.python.org/3/library/typing.html
+static IMPORTED_SUBSCRIPTS: Lazy<BTreeMap<&'static str, BTreeSet<&'static str>>> =
+    Lazy::new(|| {
+        let mut import_map = BTreeMap::new();
+        for (name, module) in [
+            // `collections`
+            ("ChainMap", "collections"),
+            ("Counter", "collections"),
+            ("OrderedDict", "collections"),
+            ("defaultdict", "collections"),
+            ("deque", "collections"),
+            // `collections.abc`
+            ("AsyncGenerator", "collections.abc"),
+            ("AsyncIterable", "collections.abc"),
+            ("AsyncIterator", "collections.abc"),
+            ("Awaitable", "collections.abc"),
+            ("ByteString", "collections.abc"),
+            ("Callable", "collections.abc"),
+            ("Collection", "collections.abc"),
+            ("Container", "collections.abc"),
+            ("Coroutine", "collections.abc"),
+            ("Generator", "collections.abc"),
+            ("ItemsView", "collections.abc"),
+            ("Iterable", "collections.abc"),
+            ("Iterator", "collections.abc"),
+            ("KeysView", "collections.abc"),
+            ("Mapping", "collections.abc"),
+            ("MappingView", "collections.abc"),
+            ("MutableMapping", "collections.abc"),
+            ("MutableSequence", "collections.abc"),
+            ("MutableSet", "collections.abc"),
+            ("Reversible", "collections.abc"),
+            ("Sequence", "collections.abc"),
+            ("Set", "collections.abc"),
+            ("ValuesView", "collections.abc"),
+            // `contextlib`
+            ("AbstractAsyncContextManager", "contextlib"),
+            ("AbstractContextManager", "contextlib"),
+            // `re`
+            ("Match", "re"),
+            ("Pattern", "re"),
+            // `typing`
+            ("AbstractSet", "typing"),
+            ("Annotated", "typing"),
+            ("AsyncContextManager", "typing"),
+            ("AsyncContextManager", "typing"),
+            ("AsyncGenerator", "typing"),
+            ("AsyncIterable", "typing"),
+            ("AsyncIterator", "typing"),
+            ("Awaitable", "typing"),
+            ("BinaryIO", "typing"),
+            ("ByteString", "typing"),
+            ("Callable", "typing"),
+            ("ChainMap", "typing"),
+            ("ClassVar", "typing"),
+            ("Collection", "typing"),
+            ("Concatenate", "typing"),
+            ("Container", "typing"),
+            ("ContextManager", "typing"),
+            ("ContextManager", "typing"),
+            ("Coroutine", "typing"),
+            ("Counter", "typing"),
+            ("DefaultDict", "typing"),
+            ("Deque", "typing"),
+            ("Dict", "typing"),
+            ("Final", "typing"),
+            ("FrozenSet", "typing"),
+            ("Generator", "typing"),
+            ("Generic", "typing"),
+            ("IO", "typing"),
+            ("ItemsView", "typing"),
+            ("Iterable", "typing"),
+            ("Iterator", "typing"),
+            ("KeysView", "typing"),
+            ("List", "typing"),
+            ("Mapping", "typing"),
+            ("Match", "typing"),
+            ("MutableMapping", "typing"),
+            ("MutableSequence", "typing"),
+            ("MutableSet", "typing"),
+            ("Optional", "typing"),
+            ("OrderedDict", "typing"),
+            ("Pattern", "typing"),
+            ("Reversible", "typing"),
+            ("Sequence", "typing"),
+            ("Set", "typing"),
+            ("TextIO", "typing"),
+            ("Tuple", "typing"),
+            ("Type", "typing"),
+            ("Type", "typing"),
+            ("TypeGuard", "typing"),
+            ("Union", "typing"),
+            ("Unpack", "typing"),
+            ("ValuesView", "typing"),
+            // `typing.io`
+            ("BinaryIO", "typing.io"),
+            ("IO", "typing.io"),
+            ("TextIO", "typing.io"),
+            // `typing.re`
+            ("Match", "typing.re"),
+            ("Pattern", "typing.re"),
+            // `weakref`
+            ("WeakKeyDictionary", "weakref"),
+            ("WeakSet", "weakref"),
+            ("WeakValueDictionary", "weakref"),
+        ] {
+            import_map
+                .entry(name)
+                .or_insert_with(BTreeSet::new)
+                .insert(module);
+        }
+        import_map
+    });
 
-pub fn is_annotated_subscript(name: &str) -> bool {
-    ANNOTATED_SUBSCRIPTS.contains(name)
-}
+// These are all assumed to come from the `typing` module.
+// See: https://peps.python.org/pep-0585/
+static PEP_585_BUILTINS_ELIGIBLE: Lazy<BTreeSet<&'static str>> =
+    Lazy::new(|| BTreeSet::from(["Dict", "FrozenSet", "List", "Set", "Tuple", "Type"]));
 
-pub fn is_pep593_annotated_subscript(name: &str) -> bool {
+// These are all assumed to come from the `typing` module.
+// See: https://peps.python.org/pep-0585/
+static PEP_585_BUILTINS: Lazy<BTreeSet<&'static str>> =
+    Lazy::new(|| BTreeSet::from(["dict", "frozenset", "list", "set", "tuple", "type"]));
+
+fn is_pep593_annotated_subscript(name: &str) -> bool {
     name == "Annotated"
 }
 
-static PEP_585_BUILTINS: Lazy<BTreeSet<&'static str>> =
-    Lazy::new(|| BTreeSet::from(["Dict", "FrozenSet", "List", "Set", "Tuple", "Type"]));
-
-pub fn is_pep585_builtin(name: &str) -> bool {
-    PEP_585_BUILTINS.contains(name)
+pub enum SubscriptKind {
+    AnnotatedSubscript,
+    PEP593AnnotatedSubscript,
+}
+
+pub fn match_annotated_subscript(
+    expr: &Expr,
+    imports: &BTreeMap<&str, BTreeSet<&str>>,
+) -> Option<SubscriptKind> {
+    match &expr.node {
+        ExprKind::Attribute { attr, value, .. } => {
+            if let ExprKind::Name { id, .. } = &value.node {
+                // If `id` is `typing` and `attr` is `Union`, verify that `typing.Union` is an
+                // annotated subscript.
+                if IMPORTED_SUBSCRIPTS
+                    .get(&attr.as_str())
+                    .map(|imports| imports.contains(&id.as_str()))
+                    .unwrap_or_default()
+                {
+                    return if is_pep593_annotated_subscript(attr) {
+                        Some(SubscriptKind::PEP593AnnotatedSubscript)
+                    } else {
+                        Some(SubscriptKind::AnnotatedSubscript)
+                    };
+                }
+            }
+        }
+        ExprKind::Name { id, .. } => {
+            // Built-ins (no import necessary).
+            if PEP_585_BUILTINS.contains(&id.as_str()) {
+                return Some(SubscriptKind::AnnotatedSubscript);
+            }
+
+            // Verify that, e.g., `Union` is a reference to `typing.Union`.
+            if let Some(modules) = IMPORTED_SUBSCRIPTS.get(&id.as_str()) {
+                for module in modules {
+                    if imports
+                        .get(module)
+                        .map(|imports| imports.contains(&id.as_str()))
+                        .unwrap_or_default()
+                    {
+                        return if is_pep593_annotated_subscript(id) {
+                            Some(SubscriptKind::PEP593AnnotatedSubscript)
+                        } else {
+                            Some(SubscriptKind::AnnotatedSubscript)
+                        };
+                    }
+                }
+            }
+        }
+        _ => {}
+    }
+    None
+}
+
+/// Returns `true` if `Expr` represents a reference to a typing object with a PEP 585 built-in.
+pub fn is_pep585_builtin(expr: &Expr, typing_imports: Option<&BTreeSet<&str>>) -> bool {
+    match &expr.node {
+        ExprKind::Attribute { attr, value, .. } => {
+            if let ExprKind::Name { id, .. } = &value.node {
+                id == "typing" && PEP_585_BUILTINS_ELIGIBLE.contains(&attr.as_str())
+            } else {
+                false
+            }
+        }
+        ExprKind::Name { id, .. } => {
+            typing_imports
+                .map(|imports| imports.contains(&id.as_str()))
+                .unwrap_or_default()
+                && PEP_585_BUILTINS_ELIGIBLE.contains(&id.as_str())
+        }
+        _ => false,
+    }
 }

src/pyupgrade/plugins/use_pep585_annotation.rs

@@ -4,22 +4,18 @@ use crate::ast::types::Range;
 use crate::autofix::Fix;
 use crate::check_ast::Checker;
 use crate::checks::{Check, CheckKind};
-use crate::python::typing;
 
 pub fn use_pep585_annotation(checker: &mut Checker, expr: &Expr, id: &str) {
-    // TODO(charlie): Verify that the builtin is imported from the `typing` module.
-    if typing::is_pep585_builtin(id) {
-        let mut check = Check::new(
-            CheckKind::UsePEP585Annotation(id.to_string()),
-            Range::from_located(expr),
-        );
-        if checker.patch() {
-            check.amend(Fix::replacement(
-                id.to_lowercase(),
-                expr.location,
-                expr.end_location.unwrap(),
-            ));
-        }
-        checker.add_check(check);
+    let mut check = Check::new(
+        CheckKind::UsePEP585Annotation(id.to_string()),
+        Range::from_located(expr),
+    );
+    if checker.patch() {
+        check.amend(Fix::replacement(
+            id.to_lowercase(),
+            expr.location,
+            expr.end_location.unwrap(),
+        ));
     }
+    checker.add_check(check);
 }

src/pyupgrade/plugins/use_pep604_annotation.rs

@@ -1,6 +1,5 @@
 use rustpython_ast::{Constant, Expr, ExprKind, Operator};
 
-use crate::ast::helpers::match_name_or_attr;
 use crate::ast::types::Range;
 use crate::autofix::Fix;
 use crate::check_ast::Checker;
@@ -43,7 +42,7 @@ fn union(elts: &[Expr]) -> Expr {
 }
 
 pub fn use_pep604_annotation(checker: &mut Checker, expr: &Expr, value: &Expr, slice: &Expr) {
-    if match_name_or_attr(value, "Optional") {
+    if checker.match_typing_module(value, "Optional") {
         let mut check = Check::new(CheckKind::UsePEP604Annotation, Range::from_located(expr));
         if checker.patch() {
             let mut generator = SourceGenerator::new();
@@ -58,7 +57,7 @@ pub fn use_pep604_annotation(checker: &mut Checker, expr: &Expr, value: &Expr, s
             }
         }
         checker.add_check(check);
-    } else if match_name_or_attr(value, "Union") {
+    } else if checker.match_typing_module(value, "Union") {
         let mut check = Check::new(CheckKind::UsePEP604Annotation, Range::from_located(expr));
         if checker.patch() {
             match &slice.node {

src/settings/configuration.rs

@@ -1,6 +1,7 @@
 //! User-provided program settings, taking into account pyproject.toml and command-line options.
 //! Structure mirrors the user-facing representation of the various parameters.
 
+use std::collections::BTreeMap;
 use std::path::PathBuf;
 
 use anyhow::{anyhow, Result};
@@ -9,7 +10,7 @@ use regex::Regex;
 
 use crate::checks_gen::CheckCodePrefix;
 use crate::settings::pyproject::load_options;
-use crate::settings::types::{FilePattern, PerFileIgnore, PythonVersion};
+use crate::settings::types::{FilePattern, PythonVersion};
 use crate::{flake8_quotes, pep8_naming};
 
 #[derive(Debug)]
@@ -21,7 +22,7 @@ pub struct Configuration {
     pub extend_select: Vec<CheckCodePrefix>,
     pub ignore: Vec<CheckCodePrefix>,
     pub line_length: usize,
-    pub per_file_ignores: Vec<PerFileIgnore>,
+    pub per_file_ignores: BTreeMap<String, Vec<CheckCodePrefix>>,
     pub select: Vec<CheckCodePrefix>,
     pub target_version: PythonVersion,
     // Plugins
@@ -80,21 +81,18 @@ impl Configuration {
                 .unwrap_or_else(|| DEFAULT_EXCLUDE.clone()),
             extend_exclude: options
                 .extend_exclude
+                .unwrap_or_default()
                 .iter()
                 .map(|path| FilePattern::from_user(path, project_root))
                 .collect(),
-            extend_ignore: options.extend_ignore,
+            extend_ignore: options.extend_ignore.unwrap_or_default(),
             select: options
                 .select
                 .unwrap_or_else(|| vec![CheckCodePrefix::E, CheckCodePrefix::F]),
-            extend_select: options.extend_select,
-            ignore: options.ignore,
+            extend_select: options.extend_select.unwrap_or_default(),
+            ignore: options.ignore.unwrap_or_default(),
             line_length: options.line_length.unwrap_or(88),
-            per_file_ignores: options
-                .per_file_ignores
-                .into_iter()
-                .map(|pair| PerFileIgnore::new(pair, project_root))
-                .collect(),
+            per_file_ignores: options.per_file_ignores.unwrap_or_default(),
             // Plugins
             flake8_quotes: options
                 .flake8_quotes

src/settings/mod.rs

@@ -1,7 +1,7 @@
 //! Effective program settings, taking into account pyproject.toml and command-line options.
 //! Structure is optimized for internal usage, as opposed to external visibility or parsing.
 
-use std::collections::BTreeSet;
+use std::collections::{BTreeMap, BTreeSet};
 use std::hash::{Hash, Hasher};
 
 use regex::Regex;
@@ -47,7 +47,7 @@ impl Settings {
             flake8_quotes: config.flake8_quotes,
             line_length: config.line_length,
             pep8_naming: config.pep8_naming,
-            per_file_ignores: config.per_file_ignores,
+            per_file_ignores: resolve_per_file_ignores(&config.per_file_ignores),
             target_version: config.target_version,
         }
     }
@@ -56,10 +56,10 @@ impl Settings {
         Self {
             dummy_variable_rgx: Regex::new("^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$").unwrap(),
             enabled: BTreeSet::from([check_code]),
-            exclude: vec![],
-            extend_exclude: vec![],
+            exclude: Default::default(),
+            extend_exclude: Default::default(),
             line_length: 88,
-            per_file_ignores: vec![],
+            per_file_ignores: Default::default(),
             target_version: PythonVersion::Py310,
             flake8_quotes: Default::default(),
             pep8_naming: Default::default(),
@@ -70,10 +70,10 @@ impl Settings {
         Self {
             dummy_variable_rgx: Regex::new("^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$").unwrap(),
             enabled: BTreeSet::from_iter(check_codes),
-            exclude: vec![],
-            extend_exclude: vec![],
+            exclude: Default::default(),
+            extend_exclude: Default::default(),
             line_length: 88,
-            per_file_ignores: vec![],
+            per_file_ignores: Default::default(),
             target_version: PythonVersion::Py310,
             flake8_quotes: Default::default(),
             pep8_naming: Default::default(),
@@ -136,6 +136,15 @@ fn resolve_codes(
     codes
 }
 
+fn resolve_per_file_ignores(
+    per_file_ignores: &BTreeMap<String, Vec<CheckCodePrefix>>,
+) -> Vec<PerFileIgnore> {
+    per_file_ignores
+        .iter()
+        .map(|(pattern, prefixes)| PerFileIgnore::new(pattern, prefixes, &None))
+        .collect()
+}
+
 #[cfg(test)]
 mod tests {
     use std::collections::BTreeSet;

src/settings/options.rs

@@ -1,27 +1,24 @@
 //! Options that the user can provide via pyproject.toml.
 
-use serde::Deserialize;
+use std::collections::BTreeMap;
+
+use serde::{Deserialize, Serialize};
 
 use crate::checks_gen::CheckCodePrefix;
-use crate::settings::types::{PythonVersion, StrCheckCodePair};
+use crate::settings::types::PythonVersion;
 use crate::{flake8_quotes, pep8_naming};
 
-#[derive(Debug, PartialEq, Eq, Deserialize, Default)]
+#[derive(Debug, PartialEq, Eq, Serialize, Deserialize, Default)]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 pub struct Options {
     pub line_length: Option<usize>,
     pub exclude: Option<Vec<String>>,
-    #[serde(default)]
-    pub extend_exclude: Vec<String>,
+    pub extend_exclude: Option<Vec<String>>,
     pub select: Option<Vec<CheckCodePrefix>>,
-    #[serde(default)]
-    pub extend_select: Vec<CheckCodePrefix>,
-    #[serde(default)]
-    pub ignore: Vec<CheckCodePrefix>,
-    #[serde(default)]
-    pub extend_ignore: Vec<CheckCodePrefix>,
-    #[serde(default)]
-    pub per_file_ignores: Vec<StrCheckCodePair>,
+    pub extend_select: Option<Vec<CheckCodePrefix>>,
+    pub ignore: Option<Vec<CheckCodePrefix>>,
+    pub extend_ignore: Option<Vec<CheckCodePrefix>>,
+    pub per_file_ignores: Option<BTreeMap<String, Vec<CheckCodePrefix>>>,
     pub dummy_variable_rgx: Option<String>,
     pub target_version: Option<PythonVersion>,
     // Plugins

src/settings/pyproject.rs

@@ -6,21 +6,31 @@ use anyhow::Result;
 use common_path::common_path_all;
 use log::debug;
 use path_absolutize::Absolutize;
-use serde::Deserialize;
+use serde::{Deserialize, Serialize};
 
 use crate::fs;
 use crate::settings::options::Options;
 
-#[derive(Debug, PartialEq, Eq, Deserialize)]
+#[derive(Debug, PartialEq, Eq, Serialize, Deserialize)]
 struct Tools {
     ruff: Option<Options>,
 }
 
-#[derive(Debug, PartialEq, Eq, Deserialize)]
-struct Pyproject {
+#[derive(Debug, PartialEq, Eq, Serialize, Deserialize)]
+pub struct Pyproject {
     tool: Option<Tools>,
 }
 
+impl Pyproject {
+    pub fn new(options: Options) -> Self {
+        Self {
+            tool: Some(Tools {
+                ruff: Some(options),
+            }),
+        }
+    }
+}
+
 fn parse_pyproject_toml(path: &Path) -> Result<Pyproject> {
     let contents = fs::read_file(path)?;
     toml::from_str(&contents).map_err(|e| e.into())
@@ -86,6 +96,7 @@ pub fn load_options(pyproject: &Option<PathBuf>) -> Result<Options> {
 
 #[cfg(test)]
 mod tests {
+    use std::collections::BTreeMap;
     use std::env::current_dir;
     use std::path::PathBuf;
     use std::str::FromStr;
@@ -97,7 +108,7 @@ mod tests {
     use crate::settings::pyproject::{
         find_project_root, find_pyproject_toml, parse_pyproject_toml, Options, Pyproject, Tools,
     };
-    use crate::settings::types::StrCheckCodePair;
+    use crate::settings::types::PatternPrefixPair;
     use crate::{flake8_quotes, pep8_naming};
 
     #[test]
@@ -124,12 +135,12 @@ mod tests {
                 ruff: Some(Options {
                     line_length: None,
                     exclude: None,
-                    extend_exclude: vec![],
+                    extend_exclude: None,
                     select: None,
-                    extend_select: vec![],
-                    ignore: vec![],
-                    extend_ignore: vec![],
-                    per_file_ignores: vec![],
+                    extend_select: None,
+                    ignore: None,
+                    extend_ignore: None,
+                    per_file_ignores: None,
                     dummy_variable_rgx: None,
                     target_version: None,
                     flake8_quotes: None,
@@ -151,12 +162,12 @@ line-length = 79
                 ruff: Some(Options {
                     line_length: Some(79),
                     exclude: None,
-                    extend_exclude: vec![],
+                    extend_exclude: None,
                     select: None,
-                    extend_select: vec![],
-                    ignore: vec![],
-                    extend_ignore: vec![],
-                    per_file_ignores: vec![],
+                    extend_select: None,
+                    ignore: None,
+                    extend_ignore: None,
+                    per_file_ignores: None,
                     dummy_variable_rgx: None,
                     target_version: None,
                     flake8_quotes: None,
@@ -178,12 +189,12 @@ exclude = ["foo.py"]
                 ruff: Some(Options {
                     line_length: None,
                     exclude: Some(vec!["foo.py".to_string()]),
-                    extend_exclude: vec![],
+                    extend_exclude: None,
                     select: None,
-                    extend_select: vec![],
-                    ignore: vec![],
-                    extend_ignore: vec![],
-                    per_file_ignores: vec![],
+                    extend_select: None,
+                    ignore: None,
+                    extend_ignore: None,
+                    per_file_ignores: None,
                     dummy_variable_rgx: None,
                     target_version: None,
                     flake8_quotes: None,
@@ -205,12 +216,12 @@ select = ["E501"]
                 ruff: Some(Options {
                     line_length: None,
                     exclude: None,
-                    extend_exclude: vec![],
+                    extend_exclude: None,
                     select: Some(vec![CheckCodePrefix::E501]),
-                    extend_select: vec![],
-                    ignore: vec![],
-                    extend_ignore: vec![],
-                    per_file_ignores: vec![],
+                    extend_select: None,
+                    ignore: None,
+                    extend_ignore: None,
+                    per_file_ignores: None,
                     dummy_variable_rgx: None,
                     target_version: None,
                     flake8_quotes: None,
@@ -233,12 +244,12 @@ ignore = ["E501"]
                 ruff: Some(Options {
                     line_length: None,
                     exclude: None,
-                    extend_exclude: vec![],
+                    extend_exclude: None,
                     select: None,
-                    extend_select: vec![CheckCodePrefix::M001],
-                    ignore: vec![CheckCodePrefix::E501],
-                    extend_ignore: vec![],
-                    per_file_ignores: vec![],
+                    extend_select: Some(vec![CheckCodePrefix::M001]),
+                    ignore: Some(vec![CheckCodePrefix::E501]),
+                    extend_ignore: None,
+                    per_file_ignores: None,
                     dummy_variable_rgx: None,
                     target_version: None,
                     flake8_quotes: None,
@@ -300,19 +311,19 @@ other-attribute = 1
             Options {
                 line_length: Some(88),
                 exclude: None,
-                extend_exclude: vec![
+                extend_exclude: Some(vec![
                     "excluded.py".to_string(),
                     "migrations".to_string(),
                     "directory/also_excluded.py".to_string(),
-                ],
+                ]),
                 select: None,
-                extend_select: vec![],
-                ignore: vec![],
-                extend_ignore: vec![],
-                per_file_ignores: vec![StrCheckCodePair {
-                    pattern: "__init__.py".to_string(),
-                    code: CheckCodePrefix::F401
-                }],
+                extend_select: None,
+                ignore: None,
+                extend_ignore: None,
+                per_file_ignores: Some(BTreeMap::from([(
+                    "__init__.py".to_string(),
+                    vec![CheckCodePrefix::F401]
+                ),])),
                 dummy_variable_rgx: None,
                 target_version: None,
                 flake8_quotes: Some(flake8_quotes::settings::Options {
@@ -347,21 +358,21 @@ other-attribute = 1
 
     #[test]
     fn str_check_code_pair_strings() {
-        let result = StrCheckCodePair::from_str("foo:E501");
+        let result = PatternPrefixPair::from_str("foo:E501");
         assert!(result.is_ok());
-        let result = StrCheckCodePair::from_str("foo: E501");
+        let result = PatternPrefixPair::from_str("foo: E501");
         assert!(result.is_ok());
-        let result = StrCheckCodePair::from_str("E501:foo");
+        let result = PatternPrefixPair::from_str("E501:foo");
         assert!(result.is_err());
-        let result = StrCheckCodePair::from_str("E501");
+        let result = PatternPrefixPair::from_str("E501");
         assert!(result.is_err());
-        let result = StrCheckCodePair::from_str("foo");
+        let result = PatternPrefixPair::from_str("foo");
         assert!(result.is_err());
-        let result = StrCheckCodePair::from_str("foo:E501:E402");
+        let result = PatternPrefixPair::from_str("foo:E501:E402");
         assert!(result.is_err());
-        let result = StrCheckCodePair::from_str("**/bar:E501");
+        let result = PatternPrefixPair::from_str("**/bar:E501");
         assert!(result.is_ok());
-        let result = StrCheckCodePair::from_str("bar:E502");
+        let result = PatternPrefixPair::from_str("bar:E502");
         assert!(result.is_err());
     }
 }

src/settings/types.rs

@@ -75,24 +75,28 @@ pub struct PerFileIgnore {
 }
 
 impl PerFileIgnore {
-    pub fn new(user_in: StrCheckCodePair, project_root: &Option<PathBuf>) -> Self {
-        let pattern = FilePattern::from_user(user_in.pattern.as_str(), project_root);
-        let codes = BTreeSet::from_iter(user_in.code.codes());
+    pub fn new(
+        pattern: &str,
+        prefixes: &[CheckCodePrefix],
+        project_root: &Option<PathBuf>,
+    ) -> Self {
+        let pattern = FilePattern::from_user(pattern, project_root);
+        let codes = BTreeSet::from_iter(prefixes.iter().flat_map(|prefix| prefix.codes()));
         Self { pattern, codes }
     }
 }
 
 #[derive(Clone, Debug, PartialEq, Eq)]
-pub struct StrCheckCodePair {
+pub struct PatternPrefixPair {
     pub pattern: String,
-    pub code: CheckCodePrefix,
+    pub prefix: CheckCodePrefix,
 }
 
-impl StrCheckCodePair {
+impl PatternPrefixPair {
     const EXPECTED_PATTERN: &'static str = "<FilePattern>:<CheckCode> pattern";
 }
 
-impl<'de> Deserialize<'de> for StrCheckCodePair {
+impl<'de> Deserialize<'de> for PatternPrefixPair {
     fn deserialize<D>(deserializer: D) -> Result<Self, D::Error>
     where
         D: Deserializer<'de>,
@@ -107,7 +111,7 @@ impl<'de> Deserialize<'de> for StrCheckCodePair {
     }
 }
 
-impl FromStr for StrCheckCodePair {
+impl FromStr for PatternPrefixPair {
     type Err = anyhow::Error;
 
     fn from_str(string: &str) -> Result<Self, Self::Err> {
@@ -118,8 +122,8 @@ impl FromStr for StrCheckCodePair {
             }
             (tokens[0].trim(), tokens[1].trim())
         };
-        let code = CheckCodePrefix::from_str(code_string)?;
         let pattern = pattern_str.into();
-        Ok(Self { pattern, code })
+        let prefix = CheckCodePrefix::from_str(code_string)?;
+        Ok(Self { pattern, prefix })
     }
 }

src/settings/user.rs

@@ -1,11 +1,12 @@
 //! Structs to render user-facing settings.
 
+use std::collections::BTreeMap;
 use std::path::PathBuf;
 
 use regex::Regex;
 
 use crate::checks_gen::CheckCodePrefix;
-use crate::settings::types::{FilePattern, PerFileIgnore, PythonVersion};
+use crate::settings::types::{FilePattern, PythonVersion};
 use crate::{flake8_quotes, pep8_naming, Configuration};
 
 /// Struct to render user-facing exclusion patterns.
@@ -41,7 +42,7 @@ pub struct UserConfiguration {
     pub extend_select: Vec<CheckCodePrefix>,
     pub ignore: Vec<CheckCodePrefix>,
     pub line_length: usize,
-    pub per_file_ignores: Vec<PerFileIgnore>,
+    pub per_file_ignores: BTreeMap<String, Vec<CheckCodePrefix>>,
     pub select: Vec<CheckCodePrefix>,
     pub target_version: PythonVersion,
     // Plugins

src/snapshots/ruff__linter__tests__F821_F821_1.py.snap

@@ -0,0 +1,41 @@
+---
+source: src/linter.rs
+expression: checks
+---
+- kind:
+    UndefinedName: Model
+  location:
+    row: 11
+    column: 9
+  end_location:
+    row: 11
+    column: 16
+  fix: ~
+- kind:
+    UndefinedName: Model
+  location:
+    row: 18
+    column: 16
+  end_location:
+    row: 18
+    column: 23
+  fix: ~
+- kind:
+    UndefinedName: Model
+  location:
+    row: 24
+    column: 12
+  end_location:
+    row: 24
+    column: 19
+  fix: ~
+- kind:
+    UndefinedName: Model
+  location:
+    row: 30
+    column: 10
+  end_location:
+    row: 30
+    column: 17
+  fix: ~
+