Add caching to formatter (#8089)

crates/ruff_cli/src/args.rs

@@ -365,6 +365,14 @@ pub struct FormatCommand {
     /// Path to the `pyproject.toml` or `ruff.toml` file to use for configuration.
     #[arg(long, conflicts_with = "isolated")]
     pub config: Option<PathBuf>,
+
+    /// Disable cache reads.
+    #[arg(short, long, help_heading = "Miscellaneous")]
+    pub no_cache: bool,
+    /// Path to the cache directory.
+    #[arg(long, env = "RUFF_CACHE_DIR", help_heading = "Miscellaneous")]
+    pub cache_dir: Option<PathBuf>,
+
     /// Respect file exclusions via `.gitignore` and other standard ignore files.
     /// Use `--no-respect-gitignore` to disable.
     #[arg(
@@ -535,6 +543,7 @@ impl FormatCommand {
                 config: self.config,
                 files: self.files,
                 isolated: self.isolated,
+                no_cache: self.no_cache,
                 stdin_filename: self.stdin_filename,
             },
             CliOverrides {
@@ -547,6 +556,8 @@ impl FormatCommand {
                 preview: resolve_bool_arg(self.preview, self.no_preview).map(PreviewMode::from),
                 force_exclude: resolve_bool_arg(self.force_exclude, self.no_force_exclude),
                 target_version: self.target_version,
+                cache_dir: self.cache_dir,
+
                 // Unsupported on the formatter CLI, but required on `Overrides`.
                 ..CliOverrides::default()
             },
@@ -590,6 +601,7 @@ pub struct CheckArguments {
 #[allow(clippy::struct_excessive_bools)]
 pub struct FormatArguments {
     pub check: bool,
+    pub no_cache: bool,
     pub diff: bool,
     pub config: Option<PathBuf>,
     pub files: Vec<PathBuf>,

crates/ruff_cli/src/cache.rs

@@ -1,4 +1,5 @@
 use std::collections::HashMap;
+use std::fmt::Debug;
 use std::fs::{self, File};
 use std::hash::Hasher;
 use std::io::{self, BufReader, BufWriter, Write};
@@ -8,6 +9,11 @@ use std::sync::Mutex;
 use std::time::{Duration, SystemTime};
 
 use anyhow::{Context, Result};
+use filetime::FileTime;
+use itertools::Itertools;
+use log::{debug, error};
+use rayon::iter::ParallelIterator;
+use rayon::iter::{IntoParallelIterator, ParallelBridge};
 use rustc_hash::FxHashMap;
 use serde::{Deserialize, Serialize};
 
@@ -15,22 +21,50 @@ use ruff_cache::{CacheKey, CacheKeyHasher};
 use ruff_diagnostics::{DiagnosticKind, Fix};
 use ruff_linter::message::Message;
 use ruff_linter::warn_user;
+use ruff_macros::CacheKey;
 use ruff_notebook::NotebookIndex;
 use ruff_python_ast::imports::ImportMap;
 use ruff_source_file::SourceFileBuilder;
 use ruff_text_size::{TextRange, TextSize};
+use ruff_workspace::resolver::{PyprojectConfig, PyprojectDiscoveryStrategy, Resolver};
 use ruff_workspace::Settings;
 
+use crate::cache;
 use crate::diagnostics::Diagnostics;
 
-/// Maximum duration for which we keep a file in cache that hasn't been seen.
-const MAX_LAST_SEEN: Duration = Duration::from_secs(30 * 24 * 60 * 60); // 30 days.
-
 /// [`Path`] that is relative to the package root in [`PackageCache`].
 pub(crate) type RelativePath = Path;
 /// [`PathBuf`] that is relative to the package root in [`PackageCache`].
 pub(crate) type RelativePathBuf = PathBuf;
 
+#[derive(CacheKey)]
+pub(crate) struct FileCacheKey {
+    /// Timestamp when the file was last modified before the (cached) check.
+    file_last_modified: FileTime,
+    /// Permissions of the file before the (cached) check.
+    file_permissions_mode: u32,
+}
+
+impl FileCacheKey {
+    pub(crate) fn from_path(path: &Path) -> io::Result<FileCacheKey> {
+        // Construct a cache key for the file
+        let metadata = path.metadata()?;
+
+        #[cfg(unix)]
+        let permissions = {
+            use std::os::unix::fs::PermissionsExt;
+            metadata.permissions().mode()
+        };
+        #[cfg(windows)]
+        let permissions: u32 = metadata.permissions().readonly().into();
+
+        Ok(FileCacheKey {
+            file_last_modified: FileTime::from_last_modification_time(&metadata),
+            file_permissions_mode: permissions,
+        })
+    }
+}
+
 /// Cache.
 ///
 /// `Cache` holds everything required to display the diagnostics for a single
@@ -50,7 +84,7 @@ pub(crate) struct Cache {
     /// Files that are linted, but are not in `package.files` or are in
     /// `package.files` but are outdated. This gets merged with `package.files`
     /// when the cache is written back to disk in [`Cache::store`].
-    new_files: Mutex<HashMap<RelativePathBuf, FileCache>>,
+    changes: Mutex<Vec<Change>>,
     /// The "current" timestamp used as cache for the updates of
     /// [`FileCache::last_seen`]
     last_seen_cache: u64,
@@ -65,7 +99,7 @@ impl Cache {
     ///
     /// Finally `settings` is used to ensure we don't open a cache for different
     /// settings. It also defines the directory where to store the cache.
-    pub(crate) fn open(package_root: PathBuf, settings: &Settings) -> Cache {
+    pub(crate) fn open(package_root: PathBuf, settings: &Settings) -> Self {
         debug_assert!(package_root.is_absolute(), "package root not canonicalized");
 
         let mut buf = itoa::Buffer::new();
@@ -105,7 +139,7 @@ impl Cache {
     }
 
     /// Create an empty `Cache`.
-    fn empty(path: PathBuf, package_root: PathBuf) -> Cache {
+    fn empty(path: PathBuf, package_root: PathBuf) -> Self {
         let package = PackageCache {
             package_root,
             files: HashMap::new(),
@@ -114,37 +148,25 @@ impl Cache {
     }
 
     #[allow(clippy::cast_possible_truncation)]
-    fn new(path: PathBuf, package: PackageCache) -> Cache {
+    fn new(path: PathBuf, package: PackageCache) -> Self {
         Cache {
             path,
             package,
-            new_files: Mutex::new(HashMap::new()),
+            changes: Mutex::new(Vec::new()),
             // SAFETY: this will be truncated to the year ~2554 (so don't use
             // this code after that!).
             last_seen_cache: SystemTime::UNIX_EPOCH.elapsed().unwrap().as_millis() as u64,
         }
     }
 
-    /// Store the cache to disk, if it has been changed.
+    /// Applies the pending changes and persists the cache to disk, if it has been changed.
-    #[allow(clippy::cast_possible_truncation)]
+    pub(crate) fn persist(mut self) -> Result<()> {
-    pub(crate) fn store(mut self) -> Result<()> {
+        if !self.save() {
-        let new_files = self.new_files.into_inner().unwrap();
-        if new_files.is_empty() {
             // No changes made, no need to write the same cache file back to
             // disk.
             return Ok(());
         }
 
-        // Remove cached files that we haven't seen in a while.
-        let now = self.last_seen_cache;
-        self.package.files.retain(|_, file| {
-            // SAFETY: this will be truncated to the year ~2554.
-            (now - *file.last_seen.get_mut()) <= MAX_LAST_SEEN.as_millis() as u64
-        });
-
-        // Apply any changes made and keep track of when we last saw files.
-        self.package.files.extend(new_files);
-
         let file = File::create(&self.path)
             .with_context(|| format!("Failed to create cache file '{}'", self.path.display()))?;
         let writer = BufWriter::new(file);
@@ -156,6 +178,53 @@ impl Cache {
         })
     }
 
+    /// Applies the pending changes without storing the cache to disk.
+    #[allow(clippy::cast_possible_truncation)]
+    pub(crate) fn save(&mut self) -> bool {
+        /// Maximum duration for which we keep a file in cache that hasn't been seen.
+        const MAX_LAST_SEEN: Duration = Duration::from_secs(30 * 24 * 60 * 60); // 30 days.
+
+        let changes = std::mem::take(self.changes.get_mut().unwrap());
+        if changes.is_empty() {
+            return false;
+        }
+
+        // Remove cached files that we haven't seen in a while.
+        let now = self.last_seen_cache;
+        self.package.files.retain(|_, file| {
+            // SAFETY: this will be truncated to the year ~2554.
+            (now - *file.last_seen.get_mut()) <= MAX_LAST_SEEN.as_millis() as u64
+        });
+
+        // Apply any changes made and keep track of when we last saw files.
+        for change in changes {
+            let entry = self
+                .package
+                .files
+                .entry(change.path)
+                .and_modify(|existing| {
+                    if existing.key != change.new_key {
+                        // Reset the data if the key change.
+                        existing.data = FileCacheData::default();
+                    }
+
+                    existing.key = change.new_key;
+                    existing
+                        .last_seen
+                        .store(self.last_seen_cache, Ordering::Relaxed);
+                })
+                .or_insert_with(|| FileCache {
+                    key: change.new_key,
+                    last_seen: AtomicU64::new(self.last_seen_cache),
+                    data: FileCacheData::default(),
+                });
+
+            change.new_data.apply(&mut entry.data);
+        }
+
+        true
+    }
+
     /// Returns the relative path based on `path` and the package root.
     ///
     /// Returns `None` if `path` is not within the package.
@@ -169,7 +238,7 @@ impl Cache {
     ///
     /// This returns `None` if `key` differs from the cached key or if the
     /// cache doesn't contain results for the file.
-    pub(crate) fn get<T: CacheKey>(&self, path: &RelativePath, key: &T) -> Option<&FileCache> {
+    pub(crate) fn get(&self, path: &RelativePath, key: &FileCacheKey) -> Option<&FileCache> {
         let file = self.package.files.get(path)?;
 
         let mut hasher = CacheKeyHasher::new();
@@ -185,50 +254,34 @@ impl Cache {
         Some(file)
     }
 
+    pub(crate) fn is_formatted(&self, path: &RelativePath, key: &FileCacheKey) -> bool {
+        self.get(path, key)
+            .is_some_and(|entry| entry.data.formatted)
+    }
+
     /// Add or update a file cache at `path` relative to the package root.
-    pub(crate) fn update<T: CacheKey>(
+    fn update(&self, path: RelativePathBuf, key: &FileCacheKey, data: ChangeData) {
-        &self,
-        path: RelativePathBuf,
-        key: T,
-        messages: &[Message],
-        imports: &ImportMap,
-        notebook_index: Option<&NotebookIndex>,
-    ) {
-        let source = if let Some(msg) = messages.first() {
-            msg.file.source_text().to_owned()
-        } else {
-            String::new() // No messages, no need to keep the source!
-        };
-
-        let messages = messages
-            .iter()
-            .map(|msg| {
-                // Make sure that all message use the same source file.
-                assert!(
-                    msg.file == messages.first().unwrap().file,
-                    "message uses a different source file"
-                );
-                CacheMessage {
-                    kind: msg.kind.clone(),
-                    range: msg.range,
-                    fix: msg.fix.clone(),
-                    noqa_offset: msg.noqa_offset,
-                }
-            })
-            .collect();
-
         let mut hasher = CacheKeyHasher::new();
         key.cache_key(&mut hasher);
 
-        let file = FileCache {
+        self.changes.lock().unwrap().push(Change {
-            key: hasher.finish(),
+            path,
-            last_seen: AtomicU64::new(self.last_seen_cache),
+            new_key: hasher.finish(),
-            imports: imports.clone(),
+            new_data: data,
-            messages,
+        });
-            source,
+    }
-            notebook_index: notebook_index.cloned(),
+
-        };
+    pub(crate) fn update_lint(
-        self.new_files.lock().unwrap().insert(path, file);
+        &self,
+        path: RelativePathBuf,
+        key: &FileCacheKey,
+        data: LintCacheData,
+    ) {
+        self.update(path, key, ChangeData::Lint(data));
+    }
+
+    pub(crate) fn set_formatted(&self, path: RelativePathBuf, key: &FileCacheKey) {
+        self.update(path, key, ChangeData::Formatted);
     }
 }
 
@@ -254,55 +307,43 @@ pub(crate) struct FileCache {
     /// Represented as the number of milliseconds since Unix epoch. This will
     /// break in 1970 + ~584 years (~2554).
     last_seen: AtomicU64,
-    /// Imports made.
+
-    imports: ImportMap,
+    data: FileCacheData,
-    /// Diagnostic messages.
-    messages: Vec<CacheMessage>,
-    /// Source code of the file.
-    ///
-    /// # Notes
-    ///
-    /// This will be empty if `messages` is empty.
-    source: String,
-    /// Notebook index if this file is a Jupyter Notebook.
-    notebook_index: Option<NotebookIndex>,
 }
 
 impl FileCache {
     /// Convert the file cache into `Diagnostics`, using `path` as file name.
-    pub(crate) fn as_diagnostics(&self, path: &Path) -> Diagnostics {
+    pub(crate) fn to_diagnostics(&self, path: &Path) -> Option<Diagnostics> {
-        let messages = if self.messages.is_empty() {
+        self.data.lint.as_ref().map(|lint| {
-            Vec::new()
+            let messages = if lint.messages.is_empty() {
-        } else {
+                Vec::new()
-            let file = SourceFileBuilder::new(path.to_string_lossy(), &*self.source).finish();
+            } else {
-            self.messages
+                let file = SourceFileBuilder::new(path.to_string_lossy(), &*lint.source).finish();
-                .iter()
+                lint.messages
-                .map(|msg| Message {
+                    .iter()
-                    kind: msg.kind.clone(),
+                    .map(|msg| Message {
-                    range: msg.range,
+                        kind: msg.kind.clone(),
-                    fix: msg.fix.clone(),
+                        range: msg.range,
-                    file: file.clone(),
+                        fix: msg.fix.clone(),
-                    noqa_offset: msg.noqa_offset,
+                        file: file.clone(),
-                })
+                        noqa_offset: msg.noqa_offset,
-                .collect()
+                    })
-        };
+                    .collect()
-        let notebook_indexes = if let Some(notebook_index) = self.notebook_index.as_ref() {
+            };
-            FxHashMap::from_iter([(path.to_string_lossy().to_string(), notebook_index.clone())])
+            let notebook_indexes = if let Some(notebook_index) = lint.notebook_index.as_ref() {
-        } else {
+                FxHashMap::from_iter([(path.to_string_lossy().to_string(), notebook_index.clone())])
-            FxHashMap::default()
+            } else {
-        };
+                FxHashMap::default()
-        Diagnostics::new(messages, self.imports.clone(), notebook_indexes)
+            };
+            Diagnostics::new(messages, lint.imports.clone(), notebook_indexes)
+        })
     }
 }
 
-/// On disk representation of a diagnostic message.
+#[derive(Debug, Default, Deserialize, Serialize)]
-#[derive(Deserialize, Debug, Serialize)]
+struct FileCacheData {
-struct CacheMessage {
+    lint: Option<LintCacheData>,
-    kind: DiagnosticKind,
+    formatted: bool,
-    /// Range into the message's [`FileCache::source`].
-    range: TextRange,
-    fix: Option<Fix>,
-    noqa_offset: TextSize,
 }
 
 /// Returns a hash key based on the `package_root`, `settings` and the crate
@@ -335,32 +376,209 @@ pub(crate) fn init(path: &Path) -> Result<()> {
     Ok(())
 }
 
+#[derive(Deserialize, Debug, Serialize, PartialEq)]
+pub(crate) struct LintCacheData {
+    /// Imports made.
+    pub(super) imports: ImportMap,
+    /// Diagnostic messages.
+    pub(super) messages: Vec<CacheMessage>,
+    /// Source code of the file.
+    ///
+    /// # Notes
+    ///
+    /// This will be empty if `messages` is empty.
+    pub(super) source: String,
+    /// Notebook index if this file is a Jupyter Notebook.
+    pub(super) notebook_index: Option<NotebookIndex>,
+}
+
+impl LintCacheData {
+    pub(crate) fn from_messages(
+        messages: &[Message],
+        imports: ImportMap,
+        notebook_index: Option<NotebookIndex>,
+    ) -> Self {
+        let source = if let Some(msg) = messages.first() {
+            msg.file.source_text().to_owned()
+        } else {
+            String::new() // No messages, no need to keep the source!
+        };
+
+        let messages = messages
+            .iter()
+            .map(|msg| {
+                // Make sure that all message use the same source file.
+                assert_eq!(
+                    msg.file,
+                    messages.first().unwrap().file,
+                    "message uses a different source file"
+                );
+                CacheMessage {
+                    kind: msg.kind.clone(),
+                    range: msg.range,
+                    fix: msg.fix.clone(),
+                    noqa_offset: msg.noqa_offset,
+                }
+            })
+            .collect();
+
+        Self {
+            imports,
+            messages,
+            source,
+            notebook_index,
+        }
+    }
+}
+
+/// On disk representation of a diagnostic message.
+#[derive(Deserialize, Debug, Serialize, PartialEq)]
+pub(super) struct CacheMessage {
+    kind: DiagnosticKind,
+    /// Range into the message's [`FileCache::source`].
+    range: TextRange,
+    fix: Option<Fix>,
+    noqa_offset: TextSize,
+}
+
+pub(crate) trait PackageCaches {
+    fn get(&self, package_root: &Path) -> Option<&Cache>;
+
+    fn persist(self) -> anyhow::Result<()>;
+}
+
+impl<T> PackageCaches for Option<T>
+where
+    T: PackageCaches,
+{
+    fn get(&self, package_root: &Path) -> Option<&Cache> {
+        match self {
+            None => None,
+            Some(caches) => caches.get(package_root),
+        }
+    }
+
+    fn persist(self) -> Result<()> {
+        match self {
+            None => Ok(()),
+            Some(caches) => caches.persist(),
+        }
+    }
+}
+
+pub(crate) struct PackageCacheMap<'a>(FxHashMap<&'a Path, Cache>);
+
+impl<'a> PackageCacheMap<'a> {
+    pub(crate) fn init(
+        pyproject_config: &PyprojectConfig,
+        package_roots: &FxHashMap<&'a Path, Option<&'a Path>>,
+        resolver: &Resolver,
+    ) -> Self {
+        fn init_cache(path: &Path) {
+            if let Err(e) = cache::init(path) {
+                error!("Failed to initialize cache at {}: {e:?}", path.display());
+            }
+        }
+
+        match pyproject_config.strategy {
+            PyprojectDiscoveryStrategy::Fixed => {
+                init_cache(&pyproject_config.settings.cache_dir);
+            }
+            PyprojectDiscoveryStrategy::Hierarchical => {
+                for settings in
+                    std::iter::once(&pyproject_config.settings).chain(resolver.settings())
+                {
+                    init_cache(&settings.cache_dir);
+                }
+            }
+        }
+
+        Self(
+            package_roots
+                .iter()
+                .map(|(package, package_root)| package_root.unwrap_or(package))
+                .unique()
+                .par_bridge()
+                .map(|cache_root| {
+                    let settings = resolver.resolve(cache_root, pyproject_config);
+                    let cache = Cache::open(cache_root.to_path_buf(), settings);
+                    (cache_root, cache)
+                })
+                .collect(),
+        )
+    }
+}
+
+impl PackageCaches for PackageCacheMap<'_> {
+    fn get(&self, package_root: &Path) -> Option<&Cache> {
+        let cache = self.0.get(package_root);
+
+        if cache.is_none() {
+            debug!("No cache found for {}", package_root.display());
+        }
+
+        cache
+    }
+
+    fn persist(self) -> Result<()> {
+        self.0
+            .into_par_iter()
+            .try_for_each(|(_, cache)| cache.persist())
+    }
+}
+
+#[derive(Debug)]
+struct Change {
+    path: PathBuf,
+    new_key: u64,
+    new_data: ChangeData,
+}
+
+#[derive(Debug)]
+enum ChangeData {
+    Lint(LintCacheData),
+    Formatted,
+}
+
+impl ChangeData {
+    fn apply(self, data: &mut FileCacheData) {
+        match self {
+            ChangeData::Lint(new_lint) => {
+                data.lint = Some(new_lint);
+            }
+            ChangeData::Formatted => {
+                data.formatted = true;
+            }
+        }
+    }
+}
+
 #[cfg(test)]
 mod tests {
-    use filetime::{set_file_mtime, FileTime};
-    use ruff_linter::settings::types::UnsafeFixes;
     use std::env::temp_dir;
     use std::fs;
     use std::io;
     use std::io::Write;
     use std::path::{Path, PathBuf};
+    use std::sync::atomic::AtomicU64;
     use std::time::SystemTime;
 
+    use anyhow::Result;
+    use filetime::{set_file_mtime, FileTime};
     use itertools::Itertools;
+    use test_case::test_case;
+
     use ruff_cache::CACHE_DIR_NAME;
     use ruff_linter::settings::flags;
-
+    use ruff_linter::settings::types::UnsafeFixes;
-    use crate::cache::RelativePathBuf;
+    use ruff_linter::source_kind::SourceKind;
-    use crate::cache::{self, Cache, FileCache};
+    use ruff_python_ast::PySourceType;
-    use crate::diagnostics::{lint_path, Diagnostics};
-
-    use std::sync::atomic::AtomicU64;
-
-    use anyhow::Result;
-    use ruff_python_ast::imports::ImportMap;
-
     use ruff_workspace::Settings;
-    use test_case::test_case;
+
+    use crate::cache::{self, FileCache, FileCacheData, FileCacheKey};
+    use crate::cache::{Cache, RelativePathBuf};
+    use crate::commands::format::{format_path, FormatCommandError, FormatMode, FormatResult};
+    use crate::diagnostics::{lint_path, Diagnostics};
 
     #[test_case("../ruff_linter/resources/test/fixtures", "ruff_tests/cache_same_results_ruff_linter"; "ruff_linter_fixtures")]
     #[test_case("../ruff_notebook/resources/test/fixtures", "ruff_tests/cache_same_results_ruff_notebook"; "ruff_notebook_fixtures")]
@@ -377,7 +595,7 @@ mod tests {
 
         let package_root = fs::canonicalize(package_root).unwrap();
         let cache = Cache::open(package_root.clone(), &settings);
-        assert_eq!(cache.new_files.lock().unwrap().len(), 0);
+        assert_eq!(cache.changes.lock().unwrap().len(), 0);
 
         let mut paths = Vec::new();
         let mut parse_errors = Vec::new();
@@ -427,7 +645,7 @@ mod tests {
         }
         assert_ne!(paths, &[] as &[std::path::PathBuf], "no files checked");
 
-        cache.store().unwrap();
+        cache.persist().unwrap();
 
         let cache = Cache::open(package_root.clone(), &settings);
         assert_ne!(cache.package.files.len(), 0);
@@ -472,21 +690,21 @@ mod tests {
         let test_cache = TestCache::new("cache_adds_file_on_lint");
         let cache = test_cache.open();
         test_cache.write_source_file("source.py", source);
-        assert_eq!(cache.new_files.lock().unwrap().len(), 0);
+        assert_eq!(cache.changes.lock().unwrap().len(), 0);
 
-        cache.store().unwrap();
+        cache.persist().unwrap();
         let cache = test_cache.open();
 
         test_cache
             .lint_file_with_cache("source.py", &cache)
             .expect("Failed to lint test file");
         assert_eq!(
-            cache.new_files.lock().unwrap().len(),
+            cache.changes.lock().unwrap().len(),
             1,
             "A single new file should be added to the cache"
         );
 
-        cache.store().unwrap();
+        cache.persist().unwrap();
     }
 
     #[test]
@@ -497,9 +715,9 @@ mod tests {
         let cache = test_cache.open();
         test_cache.write_source_file("source_1.py", source);
         test_cache.write_source_file("source_2.py", source);
-        assert_eq!(cache.new_files.lock().unwrap().len(), 0);
+        assert_eq!(cache.changes.lock().unwrap().len(), 0);
 
-        cache.store().unwrap();
+        cache.persist().unwrap();
         let cache = test_cache.open();
 
         test_cache
@@ -509,12 +727,39 @@ mod tests {
             .lint_file_with_cache("source_2.py", &cache)
             .expect("Failed to lint test file");
         assert_eq!(
-            cache.new_files.lock().unwrap().len(),
+            cache.changes.lock().unwrap().len(),
+            2,
+            "Both files should be added to the cache"
+        );
+        cache.persist().unwrap();
+    }
+
+    #[test]
+    fn cache_adds_files_on_format() {
+        let source: &[u8] = b"a = 1\n\n__all__ = list([\"a\", \"b\"])\n";
+
+        let test_cache = TestCache::new("cache_adds_files_on_format");
+        let cache = test_cache.open();
+        test_cache.write_source_file("source_1.py", source);
+        test_cache.write_source_file("source_2.py", source);
+        assert_eq!(cache.changes.lock().unwrap().len(), 0);
+
+        cache.persist().unwrap();
+        let cache = test_cache.open();
+
+        test_cache
+            .format_file_with_cache("source_1.py", &cache)
+            .expect("Failed to format test file");
+        test_cache
+            .format_file_with_cache("source_2.py", &cache)
+            .expect("Failed to format test file");
+        assert_eq!(
+            cache.changes.lock().unwrap().len(),
             2,
             "Both files should be added to the cache"
         );
 
-        cache.store().unwrap();
+        cache.persist().unwrap();
     }
 
     #[test]
@@ -524,13 +769,13 @@ mod tests {
         let test_cache = TestCache::new("cache_invalidated_on_file_modified_time");
         let cache = test_cache.open();
         let source_path = test_cache.write_source_file("source.py", source);
-        assert_eq!(cache.new_files.lock().unwrap().len(), 0);
+        assert_eq!(cache.changes.lock().unwrap().len(), 0);
 
         let expected_diagnostics = test_cache
             .lint_file_with_cache("source.py", &cache)
             .expect("Failed to lint test file");
 
-        cache.store().unwrap();
+        cache.persist().unwrap();
         let cache = test_cache.open();
 
         // Update the modified time of the file to a time in the future
@@ -545,7 +790,7 @@ mod tests {
             .expect("Failed to lint test file");
 
         assert_eq!(
-            cache.new_files.lock().unwrap().len(),
+            cache.changes.lock().unwrap().len(),
             1,
             "Cache should not be used, the file should be treated as new and added to the cache"
         );
@@ -583,13 +828,13 @@ mod tests {
         let test_cache = TestCache::new("cache_invalidated_on_permission_change");
         let cache = test_cache.open();
         let path = test_cache.write_source_file("source.py", source);
-        assert_eq!(cache.new_files.lock().unwrap().len(), 0);
+        assert_eq!(cache.changes.lock().unwrap().len(), 0);
 
         let expected_diagnostics = test_cache
             .lint_file_with_cache("source.py", &cache)
             .unwrap();
 
-        cache.store().unwrap();
+        cache.persist().unwrap();
         let cache = test_cache.open();
 
         // Flip the permissions on the file
@@ -603,7 +848,7 @@ mod tests {
             .unwrap();
 
         assert_eq!(
-            cache.new_files.lock().unwrap().len(),
+            cache.changes.lock().unwrap().len(),
             1,
             "Cache should not be used, the file should be treated as new and added to the cache"
         );
@@ -615,8 +860,8 @@ mod tests {
     }
 
     #[test]
-    fn cache_removes_stale_files_on_store() {
+    fn cache_removes_stale_files_on_persist() {
-        let test_cache = TestCache::new("cache_removes_stale_files_on_store");
+        let test_cache = TestCache::new("cache_removes_stale_files_on_persist");
         let mut cache = test_cache.open();
 
         // Add a file to the cache that hasn't been linted or seen since the '70s!
@@ -626,10 +871,7 @@ mod tests {
             FileCache {
                 key: 123,
                 last_seen: AtomicU64::new(123),
-                imports: ImportMap::new(),
+                data: FileCacheData::default(),
-                messages: Vec::new(),
-                source: String::new(),
-                notebook_index: None,
             },
         );
 
@@ -637,34 +879,125 @@ mod tests {
         let source: &[u8] = b"a = 1\n\n__all__ = list([\"a\", \"b\"])\n";
         test_cache.write_source_file("new.py", source);
         let new_path_key = RelativePathBuf::from("new.py");
-        assert_eq!(cache.new_files.lock().unwrap().len(), 0);
+        assert_eq!(cache.changes.lock().unwrap().len(), 0);
 
         test_cache
             .lint_file_with_cache("new.py", &cache)
             .expect("Failed to lint test file");
 
         // Storing the cache should remove the old (`old.py`) file.
-        cache.store().unwrap();
+        cache.persist().unwrap();
         // So we when we open the cache again it shouldn't contain `old.py`.
         let cache = test_cache.open();
 
-        assert!(
+        assert_eq!(
-            cache.package.files.keys().collect_vec() == vec![&new_path_key],
+            cache.package.files.keys().collect_vec(),
+            vec![&new_path_key],
             "Only the new file should be present"
         );
     }
 
+    #[test]
+    fn format_updates_cache_entry() {
+        let source: &[u8] = b"a = 1\n\n__all__ = list([\"a\", \"b\"])\n";
+
+        let test_cache = TestCache::new("format_updates_cache_entry");
+        let cache = test_cache.open();
+        test_cache.write_source_file("source.py", source);
+        assert_eq!(cache.changes.lock().unwrap().len(), 0);
+
+        cache.persist().unwrap();
+        let cache = test_cache.open();
+
+        // Cache the lint results
+        test_cache
+            .lint_file_with_cache("source.py", &cache)
+            .expect("Failed to lint test file");
+        cache.persist().unwrap();
+
+        let mut cache = test_cache.open();
+
+        // Now lint the file
+        test_cache
+            .format_file_with_cache("source.py", &cache)
+            .expect("Failed to format test file");
+
+        cache.save();
+
+        assert_eq!(cache.package.files.len(), 1);
+
+        let Some(file_cache) = cache.get(
+            Path::new("source.py"),
+            &FileCacheKey::from_path(&test_cache.package_root.join("source.py")).unwrap(),
+        ) else {
+            panic!("Cache entry for `source.py` is missing.");
+        };
+
+        assert!(file_cache.data.lint.is_some());
+        assert!(file_cache.data.formatted);
+    }
+
+    #[test]
+    fn file_changes_invalidate_file_cache() {
+        let source: &[u8] = b"a = 1\n\n__all__ = list([\"a\", \"b\"])\n";
+
+        let test_cache = TestCache::new("file_changes_invalidate_file_cache");
+        let cache = test_cache.open();
+        let source_path = test_cache.write_source_file("source.py", source);
+        assert_eq!(cache.changes.lock().unwrap().len(), 0);
+
+        cache.persist().unwrap();
+        let cache = test_cache.open();
+
+        // Cache the format and lint results
+        test_cache
+            .lint_file_with_cache("source.py", &cache)
+            .expect("Failed to lint test file");
+        test_cache
+            .format_file_with_cache("source.py", &cache)
+            .expect("Failed to format test file");
+
+        cache.persist().unwrap();
+
+        let mut cache = test_cache.open();
+        assert_eq!(cache.package.files.len(), 1);
+
+        set_file_mtime(
+            &source_path,
+            FileTime::from_system_time(SystemTime::now() + std::time::Duration::from_secs(1)),
+        )
+        .unwrap();
+
+        test_cache
+            .format_file_with_cache("source.py", &cache)
+            .expect("Failed to format test file");
+
+        cache.save();
+
+        assert_eq!(cache.package.files.len(), 1);
+
+        let Some(file_cache) = cache.get(
+            Path::new("source.py"),
+            &FileCacheKey::from_path(&source_path).unwrap(),
+        ) else {
+            panic!("Cache entry for `source.py` is missing.");
+        };
+
+        assert_eq!(file_cache.data.lint, None);
+        assert!(file_cache.data.formatted);
+    }
+
     struct TestCache {
         package_root: PathBuf,
         settings: Settings,
     }
 
     impl TestCache {
-        fn new(name: &str) -> Self {
+        fn new(test_case: &str) -> Self {
             // Build a new cache directory and clear it
             let mut test_dir = temp_dir();
             test_dir.push("ruff_tests/cache");
-            test_dir.push(name);
+            test_dir.push(test_case);
 
             let _ = fs::remove_dir_all(&test_dir);
 
@@ -718,6 +1051,22 @@ mod tests {
                 UnsafeFixes::Enabled,
             )
         }
+
+        fn format_file_with_cache(
+            &self,
+            path: &str,
+            cache: &Cache,
+        ) -> Result<FormatResult, FormatCommandError> {
+            let file_path = self.package_root.join(path);
+            format_path(
+                &file_path,
+                &self.settings.formatter,
+                &SourceKind::Python(std::fs::read_to_string(&file_path).unwrap()),
+                PySourceType::Python,
+                FormatMode::Write,
+                Some(cache),
+            )
+        }
     }
 
     impl Drop for TestCache {

crates/ruff_cli/src/commands/check.rs

@@ -1,4 +1,3 @@
-use std::collections::HashMap;
 use std::fmt::Write;
 use std::io;
 use std::path::{Path, PathBuf};
@@ -7,28 +6,26 @@ use std::time::Instant;
 use anyhow::Result;
 use colored::Colorize;
 use ignore::Error;
-use itertools::Itertools;
 use log::{debug, error, warn};
 #[cfg(not(target_family = "wasm"))]
 use rayon::prelude::*;
-use ruff_linter::settings::types::UnsafeFixes;
 use rustc_hash::FxHashMap;
 
 use ruff_diagnostics::Diagnostic;
 use ruff_linter::message::Message;
 use ruff_linter::registry::Rule;
+use ruff_linter::settings::types::UnsafeFixes;
 use ruff_linter::settings::{flags, LinterSettings};
 use ruff_linter::{fs, warn_user_once, IOError};
 use ruff_python_ast::imports::ImportMap;
 use ruff_source_file::SourceFileBuilder;
 use ruff_text_size::{TextRange, TextSize};
 use ruff_workspace::resolver::{
-    match_exclusion, python_files_in_path, PyprojectConfig, PyprojectDiscoveryStrategy,
+    match_exclusion, python_files_in_path, PyprojectConfig, ResolvedFile,
-    ResolvedFile,
 };
 
 use crate::args::CliOverrides;
-use crate::cache::{self, Cache};
+use crate::cache::{Cache, PackageCacheMap, PackageCaches};
 use crate::diagnostics::Diagnostics;
 use crate::panic::catch_unwind;
 
@@ -52,28 +49,6 @@ pub(crate) fn check(
         return Ok(Diagnostics::default());
     }
 
-    // Initialize the cache.
-    if cache.into() {
-        fn init_cache(path: &Path) {
-            if let Err(e) = cache::init(path) {
-                error!("Failed to initialize cache at {}: {e:?}", path.display());
-            }
-        }
-
-        match pyproject_config.strategy {
-            PyprojectDiscoveryStrategy::Fixed => {
-                init_cache(&pyproject_config.settings.cache_dir);
-            }
-            PyprojectDiscoveryStrategy::Hierarchical => {
-                for settings in
-                    std::iter::once(&pyproject_config.settings).chain(resolver.settings())
-                {
-                    init_cache(&settings.cache_dir);
-                }
-            }
-        }
-    };
-
     // Discover the package root for each Python file.
     let package_roots = resolver.package_roots(
         &paths
@@ -85,19 +60,15 @@ pub(crate) fn check(
     );
 
     // Load the caches.
-    let caches = bool::from(cache).then(|| {
+    let caches = if bool::from(cache) {
-        package_roots
+        Some(PackageCacheMap::init(
-            .iter()
+            pyproject_config,
-            .map(|(package, package_root)| package_root.unwrap_or(package))
+            &package_roots,
-            .unique()
+            &resolver,
-            .par_bridge()
+        ))
-            .map(|cache_root| {
+    } else {
-                let settings = resolver.resolve(cache_root, pyproject_config);
+        None
-                let cache = Cache::open(cache_root.to_path_buf(), settings);
+    };
-                (cache_root, cache)
-            })
-            .collect::<HashMap<&Path, Cache>>()
-    });
 
     let start = Instant::now();
     let diagnostics_per_file = paths.par_iter().filter_map(|resolved_file| {
@@ -122,14 +93,7 @@ pub(crate) fn check(
                 }
 
                 let cache_root = package.unwrap_or_else(|| path.parent().unwrap_or(path));
-                let cache = caches.as_ref().and_then(|caches| {
+                let cache = caches.get(cache_root);
-                    if let Some(cache) = caches.get(&cache_root) {
-                        Some(cache)
-                    } else {
-                        debug!("No cache found for {}", cache_root.display());
-                        None
-                    }
-                });
 
                 lint_path(
                     path,
@@ -210,11 +174,7 @@ pub(crate) fn check(
     all_diagnostics.messages.sort();
 
     // Store the caches.
-    if let Some(caches) = caches {
+    caches.persist()?;
-        caches
-            .into_par_iter()
-            .try_for_each(|(_, cache)| cache.store())?;
-    }
 
     let duration = start.elapsed();
     debug!("Checked {:?} files in: {:?}", checked_files, duration);
@@ -266,13 +226,12 @@ mod test {
     use std::os::unix::fs::OpenOptionsExt;
 
     use anyhow::Result;
-
-    use ruff_linter::settings::types::UnsafeFixes;
     use rustc_hash::FxHashMap;
     use tempfile::TempDir;
 
     use ruff_linter::message::{Emitter, EmitterContext, TextEmitter};
     use ruff_linter::registry::Rule;
+    use ruff_linter::settings::types::UnsafeFixes;
     use ruff_linter::settings::{flags, LinterSettings};
     use ruff_workspace::resolver::{PyprojectConfig, PyprojectDiscoveryStrategy};
     use ruff_workspace::Settings;

crates/ruff_cli/src/commands/format.rs

@@ -10,7 +10,7 @@ use colored::Colorize;
 use itertools::Itertools;
 use log::error;
 use rayon::iter::Either::{Left, Right};
-use rayon::iter::{IntoParallelIterator, ParallelIterator};
+use rayon::iter::{IntoParallelRefIterator, ParallelIterator};
 use similar::TextDiff;
 use thiserror::Error;
 use tracing::debug;
@@ -23,10 +23,11 @@ use ruff_linter::warn_user_once;
 use ruff_python_ast::{PySourceType, SourceType};
 use ruff_python_formatter::{format_module_source, FormatModuleError};
 use ruff_text_size::{TextLen, TextRange, TextSize};
-use ruff_workspace::resolver::{match_exclusion, python_files_in_path};
+use ruff_workspace::resolver::{match_exclusion, python_files_in_path, ResolvedFile};
 use ruff_workspace::FormatterSettings;
 
 use crate::args::{CliOverrides, FormatArguments};
+use crate::cache::{Cache, FileCacheKey, PackageCacheMap, PackageCaches};
 use crate::panic::{catch_unwind, PanicError};
 use crate::resolve::resolve;
 use crate::ExitStatus;
@@ -73,9 +74,34 @@ pub(crate) fn format(
         return Ok(ExitStatus::Success);
     }
 
+    // Discover the package root for each Python file.
+    let package_roots = resolver.package_roots(
+        &paths
+            .iter()
+            .flatten()
+            .map(ResolvedFile::path)
+            .collect::<Vec<_>>(),
+        &pyproject_config,
+    );
+
+    let caches = if cli.no_cache {
+        None
+    } else {
+        // `--no-cache` doesn't respect code changes, and so is often confusing during
+        // development.
+        #[cfg(debug_assertions)]
+        crate::warn_user!("Detected debug build without --no-cache.");
+
+        Some(PackageCacheMap::init(
+            &pyproject_config,
+            &package_roots,
+            &resolver,
+        ))
+    };
+
     let start = Instant::now();
     let (mut results, mut errors): (Vec<_>, Vec<_>) = paths
-        .into_par_iter()
+        .par_iter()
         .filter_map(|entry| {
             match entry {
                 Ok(resolved_file) => {
@@ -110,6 +136,13 @@ pub(crate) fn format(
                         }
                     };
 
+                    let package = path
+                        .parent()
+                        .and_then(|parent| package_roots.get(parent).copied())
+                        .flatten();
+                    let cache_root = package.unwrap_or_else(|| path.parent().unwrap_or(path));
+                    let cache = caches.get(cache_root);
+
                     Some(
                         match catch_unwind(|| {
                             format_path(
@@ -118,21 +151,22 @@ pub(crate) fn format(
                                 &unformatted,
                                 source_type,
                                 mode,
+                                cache,
                             )
                         }) {
                             Ok(inner) => inner.map(|result| FormatPathResult {
-                                path: resolved_file.into_path(),
+                                path: resolved_file.path().to_path_buf(),
                                 unformatted,
                                 result,
                             }),
                             Err(error) => Err(FormatCommandError::Panic(
-                                Some(resolved_file.into_path()),
+                                Some(resolved_file.path().to_path_buf()),
                                 error,
                             )),
                         },
                     )
                 }
-                Err(err) => Some(Err(FormatCommandError::Ignore(err))),
+                Err(err) => Some(Err(FormatCommandError::Ignore(err.clone()))),
             }
         })
         .partition_map(|result| match result {
@@ -168,6 +202,8 @@ pub(crate) fn format(
         duration
     );
 
+    caches.persist()?;
+
     // Report on any errors.
     for error in &errors {
         error!("{error}");
@@ -214,13 +250,26 @@ pub(crate) fn format(
 
 /// Format the file at the given [`Path`].
 #[tracing::instrument(level="debug", skip_all, fields(path = %path.display()))]
-fn format_path(
+pub(crate) fn format_path(
     path: &Path,
     settings: &FormatterSettings,
     unformatted: &SourceKind,
     source_type: PySourceType,
     mode: FormatMode,
+    cache: Option<&Cache>,
 ) -> Result<FormatResult, FormatCommandError> {
+    if let Some(cache) = cache {
+        let relative_path = cache
+            .relative_path(path)
+            .expect("wrong package cache for file");
+
+        if let Ok(cache_key) = FileCacheKey::from_path(path) {
+            if cache.is_formatted(relative_path, &cache_key) {
+                return Ok(FormatResult::Unchanged);
+            }
+        }
+    }
+
     // Format the source.
     let format_result = match format_source(unformatted, source_type, Some(path), settings)? {
         FormattedSource::Formatted(formatted) => match mode {
@@ -231,13 +280,35 @@ fn format_path(
                 formatted
                     .write(&mut writer)
                     .map_err(|err| FormatCommandError::Write(Some(path.to_path_buf()), err))?;
+
+                if let Some(cache) = cache {
+                    if let Ok(cache_key) = FileCacheKey::from_path(path) {
+                        let relative_path = cache
+                            .relative_path(path)
+                            .expect("wrong package cache for file");
+                        cache.set_formatted(relative_path.to_path_buf(), &cache_key);
+                    }
+                }
+
                 FormatResult::Formatted
             }
             FormatMode::Check => FormatResult::Formatted,
             FormatMode::Diff => FormatResult::Diff(formatted),
         },
-        FormattedSource::Unchanged => FormatResult::Unchanged,
+        FormattedSource::Unchanged => {
+            if let Some(cache) = cache {
+                if let Ok(cache_key) = FileCacheKey::from_path(path) {
+                    let relative_path = cache
+                        .relative_path(path)
+                        .expect("wrong package cache for file");
+                    cache.set_formatted(relative_path.to_path_buf(), &cache_key);
+                }
+            }
+
+            FormatResult::Unchanged
+        }
     };
+
     Ok(format_result)
 }
 

crates/ruff_cli/src/diagnostics.rs

@@ -3,16 +3,14 @@
 use std::fs::File;
 use std::io;
 use std::ops::{Add, AddAssign};
-#[cfg(unix)]
-use std::os::unix::fs::PermissionsExt;
 use std::path::Path;
 
 use anyhow::{Context, Result};
 use colored::Colorize;
-use filetime::FileTime;
 use log::{debug, error, warn};
 use rustc_hash::FxHashMap;
 
+use crate::cache::{Cache, FileCacheKey, LintCacheData};
 use ruff_diagnostics::Diagnostic;
 use ruff_linter::linter::{lint_fix, lint_only, FixTable, FixerResult, LinterResult};
 use ruff_linter::logging::DisplayParseError;
@@ -23,7 +21,6 @@ use ruff_linter::settings::types::UnsafeFixes;
 use ruff_linter::settings::{flags, LinterSettings};
 use ruff_linter::source_kind::{SourceError, SourceKind};
 use ruff_linter::{fs, IOError, SyntaxError};
-use ruff_macros::CacheKey;
 use ruff_notebook::{Notebook, NotebookError, NotebookIndex};
 use ruff_python_ast::imports::ImportMap;
 use ruff_python_ast::{SourceType, TomlSourceType};
@@ -31,33 +28,6 @@ use ruff_source_file::{LineIndex, SourceCode, SourceFileBuilder};
 use ruff_text_size::{TextRange, TextSize};
 use ruff_workspace::Settings;
 
-use crate::cache::Cache;
-
-#[derive(CacheKey)]
-pub(crate) struct FileCacheKey {
-    /// Timestamp when the file was last modified before the (cached) check.
-    file_last_modified: FileTime,
-    /// Permissions of the file before the (cached) check.
-    file_permissions_mode: u32,
-}
-
-impl FileCacheKey {
-    fn from_path(path: &Path) -> io::Result<FileCacheKey> {
-        // Construct a cache key for the file
-        let metadata = path.metadata()?;
-
-        #[cfg(unix)]
-        let permissions = metadata.permissions().mode();
-        #[cfg(windows)]
-        let permissions: u32 = metadata.permissions().readonly().into();
-
-        Ok(FileCacheKey {
-            file_last_modified: FileTime::from_last_modification_time(&metadata),
-            file_permissions_mode: permissions,
-        })
-    }
-}
-
 #[derive(Debug, Default, PartialEq)]
 pub(crate) struct Diagnostics {
     pub(crate) messages: Vec<Message>,
@@ -230,9 +200,11 @@ pub(crate) fn lint_path(
                 .expect("wrong package cache for file");
 
             let cache_key = FileCacheKey::from_path(path).context("Failed to create cache key")?;
-
+            let cached_diagnostics = cache
-            if let Some(cache) = cache.get(relative_path, &cache_key) {
+                .get(relative_path, &cache_key)
-                return Ok(cache.as_diagnostics(path));
+                .and_then(|entry| entry.to_diagnostics(path));
+            if let Some(diagnostics) = cached_diagnostics {
+                return Ok(diagnostics);
             }
 
             // Stash the file metadata for later so when we update the cache it reflects the prerun
@@ -332,12 +304,14 @@ pub(crate) fn lint_path(
     if let Some((cache, relative_path, key)) = caching {
         // We don't cache parsing errors.
         if parse_error.is_none() {
-            cache.update(
+            cache.update_lint(
                 relative_path.to_owned(),
-                key,
+                &key,
-                &messages,
+                LintCacheData::from_messages(
-                &imports,
+                    &messages,
-                source_kind.as_ipy_notebook().map(Notebook::index),
+                    imports.clone(),
+                    source_kind.as_ipy_notebook().map(Notebook::index).cloned(),
+                ),
             );
         }
     }

crates/ruff_cli/tests/format.rs

@@ -110,7 +110,7 @@ fn mixed_line_endings() -> Result<()> {
 
     assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
         .current_dir(tempdir.path())
-        .args(["format", "--diff", "--isolated"])
+        .args(["format", "--no-cache", "--diff", "--isolated"])
         .arg("."), @r###"
     success: true
     exit_code: 0
@@ -173,7 +173,7 @@ OTHER = "OTHER"
 
     assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
         .current_dir(tempdir.path())
-        .args(["format", "--check", "--config"])
+        .args(["format", "--no-cache", "--check", "--config"])
         .arg(ruff_toml.file_name().unwrap())
         // Explicitly pass test.py, should be formatted regardless of it being excluded by format.exclude
         .arg(test_path.file_name().unwrap())
@@ -322,7 +322,7 @@ format = "json"
 
 #[test]
 fn test_diff() {
-    let args = ["format", "--isolated", "--diff"];
+    let args = ["format", "--no-cache", "--isolated", "--diff"];
     let fixtures = Path::new("resources").join("test").join("fixtures");
     let paths = [
         fixtures.join("unformatted.py"),
@@ -365,7 +365,7 @@ fn test_diff() {
 
 #[test]
 fn test_diff_no_change() {
-    let args = ["format", "--isolated", "--diff"];
+    let args = ["format", "--no-cache", "--isolated", "--diff"];
     let fixtures = Path::new("resources").join("test").join("fixtures");
     let paths = [fixtures.join("unformatted.py")];
     insta::with_settings!({filters => vec![

crates/ruff_cli/tests/integration_test.rs

@@ -1305,7 +1305,7 @@ extend-unsafe-fixes = ["UP034"]
         .args([
             "--output-format",
             "text",
-            "--no-cache", 
+            "--no-cache",
             "--select",
             "F601,UP034",
         ])
@@ -1344,7 +1344,7 @@ extend-safe-fixes = ["F601"]
         .args([
             "--output-format",
             "text",
-            "--no-cache", 
+            "--no-cache",
             "--select",
             "F601,UP034",
         ])

docs/configuration.md

@@ -390,15 +390,17 @@ Options:
   -h, --help
           Print help
 
+Miscellaneous:
+  -n, --no-cache                         Disable cache reads
+      --cache-dir <CACHE_DIR>            Path to the cache directory [env: RUFF_CACHE_DIR=]
+      --isolated                         Ignore all configuration files
+      --stdin-filename <STDIN_FILENAME>  The name of the file when passing it through stdin
+
 File selection:
       --respect-gitignore       Respect file exclusions via `.gitignore` and other standard ignore files. Use `--no-respect-gitignore` to disable
       --exclude <FILE_PATTERN>  List of paths, used to omit files and/or directories from analysis
       --force-exclude           Enforce exclusions, even for paths passed to Ruff directly on the command-line. Use `--no-force-exclude` to disable
 
-Miscellaneous:
-      --isolated                         Ignore all configuration files
-      --stdin-filename <STDIN_FILENAME>  The name of the file when passing it through stdin
-
 Log levels:
   -v, --verbose  Enable verbose logging
   -q, --quiet    Print diagnostics, but nothing else