ruff server: Support Jupyter Notebook (*.ipynb) files (#11206)

## Summary

Closes https://github.com/astral-sh/ruff/issues/10858.

`ruff server` now supports `*.ipynb` (aka Jupyter Notebook) files.
Extensive internal changes have been made to facilitate this, which I've
done some work to contextualize with documentation and an pre-review
that highlights notable sections of the code.

`*.ipynb` cells should behave similarly to `*.py` documents, with one
major exception. The format command `ruff.applyFormat` will only apply
to the currently selected notebook cell - if you want to format an
entire notebook document, use `Format Notebook` from the VS Code context
menu.

## Test Plan

The VS Code extension does not yet have Jupyter Notebook support
enabled, so you'll first need to enable it manually. To do this,
checkout the `pre-release` branch and modify `src/common/server.ts` as
follows:

Before:
![Screenshot 2024-05-13 at 10 59
06 PM](c6a3c604-c405-4968-b8a2-5d670de89172)

After:
![Screenshot 2024-05-13 at 10 58
24 PM](94ab2e3d-0609-448d-9c8c-cd07c69a513b)

I recommend testing this PR with large, complicated notebook files. I
used notebook files from [this popular
repository](https://github.com/jakevdp/PythonDataScienceHandbook/tree/master/notebooks)
in my preliminary testing.

The main thing to test is ensuring that notebook cells behave the same
as Python documents, besides the aforementioned issue with
`ruff.applyFormat`. You should also test adding and deleting cells (in
particular, deleting all the code cells and ensure that doesn't break
anything), changing the kind of a cell (i.e. from markup -> code or vice
versa), and creating a new notebook file from scratch. Finally, you
should also test that source actions work as expected (and across the
entire notebook).

Note: `ruff.applyAutofix` and `ruff.applyOrganizeImports` are currently
broken for notebook files, and I suspect it has something to do with
https://github.com/astral-sh/ruff/issues/11248. Once this is fixed, I
will update the test plan accordingly.

---------

Co-authored-by: nolan <nolan.king90@gmail.com>

Cargo.lock

@@ -1300,8 +1300,7 @@ dependencies = [
 [[package]]
 name = "lsp-types"
 version = "0.95.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
+source = "git+https://github.com/astral-sh/lsp-types.git?rev=3512a9f#3512a9f33eadc5402cfab1b8f7340824c8ca1439"
-checksum = "8e34d33a8e9b006cd3fc4fe69a921affa097bae4bb65f76271f4644f9a334365"
 dependencies = [
  "bitflags 1.3.2",
  "serde",
@@ -2377,6 +2376,7 @@ dependencies = [
  "ruff_diagnostics",
  "ruff_formatter",
  "ruff_linter",
+ "ruff_notebook",
  "ruff_python_ast",
  "ruff_python_codegen",
  "ruff_python_formatter",

Cargo.toml

@@ -81,7 +81,7 @@ libc = { version = "0.2.153" }
 libcst = { version = "1.1.0", default-features = false }
 log = { version = "0.4.17" }
 lsp-server = { version = "0.7.6" }
-lsp-types = { version = "0.95.0", features = ["proposed"] }
+lsp-types = { git="https://github.com/astral-sh/lsp-types.git", rev = "3512a9f", features = ["proposed"] }
 matchit = { version = "0.8.1" }
 memchr = { version = "2.7.1" }
 mimalloc = { version = "0.1.39" }

crates/ruff_notebook/src/cell.rs

@@ -23,7 +23,7 @@ impl fmt::Display for SourceValue {
 
 impl Cell {
     /// Return the [`SourceValue`] of the cell.
-    pub(crate) fn source(&self) -> &SourceValue {
+    pub fn source(&self) -> &SourceValue {
         match self {
             Cell::Code(cell) => &cell.source,
             Cell::Markdown(cell) => &cell.source,

crates/ruff_notebook/src/notebook.rs

@@ -98,7 +98,7 @@ impl Notebook {
             reader.read_exact(&mut buf).is_ok_and(|()| buf[0] == b'\n')
         });
         reader.rewind()?;
-        let mut raw_notebook: RawNotebook = match serde_json::from_reader(reader.by_ref()) {
+        let raw_notebook: RawNotebook = match serde_json::from_reader(reader.by_ref()) {
             Ok(notebook) => notebook,
             Err(err) => {
                 // Translate the error into a diagnostic
@@ -113,7 +113,13 @@ impl Notebook {
                 });
             }
         };
+        Self::from_raw_notebook(raw_notebook, trailing_newline)
+    }
 
+    pub fn from_raw_notebook(
+        mut raw_notebook: RawNotebook,
+        trailing_newline: bool,
+    ) -> Result<Self, NotebookError> {
         // v4 is what everybody uses
         if raw_notebook.nbformat != 4 {
             // bail because we should have already failed at the json schema stage

crates/ruff_server/Cargo.toml

@@ -21,6 +21,7 @@ ruff_python_codegen = { workspace = true }
 ruff_python_formatter = { workspace = true }
 ruff_python_index = { workspace = true }
 ruff_python_parser = { workspace = true }
+ruff_notebook = { path = "../ruff_notebook" }
 ruff_source_file = { workspace = true }
 ruff_text_size = { workspace = true }
 ruff_workspace = { workspace = true }

crates/ruff_server/src/edit.rs

@@ -1,18 +1,20 @@
 //! Types and utilities for working with text, modifying source files, and `Ruff <-> LSP` type conversion.
 
 mod document;
+mod notebook;
 mod range;
 mod replacement;
 
-use std::collections::HashMap;
+use std::{collections::HashMap, path::PathBuf};
 
-pub use document::Document;
 pub(crate) use document::DocumentVersion;
+pub use document::TextDocument;
 use lsp_types::PositionEncodingKind;
-pub(crate) use range::{RangeExt, ToRangeExt};
+pub(crate) use notebook::NotebookDocument;
+pub(crate) use range::{NotebookRange, RangeExt, ToRangeExt};
 pub(crate) use replacement::Replacement;
 
-use crate::session::ResolvedClientCapabilities;
+use crate::{fix::Fixes, session::ResolvedClientCapabilities};
 
 /// A convenient enumeration for supported text encodings. Can be converted to [`lsp_types::PositionEncodingKind`].
 // Please maintain the order from least to greatest priority for the derived `Ord` impl.
@@ -29,6 +31,37 @@ pub enum PositionEncoding {
     UTF8,
 }
 
+/// A unique document ID, derived from a URL passed as part of an LSP request.
+/// This document ID can point to either be a standalone Python file, a full notebook, or a cell within a notebook.
+#[derive(Clone, Debug)]
+pub(crate) enum DocumentKey {
+    Notebook(PathBuf),
+    NotebookCell(lsp_types::Url),
+    Text(PathBuf),
+}
+
+impl DocumentKey {
+    /// Converts the key back into its original URL.
+    pub(crate) fn into_url(self) -> lsp_types::Url {
+        match self {
+            DocumentKey::NotebookCell(url) => url,
+            DocumentKey::Notebook(path) | DocumentKey::Text(path) => {
+                lsp_types::Url::from_file_path(path)
+                    .expect("file path originally from URL should convert back to URL")
+            }
+        }
+    }
+}
+
+impl std::fmt::Display for DocumentKey {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            Self::NotebookCell(url) => url.fmt(f),
+            Self::Notebook(path) | Self::Text(path) => path.display().fmt(f),
+        }
+    }
+}
+
 /// Tracks multi-document edits to eventually merge into a `WorkspaceEdit`.
 /// Compatible with clients that don't support `workspace.workspaceEdit.documentChanges`.
 #[derive(Debug)]
@@ -72,13 +105,25 @@ impl WorkspaceEditTracker {
         }
     }
 
+    /// Sets a series of [`Fixes`] for a text or notebook document.
+    pub(crate) fn set_fixes_for_document(
+        &mut self,
+        fixes: Fixes,
+        version: DocumentVersion,
+    ) -> crate::Result<()> {
+        for (uri, edits) in fixes {
+            self.set_edits_for_document(uri, version, edits)?;
+        }
+        Ok(())
+    }
+
     /// Sets the edits made to a specific document. This should only be called
     /// once for each document `uri`, and will fail if this is called for the same `uri`
     /// multiple times.
     pub(crate) fn set_edits_for_document(
         &mut self,
         uri: lsp_types::Url,
-        version: DocumentVersion,
+        _version: DocumentVersion,
         edits: Vec<lsp_types::TextEdit>,
     ) -> crate::Result<()> {
         match self {
@@ -94,7 +139,8 @@ impl WorkspaceEditTracker {
                 document_edits.push(lsp_types::TextDocumentEdit {
                     text_document: lsp_types::OptionalVersionedTextDocumentIdentifier {
                         uri,
-                        version: Some(version),
+                        // TODO(jane): Re-enable versioned edits after investigating whether it could work with notebook cells
+                        version: None,
                     },
                     edits: edits.into_iter().map(lsp_types::OneOf::Left).collect(),
                 });

crates/ruff_server/src/edit/document.rs

@@ -7,10 +7,10 @@ use super::RangeExt;
 
 pub(crate) type DocumentVersion = i32;
 
-/// The state for an individual document in the server. Stays up-to-date
+/// The state of an individual document in the server. Stays up-to-date
 /// with changes made by the user, including unsaved changes.
 #[derive(Debug, Clone)]
-pub struct Document {
+pub struct TextDocument {
     /// The string contents of the document.
     contents: String,
     /// A computed line index for the document. This should always reflect
@@ -22,7 +22,7 @@ pub struct Document {
     version: DocumentVersion,
 }
 
-impl Document {
+impl TextDocument {
     pub fn new(contents: String, version: DocumentVersion) -> Self {
         let index = LineIndex::from_source_text(&contents);
         Self {

crates/ruff_server/src/edit/notebook.rs

@@ -0,0 +1,202 @@
+use std::{collections::HashMap, hash::BuildHasherDefault};
+
+use anyhow::Ok;
+use lsp_types::{NotebookCellKind, Url};
+use rustc_hash::FxHashMap;
+
+use crate::{PositionEncoding, TextDocument};
+
+use super::DocumentVersion;
+
+pub(super) type CellId = usize;
+
+/// The state of a notebook document in the server. Contains an array of cells whose
+/// contents are internally represented by [`TextDocument`]s.
+#[derive(Clone, Debug)]
+pub(crate) struct NotebookDocument {
+    cells: Vec<NotebookCell>,
+    metadata: ruff_notebook::RawNotebookMetadata,
+    version: DocumentVersion,
+    // Used to quickly find the index of a cell for a given URL.
+    cell_index: FxHashMap<lsp_types::Url, CellId>,
+}
+
+/// A single cell within a notebook, which has text contents represented as a `TextDocument`.
+#[derive(Clone, Debug)]
+struct NotebookCell {
+    url: Url,
+    kind: NotebookCellKind,
+    document: TextDocument,
+}
+
+impl NotebookDocument {
+    pub(crate) fn new(
+        version: DocumentVersion,
+        cells: Vec<lsp_types::NotebookCell>,
+        metadata: serde_json::Map<String, serde_json::Value>,
+        cell_documents: Vec<lsp_types::TextDocumentItem>,
+    ) -> crate::Result<Self> {
+        let mut cell_contents: FxHashMap<_, _> = cell_documents
+            .into_iter()
+            .map(|document| (document.uri, document.text))
+            .collect();
+
+        let cells: Vec<_> = cells
+            .into_iter()
+            .map(|cell| {
+                let contents = cell_contents.remove(&cell.document).unwrap_or_default();
+                NotebookCell::new(cell, contents, version)
+            })
+            .collect();
+
+        Ok(Self {
+            version,
+            cell_index: Self::make_cell_index(cells.as_slice()),
+            metadata: serde_json::from_value(serde_json::Value::Object(metadata))?,
+            cells,
+        })
+    }
+
+    /// Generates a pseudo-representation of a notebook that lacks per-cell metadata and contextual information
+    /// but should still work with Ruff's linter.
+    pub(crate) fn make_ruff_notebook(&self) -> ruff_notebook::Notebook {
+        let cells = self
+            .cells
+            .iter()
+            .map(|cell| match cell.kind {
+                NotebookCellKind::Code => ruff_notebook::Cell::Code(ruff_notebook::CodeCell {
+                    execution_count: None,
+                    id: None,
+                    metadata: serde_json::Value::Null,
+                    outputs: vec![],
+                    source: ruff_notebook::SourceValue::String(
+                        cell.document.contents().to_string(),
+                    ),
+                }),
+                NotebookCellKind::Markup => {
+                    ruff_notebook::Cell::Markdown(ruff_notebook::MarkdownCell {
+                        attachments: None,
+                        id: None,
+                        metadata: serde_json::Value::Null,
+                        source: ruff_notebook::SourceValue::String(
+                            cell.document.contents().to_string(),
+                        ),
+                    })
+                }
+            })
+            .collect();
+        let raw_notebook = ruff_notebook::RawNotebook {
+            cells,
+            metadata: self.metadata.clone(),
+            nbformat: 4,
+            nbformat_minor: 5,
+        };
+
+        ruff_notebook::Notebook::from_raw_notebook(raw_notebook, false)
+            .unwrap_or_else(|err| panic!("Server notebook document could not be converted to Ruff's notebook document format: {err}"))
+    }
+
+    pub(crate) fn update(
+        &mut self,
+        cells: Option<lsp_types::NotebookDocumentCellChange>,
+        metadata_change: Option<serde_json::Map<String, serde_json::Value>>,
+        version: DocumentVersion,
+        encoding: PositionEncoding,
+    ) -> crate::Result<()> {
+        self.version = version;
+
+        if let Some(lsp_types::NotebookDocumentCellChange {
+            structure,
+            data,
+            text_content,
+        }) = cells
+        {
+            if let Some(structure) = structure {
+                let start = structure.array.start as usize;
+                let delete = structure.array.delete_count as usize;
+                if delete > 0 {
+                    for cell in self.cells.drain(start..start + delete) {
+                        self.cell_index.remove(&cell.url);
+                    }
+                }
+                for cell in structure.array.cells.into_iter().flatten().rev() {
+                    self.cells
+                        .insert(start, NotebookCell::new(cell, String::new(), version));
+                }
+
+                // register any new cells in the index and update existing ones that came after the insertion
+                for (i, cell) in self.cells.iter().enumerate().skip(start) {
+                    self.cell_index.insert(cell.url.clone(), i);
+                }
+            }
+            if let Some(cell_data) = data {
+                for cell in cell_data {
+                    if let Some(existing_cell) = self.cell_by_uri_mut(&cell.document) {
+                        existing_cell.kind = cell.kind;
+                    }
+                }
+            }
+            if let Some(content_changes) = text_content {
+                for content_change in content_changes {
+                    if let Some(cell) = self.cell_by_uri_mut(&content_change.document.uri) {
+                        cell.document
+                            .apply_changes(content_change.changes, version, encoding);
+                    }
+                }
+            }
+        }
+        if let Some(metadata_change) = metadata_change {
+            self.metadata = serde_json::from_value(serde_json::Value::Object(metadata_change))?;
+        }
+        Ok(())
+    }
+
+    /// Get the current version of the notebook document.
+    pub(crate) fn version(&self) -> DocumentVersion {
+        self.version
+    }
+
+    /// Get the URI for a cell by its index within the cell array.
+    pub(crate) fn cell_uri_by_index(&self, index: CellId) -> Option<&lsp_types::Url> {
+        self.cells.get(index).map(|cell| &cell.url)
+    }
+
+    /// Get the text document representing the contents of a cell by the cell URI.
+    pub(crate) fn cell_document_by_uri(&self, uri: &lsp_types::Url) -> Option<&TextDocument> {
+        self.cells
+            .get(*self.cell_index.get(uri)?)
+            .map(|cell| &cell.document)
+    }
+
+    /// Returns a list of cell URIs in the order they appear in the array.
+    pub(crate) fn urls(&self) -> impl Iterator<Item = &lsp_types::Url> {
+        self.cells.iter().map(|cell| &cell.url)
+    }
+
+    fn cell_by_uri_mut(&mut self, uri: &lsp_types::Url) -> Option<&mut NotebookCell> {
+        self.cells.get_mut(*self.cell_index.get(uri)?)
+    }
+
+    fn make_cell_index(cells: &[NotebookCell]) -> FxHashMap<lsp_types::Url, CellId> {
+        let mut index =
+            HashMap::with_capacity_and_hasher(cells.len(), BuildHasherDefault::default());
+        for (i, cell) in cells.iter().enumerate() {
+            index.insert(cell.url.clone(), i);
+        }
+        index
+    }
+}
+
+impl NotebookCell {
+    pub(crate) fn new(
+        cell: lsp_types::NotebookCell,
+        contents: String,
+        version: DocumentVersion,
+    ) -> Self {
+        Self {
+            url: cell.document,
+            kind: cell.kind,
+            document: TextDocument::new(contents, version),
+        }
+    }
+}

crates/ruff_server/src/edit/range.rs

@@ -1,9 +1,16 @@
+use super::notebook;
 use super::PositionEncoding;
 use lsp_types as types;
+use ruff_notebook::NotebookIndex;
 use ruff_source_file::OneIndexed;
 use ruff_source_file::{LineIndex, SourceLocation};
 use ruff_text_size::{TextRange, TextSize};
 
+pub(crate) struct NotebookRange {
+    pub(crate) cell: notebook::CellId,
+    pub(crate) range: types::Range,
+}
+
 pub(crate) trait RangeExt {
     fn to_text_range(&self, text: &str, index: &LineIndex, encoding: PositionEncoding)
         -> TextRange;
@@ -11,6 +18,13 @@ pub(crate) trait RangeExt {
 
 pub(crate) trait ToRangeExt {
     fn to_range(&self, text: &str, index: &LineIndex, encoding: PositionEncoding) -> types::Range;
+    fn to_notebook_range(
+        &self,
+        text: &str,
+        source_index: &LineIndex,
+        notebook_index: &NotebookIndex,
+        encoding: PositionEncoding,
+    ) -> NotebookRange;
 }
 
 fn u32_index_to_usize(index: u32) -> usize {
@@ -83,8 +97,54 @@ impl RangeExt for lsp_types::Range {
 impl ToRangeExt for TextRange {
     fn to_range(&self, text: &str, index: &LineIndex, encoding: PositionEncoding) -> types::Range {
         types::Range {
-            start: offset_to_position(self.start(), text, index, encoding),
+            start: source_location_to_position(&offset_to_source_location(
-            end: offset_to_position(self.end(), text, index, encoding),
+                self.start(),
+                text,
+                index,
+                encoding,
+            )),
+            end: source_location_to_position(&offset_to_source_location(
+                self.end(),
+                text,
+                index,
+                encoding,
+            )),
+        }
+    }
+
+    fn to_notebook_range(
+        &self,
+        text: &str,
+        source_index: &LineIndex,
+        notebook_index: &NotebookIndex,
+        encoding: PositionEncoding,
+    ) -> NotebookRange {
+        let start = offset_to_source_location(self.start(), text, source_index, encoding);
+        let mut end = offset_to_source_location(self.end(), text, source_index, encoding);
+        let starting_cell = notebook_index.cell(start.row);
+
+        // weird edge case here - if the end of the range is where the newline after the cell got added (making it 'out of bounds')
+        // we need to move it one character back (which should place it at the end of the last line).
+        // we test this by checking if the ending offset is in a different (or nonexistent) cell compared to the cell of the starting offset.
+        if notebook_index.cell(end.row) != starting_cell {
+            end.row = end.row.saturating_sub(1);
+            end.column = offset_to_source_location(
+                self.end().checked_sub(1.into()).unwrap_or_default(),
+                text,
+                source_index,
+                encoding,
+            )
+            .column;
+        }
+
+        let start = source_location_to_position(&notebook_index.translate_location(&start));
+        let end = source_location_to_position(&notebook_index.translate_location(&end));
+
+        NotebookRange {
+            cell: starting_cell
+                .map(OneIndexed::to_zero_indexed)
+                .unwrap_or_default(),
+            range: types::Range { start, end },
         }
     }
 }
@@ -111,13 +171,13 @@ fn utf8_column_offset(utf16_code_unit_offset: u32, line: &str) -> TextSize {
     utf8_code_unit_offset
 }
 
-fn offset_to_position(
+fn offset_to_source_location(
     offset: TextSize,
     text: &str,
     index: &LineIndex,
     encoding: PositionEncoding,
-) -> types::Position {
+) -> SourceLocation {
-    let location = match encoding {
+    match encoding {
         PositionEncoding::UTF8 => {
             let row = index.line_index(offset);
             let column = offset - index.line_start(row, text);
@@ -143,8 +203,10 @@ fn offset_to_position(
             }
         }
         PositionEncoding::UTF32 => index.source_location(offset, text),
-    };
+    }
+}
 
+fn source_location_to_position(location: &SourceLocation) -> types::Position {
     types::Position {
         line: u32::try_from(location.row.to_zero_indexed()).expect("row usize fits in u32"),
         character: u32::try_from(location.column.to_zero_indexed())

crates/ruff_server/src/fix.rs

@@ -2,28 +2,29 @@ use ruff_linter::{
     linter::{FixerResult, LinterResult},
     packaging::detect_package_root,
     settings::{flags, types::UnsafeFixes, LinterSettings},
-    source_kind::SourceKind,
 };
-use ruff_python_ast::PySourceType;
+use ruff_notebook::SourceValue;
 use ruff_source_file::LineIndex;
+use rustc_hash::FxHashMap;
 use std::borrow::Cow;
 
 use crate::{
     edit::{Replacement, ToRangeExt},
+    session::DocumentQuery,
     PositionEncoding,
 };
 
+/// A simultaneous fix made across a single text document or among an arbitrary
+/// number of notebook cells.
+pub(crate) type Fixes = FxHashMap<lsp_types::Url, Vec<lsp_types::TextEdit>>;
+
 pub(crate) fn fix_all(
-    document: &crate::edit::Document,
+    query: &DocumentQuery,
-    document_url: &lsp_types::Url,
     linter_settings: &LinterSettings,
     encoding: PositionEncoding,
-) -> crate::Result<Vec<lsp_types::TextEdit>> {
+) -> crate::Result<Fixes> {
-    let source = document.contents();
+    let document_path = query.file_path();
-
+    let source_kind = query.make_source_kind();
-    let document_path = document_url
-        .to_file_path()
-        .expect("document URL should be a valid file path");
 
     let package = detect_package_root(
         document_path
@@ -32,10 +33,7 @@ pub(crate) fn fix_all(
         &linter_settings.namespace_packages,
     );
 
-    let source_type = PySourceType::default();
+    let source_type = query.source_type();
-
-    // TODO(jane): Support Jupyter Notebooks
-    let source_kind = SourceKind::Python(source.to_string());
 
     // We need to iteratively apply all safe fixes onto a single file and then
     // create a diff between the modified file and the original source to use as a single workspace
@@ -48,7 +46,7 @@ pub(crate) fn fix_all(
         result: LinterResult { error, .. },
         ..
     } = ruff_linter::linter::lint_fix(
-        &document_path,
+        document_path,
         package,
         flags::Noqa::Enabled,
         UnsafeFixes::Disabled,
@@ -66,27 +64,79 @@ pub(crate) fn fix_all(
 
     // fast path: if `transformed` is still borrowed, no changes were made and we can return early
     if let Cow::Borrowed(_) = transformed {
-        return Ok(vec![]);
+        return Ok(Fixes::default());
     }
 
-    let modified = transformed.source_code();
+    if let (Some(source_notebook), Some(modified_notebook)) =
+        (source_kind.as_ipy_notebook(), transformed.as_ipy_notebook())
+    {
+        fn cell_source(cell: &ruff_notebook::Cell) -> String {
+            match cell.source() {
+                SourceValue::String(string) => string.clone(),
+                SourceValue::StringArray(array) => array.join(""),
+            }
+        }
 
-    let modified_index = LineIndex::from_source_text(modified);
+        let Some(notebook) = query.as_notebook() else {
-
+            anyhow::bail!("Notebook document expected from notebook source kind");
-    let source_index = document.index();
+        };
+        let mut fixes = Fixes::default();
+        for ((source, modified), url) in source_notebook
+            .cells()
+            .iter()
+            .map(cell_source)
+            .zip(modified_notebook.cells().iter().map(cell_source))
+            .zip(notebook.urls())
+        {
+            let source_index = LineIndex::from_source_text(&source);
+            let modified_index = LineIndex::from_source_text(&modified);
 
             let Replacement {
                 source_range,
                 modified_range,
             } = Replacement::between(
-        source,
+                &source,
+                source_index.line_starts(),
+                &modified,
+                modified_index.line_starts(),
+            );
+
+            fixes.insert(
+                url.clone(),
+                vec![lsp_types::TextEdit {
+                    range: source_range.to_range(
+                        source_kind.source_code(),
+                        &source_index,
+                        encoding,
+                    ),
+                    new_text: modified[modified_range].to_owned(),
+                }],
+            );
+        }
+        Ok(fixes)
+    } else {
+        let source_index = LineIndex::from_source_text(source_kind.source_code());
+
+        let modified = transformed.source_code();
+        let modified_index = LineIndex::from_source_text(modified);
+
+        let Replacement {
+            source_range,
+            modified_range,
+        } = Replacement::between(
+            source_kind.source_code(),
             source_index.line_starts(),
             modified,
             modified_index.line_starts(),
         );
-
+        Ok([(
-    Ok(vec![lsp_types::TextEdit {
+            query.make_key().into_url(),
-        range: source_range.to_range(source, source_index, encoding),
+            vec![lsp_types::TextEdit {
+                range: source_range.to_range(source_kind.source_code(), &source_index, encoding),
                 new_text: modified[modified_range].to_owned(),
-    }])
+            }],
+        )]
+        .into_iter()
+        .collect())
+    }
 }

crates/ruff_server/src/format.rs

@@ -1,29 +1,28 @@
 use ruff_formatter::PrintedRange;
+use ruff_python_ast::PySourceType;
 use ruff_python_formatter::format_module_source;
 use ruff_text_size::TextRange;
 use ruff_workspace::FormatterSettings;
 
-use crate::edit::Document;
+use crate::edit::TextDocument;
 
 pub(crate) fn format(
-    document: &Document,
+    document: &TextDocument,
+    source_type: PySourceType,
     formatter_settings: &FormatterSettings,
 ) -> crate::Result<String> {
-    // TODO(jane): support Jupyter Notebook
+    let format_options = formatter_settings.to_format_options(source_type, document.contents());
-    let format_options = formatter_settings
-        .to_format_options(ruff_python_ast::PySourceType::Python, document.contents());
     let formatted = format_module_source(document.contents(), format_options)?;
     Ok(formatted.into_code())
 }
 
 pub(crate) fn format_range(
-    document: &Document,
+    document: &TextDocument,
+    source_type: PySourceType,
     formatter_settings: &FormatterSettings,
     range: TextRange,
 ) -> crate::Result<PrintedRange> {
-    // TODO(jane): support Jupyter Notebook
+    let format_options = formatter_settings.to_format_options(source_type, document.contents());
-    let format_options = formatter_settings
-        .to_format_options(ruff_python_ast::PySourceType::Python, document.contents());
 
     Ok(ruff_python_formatter::format_range(
         document.contents(),

crates/ruff_server/src/lib.rs

@@ -1,6 +1,6 @@
 //! ## The Ruff Language Server
 
-pub use edit::{Document, PositionEncoding};
+pub use edit::{PositionEncoding, TextDocument};
 use lsp_types::CodeActionKind;
 pub use server::Server;
 
@@ -19,6 +19,10 @@ pub(crate) const DIAGNOSTIC_NAME: &str = "Ruff";
 pub(crate) const SOURCE_FIX_ALL_RUFF: CodeActionKind = CodeActionKind::new("source.fixAll.ruff");
 pub(crate) const SOURCE_ORGANIZE_IMPORTS_RUFF: CodeActionKind =
     CodeActionKind::new("source.organizeImports.ruff");
+pub(crate) const NOTEBOOK_SOURCE_FIX_ALL_RUFF: CodeActionKind =
+    CodeActionKind::new("notebook.source.fixAll.ruff");
+pub(crate) const NOTEBOOK_SOURCE_ORGANIZE_IMPORTS_RUFF: CodeActionKind =
+    CodeActionKind::new("notebook.source.organizeImports.ruff");
 
 /// A common result type used in most cases where a
 /// result type is needed.

crates/ruff_server/src/lint.rs

@@ -10,26 +10,32 @@ use ruff_linter::{
     settings::{flags, LinterSettings},
     source_kind::SourceKind,
 };
-use ruff_python_ast::PySourceType;
+use ruff_notebook::Notebook;
 use ruff_python_codegen::Stylist;
 use ruff_python_index::Indexer;
 use ruff_python_parser::AsMode;
-use ruff_source_file::Locator;
+use ruff_source_file::{LineIndex, Locator};
-use ruff_text_size::Ranged;
+use ruff_text_size::{Ranged, TextRange};
+use rustc_hash::FxHashMap;
 use serde::{Deserialize, Serialize};
 
-use crate::{edit::ToRangeExt, PositionEncoding, DIAGNOSTIC_NAME};
+use crate::{
+    edit::{NotebookRange, ToRangeExt},
+    session::DocumentQuery,
+    PositionEncoding, DIAGNOSTIC_NAME,
+};
 
 /// This is serialized on the diagnostic `data` field.
 #[derive(Serialize, Deserialize, Debug, Clone)]
 pub(crate) struct AssociatedDiagnosticData {
     pub(crate) kind: DiagnosticKind,
-    /// A possible fix for the associated diagnostic.
+    /// Edits to fix the diagnostic. If this is empty, a fix
-    pub(crate) fix: Option<Fix>,
+    /// does not exist.
+    pub(crate) edits: Vec<lsp_types::TextEdit>,
     /// The NOQA code for the diagnostic.
     pub(crate) code: String,
     /// Possible edit to add a `noqa` comment which will disable this diagnostic.
-    pub(crate) noqa_edit: Option<ruff_diagnostics::Edit>,
+    pub(crate) noqa_edit: Option<lsp_types::TextEdit>,
 }
 
 /// Describes a fix for `fixed_diagnostic` that may have quick fix
@@ -49,18 +55,16 @@ pub(crate) struct DiagnosticFix {
     pub(crate) noqa_edit: Option<lsp_types::TextEdit>,
 }
 
+/// A series of diagnostics across a single text document or an arbitrary number of notebook cells.
+pub(crate) type Diagnostics = FxHashMap<lsp_types::Url, Vec<lsp_types::Diagnostic>>;
+
 pub(crate) fn check(
-    document: &crate::edit::Document,
+    query: &DocumentQuery,
-    document_url: &lsp_types::Url,
     linter_settings: &LinterSettings,
     encoding: PositionEncoding,
-) -> Vec<lsp_types::Diagnostic> {
+) -> Diagnostics {
-    let contents = document.contents();
+    let document_path = query.file_path();
-    let index = document.index().clone();
+    let source_kind = query.make_source_kind();
-
-    let document_path = document_url
-        .to_file_path()
-        .expect("document URL should be a valid file path");
 
     let package = detect_package_root(
         document_path
@@ -69,16 +73,15 @@ pub(crate) fn check(
         &linter_settings.namespace_packages,
     );
 
-    let source_type = PySourceType::default();
+    let source_type = query.source_type();
-
-    // TODO(jane): Support Jupyter Notebooks
-    let source_kind = SourceKind::Python(contents.to_string());
 
     // Tokenize once.
-    let tokens = ruff_python_parser::tokenize(contents, source_type.as_mode());
+    let tokens = ruff_python_parser::tokenize(source_kind.source_code(), source_type.as_mode());
+
+    let index = LineIndex::from_source_text(source_kind.source_code());
 
     // Map row and column locations to byte slices (lazily).
-    let locator = Locator::with_index(contents, index);
+    let locator = Locator::with_index(source_kind.source_code(), index.clone());
 
     // Detect the current code style (lazily).
     let stylist = Stylist::from_tokens(&tokens, &locator);
@@ -90,10 +93,8 @@ pub(crate) fn check(
     let directives = extract_directives(&tokens, Flags::all(), &locator, &indexer);
 
     // Generate checks.
-    let LinterResult {
+    let LinterResult { data, .. } = check_path(
-        data: diagnostics, ..
+        document_path,
-    } = check_path(
-        &document_path,
         package,
         &locator,
         &stylist,
@@ -107,8 +108,8 @@ pub(crate) fn check(
     );
 
     let noqa_edits = generate_noqa_edits(
-        &document_path,
+        document_path,
-        diagnostics.as_slice(),
+        data.as_slice(),
         &locator,
         indexer.comment_ranges(),
         &linter_settings.external,
@@ -116,16 +117,45 @@ pub(crate) fn check(
         stylist.line_ending(),
     );
 
-    diagnostics
+    let mut diagnostics = Diagnostics::default();
-        .into_iter()
+
-        .zip(noqa_edits)
+    // Populate all cell URLs with an empty diagnostic list.
-        .map(|(diagnostic, noqa_edit)| to_lsp_diagnostic(diagnostic, noqa_edit, document, encoding))
+    // This ensures that cells without diagnostics still get updated.
-        .collect()
+    if let Some(notebook) = query.as_notebook() {
+        for url in notebook.urls() {
+            diagnostics.entry(url.clone()).or_default();
+        }
     }
 
+    let lsp_diagnostics = data
+        .into_iter()
+        .zip(noqa_edits)
+        .map(|(diagnostic, noqa_edit)| {
+            to_lsp_diagnostic(diagnostic, &noqa_edit, &source_kind, &index, encoding)
+        });
+
+    if let Some(notebook) = query.as_notebook() {
+        for (index, diagnostic) in lsp_diagnostics {
+            let Some(uri) = notebook.cell_uri_by_index(index) else {
+                tracing::warn!("Unable to find notebook cell at index {index}.");
+                continue;
+            };
+            diagnostics.entry(uri.clone()).or_default().push(diagnostic);
+        }
+    } else {
+        for (_, diagnostic) in lsp_diagnostics {
+            diagnostics
+                .entry(query.make_key().into_url())
+                .or_default()
+                .push(diagnostic);
+        }
+    }
+
+    diagnostics
+}
+
+/// Converts LSP diagnostics to a list of `DiagnosticFix`es by deserializing associated data on each diagnostic.
 pub(crate) fn fixes_for_diagnostics(
-    document: &crate::edit::Document,
-    encoding: PositionEncoding,
     diagnostics: Vec<lsp_types::Diagnostic>,
 ) -> crate::Result<Vec<DiagnosticFix>> {
     diagnostics
@@ -139,36 +169,6 @@ pub(crate) fn fixes_for_diagnostics(
                 serde_json::from_value(data).map_err(|err| {
                     anyhow::anyhow!("failed to deserialize diagnostic data: {err}")
                 })?;
-            let edits = associated_data
-                .fix
-                .map(|fix| {
-                    fix.edits()
-                        .iter()
-                        .map(|edit| lsp_types::TextEdit {
-                            range: edit.range().to_range(
-                                document.contents(),
-                                document.index(),
-                                encoding,
-                            ),
-                            new_text: edit.content().unwrap_or_default().to_string(),
-                        })
-                        .collect()
-                })
-                .unwrap_or_default();
-
-            let noqa_edit =
-                associated_data
-                    .noqa_edit
-                    .as_ref()
-                    .map(|noqa_edit| lsp_types::TextEdit {
-                        range: noqa_edit.range().to_range(
-                            document.contents(),
-                            document.index(),
-                            encoding,
-                        ),
-                        new_text: noqa_edit.content().unwrap_or_default().to_string(),
-                    });
-
             Ok(Some(DiagnosticFix {
                 fixed_diagnostic,
                 code: associated_data.code,
@@ -176,22 +176,28 @@ pub(crate) fn fixes_for_diagnostics(
                     .kind
                     .suggestion
                     .unwrap_or(associated_data.kind.name),
-                edits,
+                noqa_edit: associated_data.noqa_edit,
-                noqa_edit,
+                edits: associated_data.edits,
             }))
         })
         .filter_map(crate::Result::transpose)
         .collect()
 }
 
+/// Generates an LSP diagnostic with an associated cell index for the diagnostic to go in.
+/// If the source kind is a text document, the cell index will always be `0`.
 fn to_lsp_diagnostic(
     diagnostic: Diagnostic,
-    noqa_edit: Option<Edit>,
+    noqa_edit: &Option<Edit>,
-    document: &crate::edit::Document,
+    source_kind: &SourceKind,
+    index: &LineIndex,
     encoding: PositionEncoding,
-) -> lsp_types::Diagnostic {
+) -> (usize, lsp_types::Diagnostic) {
     let Diagnostic {
-        kind, range, fix, ..
+        kind,
+        range: diagnostic_range,
+        fix,
+        ..
     } = diagnostic;
 
     let rule = kind.rule();
@@ -200,11 +206,24 @@ fn to_lsp_diagnostic(
 
     let data = (fix.is_some() || noqa_edit.is_some())
         .then(|| {
-            serde_json::to_value(&AssociatedDiagnosticData {
+            let edits = fix
+                .as_ref()
+                .into_iter()
+                .flat_map(Fix::edits)
+                .map(|edit| lsp_types::TextEdit {
+                    range: diagnostic_edit_range(edit.range(), source_kind, index, encoding),
+                    new_text: edit.content().unwrap_or_default().to_string(),
+                })
+                .collect();
+            let noqa_edit = noqa_edit.as_ref().map(|noqa_edit| lsp_types::TextEdit {
+                range: diagnostic_edit_range(noqa_edit.range(), source_kind, index, encoding),
+                new_text: noqa_edit.content().unwrap_or_default().to_string(),
+            });
+            serde_json::to_value(AssociatedDiagnosticData {
                 kind: kind.clone(),
-                fix,
-                code: rule.noqa_code().to_string(),
                 noqa_edit,
+                edits,
+                code: rule.noqa_code().to_string(),
             })
             .ok()
         })
@@ -212,8 +231,25 @@ fn to_lsp_diagnostic(
 
     let code = rule.noqa_code().to_string();
 
+    let range: lsp_types::Range;
+    let cell: usize;
+
+    if let Some(notebook_index) = source_kind.as_ipy_notebook().map(Notebook::index) {
+        NotebookRange { cell, range } = diagnostic_range.to_notebook_range(
+            source_kind.source_code(),
+            index,
+            notebook_index,
+            encoding,
+        );
+    } else {
+        cell = usize::default();
+        range = diagnostic_range.to_range(source_kind.source_code(), index, encoding);
+    }
+
+    (
+        cell,
         lsp_types::Diagnostic {
-        range: range.to_range(document.contents(), document.index(), encoding),
+            range,
             severity: Some(severity(&code)),
             tags: tags(&code),
             code: Some(lsp_types::NumberOrString::String(code)),
@@ -226,6 +262,22 @@ fn to_lsp_diagnostic(
             message: kind.body,
             related_information: None,
             data,
+        },
+    )
+}
+
+fn diagnostic_edit_range(
+    range: TextRange,
+    source_kind: &SourceKind,
+    index: &LineIndex,
+    encoding: PositionEncoding,
+) -> lsp_types::Range {
+    if let Some(notebook_index) = source_kind.as_ipy_notebook().map(Notebook::index) {
+        range
+            .to_notebook_range(source_kind.source_code(), index, notebook_index, encoding)
+            .range
+    } else {
+        range.to_range(source_kind.source_code(), index, encoding)
     }
 }
 

crates/ruff_server/src/server.rs

@@ -1,6 +1,7 @@
 //! Scheduling, I/O, and API endpoints.
 
 use std::num::NonZeroUsize;
+use std::path::PathBuf;
 
 use lsp_server as lsp;
 use lsp_types as types;
@@ -10,6 +11,9 @@ use types::CodeActionOptions;
 use types::DiagnosticOptions;
 use types::DidChangeWatchedFilesRegistrationOptions;
 use types::FileSystemWatcher;
+use types::NotebookCellSelector;
+use types::NotebookDocumentSyncOptions;
+use types::NotebookSelector;
 use types::OneOf;
 use types::TextDocumentSyncCapability;
 use types::TextDocumentSyncKind;
@@ -67,26 +71,26 @@ impl Server {
             mut workspace_settings,
         } = AllSettings::from_value(init_params.initialization_options.unwrap_or_default());
 
-        let mut workspace_for_uri = |uri| {
+        let mut workspace_for_path = |path: PathBuf| {
             let Some(workspace_settings) = workspace_settings.as_mut() else {
-                return (uri, ClientSettings::default());
+                return (path, ClientSettings::default());
             };
-            let settings = workspace_settings.remove(&uri).unwrap_or_else(|| {
+            let settings = workspace_settings.remove(&path).unwrap_or_else(|| {
-                tracing::warn!("No workspace settings found for {uri}");
+                tracing::warn!("No workspace settings found for {}", path.display());
                 ClientSettings::default()
             });
-            (uri, settings)
+            (path, settings)
         };
 
         let workspaces = init_params
             .workspace_folders
             .map(|folders| folders.into_iter().map(|folder| {
-                workspace_for_uri(folder.uri)
+                workspace_for_path(folder.uri.to_file_path().unwrap())
             }).collect())
             .or_else(|| {
                 tracing::debug!("No workspace(s) were provided during initialization. Using the current working directory as a default workspace...");
                 let uri = types::Url::from_file_path(std::env::current_dir().ok()?).ok()?;
-                Some(vec![workspace_for_uri(uri)])
+                Some(vec![workspace_for_path(uri.to_file_path().unwrap())])
             })
             .ok_or_else(|| {
                 anyhow::anyhow!("Failed to get the current working directory while creating a default workspace.")
@@ -100,7 +104,7 @@ impl Server {
                 position_encoding,
                 global_settings,
                 workspaces,
-            )?,
+            ),
             client_capabilities,
         })
     }
@@ -252,6 +256,16 @@ impl Server {
                 },
             )),
             hover_provider: Some(types::HoverProviderCapability::Simple(true)),
+            notebook_document_sync: Some(types::OneOf::Left(NotebookDocumentSyncOptions {
+                save: Some(false),
+                notebook_selector: [NotebookSelector::ByCells {
+                    notebook: None,
+                    cells: vec![NotebookCellSelector {
+                        language: "python".to_string(),
+                    }],
+                }]
+                .to_vec(),
+            })),
             text_document_sync: Some(TextDocumentSyncCapability::Options(
                 TextDocumentSyncOptions {
                     open_close: Some(true),
@@ -278,8 +292,15 @@ pub(crate) enum SupportedCodeAction {
     SourceFixAll,
     /// Maps to `source.organizeImports` and `source.organizeImports.ruff` code action kinds.
     /// This is a source action that applies import sorting fixes to the currently open document.
-    #[allow(dead_code)] // TODO: remove
     SourceOrganizeImports,
+    /// Maps to the `notebook.source.fixAll` and `notebook.source.fixAll.ruff` code action kinds.
+    /// This is a source action, specifically for notebooks, that applies all safe fixes
+    /// to the currently open document.
+    NotebookSourceFixAll,
+    /// Maps to `source.organizeImports` and `source.organizeImports.ruff` code action kinds.
+    /// This is a source action, specifically for notebooks, that applies import sorting fixes
+    /// to the currently open document.
+    NotebookSourceOrganizeImports,
 }
 
 impl SupportedCodeAction {
@@ -289,6 +310,8 @@ impl SupportedCodeAction {
             Self::QuickFix => CodeActionKind::QUICKFIX,
             Self::SourceFixAll => crate::SOURCE_FIX_ALL_RUFF,
             Self::SourceOrganizeImports => crate::SOURCE_ORGANIZE_IMPORTS_RUFF,
+            Self::NotebookSourceFixAll => crate::NOTEBOOK_SOURCE_FIX_ALL_RUFF,
+            Self::NotebookSourceOrganizeImports => crate::NOTEBOOK_SOURCE_ORGANIZE_IMPORTS_RUFF,
         }
     }
 
@@ -304,6 +327,8 @@ impl SupportedCodeAction {
             Self::QuickFix,
             Self::SourceFixAll,
             Self::SourceOrganizeImports,
+            Self::NotebookSourceFixAll,
+            Self::NotebookSourceOrganizeImports,
         ]
         .into_iter()
     }

crates/ruff_server/src/server/api.rs

@@ -84,6 +84,15 @@ pub(super) fn notification<'a>(notif: server::Notification) -> Task<'a> {
         }
         notification::DidClose::METHOD => local_notification_task::<notification::DidClose>(notif),
         notification::DidOpen::METHOD => local_notification_task::<notification::DidOpen>(notif),
+        notification::DidOpenNotebook::METHOD => {
+            local_notification_task::<notification::DidOpenNotebook>(notif)
+        }
+        notification::DidChangeNotebook::METHOD => {
+            local_notification_task::<notification::DidChangeNotebook>(notif)
+        }
+        notification::DidCloseNotebook::METHOD => {
+            local_notification_task::<notification::DidCloseNotebook>(notif)
+        }
         method => {
             tracing::warn!("Received notification {method} which does not have a handler.");
             return Task::nothing();

crates/ruff_server/src/server/api/diagnostics.rs

@@ -1,17 +1,20 @@
-use crate::{server::client::Notifier, session::DocumentSnapshot};
+use crate::{
+    lint::Diagnostics,
+    server::client::Notifier,
+    session::{DocumentQuery, DocumentSnapshot},
+};
 
 use super::LSPResult;
 
-pub(super) fn generate_diagnostics(snapshot: &DocumentSnapshot) -> Vec<lsp_types::Diagnostic> {
+pub(super) fn generate_diagnostics(snapshot: &DocumentSnapshot) -> Diagnostics {
     if snapshot.client_settings().lint() {
         crate::lint::check(
-            snapshot.document(),
+            snapshot.query(),
-            snapshot.url(),
+            snapshot.query().settings().linter(),
-            snapshot.settings().linter(),
             snapshot.encoding(),
         )
     } else {
-        vec![]
+        Diagnostics::default()
     }
 }
 
@@ -19,31 +22,31 @@ pub(super) fn publish_diagnostics_for_document(
     snapshot: &DocumentSnapshot,
     notifier: &Notifier,
 ) -> crate::server::Result<()> {
-    let diagnostics = generate_diagnostics(snapshot);
+    for (uri, diagnostics) in generate_diagnostics(snapshot) {
-
         notifier
             .notify::<lsp_types::notification::PublishDiagnostics>(
                 lsp_types::PublishDiagnosticsParams {
-                uri: snapshot.url().clone(),
+                    uri,
                     diagnostics,
-                version: Some(snapshot.document().version()),
+                    version: Some(snapshot.query().version()),
                 },
             )
             .with_failure_code(lsp_server::ErrorCode::InternalError)?;
+    }
 
     Ok(())
 }
 
 pub(super) fn clear_diagnostics_for_document(
-    snapshot: &DocumentSnapshot,
+    query: &DocumentQuery,
     notifier: &Notifier,
 ) -> crate::server::Result<()> {
     notifier
         .notify::<lsp_types::notification::PublishDiagnostics>(
             lsp_types::PublishDiagnosticsParams {
-                uri: snapshot.url().clone(),
+                uri: query.make_key().into_url(),
                 diagnostics: vec![],
-                version: Some(snapshot.document().version()),
+                version: Some(query.version()),
             },
         )
         .with_failure_code(lsp_server::ErrorCode::InternalError)?;

crates/ruff_server/src/server/api/notifications.rs

@@ -1,16 +1,22 @@
 mod cancel;
 mod did_change;
 mod did_change_configuration;
+mod did_change_notebook;
 mod did_change_watched_files;
 mod did_change_workspace;
 mod did_close;
+mod did_close_notebook;
 mod did_open;
+mod did_open_notebook;
 
 use super::traits::{NotificationHandler, SyncNotificationHandler};
 pub(super) use cancel::Cancel;
 pub(super) use did_change::DidChange;
 pub(super) use did_change_configuration::DidChangeConfiguration;
+pub(super) use did_change_notebook::DidChangeNotebook;
 pub(super) use did_change_watched_files::DidChangeWatchedFiles;
 pub(super) use did_change_workspace::DidChangeWorkspace;
 pub(super) use did_close::DidClose;
+pub(super) use did_close_notebook::DidCloseNotebook;
 pub(super) use did_open::DidOpen;
+pub(super) use did_open_notebook::DidOpenNotebook;

crates/ruff_server/src/server/api/notifications/cancel.rs

@@ -11,7 +11,6 @@ impl super::NotificationHandler for Cancel {
 }
 
 impl super::SyncNotificationHandler for Cancel {
-    #[tracing::instrument(skip_all)]
     fn run(
         _session: &mut Session,
         _notifier: Notifier,

crates/ruff_server/src/server/api/notifications/did_change.rs

@@ -3,6 +3,7 @@ use crate::server::api::LSPResult;
 use crate::server::client::{Notifier, Requester};
 use crate::server::Result;
 use crate::session::Session;
+use lsp_server::ErrorCode;
 use lsp_types as types;
 use lsp_types::notification as notif;
 
@@ -13,7 +14,6 @@ impl super::NotificationHandler for DidChange {
 }
 
 impl super::SyncNotificationHandler for DidChange {
-    #[tracing::instrument(skip_all, fields(file=%uri))]
     fn run(
         session: &mut Session,
         notifier: Notifier,
@@ -27,19 +27,13 @@ impl super::SyncNotificationHandler for DidChange {
             content_changes,
         }: types::DidChangeTextDocumentParams,
     ) -> Result<()> {
-        let encoding = session.encoding();
+        let key = session
-        let document = session
+            .key_from_url(&uri)
-            .document_controller(&uri)
+            .with_failure_code(ErrorCode::InternalError)?;
-            .with_failure_code(lsp_server::ErrorCode::InvalidParams)?;
 
-        if content_changes.is_empty() {
+        session
-            document.make_mut().update_version(new_version);
+            .update_text_document(&key, content_changes, new_version)
-            return Ok(());
+            .with_failure_code(ErrorCode::InternalError)?;
-        }
-
-        document
-            .make_mut()
-            .apply_changes(content_changes, new_version, encoding);
 
         // Publish diagnostics if the client doesnt support pull diagnostics
         if !session.resolved_client_capabilities().pull_diagnostics {

crates/ruff_server/src/server/api/notifications/did_change_notebook.rs

@@ -0,0 +1,41 @@
+use crate::server::api::diagnostics::publish_diagnostics_for_document;
+use crate::server::api::LSPResult;
+use crate::server::client::{Notifier, Requester};
+use crate::server::Result;
+use crate::session::Session;
+use lsp_server::ErrorCode;
+use lsp_types as types;
+use lsp_types::notification as notif;
+
+pub(crate) struct DidChangeNotebook;
+
+impl super::NotificationHandler for DidChangeNotebook {
+    type NotificationType = notif::DidChangeNotebookDocument;
+}
+
+impl super::SyncNotificationHandler for DidChangeNotebook {
+    fn run(
+        session: &mut Session,
+        notifier: Notifier,
+        _requester: &mut Requester,
+        types::DidChangeNotebookDocumentParams {
+            notebook_document: types::VersionedNotebookDocumentIdentifier { uri, version },
+            change: types::NotebookDocumentChangeEvent { cells, metadata },
+        }: types::DidChangeNotebookDocumentParams,
+    ) -> Result<()> {
+        let key = session
+            .key_from_url(&uri)
+            .with_failure_code(ErrorCode::InternalError)?;
+        session
+            .update_notebook_document(&key, cells, metadata, version)
+            .with_failure_code(ErrorCode::InternalError)?;
+
+        // publish new diagnostics
+        let snapshot = session
+            .take_snapshot(&uri)
+            .expect("snapshot should be available");
+        publish_diagnostics_for_document(&snapshot, &notifier)?;
+
+        Ok(())
+    }
+}

crates/ruff_server/src/server/api/notifications/did_change_watched_files.rs

@@ -20,9 +20,7 @@ impl super::SyncNotificationHandler for DidChangeWatchedFiles {
         params: types::DidChangeWatchedFilesParams,
     ) -> Result<()> {
         for change in &params.changes {
-            session
+            session.reload_settings(&change.uri.to_file_path().unwrap());
-                .reload_settings(&change.uri)
-                .with_failure_code(lsp_server::ErrorCode::InternalError)?;
         }
 
         if session.resolved_client_capabilities().workspace_refresh && !params.changes.is_empty() {

crates/ruff_server/src/server/api/notifications/did_change_workspace.rs

@@ -2,6 +2,8 @@ use crate::server::api::LSPResult;
 use crate::server::client::{Notifier, Requester};
 use crate::server::Result;
 use crate::session::Session;
+use anyhow::anyhow;
+use lsp_server::ErrorCode;
 use lsp_types as types;
 use lsp_types::notification as notif;
 
@@ -18,14 +20,21 @@ impl super::SyncNotificationHandler for DidChangeWorkspace {
         _requester: &mut Requester,
         params: types::DidChangeWorkspaceFoldersParams,
     ) -> Result<()> {
-        for new in params.event.added {
+        for types::WorkspaceFolder { ref uri, .. } in params.event.added {
-            session
+            let workspace_path = uri
-                .open_workspace_folder(&new.uri)
+                .to_file_path()
-                .with_failure_code(lsp_server::ErrorCode::InvalidParams)?;
+                .map_err(|()| anyhow!("expected document URI {uri} to be a valid file path"))
+                .with_failure_code(ErrorCode::InvalidParams)?;
+
+            session.open_workspace_folder(workspace_path);
         }
-        for removed in params.event.removed {
+        for types::WorkspaceFolder { ref uri, .. } in params.event.removed {
+            let workspace_path = uri
+                .to_file_path()
+                .map_err(|()| anyhow!("expected document URI {uri} to be a valid file path"))
+                .with_failure_code(ErrorCode::InvalidParams)?;
             session
-                .close_workspace_folder(&removed.uri)
+                .close_workspace_folder(&workspace_path)
                 .with_failure_code(lsp_server::ErrorCode::InvalidParams)?;
         }
         Ok(())

crates/ruff_server/src/server/api/notifications/did_close.rs

@@ -1,3 +1,4 @@
+use crate::edit::DocumentKey;
 use crate::server::api::diagnostics::clear_diagnostics_for_document;
 use crate::server::api::LSPResult;
 use crate::server::client::{Notifier, Requester};
@@ -13,7 +14,6 @@ impl super::NotificationHandler for DidClose {
 }
 
 impl super::SyncNotificationHandler for DidClose {
-    #[tracing::instrument(skip_all, fields(file=%uri))]
     fn run(
         session: &mut Session,
         notifier: Notifier,
@@ -22,20 +22,24 @@ impl super::SyncNotificationHandler for DidClose {
             text_document: types::TextDocumentIdentifier { uri },
         }: types::DidCloseTextDocumentParams,
     ) -> Result<()> {
-        // Publish an empty diagnostic report for the document if the client does not support pull diagnostics.
+        // Publish an empty diagnostic report for the document. This will de-register any existing diagnostics.
-        // This will de-register any existing diagnostics.
-        if !session.resolved_client_capabilities().pull_diagnostics {
         let snapshot = session
             .take_snapshot(&uri)
-                .ok_or_else(|| {
+            .ok_or_else(|| anyhow::anyhow!("Unable to take snapshot for document with URL {uri}"))
-                    anyhow::anyhow!("Unable to take snapshot for document with URL {uri}")
-                })
             .with_failure_code(lsp_server::ErrorCode::InternalError)?;
-            clear_diagnostics_for_document(&snapshot, &notifier)?;
+        clear_diagnostics_for_document(snapshot.query(), &notifier)?;
+
+        let key = snapshot.query().make_key();
+
+        // Notebook cells will go through the `textDocument/didClose` path.
+        // We still want to publish empty diagnostics for them, but we
+        // shouldn't call `session.close_document` on them.
+        if matches!(key, DocumentKey::NotebookCell(_)) {
+            return Ok(());
         }
 
         session
-            .close_document(&uri)
+            .close_document(&key)
             .with_failure_code(lsp_server::ErrorCode::InternalError)
     }
 }

crates/ruff_server/src/server/api/notifications/did_close_notebook.rs

@@ -0,0 +1,35 @@
+use crate::server::api::LSPResult;
+use crate::server::client::{Notifier, Requester};
+use crate::server::Result;
+use crate::session::Session;
+use lsp_server::ErrorCode;
+use lsp_types as types;
+use lsp_types::notification as notif;
+
+pub(crate) struct DidCloseNotebook;
+
+impl super::NotificationHandler for DidCloseNotebook {
+    type NotificationType = notif::DidCloseNotebookDocument;
+}
+
+impl super::SyncNotificationHandler for DidCloseNotebook {
+    fn run(
+        session: &mut Session,
+        _notifier: Notifier,
+        _requester: &mut Requester,
+        types::DidCloseNotebookDocumentParams {
+            notebook_document: types::NotebookDocumentIdentifier { uri },
+            ..
+        }: types::DidCloseNotebookDocumentParams,
+    ) -> Result<()> {
+        let key = session
+            .key_from_url(&uri)
+            .with_failure_code(ErrorCode::InternalError)?;
+
+        session
+            .close_document(&key)
+            .with_failure_code(ErrorCode::InternalError)?;
+
+        Ok(())
+    }
+}

crates/ruff_server/src/server/api/notifications/did_open.rs

@@ -3,6 +3,9 @@ use crate::server::api::LSPResult;
 use crate::server::client::{Notifier, Requester};
 use crate::server::Result;
 use crate::session::Session;
+use crate::TextDocument;
+use anyhow::anyhow;
+use lsp_server::ErrorCode;
 use lsp_types as types;
 use lsp_types::notification as notif;
 
@@ -13,7 +16,6 @@ impl super::NotificationHandler for DidOpen {
 }
 
 impl super::SyncNotificationHandler for DidOpen {
-    #[tracing::instrument(skip_all, fields(file=%url))]
     fn run(
         session: &mut Session,
         notifier: Notifier,
@@ -21,21 +23,28 @@ impl super::SyncNotificationHandler for DidOpen {
         types::DidOpenTextDocumentParams {
             text_document:
                 types::TextDocumentItem {
-                    uri: ref url,
+                    ref uri,
                     text,
                     version,
                     ..
                 },
         }: types::DidOpenTextDocumentParams,
     ) -> Result<()> {
-        session.open_document(url, text, version);
+        let document_path: std::path::PathBuf = uri
+            .to_file_path()
+            .map_err(|()| anyhow!("expected document URI {uri} to be a valid file path"))
+            .with_failure_code(ErrorCode::InvalidParams)?;
+
+        let document = TextDocument::new(text, version);
+
+        session.open_text_document(document_path, document);
 
         // Publish diagnostics if the client doesnt support pull diagnostics
         if !session.resolved_client_capabilities().pull_diagnostics {
             let snapshot = session
-                .take_snapshot(url)
+                .take_snapshot(uri)
                 .ok_or_else(|| {
-                    anyhow::anyhow!("Unable to take snapshot for document with URL {url}")
+                    anyhow::anyhow!("Unable to take snapshot for document with URL {uri}")
                 })
                 .with_failure_code(lsp_server::ErrorCode::InternalError)?;
             publish_diagnostics_for_document(&snapshot, &notifier)?;

crates/ruff_server/src/server/api/notifications/did_open_notebook.rs

@@ -0,0 +1,58 @@
+use crate::edit::NotebookDocument;
+use crate::server::api::diagnostics::publish_diagnostics_for_document;
+use crate::server::api::LSPResult;
+use crate::server::client::{Notifier, Requester};
+use crate::server::Result;
+use crate::session::Session;
+use anyhow::anyhow;
+use lsp_server::ErrorCode;
+use lsp_types as types;
+use lsp_types::notification as notif;
+
+pub(crate) struct DidOpenNotebook;
+
+impl super::NotificationHandler for DidOpenNotebook {
+    type NotificationType = notif::DidOpenNotebookDocument;
+}
+
+impl super::SyncNotificationHandler for DidOpenNotebook {
+    fn run(
+        session: &mut Session,
+        notifier: Notifier,
+        _requester: &mut Requester,
+        types::DidOpenNotebookDocumentParams {
+            notebook_document:
+                types::NotebookDocument {
+                    uri,
+                    version,
+                    cells,
+                    metadata,
+                    ..
+                },
+            cell_text_documents,
+        }: types::DidOpenNotebookDocumentParams,
+    ) -> Result<()> {
+        let notebook = NotebookDocument::new(
+            version,
+            cells,
+            metadata.unwrap_or_default(),
+            cell_text_documents,
+        )
+        .with_failure_code(ErrorCode::InternalError)?;
+
+        let notebook_path = uri
+            .to_file_path()
+            .map_err(|()| anyhow!("expected notebook URI {uri} to be a valid file path"))
+            .with_failure_code(ErrorCode::InvalidParams)?;
+
+        session.open_notebook_document(notebook_path, notebook);
+
+        // publish diagnostics
+        let snapshot = session
+            .take_snapshot(&uri)
+            .expect("snapshot should be available");
+        publish_diagnostics_for_document(&snapshot, &notifier)?;
+
+        Ok(())
+    }
+}

crates/ruff_server/src/server/api/requests/code_action.rs

@@ -29,11 +29,7 @@ impl super::BackgroundDocumentRequestHandler for CodeActions {
 
         let supported_code_actions = supported_code_actions(params.context.only.clone());
 
-        let fixes = fixes_for_diagnostics(
+        let fixes = fixes_for_diagnostics(params.context.diagnostics)
-            snapshot.document(),
-            snapshot.encoding(),
-            params.context.diagnostics,
-        )
             .with_failure_code(ErrorCode::InternalError)?;
 
         if snapshot.client_settings().fix_violation()
@@ -61,6 +57,20 @@ impl super::BackgroundDocumentRequestHandler for CodeActions {
             response.push(organize_imports(&snapshot).with_failure_code(ErrorCode::InternalError)?);
         }
 
+        if snapshot.client_settings().fix_all()
+            && supported_code_actions.contains(&SupportedCodeAction::NotebookSourceFixAll)
+        {
+            response.push(notebook_fix_all(&snapshot).with_failure_code(ErrorCode::InternalError)?);
+        }
+
+        if snapshot.client_settings().organize_imports()
+            && supported_code_actions.contains(&SupportedCodeAction::NotebookSourceOrganizeImports)
+        {
+            response.push(
+                notebook_organize_imports(&snapshot).with_failure_code(ErrorCode::InternalError)?,
+            );
+        }
+
         Ok(Some(response))
     }
 }
@@ -69,7 +79,8 @@ fn quick_fix(
     snapshot: &DocumentSnapshot,
     fixes: &[DiagnosticFix],
 ) -> crate::Result<Vec<CodeActionOrCommand>> {
-    let document = snapshot.document();
+    let document = snapshot.query();
+
     fixes
         .iter()
         .filter(|fix| !fix.edits.is_empty())
@@ -77,7 +88,7 @@ fn quick_fix(
             let mut tracker = WorkspaceEditTracker::new(snapshot.resolved_client_capabilities());
 
             tracker.set_edits_for_document(
-                snapshot.url().clone(),
+                snapshot.query().make_key().into_url(),
                 document.version(),
                 fix.edits.clone(),
             )?;
@@ -88,7 +99,8 @@ fn quick_fix(
                 edit: Some(tracker.into_workspace_edit()),
                 diagnostics: Some(vec![fix.fixed_diagnostic.clone()]),
                 data: Some(
-                    serde_json::to_value(snapshot.url()).expect("document url to serialize"),
+                    serde_json::to_value(snapshot.query().make_key().into_url())
+                        .expect("document url should serialize"),
                 ),
                 ..Default::default()
             }))
@@ -106,8 +118,8 @@ fn noqa_comments(snapshot: &DocumentSnapshot, fixes: &[DiagnosticFix]) -> Vec<Co
 
             tracker
                 .set_edits_for_document(
-                    snapshot.url().clone(),
+                    snapshot.query().make_key().into_url(),
-                    snapshot.document().version(),
+                    snapshot.query().version(),
                     vec![edit],
                 )
                 .ok()?;
@@ -118,7 +130,8 @@ fn noqa_comments(snapshot: &DocumentSnapshot, fixes: &[DiagnosticFix]) -> Vec<Co
                 edit: Some(tracker.into_workspace_edit()),
                 diagnostics: Some(vec![fix.fixed_diagnostic.clone()]),
                 data: Some(
-                    serde_json::to_value(snapshot.url()).expect("document url to serialize"),
+                    serde_json::to_value(snapshot.query().make_key().into_url())
+                        .expect("document url should serialize"),
                 ),
                 ..Default::default()
             }))
@@ -127,7 +140,7 @@ fn noqa_comments(snapshot: &DocumentSnapshot, fixes: &[DiagnosticFix]) -> Vec<Co
 }
 
 fn fix_all(snapshot: &DocumentSnapshot) -> crate::Result<CodeActionOrCommand> {
-    let document = snapshot.document();
+    let document = snapshot.query();
 
     let (edit, data) = if snapshot
         .resolved_client_capabilities()
@@ -136,17 +149,18 @@ fn fix_all(snapshot: &DocumentSnapshot) -> crate::Result<CodeActionOrCommand> {
         // The editor will request the edit in a `CodeActionsResolve` request
         (
             None,
-            Some(serde_json::to_value(snapshot.url()).expect("document url to serialize")),
+            Some(
+                serde_json::to_value(snapshot.query().make_key().into_url())
+                    .expect("document url should serialize"),
+            ),
         )
     } else {
         (
             Some(resolve_edit_for_fix_all(
                 document,
                 snapshot.resolved_client_capabilities(),
-                snapshot.url(),
+                snapshot.query().settings().linter(),
-                snapshot.settings().linter(),
                 snapshot.encoding(),
-                document.version(),
             )?),
             None,
         )
@@ -161,8 +175,44 @@ fn fix_all(snapshot: &DocumentSnapshot) -> crate::Result<CodeActionOrCommand> {
     }))
 }
 
+fn notebook_fix_all(snapshot: &DocumentSnapshot) -> crate::Result<CodeActionOrCommand> {
+    let document = snapshot.query();
+
+    let (edit, data) = if snapshot
+        .resolved_client_capabilities()
+        .code_action_deferred_edit_resolution
+    {
+        // The editor will request the edit in a `CodeActionsResolve` request
+        (
+            None,
+            Some(
+                serde_json::to_value(snapshot.query().make_key().into_url())
+                    .expect("document url should serialize"),
+            ),
+        )
+    } else {
+        (
+            Some(resolve_edit_for_fix_all(
+                document,
+                snapshot.resolved_client_capabilities(),
+                snapshot.query().settings().linter(),
+                snapshot.encoding(),
+            )?),
+            None,
+        )
+    };
+
+    Ok(CodeActionOrCommand::CodeAction(types::CodeAction {
+        title: format!("{DIAGNOSTIC_NAME}: Fix all auto-fixable problems"),
+        kind: Some(crate::NOTEBOOK_SOURCE_FIX_ALL_RUFF),
+        edit,
+        data,
+        ..Default::default()
+    }))
+}
+
 fn organize_imports(snapshot: &DocumentSnapshot) -> crate::Result<CodeActionOrCommand> {
-    let document = snapshot.document();
+    let document = snapshot.query();
 
     let (edit, data) = if snapshot
         .resolved_client_capabilities()
@@ -171,17 +221,18 @@ fn organize_imports(snapshot: &DocumentSnapshot) -> crate::Result<CodeActionOrCo
         // The edit will be resolved later in the `CodeActionsResolve` request
         (
             None,
-            Some(serde_json::to_value(snapshot.url()).expect("document url to serialize")),
+            Some(
+                serde_json::to_value(snapshot.query().make_key().into_url())
+                    .expect("document url should serialize"),
+            ),
         )
     } else {
         (
             Some(resolve_edit_for_organize_imports(
                 document,
                 snapshot.resolved_client_capabilities(),
-                snapshot.url(),
+                snapshot.query().settings().linter(),
-                snapshot.settings().linter(),
                 snapshot.encoding(),
-                document.version(),
             )?),
             None,
         )
@@ -196,6 +247,42 @@ fn organize_imports(snapshot: &DocumentSnapshot) -> crate::Result<CodeActionOrCo
     }))
 }
 
+fn notebook_organize_imports(snapshot: &DocumentSnapshot) -> crate::Result<CodeActionOrCommand> {
+    let document = snapshot.query();
+
+    let (edit, data) = if snapshot
+        .resolved_client_capabilities()
+        .code_action_deferred_edit_resolution
+    {
+        // The edit will be resolved later in the `CodeActionsResolve` request
+        (
+            None,
+            Some(
+                serde_json::to_value(snapshot.query().make_key().into_url())
+                    .expect("document url should serialize"),
+            ),
+        )
+    } else {
+        (
+            Some(resolve_edit_for_organize_imports(
+                document,
+                snapshot.resolved_client_capabilities(),
+                snapshot.query().settings().linter(),
+                snapshot.encoding(),
+            )?),
+            None,
+        )
+    };
+
+    Ok(CodeActionOrCommand::CodeAction(types::CodeAction {
+        title: format!("{DIAGNOSTIC_NAME}: Organize imports"),
+        kind: Some(crate::NOTEBOOK_SOURCE_ORGANIZE_IMPORTS_RUFF),
+        edit,
+        data,
+        ..Default::default()
+    }))
+}
+
 /// If `action_filter` is `None`, this returns [`SupportedCodeActionKind::all()`]. Otherwise,
 /// the list is filtered.
 fn supported_code_actions(

crates/ruff_server/src/server/api/requests/code_action_resolve.rs

@@ -1,10 +1,11 @@
 use std::borrow::Cow;
 
-use crate::edit::{DocumentVersion, WorkspaceEditTracker};
+use crate::edit::WorkspaceEditTracker;
+use crate::fix::Fixes;
 use crate::server::api::LSPResult;
 use crate::server::SupportedCodeAction;
 use crate::server::{client::Notifier, Result};
-use crate::session::{DocumentSnapshot, ResolvedClientCapabilities};
+use crate::session::{DocumentQuery, DocumentSnapshot, ResolvedClientCapabilities};
 use crate::PositionEncoding;
 use lsp_server::ErrorCode;
 use lsp_types::{self as types, request as req};
@@ -28,7 +29,7 @@ impl super::BackgroundDocumentRequestHandler for CodeActionResolve {
         _notifier: Notifier,
         mut action: types::CodeAction,
     ) -> Result<types::CodeAction> {
-        let document = snapshot.document();
+        let query = snapshot.query();
 
         let code_actions = SupportedCodeAction::from_kind(
             action
@@ -49,25 +50,22 @@ impl super::BackgroundDocumentRequestHandler for CodeActionResolve {
         };
 
         action.edit = match action_kind {
-            SupportedCodeAction::SourceFixAll => Some(
+            SupportedCodeAction::SourceFixAll | SupportedCodeAction::NotebookSourceFixAll => Some(
                 resolve_edit_for_fix_all(
-                    document,
+                    query,
                     snapshot.resolved_client_capabilities(),
-                    snapshot.url(),
+                    query.settings().linter(),
-                    snapshot.settings().linter(),
                     snapshot.encoding(),
-                    document.version(),
                 )
                 .with_failure_code(ErrorCode::InternalError)?,
             ),
-            SupportedCodeAction::SourceOrganizeImports => Some(
+            SupportedCodeAction::SourceOrganizeImports
+            | SupportedCodeAction::NotebookSourceOrganizeImports => Some(
                 resolve_edit_for_organize_imports(
-                    document,
+                    query,
                     snapshot.resolved_client_capabilities(),
-                    snapshot.url(),
+                    query.settings().linter(),
-                    snapshot.settings().linter(),
                     snapshot.encoding(),
-                    document.version(),
                 )
                 .with_failure_code(ErrorCode::InternalError)?,
             ),
@@ -84,54 +82,46 @@ impl super::BackgroundDocumentRequestHandler for CodeActionResolve {
 }
 
 pub(super) fn resolve_edit_for_fix_all(
-    document: &crate::edit::Document,
+    query: &DocumentQuery,
     client_capabilities: &ResolvedClientCapabilities,
-    url: &types::Url,
     linter_settings: &LinterSettings,
     encoding: PositionEncoding,
-    version: DocumentVersion,
 ) -> crate::Result<types::WorkspaceEdit> {
     let mut tracker = WorkspaceEditTracker::new(client_capabilities);
-    tracker.set_edits_for_document(
+    tracker.set_fixes_for_document(
-        url.clone(),
+        fix_all_edit(query, linter_settings, encoding)?,
-        version,
+        query.version(),
-        fix_all_edit(document, url, linter_settings, encoding)?,
     )?;
     Ok(tracker.into_workspace_edit())
 }
 
 pub(super) fn fix_all_edit(
-    document: &crate::edit::Document,
+    query: &DocumentQuery,
-    document_url: &types::Url,
     linter_settings: &LinterSettings,
     encoding: PositionEncoding,
-) -> crate::Result<Vec<types::TextEdit>> {
+) -> crate::Result<Fixes> {
-    crate::fix::fix_all(document, document_url, linter_settings, encoding)
+    crate::fix::fix_all(query, linter_settings, encoding)
 }
 
 pub(super) fn resolve_edit_for_organize_imports(
-    document: &crate::edit::Document,
+    query: &DocumentQuery,
     client_capabilities: &ResolvedClientCapabilities,
-    url: &types::Url,
     linter_settings: &ruff_linter::settings::LinterSettings,
     encoding: PositionEncoding,
-    version: DocumentVersion,
 ) -> crate::Result<types::WorkspaceEdit> {
     let mut tracker = WorkspaceEditTracker::new(client_capabilities);
-    tracker.set_edits_for_document(
+    tracker.set_fixes_for_document(
-        url.clone(),
+        organize_imports_edit(query, linter_settings, encoding)?,
-        version,
+        query.version(),
-        organize_imports_edit(document, url, linter_settings, encoding)?,
     )?;
     Ok(tracker.into_workspace_edit())
 }
 
 pub(super) fn organize_imports_edit(
-    document: &crate::edit::Document,
+    query: &DocumentQuery,
-    document_url: &types::Url,
     linter_settings: &LinterSettings,
     encoding: PositionEncoding,
-) -> crate::Result<Vec<types::TextEdit>> {
+) -> crate::Result<Fixes> {
     let mut linter_settings = linter_settings.clone();
     linter_settings.rules = [
         Rule::UnsortedImports,       // I001
@@ -140,5 +130,5 @@ pub(super) fn organize_imports_edit(
     .into_iter()
     .collect();
 
-    crate::fix::fix_all(document, document_url, &linter_settings, encoding)
+    crate::fix::fix_all(query, &linter_settings, encoding)
 }

crates/ruff_server/src/server/api/requests/diagnostic.rs

@@ -26,7 +26,13 @@ impl super::BackgroundDocumentRequestHandler for DocumentDiagnostic {
                 full_document_diagnostic_report: FullDocumentDiagnosticReport {
                     // TODO(jane): eventually this will be important for caching diagnostic information.
                     result_id: None,
-                    items: generate_diagnostics(&snapshot),
+                    // Pull diagnostic requests are only called for text documents.
+                    // Since diagnostic requests generate
+                    items: generate_diagnostics(&snapshot)
+                        .into_iter()
+                        .next()
+                        .map(|(_, diagnostics)| diagnostics)
+                        .unwrap_or_default(),
                 },
             }),
         ))

crates/ruff_server/src/server/api/requests/execute_command.rs

@@ -21,7 +21,7 @@ enum Command {
 pub(crate) struct ExecuteCommand;
 
 #[derive(Deserialize)]
-struct TextDocumentArgument {
+struct Argument {
     uri: types::Url,
     version: DocumentVersion,
 }
@@ -45,7 +45,7 @@ impl super::SyncRequestHandler for ExecuteCommand {
             return Err(anyhow::anyhow!("Cannot execute the '{}' command: the client does not support `workspace/applyEdit`", command.label())).with_failure_code(ErrorCode::InternalError);
         }
 
-        let mut arguments: Vec<TextDocumentArgument> = params
+        let mut arguments: Vec<Argument> = params
             .arguments
             .into_iter()
             .map(|value| serde_json::from_value(value).with_failure_code(ErrorCode::InvalidParams))
@@ -55,22 +55,21 @@ impl super::SyncRequestHandler for ExecuteCommand {
         arguments.dedup_by(|a, b| a.uri == b.uri);
 
         let mut edit_tracker = WorkspaceEditTracker::new(session.resolved_client_capabilities());
-        for TextDocumentArgument { uri, version } in arguments {
+        for Argument { uri, version } in arguments {
             let snapshot = session
                 .take_snapshot(&uri)
                 .ok_or(anyhow::anyhow!("Document snapshot not available for {uri}",))
                 .with_failure_code(ErrorCode::InternalError)?;
             match command {
                 Command::FixAll => {
-                    let edits = super::code_action_resolve::fix_all_edit(
+                    let fixes = super::code_action_resolve::fix_all_edit(
-                        snapshot.document(),
+                        snapshot.query(),
-                        snapshot.url(),
+                        snapshot.query().settings().linter(),
-                        snapshot.settings().linter(),
                         snapshot.encoding(),
                     )
                     .with_failure_code(ErrorCode::InternalError)?;
                     edit_tracker
-                        .set_edits_for_document(uri, version, edits)
+                        .set_fixes_for_document(fixes, snapshot.query().version())
                         .with_failure_code(ErrorCode::InternalError)?;
                 }
                 Command::Format => {
@@ -82,15 +81,14 @@ impl super::SyncRequestHandler for ExecuteCommand {
                     }
                 }
                 Command::OrganizeImports => {
-                    let edits = super::code_action_resolve::organize_imports_edit(
+                    let fixes = super::code_action_resolve::organize_imports_edit(
-                        snapshot.document(),
+                        snapshot.query(),
-                        snapshot.url(),
+                        snapshot.query().settings().linter(),
-                        snapshot.settings().linter(),
                         snapshot.encoding(),
                     )
                     .with_failure_code(ErrorCode::InternalError)?;
                     edit_tracker
-                        .set_edits_for_document(uri, version, edits)
+                        .set_fixes_for_document(fixes, snapshot.query().version())
                         .with_failure_code(ErrorCode::InternalError)?;
                 }
             }

crates/ruff_server/src/server/api/requests/format.rs

@@ -24,14 +24,37 @@ impl super::BackgroundDocumentRequestHandler for Format {
 }
 
 pub(super) fn format_document(snapshot: &DocumentSnapshot) -> Result<super::FormatResponse> {
-    let doc = snapshot.document();
+    let doc = snapshot
+        .query()
+        .as_single_document()
+        .expect("format should only be called on text documents or notebook cells");
     let source = doc.contents();
-    let formatted = crate::format::format(doc, snapshot.settings().formatter())
+    let mut formatted = crate::format::format(
+        doc,
+        snapshot.query().source_type(),
+        snapshot.query().settings().formatter(),
+    )
     .with_failure_code(lsp_server::ErrorCode::InternalError)?;
     // fast path - if the code is the same, return early
     if formatted == source {
         return Ok(None);
     }
+
+    // special case - avoid adding a newline to a notebook cell if it didn't already exist
+    if snapshot.query().as_notebook().is_some() {
+        let mut trimmed = formatted.as_str();
+        if !source.ends_with("\r\n") {
+            trimmed = trimmed.trim_end_matches("\r\n");
+        }
+        if !source.ends_with('\n') {
+            trimmed = trimmed.trim_end_matches('\n');
+        }
+        if !source.ends_with('\r') {
+            trimmed = trimmed.trim_end_matches('\r');
+        }
+        formatted = trimmed.to_string();
+    }
+
     let formatted_index: LineIndex = LineIndex::from_source_text(&formatted);
 
     let unformatted_index = doc.index();

crates/ruff_server/src/server/api/requests/format_range.rs

@@ -17,12 +17,19 @@ impl super::BackgroundDocumentRequestHandler for FormatRange {
         _notifier: Notifier,
         params: types::DocumentRangeFormattingParams,
     ) -> Result<super::FormatResponse> {
-        let document = snapshot.document();
+        let document = snapshot
+            .query()
+            .as_single_document()
+            .expect("hover should only be called on text documents or notebook cells");
         let text = document.contents();
         let index = document.index();
         let range = params.range.to_text_range(text, index, snapshot.encoding());
-        let formatted_range =
+        let formatted_range = crate::format::format_range(
-            crate::format::format_range(document, snapshot.settings().formatter(), range)
+            document,
+            snapshot.query().source_type(),
+            snapshot.query().settings().formatter(),
+            range,
+        )
         .with_failure_code(lsp_server::ErrorCode::InternalError)?;
         Ok(Some(vec![types::TextEdit {
             range: formatted_range

crates/ruff_server/src/server/api/requests/hover.rs

@@ -29,7 +29,11 @@ pub(crate) fn hover(
     snapshot: &DocumentSnapshot,
     position: &types::TextDocumentPositionParams,
 ) -> Option<types::Hover> {
-    let document = snapshot.document();
+    // Hover only operates on text documents or notebook cells
+    let document = snapshot
+        .query()
+        .as_single_document()
+        .expect("hover should only be called on text documents or notebook cells");
     let line_number: usize = position
         .position
         .line

crates/ruff_server/src/session.rs

@@ -1,24 +1,26 @@
 //! Data model, state management, and configuration resolution.
 
 mod capabilities;
+mod index;
 mod settings;
-mod workspace;
 
+use std::path::PathBuf;
 use std::sync::Arc;
 
 use anyhow::anyhow;
-use lsp_types::{ClientCapabilities, Url};
+use lsp_types::{ClientCapabilities, NotebookDocumentCellChange, Url};
 
-use crate::edit::DocumentVersion;
+use crate::edit::{DocumentKey, DocumentVersion, NotebookDocument};
-use crate::PositionEncoding;
+use crate::{PositionEncoding, TextDocument};
 
 pub(crate) use self::capabilities::ResolvedClientCapabilities;
+pub(crate) use self::index::DocumentQuery;
 pub(crate) use self::settings::{AllSettings, ClientSettings};
 
 /// The global state for the LSP
 pub(crate) struct Session {
-    /// Workspace folders in the current session, which contain the state of all open files.
+    /// Used to retrieve information about open documents and settings.
-    workspaces: workspace::Workspaces,
+    index: index::Index,
     /// The global position encoding, negotiated during LSP initialization.
     position_encoding: PositionEncoding,
     /// Global settings provided by the client.
@@ -32,9 +34,8 @@ pub(crate) struct Session {
 pub(crate) struct DocumentSnapshot {
     resolved_client_capabilities: Arc<ResolvedClientCapabilities>,
     client_settings: settings::ResolvedClientSettings,
-    document_ref: workspace::DocumentRef,
+    document_ref: index::DocumentQuery,
     position_encoding: PositionEncoding,
-    url: Url,
 }
 
 impl Session {
@@ -42,58 +43,100 @@ impl Session {
         client_capabilities: &ClientCapabilities,
         position_encoding: PositionEncoding,
         global_settings: ClientSettings,
-        workspaces: Vec<(Url, ClientSettings)>,
+        workspace_folders: Vec<(PathBuf, ClientSettings)>,
-    ) -> crate::Result<Self> {
+    ) -> Self {
-        Ok(Self {
+        Self {
             position_encoding,
-            workspaces: workspace::Workspaces::new(workspaces, &global_settings)?,
+            index: index::Index::new(workspace_folders, &global_settings),
             global_settings,
             resolved_client_capabilities: Arc::new(ResolvedClientCapabilities::new(
                 client_capabilities,
             )),
-        })
+        }
     }
 
+    pub(crate) fn key_from_url(&self, url: &lsp_types::Url) -> crate::Result<DocumentKey> {
+        self.index
+            .key_from_url(url)
+            .ok_or_else(|| anyhow!("No document found for {url}"))
+    }
+
+    /// Creates a document snapshot with the URL referencing the document to snapshot.
     pub(crate) fn take_snapshot(&self, url: &Url) -> Option<DocumentSnapshot> {
+        let key = self.key_from_url(url).ok()?;
         Some(DocumentSnapshot {
             resolved_client_capabilities: self.resolved_client_capabilities.clone(),
-            client_settings: self.workspaces.client_settings(url, &self.global_settings),
+            client_settings: self.index.client_settings(&key, &self.global_settings),
-            document_ref: self.workspaces.snapshot(url)?,
+            document_ref: self.index.make_document_ref(key)?,
             position_encoding: self.position_encoding,
-            url: url.clone(),
         })
     }
 
-    pub(crate) fn open_document(&mut self, url: &Url, contents: String, version: DocumentVersion) {
+    /// Updates a text document at the associated `key`.
-        self.workspaces.open(url, contents, version);
+    ///
-    }
+    /// The document key must point to a text document, or this will throw an error.
-
+    pub(crate) fn update_text_document(
-    pub(crate) fn close_document(&mut self, url: &Url) -> crate::Result<()> {
-        self.workspaces.close(url)?;
-        Ok(())
-    }
-
-    pub(crate) fn document_controller(
         &mut self,
-        url: &Url,
+        key: &DocumentKey,
-    ) -> crate::Result<&mut workspace::DocumentController> {
+        content_changes: Vec<lsp_types::TextDocumentContentChangeEvent>,
-        self.workspaces
+        new_version: DocumentVersion,
-            .controller(url)
+    ) -> crate::Result<()> {
-            .ok_or_else(|| anyhow!("Tried to open unavailable document `{url}`"))
+        let encoding = self.encoding();
+
+        self.index
+            .update_text_document(key, content_changes, new_version, encoding)
     }
 
-    pub(crate) fn reload_settings(&mut self, url: &Url) -> crate::Result<()> {
+    /// Updates a notebook document at the associated `key` with potentially new
-        self.workspaces.reload_settings(url)
+    /// cell, metadata, and version values.
+    ///
+    /// The document key must point to a notebook document or cell, or this will
+    /// throw an error.
+    pub(crate) fn update_notebook_document(
+        &mut self,
+        key: &DocumentKey,
+        cells: Option<NotebookDocumentCellChange>,
+        metadata: Option<serde_json::Map<String, serde_json::Value>>,
+        version: DocumentVersion,
+    ) -> crate::Result<()> {
+        let encoding = self.encoding();
+        self.index
+            .update_notebook_document(key, cells, metadata, version, encoding)
     }
 
-    pub(crate) fn open_workspace_folder(&mut self, url: &Url) -> crate::Result<()> {
+    /// Registers a notebook document at the provided `path`.
-        self.workspaces
+    /// If a document is already open here, it will be overwritten.
-            .open_workspace_folder(url, &self.global_settings)?;
+    pub(crate) fn open_notebook_document(&mut self, path: PathBuf, document: NotebookDocument) {
+        self.index.open_notebook_document(path, document);
+    }
+
+    /// Registers a text document at the provided `path`.
+    /// If a document is already open here, it will be overwritten.
+    pub(crate) fn open_text_document(&mut self, path: PathBuf, document: TextDocument) {
+        self.index.open_text_document(path, document);
+    }
+
+    /// De-registers a document, specified by its key.
+    /// Calling this multiple times for the same document is a logic error.
+    pub(crate) fn close_document(&mut self, key: &DocumentKey) -> crate::Result<()> {
+        self.index.close_document(key)?;
         Ok(())
     }
 
-    pub(crate) fn close_workspace_folder(&mut self, url: &Url) -> crate::Result<()> {
+    /// Reloads the settings index
-        self.workspaces.close_workspace_folder(url)?;
+    pub(crate) fn reload_settings(&mut self, changed_path: &PathBuf) {
+        self.index.reload_settings(changed_path);
+    }
+
+    /// Open a workspace folder at the given `path`.
+    pub(crate) fn open_workspace_folder(&mut self, path: PathBuf) {
+        self.index
+            .open_workspace_folder(path, &self.global_settings);
+    }
+
+    /// Close a workspace folder at the given `path`.
+    pub(crate) fn close_workspace_folder(&mut self, path: &PathBuf) -> crate::Result<()> {
+        self.index.close_workspace_folder(path)?;
         Ok(())
     }
 
@@ -107,10 +150,6 @@ impl Session {
 }
 
 impl DocumentSnapshot {
-    pub(crate) fn settings(&self) -> &workspace::RuffSettings {
-        self.document().settings()
-    }
-
     pub(crate) fn resolved_client_capabilities(&self) -> &ResolvedClientCapabilities {
         &self.resolved_client_capabilities
     }
@@ -119,15 +158,11 @@ impl DocumentSnapshot {
         &self.client_settings
     }
 
-    pub(crate) fn document(&self) -> &workspace::DocumentRef {
+    pub(crate) fn query(&self) -> &index::DocumentQuery {
         &self.document_ref
     }
 
     pub(crate) fn encoding(&self) -> PositionEncoding {
         self.position_encoding
     }
-
-    pub(crate) fn url(&self) -> &Url {
-        &self.url
-    }
 }

crates/ruff_server/src/session/index.rs

@@ -0,0 +1,464 @@
+use anyhow::anyhow;
+use rustc_hash::FxHashMap;
+use std::{
+    collections::BTreeMap,
+    path::{Path, PathBuf},
+    sync::Arc,
+};
+
+use crate::{
+    edit::{DocumentKey, DocumentVersion, NotebookDocument},
+    PositionEncoding, TextDocument,
+};
+
+use super::{
+    settings::{self, ResolvedClientSettings},
+    ClientSettings,
+};
+
+mod ruff_settings;
+
+pub(crate) use ruff_settings::RuffSettings;
+
+type DocumentIndex = FxHashMap<PathBuf, DocumentController>;
+type NotebookCellIndex = FxHashMap<lsp_types::Url, PathBuf>;
+type SettingsIndex = BTreeMap<PathBuf, WorkspaceSettings>;
+
+/// Stores and tracks all open documents in a session, along with their associated settings.
+#[derive(Default)]
+pub(crate) struct Index {
+    /// Maps all document file paths to the associated document controller
+    documents: DocumentIndex,
+    /// Maps opaque cell URLs to a notebook path
+    notebook_cells: NotebookCellIndex,
+    /// Maps a workspace folder root to its settings.
+    settings: SettingsIndex,
+}
+
+/// Settings associated with a workspace.
+struct WorkspaceSettings {
+    client_settings: ResolvedClientSettings,
+    workspace_settings_index: ruff_settings::RuffSettingsIndex,
+}
+
+/// A mutable handler to an underlying document.
+enum DocumentController {
+    Text(Arc<TextDocument>),
+    Notebook(Arc<NotebookDocument>),
+}
+
+/// A read-only query to an open document.
+/// This query can 'select' a text document, full notebook, or a specific notebook cell.
+/// It also includes document settings.
+#[derive(Clone)]
+pub(crate) enum DocumentQuery {
+    Text {
+        file_path: PathBuf,
+        document: Arc<TextDocument>,
+        settings: Arc<RuffSettings>,
+    },
+    Notebook {
+        /// The selected notebook cell, if it exists.
+        cell_uri: Option<lsp_types::Url>,
+        file_path: PathBuf,
+        notebook: Arc<NotebookDocument>,
+        settings: Arc<RuffSettings>,
+    },
+}
+
+impl Index {
+    pub(super) fn new(
+        workspace_folders: Vec<(PathBuf, ClientSettings)>,
+        global_settings: &ClientSettings,
+    ) -> Self {
+        let mut settings_index = BTreeMap::new();
+        for (path, workspace_settings) in workspace_folders {
+            Self::register_workspace_settings(
+                &mut settings_index,
+                path,
+                Some(workspace_settings),
+                global_settings,
+            );
+        }
+
+        Self {
+            documents: FxHashMap::default(),
+            notebook_cells: FxHashMap::default(),
+            settings: settings_index,
+        }
+    }
+
+    pub(super) fn update_text_document(
+        &mut self,
+        key: &DocumentKey,
+        content_changes: Vec<lsp_types::TextDocumentContentChangeEvent>,
+        new_version: DocumentVersion,
+        encoding: PositionEncoding,
+    ) -> crate::Result<()> {
+        let controller = self.document_controller_for_key(key)?;
+        let Some(document) = controller.as_text_mut() else {
+            anyhow::bail!("Text document URI does not point to a text document");
+        };
+
+        if content_changes.is_empty() {
+            document.update_version(new_version);
+            return Ok(());
+        }
+
+        document.apply_changes(content_changes, new_version, encoding);
+
+        Ok(())
+    }
+
+    pub(super) fn key_from_url(&self, url: &lsp_types::Url) -> Option<DocumentKey> {
+        if self.notebook_cells.contains_key(url) {
+            return Some(DocumentKey::NotebookCell(url.clone()));
+        }
+        let path = url.to_file_path().ok()?;
+        Some(
+            match path
+                .extension()
+                .unwrap_or_default()
+                .to_str()
+                .unwrap_or_default()
+            {
+                "ipynb" => DocumentKey::Notebook(path),
+                _ => DocumentKey::Text(path),
+            },
+        )
+    }
+
+    pub(super) fn update_notebook_document(
+        &mut self,
+        key: &DocumentKey,
+        cells: Option<lsp_types::NotebookDocumentCellChange>,
+        metadata: Option<serde_json::Map<String, serde_json::Value>>,
+        new_version: DocumentVersion,
+        encoding: PositionEncoding,
+    ) -> crate::Result<()> {
+        // update notebook cell index
+        if let Some(lsp_types::NotebookDocumentCellChangeStructure {
+            did_open,
+            did_close,
+            ..
+        }) = cells.as_ref().and_then(|cells| cells.structure.as_ref())
+        {
+            let Some(path) = self.path_for_key(key).cloned() else {
+                anyhow::bail!("Tried to open unavailable document `{key}`");
+            };
+
+            for opened_cell in did_open.iter().flatten() {
+                self.notebook_cells
+                    .insert(opened_cell.uri.clone(), path.clone());
+            }
+            for closed_cell in did_close.iter().flatten() {
+                if self.notebook_cells.remove(&closed_cell.uri).is_none() {
+                    tracing::warn!(
+                        "Tried to remove a notebook cell that does not exist: {}",
+                        closed_cell.uri
+                    );
+                }
+            }
+        }
+
+        let controller = self.document_controller_for_key(key)?;
+        let Some(notebook) = controller.as_notebook_mut() else {
+            anyhow::bail!("Notebook document URI does not point to a notebook document");
+        };
+
+        notebook.update(cells, metadata, new_version, encoding)?;
+        Ok(())
+    }
+
+    pub(super) fn open_workspace_folder(
+        &mut self,
+        path: PathBuf,
+        global_settings: &ClientSettings,
+    ) {
+        // TODO(jane): Find a way for workspace client settings to be added or changed dynamically.
+        Self::register_workspace_settings(&mut self.settings, path, None, global_settings);
+    }
+
+    fn register_workspace_settings(
+        settings_index: &mut SettingsIndex,
+        workspace_path: PathBuf,
+        workspace_settings: Option<ClientSettings>,
+        global_settings: &ClientSettings,
+    ) {
+        let client_settings = if let Some(workspace_settings) = workspace_settings {
+            ResolvedClientSettings::with_workspace(&workspace_settings, global_settings)
+        } else {
+            ResolvedClientSettings::global(global_settings)
+        };
+        let workspace_settings_index = ruff_settings::RuffSettingsIndex::new(
+            &workspace_path,
+            client_settings.editor_settings(),
+        );
+
+        settings_index.insert(
+            workspace_path,
+            WorkspaceSettings {
+                client_settings,
+                workspace_settings_index,
+            },
+        );
+    }
+
+    pub(super) fn close_workspace_folder(&mut self, workspace_path: &PathBuf) -> crate::Result<()> {
+        self.settings.remove(workspace_path).ok_or_else(|| {
+            anyhow!(
+                "Tried to remove non-existent folder {}",
+                workspace_path.display()
+            )
+        })?;
+        // O(n) complexity, which isn't ideal... but this is an uncommon operation.
+        self.documents
+            .retain(|path, _| !path.starts_with(workspace_path));
+        self.notebook_cells
+            .retain(|_, path| !path.starts_with(workspace_path));
+        Ok(())
+    }
+
+    pub(super) fn make_document_ref(&self, key: DocumentKey) -> Option<DocumentQuery> {
+        let path = self.path_for_key(&key)?.clone();
+        let document_settings = self
+            .settings_for_path(&path)?
+            .workspace_settings_index
+            .get(&path);
+
+        let controller = self.documents.get(&path)?;
+        let cell_uri = match key {
+            DocumentKey::NotebookCell(uri) => Some(uri),
+            _ => None,
+        };
+        Some(controller.make_ref(cell_uri, path, document_settings))
+    }
+
+    pub(super) fn reload_settings(&mut self, changed_path: &PathBuf) {
+        for (root, settings) in self
+            .settings
+            .iter_mut()
+            .filter(|(path, _)| path.starts_with(changed_path))
+        {
+            settings.workspace_settings_index = ruff_settings::RuffSettingsIndex::new(
+                root,
+                settings.client_settings.editor_settings(),
+            );
+        }
+    }
+
+    pub(super) fn open_text_document(&mut self, path: PathBuf, document: TextDocument) {
+        self.documents
+            .insert(path, DocumentController::new_text(document));
+    }
+
+    pub(super) fn open_notebook_document(&mut self, path: PathBuf, document: NotebookDocument) {
+        for url in document.urls() {
+            self.notebook_cells.insert(url.clone(), path.clone());
+        }
+        self.documents
+            .insert(path, DocumentController::new_notebook(document));
+    }
+
+    pub(super) fn close_document(&mut self, key: &DocumentKey) -> crate::Result<()> {
+        let Some(path) = self.path_for_key(key).cloned() else {
+            anyhow::bail!("Tried to open unavailable document `{key}`");
+        };
+
+        let Some(controller) = self.documents.remove(&path) else {
+            anyhow::bail!(
+                "tried to close document that didn't exist at {}",
+                path.display()
+            )
+        };
+        if let Some(notebook) = controller.as_notebook() {
+            for url in notebook.urls() {
+                self.notebook_cells.remove(url).ok_or_else(|| {
+                    anyhow!("tried to de-register notebook cell with URL {url} that didn't exist")
+                })?;
+            }
+        }
+        Ok(())
+    }
+
+    pub(super) fn client_settings(
+        &self,
+        key: &DocumentKey,
+        global_settings: &ClientSettings,
+    ) -> settings::ResolvedClientSettings {
+        let Some(path) = self.path_for_key(key) else {
+            return ResolvedClientSettings::global(global_settings);
+        };
+        let Some(WorkspaceSettings {
+            client_settings, ..
+        }) = self.settings_for_path(path)
+        else {
+            return ResolvedClientSettings::global(global_settings);
+        };
+        client_settings.clone()
+    }
+
+    fn document_controller_for_key(
+        &mut self,
+        key: &DocumentKey,
+    ) -> crate::Result<&mut DocumentController> {
+        let Some(path) = self.path_for_key(key).cloned() else {
+            anyhow::bail!("Tried to open unavailable document `{key}`");
+        };
+        let Some(controller) = self.documents.get_mut(&path) else {
+            anyhow::bail!("Document controller not available at `{}`", path.display());
+        };
+        Ok(controller)
+    }
+
+    fn path_for_key<'a>(&'a self, key: &'a DocumentKey) -> Option<&'a PathBuf> {
+        match key {
+            DocumentKey::Notebook(path) | DocumentKey::Text(path) => Some(path),
+            DocumentKey::NotebookCell(uri) => self.notebook_cells.get(uri),
+        }
+    }
+
+    fn settings_for_path(&self, path: &Path) -> Option<&WorkspaceSettings> {
+        self.settings
+            .range(..path.to_path_buf())
+            .next_back()
+            .map(|(_, settings)| settings)
+    }
+}
+
+impl DocumentController {
+    fn new_text(document: TextDocument) -> Self {
+        Self::Text(Arc::new(document))
+    }
+
+    fn new_notebook(document: NotebookDocument) -> Self {
+        Self::Notebook(Arc::new(document))
+    }
+
+    fn make_ref(
+        &self,
+        cell_uri: Option<lsp_types::Url>,
+        file_path: PathBuf,
+        settings: Arc<RuffSettings>,
+    ) -> DocumentQuery {
+        match &self {
+            Self::Notebook(notebook) => DocumentQuery::Notebook {
+                cell_uri,
+                file_path,
+                notebook: notebook.clone(),
+                settings,
+            },
+            Self::Text(document) => DocumentQuery::Text {
+                file_path,
+                document: document.clone(),
+                settings,
+            },
+        }
+    }
+
+    pub(crate) fn as_notebook_mut(&mut self) -> Option<&mut NotebookDocument> {
+        Some(match self {
+            Self::Notebook(notebook) => Arc::make_mut(notebook),
+            Self::Text(_) => return None,
+        })
+    }
+
+    pub(crate) fn as_notebook(&self) -> Option<&NotebookDocument> {
+        match self {
+            Self::Notebook(notebook) => Some(notebook),
+            Self::Text(_) => None,
+        }
+    }
+
+    #[allow(dead_code)]
+    pub(crate) fn as_text(&self) -> Option<&TextDocument> {
+        match self {
+            Self::Text(document) => Some(document),
+            Self::Notebook(_) => None,
+        }
+    }
+
+    pub(crate) fn as_text_mut(&mut self) -> Option<&mut TextDocument> {
+        Some(match self {
+            Self::Text(document) => Arc::make_mut(document),
+            Self::Notebook(_) => return None,
+        })
+    }
+}
+
+impl DocumentQuery {
+    /// Retrieve the original key that describes this document query.
+    pub(crate) fn make_key(&self) -> DocumentKey {
+        match self {
+            Self::Text { file_path, .. } => DocumentKey::Text(file_path.clone()),
+            Self::Notebook {
+                cell_uri: Some(cell_uri),
+                ..
+            } => DocumentKey::NotebookCell(cell_uri.clone()),
+            Self::Notebook { file_path, .. } => DocumentKey::Notebook(file_path.clone()),
+        }
+    }
+
+    /// Get the document settings associated with this query.
+    pub(crate) fn settings(&self) -> &RuffSettings {
+        match self {
+            Self::Text { settings, .. } | Self::Notebook { settings, .. } => settings,
+        }
+    }
+
+    /// Generate a source kind used by the linter.
+    pub(crate) fn make_source_kind(&self) -> ruff_linter::source_kind::SourceKind {
+        match self {
+            Self::Text { document, .. } => {
+                ruff_linter::source_kind::SourceKind::Python(document.contents().to_string())
+            }
+            Self::Notebook { notebook, .. } => {
+                ruff_linter::source_kind::SourceKind::IpyNotebook(notebook.make_ruff_notebook())
+            }
+        }
+    }
+
+    /// Attempts to access the underlying notebook document that this query is selecting.
+    pub(crate) fn as_notebook(&self) -> Option<&NotebookDocument> {
+        match self {
+            Self::Notebook { notebook, .. } => Some(notebook),
+            Self::Text { .. } => None,
+        }
+    }
+
+    /// Get the source type of the document associated with this query.
+    pub(crate) fn source_type(&self) -> ruff_python_ast::PySourceType {
+        match self {
+            Self::Text { .. } => ruff_python_ast::PySourceType::Python,
+            Self::Notebook { .. } => ruff_python_ast::PySourceType::Ipynb,
+        }
+    }
+
+    /// Get the version of document selected by this query.
+    pub(crate) fn version(&self) -> DocumentVersion {
+        match self {
+            Self::Text { document, .. } => document.version(),
+            Self::Notebook { notebook, .. } => notebook.version(),
+        }
+    }
+
+    /// Get the underlying file path for the document selected by this query.
+    pub(crate) fn file_path(&self) -> &PathBuf {
+        match self {
+            Self::Text { file_path, .. } | Self::Notebook { file_path, .. } => file_path,
+        }
+    }
+
+    /// Attempt to access the single inner text document selected by the query.
+    /// If this query is selecting an entire notebook document, this will return `None`.
+    pub(crate) fn as_single_document(&self) -> Option<&TextDocument> {
+        match self {
+            Self::Text { document, .. } => Some(document),
+            Self::Notebook {
+                notebook, cell_uri, ..
+            } => cell_uri
+                .as_ref()
+                .and_then(|cell_uri| notebook.cell_document_by_uri(cell_uri)),
+        }
+    }
+}

crates/ruff_server/src/session/settings.rs

@@ -7,7 +7,7 @@ use serde::Deserialize;
 use ruff_linter::{line_width::LineLength, RuleSelector};
 
 /// Maps a workspace URI to its associated client settings. Used during server initialization.
-pub(crate) type WorkspaceSettingsMap = FxHashMap<Url, ClientSettings>;
+pub(crate) type WorkspaceSettingsMap = FxHashMap<PathBuf, ClientSettings>;
 
 /// Resolved client settings for a specific document. These settings are meant to be
 /// used directly by the server, and are *not* a 1:1 representation with how the client
@@ -169,7 +169,12 @@ impl AllSettings {
             workspace_settings: workspace_settings.map(|workspace_settings| {
                 workspace_settings
                     .into_iter()
-                    .map(|settings| (settings.workspace, settings.settings))
+                    .map(|settings| {
+                        (
+                            settings.workspace.to_file_path().unwrap(),
+                            settings.settings,
+                        )
+                    })
                     .collect()
             }),
         }
@@ -360,7 +365,7 @@ mod tests {
         serde_json::from_str(content).expect("test fixture JSON should deserialize")
     }
 
-    #[test]
+    #[cfg_attr(not(windows), test)]
     fn test_vs_code_init_options_deserialize() {
         let options: InitializationOptions = deserialize_fixture(VS_CODE_INIT_OPTIONS_FIXTURE);
 
@@ -545,19 +550,19 @@ mod tests {
         "###);
     }
 
-    #[test]
+    #[cfg_attr(not(windows), test)]
     fn test_vs_code_workspace_settings_resolve() {
         let options = deserialize_fixture(VS_CODE_INIT_OPTIONS_FIXTURE);
         let AllSettings {
             global_settings,
             workspace_settings,
         } = AllSettings::from_init_options(options);
-        let url = Url::parse("file:///Users/test/projects/pandas").expect("url should parse");
+        let path = PathBuf::from_str("/Users/test/projects/pandas").expect("path should be valid");
         let workspace_settings = workspace_settings.expect("workspace settings should exist");
         assert_eq!(
             ResolvedClientSettings::with_workspace(
                 workspace_settings
-                    .get(&url)
+                    .get(&path)
                     .expect("workspace setting should exist"),
                 &global_settings
             ),
@@ -583,11 +588,11 @@ mod tests {
                 }
             }
         );
-        let url = Url::parse("file:///Users/test/projects/scipy").expect("url should parse");
+        let path = PathBuf::from_str("/Users/test/projects/scipy").expect("path should be valid");
         assert_eq!(
             ResolvedClientSettings::with_workspace(
                 workspace_settings
-                    .get(&url)
+                    .get(&path)
                     .expect("workspace setting should exist"),
                 &global_settings
             ),

crates/ruff_server/src/session/workspace.rs

@@ -1,269 +0,0 @@
-use anyhow::anyhow;
-use lsp_types::Url;
-use rustc_hash::FxHashMap;
-use std::{
-    collections::BTreeMap,
-    ops::Deref,
-    path::{Path, PathBuf},
-    sync::Arc,
-};
-
-use crate::{edit::DocumentVersion, Document};
-
-use self::ruff_settings::RuffSettingsIndex;
-
-use super::{
-    settings::{self, ResolvedClientSettings, ResolvedEditorSettings},
-    ClientSettings,
-};
-
-mod ruff_settings;
-
-pub(crate) use ruff_settings::RuffSettings;
-
-#[derive(Default)]
-pub(crate) struct Workspaces(BTreeMap<PathBuf, Workspace>);
-
-pub(crate) struct Workspace {
-    open_documents: OpenDocuments,
-    settings: ResolvedClientSettings,
-}
-
-pub(crate) struct OpenDocuments {
-    documents: FxHashMap<Url, DocumentController>,
-    settings_index: ruff_settings::RuffSettingsIndex,
-}
-
-/// A mutable handler to an underlying document.
-/// Handles copy-on-write mutation automatically when
-/// calling `deref_mut`.
-pub(crate) struct DocumentController {
-    document: Arc<Document>,
-}
-
-/// A read-only reference to a document.
-#[derive(Clone)]
-pub(crate) struct DocumentRef {
-    document: Arc<Document>,
-    settings: Arc<RuffSettings>,
-}
-
-impl Workspaces {
-    pub(super) fn new(
-        workspaces: Vec<(Url, ClientSettings)>,
-        global_settings: &ClientSettings,
-    ) -> crate::Result<Self> {
-        Ok(Self(
-            workspaces
-                .into_iter()
-                .map(|(url, workspace_settings)| {
-                    Workspace::new(&url, &workspace_settings, global_settings)
-                })
-                .collect::<crate::Result<_>>()?,
-        ))
-    }
-
-    pub(super) fn open_workspace_folder(
-        &mut self,
-        folder_url: &Url,
-        global_settings: &ClientSettings,
-    ) -> crate::Result<()> {
-        // TODO(jane): find a way to allow for workspace settings to be updated dynamically
-        let (path, workspace) =
-            Workspace::new(folder_url, &ClientSettings::default(), global_settings)?;
-        self.0.insert(path, workspace);
-        Ok(())
-    }
-
-    pub(super) fn close_workspace_folder(&mut self, folder_url: &Url) -> crate::Result<()> {
-        let path = folder_url
-            .to_file_path()
-            .map_err(|()| anyhow!("Folder URI was not a proper file path"))?;
-        self.0
-            .remove(&path)
-            .ok_or_else(|| anyhow!("Tried to remove non-existent folder {}", path.display()))?;
-        Ok(())
-    }
-
-    pub(super) fn snapshot(&self, document_url: &Url) -> Option<DocumentRef> {
-        self.workspace_for_url(document_url)?
-            .open_documents
-            .snapshot(document_url)
-    }
-
-    pub(super) fn controller(&mut self, document_url: &Url) -> Option<&mut DocumentController> {
-        self.workspace_for_url_mut(document_url)?
-            .open_documents
-            .controller(document_url)
-    }
-
-    pub(super) fn reload_settings(&mut self, changed_url: &Url) -> crate::Result<()> {
-        let (root, workspace) = self
-            .entry_for_url_mut(changed_url)
-            .ok_or_else(|| anyhow!("Workspace not found for {changed_url}"))?;
-        workspace.reload_settings(root);
-        Ok(())
-    }
-
-    pub(super) fn open(&mut self, url: &Url, contents: String, version: DocumentVersion) {
-        if let Some(workspace) = self.workspace_for_url_mut(url) {
-            workspace.open_documents.open(url, contents, version);
-        }
-    }
-
-    pub(super) fn close(&mut self, url: &Url) -> crate::Result<()> {
-        self.workspace_for_url_mut(url)
-            .ok_or_else(|| anyhow!("Workspace not found for {url}"))?
-            .open_documents
-            .close(url)
-    }
-
-    pub(super) fn client_settings(
-        &self,
-        url: &Url,
-        global_settings: &ClientSettings,
-    ) -> settings::ResolvedClientSettings {
-        self.workspace_for_url(url).map_or_else(
-            || {
-                tracing::warn!(
-                    "Workspace not found for {url}. Global settings will be used for this document"
-                );
-                settings::ResolvedClientSettings::global(global_settings)
-            },
-            |workspace| workspace.settings.clone(),
-        )
-    }
-
-    fn workspace_for_url(&self, url: &Url) -> Option<&Workspace> {
-        Some(self.entry_for_url(url)?.1)
-    }
-
-    fn workspace_for_url_mut(&mut self, url: &Url) -> Option<&mut Workspace> {
-        Some(self.entry_for_url_mut(url)?.1)
-    }
-
-    fn entry_for_url(&self, url: &Url) -> Option<(&Path, &Workspace)> {
-        let path = url.to_file_path().ok()?;
-        self.0
-            .range(..path)
-            .next_back()
-            .map(|(path, workspace)| (path.as_path(), workspace))
-    }
-
-    fn entry_for_url_mut(&mut self, url: &Url) -> Option<(&Path, &mut Workspace)> {
-        let path = url.to_file_path().ok()?;
-        self.0
-            .range_mut(..path)
-            .next_back()
-            .map(|(path, workspace)| (path.as_path(), workspace))
-    }
-}
-
-impl Workspace {
-    pub(crate) fn new(
-        root: &Url,
-        workspace_settings: &ClientSettings,
-        global_settings: &ClientSettings,
-    ) -> crate::Result<(PathBuf, Self)> {
-        let path = root
-            .to_file_path()
-            .map_err(|()| anyhow!("workspace URL was not a file path!"))?;
-
-        let settings = ResolvedClientSettings::with_workspace(workspace_settings, global_settings);
-
-        let workspace = Self {
-            open_documents: OpenDocuments::new(&path, settings.editor_settings()),
-            settings,
-        };
-
-        Ok((path, workspace))
-    }
-
-    fn reload_settings(&mut self, root: &Path) {
-        self.open_documents
-            .reload_settings(root, self.settings.editor_settings());
-    }
-}
-
-impl OpenDocuments {
-    fn new(path: &Path, editor_settings: &ResolvedEditorSettings) -> Self {
-        Self {
-            documents: FxHashMap::default(),
-            settings_index: RuffSettingsIndex::new(path, editor_settings),
-        }
-    }
-
-    fn snapshot(&self, url: &Url) -> Option<DocumentRef> {
-        let path = url
-            .to_file_path()
-            .expect("document URL should convert to file path: {url}");
-        let document_settings = self.settings_index.get(&path);
-        Some(self.documents.get(url)?.make_ref(document_settings))
-    }
-
-    fn controller(&mut self, url: &Url) -> Option<&mut DocumentController> {
-        self.documents.get_mut(url)
-    }
-
-    fn open(&mut self, url: &Url, contents: String, version: DocumentVersion) {
-        if self
-            .documents
-            .insert(url.clone(), DocumentController::new(contents, version))
-            .is_some()
-        {
-            tracing::warn!("Opening document `{url}` that is already open!");
-        }
-    }
-
-    fn close(&mut self, url: &Url) -> crate::Result<()> {
-        let Some(_) = self.documents.remove(url) else {
-            return Err(anyhow!(
-                "Tried to close document `{url}`, which was not open"
-            ));
-        };
-        Ok(())
-    }
-
-    fn reload_settings(&mut self, root: &Path, editor_settings: &ResolvedEditorSettings) {
-        self.settings_index = RuffSettingsIndex::new(root, editor_settings);
-    }
-}
-
-impl DocumentController {
-    fn new(contents: String, version: DocumentVersion) -> Self {
-        Self {
-            document: Arc::new(Document::new(contents, version)),
-        }
-    }
-
-    pub(crate) fn make_ref(&self, document_settings: Arc<RuffSettings>) -> DocumentRef {
-        DocumentRef {
-            document: self.document.clone(),
-            settings: document_settings,
-        }
-    }
-
-    pub(crate) fn make_mut(&mut self) -> &mut Document {
-        Arc::make_mut(&mut self.document)
-    }
-}
-
-impl Deref for DocumentController {
-    type Target = Document;
-    fn deref(&self) -> &Self::Target {
-        &self.document
-    }
-}
-
-impl Deref for DocumentRef {
-    type Target = Document;
-    fn deref(&self) -> &Self::Target {
-        &self.document
-    }
-}
-
-impl DocumentRef {
-    pub(crate) fn settings(&self) -> &RuffSettings {
-        &self.settings
-    }
-}

crates/ruff_server/tests/document.rs

@@ -1,11 +1,11 @@
 const PANDAS_HTML_SRC: &str = include_str!("../resources/test/fixtures/pandas_html.py");
 
 use lsp_types::{Position, Range, TextDocumentContentChangeEvent};
-use ruff_server::{Document, PositionEncoding};
+use ruff_server::{PositionEncoding, TextDocument};
 
 #[test]
 fn delete_lines_pandas_html() {
-    let mut document = Document::new(PANDAS_HTML_SRC.to_string(), 1);
+    let mut document = TextDocument::new(PANDAS_HTML_SRC.to_string(), 1);
 
     let changes = vec![
         TextDocumentContentChangeEvent {