Check context parameters directly from function definition

add lint rule to show error for removed context variables in airflow

.gitattributes

@@ -14,5 +14,7 @@ crates/ruff_python_parser/resources/invalid/re_lex_logical_token_mac_eol.py text
 
 crates/ruff_python_parser/resources/inline linguist-generated=true
 
-ruff.schema.json linguist-generated=true text=auto eol=lf
+ruff.schema.json -diff linguist-generated=true text=auto eol=lf
+crates/ruff_python_ast/src/generated.rs -diff linguist-generated=true text=auto eol=lf
+crates/ruff_python_formatter/src/generated.rs -diff linguist-generated=true text=auto eol=lf
 *.md.snap linguist-language=Markdown

.github/actionlint.yaml

@@ -6,4 +6,5 @@ self-hosted-runner:
   labels:
     - depot-ubuntu-latest-8
     - depot-ubuntu-22.04-16
-    - windows-latest-xlarge
+    - github-windows-2025-x86_64-8
+    - github-windows-2025-x86_64-16

.github/workflows/ci.yaml

@@ -203,7 +203,7 @@ jobs:
 
   cargo-test-windows:
     name: "cargo test (windows)"
-    runs-on: windows-latest-xlarge
+    runs-on: github-windows-2025-x86_64-16
     needs: determine_changes
     if: ${{ needs.determine_changes.outputs.code == 'true' || github.ref == 'refs/heads/main' }}
     timeout-minutes: 20
@@ -386,6 +386,12 @@ jobs:
       - name: "Install Rust toolchain"
         run: rustup component add rustfmt
       - uses: Swatinem/rust-cache@v2
+      # Run all code generation scripts, and verify that the current output is
+      # already checked into git.
+      - run: python crates/ruff_python_ast/generate.py
+      - run: python crates/ruff_python_formatter/generate.py
+      - run: test -z "$(git status --porcelain)"
+      # Verify that adding a plugin or rule produces clean code.
       - run: ./scripts/add_rule.py --name DoTheThing --prefix F --code 999 --linter pyflakes
       - run: cargo check
       - run: cargo fmt --all --check

.github/workflows/publish-playground.yml

@@ -49,7 +49,7 @@ jobs:
         working-directory: playground
       - name: "Deploy to Cloudflare Pages"
         if: ${{ env.CF_API_TOKEN_EXISTS == 'true' }}
-        uses: cloudflare/wrangler-action@v3.13.0
+        uses: cloudflare/wrangler-action@v3.13.1
         with:
           apiToken: ${{ secrets.CF_API_TOKEN }}
           accountId: ${{ secrets.CF_ACCOUNT_ID }}

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ exclude: |
   (?x)^(
     .github/workflows/release.yml|
     crates/red_knot_vendored/vendor/.*|
-    crates/red_knot_workspace/resources/.*|
+    crates/red_knot_project/resources/.*|
     crates/ruff_linter/resources/.*|
     crates/ruff_linter/src/rules/.*/snapshots/.*|
     crates/ruff_notebook/resources/.*|
@@ -73,7 +73,7 @@ repos:
         pass_filenames: false # This makes it a lot faster
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.1
+    rev: v0.9.2
     hooks:
       - id: ruff-format
       - id: ruff
@@ -91,7 +91,7 @@ repos:
   # zizmor detects security vulnerabilities in GitHub Actions workflows.
   # Additional configuration for the tool is found in `.github/zizmor.yml`
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.0.1
+    rev: v1.1.1
     hooks:
       - id: zizmor
 
@@ -103,7 +103,7 @@ repos:
   # `actionlint` hook, for verifying correct syntax in GitHub Actions workflows.
   # Some additional configuration for `actionlint` can be found in `.github/actionlint.yaml`.
   - repo: https://github.com/rhysd/actionlint
-    rev: v1.7.6
+    rev: v1.7.7
     hooks:
       - id: actionlint
         stages:

Cargo.lock

@@ -212,9 +212,9 @@ checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
 
 [[package]]
 name = "bitflags"
-version = "2.7.0"
+version = "2.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1be3f42a67d6d345ecd59f675f3f012d6974981560836e938c22b424b85ce1be"
+checksum = "8f68f53c83ab957f72c32642f3868eec03eb974d1fb82e453128456482613d36"
 
 [[package]]
 name = "block-buffer"
@@ -477,7 +477,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "117725a109d387c937a1533ce01b450cbde6b88abceea8473c4d7a85853cda3c"
 dependencies = [
  "lazy_static",
- "windows-sys 0.48.0",
+ "windows-sys 0.59.0",
 ]
 
 [[package]]
@@ -1062,7 +1062,7 @@ version = "0.9.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0bf760ebf69878d9fd8f110c89703d90ce35095324d1f1edcb595c63945ee757"
 dependencies = [
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "ignore",
  "walkdir",
 ]
@@ -1343,9 +1343,9 @@ dependencies = [
 
 [[package]]
 name = "indexmap"
-version = "2.7.0"
+version = "2.7.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "62f822373a4fe84d4bb149bf54e584a7f4abec90e072ed49cda0edea5b95471f"
+checksum = "8c9c992b02b5b4c94ea26e32fe5bccb7aa7d9f390ab5c1221ff895bc7ea8b652"
 dependencies = [
  "equivalent",
  "hashbrown 0.15.2",
@@ -1374,11 +1374,11 @@ checksum = "b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5"
 
 [[package]]
 name = "inotify"
-version = "0.10.2"
+version = "0.11.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fdd168d97690d0b8c412d6b6c10360277f4d7ee495c5d0d5d5fe0854923255cc"
+checksum = "f37dccff2791ab604f9babef0ba14fbe0be30bd368dc541e2b08d07c8aa908f3"
 dependencies = [
- "bitflags 1.3.2",
+ "bitflags 2.8.0",
  "inotify-sys",
  "libc",
 ]
@@ -1422,15 +1422,6 @@ dependencies = [
  "serde_json",
 ]
 
-[[package]]
-name = "instant"
-version = "0.1.12"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c"
-dependencies = [
- "cfg-if",
-]
-
 [[package]]
 name = "is-docker"
 version = "0.2.0"
@@ -1610,7 +1601,7 @@ version = "0.1.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c0ff37bd590ca25063e35af745c343cb7a0271906fb7b37e4813e8f79f00268d"
 dependencies = [
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "libc",
  "redox_syscall 0.5.3",
 ]
@@ -1657,9 +1648,9 @@ dependencies = [
 
 [[package]]
 name = "log"
-version = "0.4.22"
+version = "0.4.25"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24"
+checksum = "04cbf5b083de1c7e0222a7a51dbfdba1cbe1c6ab0b15e29fff3f6c077fd9cd9f"
 
 [[package]]
 name = "lsp-server"
@@ -1781,7 +1772,7 @@ version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "71e2746dc3a24dd78b3cfcb7be93368c6de9963d30f43a6a73998a9cf4b17b46"
 dependencies = [
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "cfg-if",
  "cfg_aliases",
  "libc",
@@ -1805,11 +1796,11 @@ checksum = "61807f77802ff30975e01f4f071c8ba10c022052f98b3294119f3e615d13e5be"
 
 [[package]]
 name = "notify"
-version = "7.0.0"
+version = "8.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c533b4c39709f9ba5005d8002048266593c1cfaf3c5f0739d5b8ab0c6c504009"
+checksum = "2fee8403b3d66ac7b26aee6e40a897d85dc5ce26f44da36b8b73e987cc52e943"
 dependencies = [
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "filetime",
  "fsevent-sys",
  "inotify",
@@ -1819,17 +1810,14 @@ dependencies = [
  "mio",
  "notify-types",
  "walkdir",
- "windows-sys 0.52.0",
+ "windows-sys 0.59.0",
 ]
 
 [[package]]
 name = "notify-types"
-version = "1.0.0"
+version = "2.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7393c226621f817964ffb3dc5704f9509e107a8b024b489cc2c1b217378785df"
-dependencies = [
- "instant",
-]
+checksum = "5e0826a989adedc2a244799e823aece04662b66609d96af8dff7ac6df9a8925d"
 
 [[package]]
 name = "nu-ansi-term"
@@ -1895,9 +1883,9 @@ checksum = "04744f49eae99ab78e0d5c0b603ab218f515ea8cfe5a456d7629ad883a3b6e7d"
 
 [[package]]
 name = "ordermap"
-version = "0.5.4"
+version = "0.5.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f80a48eb68b6a7da9829b8b0429011708f775af80676a91063d023a66a656106"
+checksum = "c55fdf45a2b1e929e3656d404395767e05c98b6ebd8157eb31e370077d545160"
 dependencies = [
  "indexmap",
 ]
@@ -2336,25 +2324,55 @@ dependencies = [
  "crossbeam",
  "ctrlc",
  "filetime",
+ "insta",
+ "insta-cmd",
  "rayon",
+ "red_knot_project",
  "red_knot_python_semantic",
  "red_knot_server",
- "red_knot_workspace",
+ "regex",
  "ruff_db",
  "salsa",
  "tempfile",
+ "toml",
  "tracing",
  "tracing-flame",
  "tracing-subscriber",
  "tracing-tree",
 ]
 
+[[package]]
+name = "red_knot_project"
+version = "0.0.0"
+dependencies = [
+ "anyhow",
+ "crossbeam",
+ "glob",
+ "insta",
+ "notify",
+ "pep440_rs",
+ "rayon",
+ "red_knot_python_semantic",
+ "red_knot_vendored",
+ "ruff_cache",
+ "ruff_db",
+ "ruff_macros",
+ "ruff_python_ast",
+ "ruff_text_size",
+ "rustc-hash 2.1.0",
+ "salsa",
+ "serde",
+ "thiserror 2.0.11",
+ "toml",
+ "tracing",
+]
+
 [[package]]
 name = "red_knot_python_semantic"
 version = "0.0.0"
 dependencies = [
  "anyhow",
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "camino",
  "compact_str",
  "countme",
@@ -2401,7 +2419,7 @@ dependencies = [
  "libc",
  "lsp-server",
  "lsp-types",
- "red_knot_workspace",
+ "red_knot_project",
  "ruff_db",
  "ruff_notebook",
  "ruff_python_ast",
@@ -2456,39 +2474,14 @@ dependencies = [
  "console_log",
  "js-sys",
  "log",
+ "red_knot_project",
  "red_knot_python_semantic",
- "red_knot_workspace",
  "ruff_db",
  "ruff_notebook",
  "wasm-bindgen",
  "wasm-bindgen-test",
 ]
 
-[[package]]
-name = "red_knot_workspace"
-version = "0.0.0"
-dependencies = [
- "anyhow",
- "crossbeam",
- "glob",
- "insta",
- "notify",
- "pep440_rs",
- "rayon",
- "red_knot_python_semantic",
- "red_knot_vendored",
- "ruff_cache",
- "ruff_db",
- "ruff_python_ast",
- "ruff_text_size",
- "rustc-hash 2.1.0",
- "salsa",
- "serde",
- "thiserror 2.0.11",
- "toml",
- "tracing",
-]
-
 [[package]]
 name = "redox_syscall"
 version = "0.4.1"
@@ -2504,7 +2497,7 @@ version = "0.5.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2a908a6e00f1fdd0dfd9c0eb08ce85126f6d8bbda50017e74bc4a4b7d4a926a4"
 dependencies = [
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
 ]
 
 [[package]]
@@ -2596,7 +2589,7 @@ dependencies = [
  "argfile",
  "assert_fs",
  "bincode",
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "cachedir",
  "chrono",
  "clap",
@@ -2668,8 +2661,8 @@ dependencies = [
  "criterion",
  "mimalloc",
  "rayon",
+ "red_knot_project",
  "red_knot_python_semantic",
- "red_knot_workspace",
  "ruff_db",
  "ruff_linter",
  "ruff_python_ast",
@@ -2828,7 +2821,7 @@ version = "0.9.2"
 dependencies = [
  "aho-corasick",
  "anyhow",
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "chrono",
  "clap",
  "colored 3.0.0",
@@ -2918,7 +2911,7 @@ name = "ruff_python_ast"
 version = "0.0.0"
 dependencies = [
  "aho-corasick",
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "compact_str",
  "is-macro",
  "itertools 0.14.0",
@@ -3000,7 +2993,7 @@ dependencies = [
 name = "ruff_python_literal"
 version = "0.0.0"
 dependencies = [
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "itertools 0.14.0",
  "ruff_python_ast",
  "unic-ucd-category",
@@ -3011,7 +3004,7 @@ name = "ruff_python_parser"
 version = "0.0.0"
 dependencies = [
  "anyhow",
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "bstr",
  "compact_str",
  "insta",
@@ -3043,7 +3036,7 @@ dependencies = [
 name = "ruff_python_semantic"
 version = "0.0.0"
 dependencies = [
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "is-macro",
  "ruff_cache",
  "ruff_index",
@@ -3062,7 +3055,7 @@ dependencies = [
 name = "ruff_python_stdlib"
 version = "0.0.0"
 dependencies = [
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "unicode-ident",
 ]
 
@@ -3229,7 +3222,7 @@ version = "0.38.40"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "99e4ea3e1cdc4b559b8e5650f9c8e5998e3e5c1343b4eaf034565f32318d63c0"
 dependencies = [
- "bitflags 2.7.0",
+ "bitflags 2.8.0",
  "errno",
  "libc",
  "linux-raw-sys",
@@ -3412,9 +3405,9 @@ dependencies = [
 
 [[package]]
 name = "serde_json"
-version = "1.0.135"
+version = "1.0.137"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2b0d7ba2887406110130a978386c4e1befb98c674b4fba677954e4db976630d9"
+checksum = "930cfb6e6abf99298aaad7d29abbef7a9999a9a8806a40088f55f0dcec03146b"
 dependencies = [
  "itoa",
  "memchr",
@@ -3511,9 +3504,9 @@ checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64"
 
 [[package]]
 name = "similar"
-version = "2.6.0"
+version = "2.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1de1d4f81173b03af4c0cbed3c898f6bff5b870e4a7f5d6f4057d62a7a4b686e"
+checksum = "bbbb5d9659141646ae647b42fe094daf6c6192d1620870b449d9557f748b2daa"
 
 [[package]]
 name = "siphasher"
@@ -3933,9 +3926,9 @@ dependencies = [
 
 [[package]]
 name = "tracing-indicatif"
-version = "0.3.8"
+version = "0.3.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "74ba258e9de86447f75edf6455fded8e5242704c6fccffe7bf8d7fb6daef1180"
+checksum = "8201ca430e0cd893ef978226fd3516c06d9c494181c8bf4e5b32e30ed4b40aa1"
 dependencies = [
  "indicatif",
  "tracing",
@@ -4176,9 +4169,9 @@ checksum = "711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a"
 
 [[package]]
 name = "uuid"
-version = "1.11.1"
+version = "1.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b913a3b5fe84142e269d63cc62b64319ccaf89b748fc31fe025177f767a756c4"
+checksum = "744018581f9a3454a9e15beb8a33b017183f1e7c0cd170232a2d1453b23a51c4"
 dependencies = [
  "getrandom",
  "rand",
@@ -4188,9 +4181,9 @@ dependencies = [
 
 [[package]]
 name = "uuid-macro-internal"
-version = "1.11.1"
+version = "1.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c91084647266237a48351d05d55dee65bba9e1b597f555fcf54680f820284a1c"
+checksum = "144b419c512fdd5eaa4c2998813e32aaab2b257746ee038de93985a99635501d"
 dependencies = [
  "proc-macro2",
  "quote",

Cargo.toml

@@ -41,7 +41,7 @@ ruff_workspace = { path = "crates/ruff_workspace" }
 red_knot_python_semantic = { path = "crates/red_knot_python_semantic" }
 red_knot_server = { path = "crates/red_knot_server" }
 red_knot_test = { path = "crates/red_knot_test" }
-red_knot_workspace = { path = "crates/red_knot_workspace", default-features = false }
+red_knot_project = { path = "crates/red_knot_project", default-features = false }
 
 aho-corasick = { version = "1.1.3" }
 anstream = { version = "0.6.18" }
@@ -105,7 +105,7 @@ matchit = { version = "0.8.1" }
 memchr = { version = "2.7.1" }
 mimalloc = { version = "0.1.39" }
 natord = { version = "1.0.9" }
-notify = { version = "7.0.0" }
+notify = { version = "8.0.0" }
 ordermap = { version = "0.5.0" }
 path-absolutize = { version = "3.1.1" }
 path-slash = { version = "0.2.1" }

crates/red_knot/Cargo.toml

@@ -13,7 +13,7 @@ license.workspace = true
 
 [dependencies]
 red_knot_python_semantic = { workspace = true }
-red_knot_workspace = { workspace = true, features = ["zstd"] }
+red_knot_project = { workspace = true, features = ["zstd"] }
 red_knot_server = { workspace = true }
 ruff_db = { workspace = true, features = ["os", "cache"] }
 
@@ -32,9 +32,14 @@ tracing-flame = { workspace = true }
 tracing-tree = { workspace = true }
 
 [dev-dependencies]
-filetime = { workspace = true }
-tempfile = { workspace = true }
 ruff_db = { workspace = true, features = ["testing"] }
 
+insta = { workspace = true, features = ["filters"] }
+insta-cmd = { workspace = true }
+filetime = { workspace = true }
+regex = { workspace = true }
+tempfile = { workspace = true }
+toml = { workspace = true }
+
 [lints]
 workspace = true

crates/red_knot/src/main.rs

@@ -6,13 +6,11 @@ use clap::Parser;
 use colored::Colorize;
 use crossbeam::channel as crossbeam_channel;
 use python_version::PythonVersion;
-use red_knot_python_semantic::SitePackages;
+use red_knot_project::metadata::options::{EnvironmentOptions, Options};
+use red_knot_project::watch;
+use red_knot_project::watch::ProjectWatcher;
+use red_knot_project::{ProjectDatabase, ProjectMetadata};
 use red_knot_server::run_server;
-use red_knot_workspace::db::ProjectDatabase;
-use red_knot_workspace::project::settings::Configuration;
-use red_knot_workspace::project::ProjectMetadata;
-use red_knot_workspace::watch;
-use red_knot_workspace::watch::ProjectWatcher;
 use ruff_db::diagnostic::Diagnostic;
 use ruff_db::system::{OsSystem, System, SystemPath, SystemPathBuf};
 use salsa::plumbing::ZalsaDatabase;
@@ -71,31 +69,28 @@ struct Args {
 }
 
 impl Args {
-    fn to_configuration(&self, cli_cwd: &SystemPath) -> Configuration {
-        let mut configuration = Configuration::default();
-
-        if let Some(python_version) = self.python_version {
-            configuration.python_version = Some(python_version.into());
+    fn to_options(&self, cli_cwd: &SystemPath) -> Options {
+        Options {
+            environment: Some(EnvironmentOptions {
+                python_version: self.python_version.map(Into::into),
+                venv_path: self
+                    .venv_path
+                    .as_ref()
+                    .map(|venv_path| SystemPath::absolute(venv_path, cli_cwd)),
+                typeshed: self
+                    .typeshed
+                    .as_ref()
+                    .map(|typeshed| SystemPath::absolute(typeshed, cli_cwd)),
+                extra_paths: self.extra_search_path.as_ref().map(|extra_search_paths| {
+                    extra_search_paths
+                        .iter()
+                        .map(|path| SystemPath::absolute(path, cli_cwd))
+                        .collect()
+                }),
+                ..EnvironmentOptions::default()
+            }),
+            ..Default::default()
         }
-
-        if let Some(venv_path) = &self.venv_path {
-            configuration.search_paths.site_packages = Some(SitePackages::Derived {
-                venv_path: SystemPath::absolute(venv_path, cli_cwd),
-            });
-        }
-
-        if let Some(typeshed) = &self.typeshed {
-            configuration.search_paths.typeshed = Some(SystemPath::absolute(typeshed, cli_cwd));
-        }
-
-        if let Some(extra_search_paths) = &self.extra_search_path {
-            configuration.search_paths.extra_paths = extra_search_paths
-                .iter()
-                .map(|path| Some(SystemPath::absolute(path, cli_cwd)))
-                .collect();
-        }
-
-        configuration
     }
 }
 
@@ -164,18 +159,13 @@ fn run() -> anyhow::Result<ExitStatus> {
         .unwrap_or_else(|| cli_base_path.clone());
 
     let system = OsSystem::new(cwd.clone());
-    let cli_configuration = args.to_configuration(&cwd);
-    let workspace_metadata = ProjectMetadata::discover(
-        system.current_directory(),
-        &system,
-        Some(&cli_configuration),
-    )?;
+    let cli_options = args.to_options(&cwd);
+    let mut workspace_metadata = ProjectMetadata::discover(system.current_directory(), &system)?;
+    workspace_metadata.apply_cli_options(cli_options.clone());
 
-    // TODO: Use the `program_settings` to compute the key for the database's persistent
-    //   cache and load the cache if it exists.
     let mut db = ProjectDatabase::new(workspace_metadata, system)?;
 
-    let (main_loop, main_loop_cancellation_token) = MainLoop::new(cli_configuration);
+    let (main_loop, main_loop_cancellation_token) = MainLoop::new(cli_options);
 
     // Listen to Ctrl+C and abort the watch mode.
     let main_loop_cancellation_token = Mutex::new(Some(main_loop_cancellation_token));
@@ -228,11 +218,11 @@ struct MainLoop {
     /// The file system watcher, if running in watch mode.
     watcher: Option<ProjectWatcher>,
 
-    cli_configuration: Configuration,
+    cli_options: Options,
 }
 
 impl MainLoop {
-    fn new(cli_configuration: Configuration) -> (Self, MainLoopCancellationToken) {
+    fn new(cli_options: Options) -> (Self, MainLoopCancellationToken) {
         let (sender, receiver) = crossbeam_channel::bounded(10);
 
         (
@@ -240,7 +230,7 @@ impl MainLoop {
                 sender: sender.clone(),
                 receiver,
                 watcher: None,
-                cli_configuration,
+                cli_options,
             },
             MainLoopCancellationToken { sender },
         )
@@ -324,7 +314,7 @@ impl MainLoop {
                 MainLoopMessage::ApplyChanges(changes) => {
                     revision += 1;
                     // Automatically cancels any pending queries and waits for them to complete.
-                    db.apply_changes(changes, Some(&self.cli_configuration));
+                    db.apply_changes(changes, Some(&self.cli_options));
                     if let Some(watcher) = self.watcher.as_mut() {
                         watcher.update(db);
                     }

crates/red_knot/tests/cli.rs

@@ -0,0 +1,60 @@
+use anyhow::Context;
+use insta_cmd::{assert_cmd_snapshot, get_cargo_bin};
+use std::process::Command;
+use tempfile::TempDir;
+
+/// Specifying an option on the CLI should take precedence over the same setting in the
+/// project's configuration.
+#[test]
+fn test_config_override() -> anyhow::Result<()> {
+    let tempdir = TempDir::new()?;
+
+    std::fs::write(
+        tempdir.path().join("pyproject.toml"),
+        r#"
+[tool.knot.environment]
+python-version = "3.11"
+"#,
+    )
+    .context("Failed to write settings")?;
+
+    std::fs::write(
+        tempdir.path().join("test.py"),
+        r#"
+import sys
+
+# Access `sys.last_exc` that was only added in Python 3.12
+print(sys.last_exc)
+"#,
+    )
+    .context("Failed to write test.py")?;
+
+    insta::with_settings!({filters => vec![(&*tempdir_filter(&tempdir), "<temp_dir>/")]}, {
+        assert_cmd_snapshot!(knot().arg("--project").arg(tempdir.path()), @r"
+        success: false
+        exit_code: 1
+        ----- stdout -----
+        error[lint:unresolved-attribute] <temp_dir>/test.py:5:7 Type `<module 'sys'>` has no attribute `last_exc`
+
+        ----- stderr -----
+        ");
+    });
+
+    assert_cmd_snapshot!(knot().arg("--project").arg(tempdir.path()).arg("--python-version").arg("3.12"), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    ");
+
+    Ok(())
+}
+
+fn knot() -> Command {
+    Command::new(get_cargo_bin("red_knot"))
+}
+
+fn tempdir_filter(tempdir: &TempDir) -> String {
+    format!(r"{}\\?/?", regex::escape(tempdir.path().to_str().unwrap()))
+}

crates/red_knot/tests/file_watching.rs

@@ -4,11 +4,11 @@ use std::io::Write;
 use std::time::{Duration, Instant};
 
 use anyhow::{anyhow, Context};
-use red_knot_python_semantic::{resolve_module, ModuleName, Program, PythonVersion, SitePackages};
-use red_knot_workspace::db::{Db, ProjectDatabase};
-use red_knot_workspace::project::settings::{Configuration, SearchPathConfiguration};
-use red_knot_workspace::project::ProjectMetadata;
-use red_knot_workspace::watch::{directory_watcher, ChangeEvent, ProjectWatcher};
+use red_knot_project::metadata::options::{EnvironmentOptions, Options};
+use red_knot_project::metadata::pyproject::{PyProject, Tool};
+use red_knot_project::watch::{directory_watcher, ChangeEvent, ProjectWatcher};
+use red_knot_project::{Db, ProjectDatabase, ProjectMetadata};
+use red_knot_python_semantic::{resolve_module, ModuleName, PythonPlatform, PythonVersion};
 use ruff_db::files::{system_path_to_file, File, FileError};
 use ruff_db::source::source_text;
 use ruff_db::system::{OsSystem, SystemPath, SystemPathBuf};
@@ -22,7 +22,6 @@ struct TestCase {
     /// We need to hold on to it in the test case or the temp files get deleted.
     _temp_dir: tempfile::TempDir,
     root_dir: SystemPathBuf,
-    configuration: Configuration,
 }
 
 impl TestCase {
@@ -112,19 +111,44 @@ impl TestCase {
         Ok(all_events)
     }
 
-    fn take_watch_changes(&self) -> Vec<ChangeEvent> {
-        self.try_take_watch_changes(Duration::from_secs(10))
+    fn take_watch_changes<M: MatchEvent>(&self, matcher: M) -> Vec<ChangeEvent> {
+        self.try_take_watch_changes(matcher, Duration::from_secs(10))
             .expect("Expected watch changes but observed none")
     }
 
-    fn try_take_watch_changes(&self, timeout: Duration) -> Option<Vec<ChangeEvent>> {
-        let watcher = self.watcher.as_ref()?;
+    fn try_take_watch_changes<M: MatchEvent>(
+        &self,
+        mut matcher: M,
+        timeout: Duration,
+    ) -> Result<Vec<ChangeEvent>, Vec<ChangeEvent>> {
+        let watcher = self
+            .watcher
+            .as_ref()
+            .expect("Cannot call `try_take_watch_changes` after `stop_watch`");
 
-        let mut all_events = self
-            .changes_receiver
-            .recv_timeout(timeout)
-            .unwrap_or_default();
-        watcher.flush();
+        let start = Instant::now();
+        let mut all_events = Vec::new();
+
+        loop {
+            let events = self
+                .changes_receiver
+                .recv_timeout(Duration::from_millis(100))
+                .unwrap_or_default();
+
+            if events
+                .iter()
+                .any(|event| matcher.match_event(event) || event.is_rescan())
+            {
+                all_events.extend(events);
+                break;
+            }
+
+            all_events.extend(events);
+
+            if start.elapsed() > timeout {
+                return Err(all_events);
+            }
+        }
 
         while let Ok(event) = self
             .changes_receiver
@@ -134,26 +158,28 @@ impl TestCase {
             watcher.flush();
         }
 
-        if all_events.is_empty() {
-            return None;
-        }
-        Some(all_events)
+        Ok(all_events)
     }
 
     fn apply_changes(&mut self, changes: Vec<ChangeEvent>) {
-        self.db.apply_changes(changes, Some(&self.configuration));
+        self.db.apply_changes(changes, None);
     }
 
-    fn update_search_path_settings(
-        &mut self,
-        configuration: SearchPathConfiguration,
-    ) -> anyhow::Result<()> {
-        let program = Program::get(self.db());
+    fn update_options(&mut self, options: Options) -> anyhow::Result<()> {
+        std::fs::write(
+            self.project_path("pyproject.toml").as_std_path(),
+            toml::to_string(&PyProject {
+                project: None,
+                tool: Some(Tool {
+                    knot: Some(options),
+                }),
+            })
+            .context("Failed to serialize options")?,
+        )
+        .context("Failed to write configuration")?;
 
-        let new_settings = configuration.to_settings(self.db.project().root(&self.db));
-        self.configuration.search_paths = configuration;
-
-        program.update_search_paths(&mut self.db, &new_settings)?;
+        let changes = self.take_watch_changes(event_for_file("pyproject.toml"));
+        self.apply_changes(changes);
 
         if let Some(watcher) = &mut self.watcher {
             watcher.update(&self.db);
@@ -234,14 +260,13 @@ fn setup<F>(setup_files: F) -> anyhow::Result<TestCase>
 where
     F: SetupFiles,
 {
-    setup_with_search_paths(setup_files, |_root, _project_path| {
-        SearchPathConfiguration::default()
-    })
+    setup_with_options(setup_files, |_root, _project_path| None)
 }
 
-fn setup_with_search_paths<F>(
+// TODO: Replace with configuration?
+fn setup_with_options<F>(
     setup_files: F,
-    create_search_paths: impl FnOnce(&SystemPath, &SystemPath) -> SearchPathConfiguration,
+    create_options: impl FnOnce(&SystemPath, &SystemPath) -> Option<Options>,
 ) -> anyhow::Result<TestCase>
 where
     F: SetupFiles,
@@ -275,32 +300,33 @@ where
 
     let system = OsSystem::new(&project_path);
 
-    let search_paths = create_search_paths(&root_path, &project_path);
+    if let Some(options) = create_options(&root_path, &project_path) {
+        std::fs::write(
+            project_path.join("pyproject.toml").as_std_path(),
+            toml::to_string(&PyProject {
+                project: None,
+                tool: Some(Tool {
+                    knot: Some(options),
+                }),
+            })
+            .context("Failed to serialize options")?,
+        )
+        .context("Failed to write configuration")?;
+    }
 
-    for path in search_paths
+    let project = ProjectMetadata::discover(&project_path, &system)?;
+    let program_settings = project.to_program_settings(&system);
+
+    for path in program_settings
+        .search_paths
         .extra_paths
         .iter()
-        .flatten()
-        .chain(search_paths.typeshed.iter())
-        .chain(search_paths.site_packages.iter().flat_map(|site_packages| {
-            if let SitePackages::Known(path) = site_packages {
-                path.as_slice()
-            } else {
-                &[]
-            }
-        }))
+        .chain(program_settings.search_paths.typeshed.as_ref())
     {
         std::fs::create_dir_all(path.as_std_path())
             .with_context(|| format!("Failed to create search path `{path}`"))?;
     }
 
-    let configuration = Configuration {
-        python_version: Some(PythonVersion::PY312),
-        search_paths,
-    };
-
-    let project = ProjectMetadata::discover(&project_path, &system, Some(&configuration))?;
-
     let db = ProjectDatabase::new(project, system)?;
 
     let (sender, receiver) = crossbeam::channel::unbounded();
@@ -316,12 +342,12 @@ where
         watcher: Some(watcher),
         _temp_dir: temp_dir,
         root_dir: root_path,
-        configuration,
     };
 
     // Sometimes the file watcher reports changes for events that happened before the watcher was started.
     // Do a best effort at dropping these events.
-    test_case.try_take_watch_changes(Duration::from_millis(100));
+    let _ =
+        test_case.try_take_watch_changes(|_event: &ChangeEvent| true, Duration::from_millis(100));
 
     Ok(test_case)
 }
@@ -762,13 +788,15 @@ fn directory_deleted() -> anyhow::Result<()> {
 
 #[test]
 fn search_path() -> anyhow::Result<()> {
-    let mut case =
-        setup_with_search_paths([("bar.py", "import sub.a")], |root_path, _project_path| {
-            SearchPathConfiguration {
-                site_packages: Some(SitePackages::Known(vec![root_path.join("site_packages")])),
-                ..SearchPathConfiguration::default()
-            }
-        })?;
+    let mut case = setup_with_options([("bar.py", "import sub.a")], |root_path, _project_path| {
+        Some(Options {
+            environment: Some(EnvironmentOptions {
+                extra_paths: Some(vec![root_path.join("site_packages")]),
+                ..EnvironmentOptions::default()
+            }),
+            ..Options::default()
+        })
+    })?;
 
     let site_packages = case.root_path().join("site_packages");
 
@@ -802,9 +830,12 @@ fn add_search_path() -> anyhow::Result<()> {
     assert!(resolve_module(case.db().upcast(), &ModuleName::new_static("a").unwrap()).is_none());
 
     // Register site-packages as a search path.
-    case.update_search_path_settings(SearchPathConfiguration {
-        site_packages: Some(SitePackages::Known(vec![site_packages.clone()])),
-        ..SearchPathConfiguration::default()
+    case.update_options(Options {
+        environment: Some(EnvironmentOptions {
+            extra_paths: Some(vec![site_packages.clone()]),
+            ..EnvironmentOptions::default()
+        }),
+        ..Options::default()
     })
     .expect("Search path settings to be valid");
 
@@ -821,19 +852,22 @@ fn add_search_path() -> anyhow::Result<()> {
 
 #[test]
 fn remove_search_path() -> anyhow::Result<()> {
-    let mut case =
-        setup_with_search_paths([("bar.py", "import sub.a")], |root_path, _project_path| {
-            SearchPathConfiguration {
-                site_packages: Some(SitePackages::Known(vec![root_path.join("site_packages")])),
-                ..SearchPathConfiguration::default()
-            }
-        })?;
+    let mut case = setup_with_options([("bar.py", "import sub.a")], |root_path, _project_path| {
+        Some(Options {
+            environment: Some(EnvironmentOptions {
+                extra_paths: Some(vec![root_path.join("site_packages")]),
+                ..EnvironmentOptions::default()
+            }),
+            ..Options::default()
+        })
+    })?;
 
     // Remove site packages from the search path settings.
     let site_packages = case.root_path().join("site_packages");
-    case.update_search_path_settings(SearchPathConfiguration {
-        site_packages: None,
-        ..SearchPathConfiguration::default()
+
+    case.update_options(Options {
+        environment: None,
+        ..Options::default()
     })
     .expect("Search path settings to be valid");
 
@@ -846,9 +880,63 @@ fn remove_search_path() -> anyhow::Result<()> {
     Ok(())
 }
 
+#[test]
+fn change_python_version_and_platform() -> anyhow::Result<()> {
+    let mut case = setup_with_options(
+        // `sys.last_exc` is a Python 3.12 only feature
+        // `os.getegid()` is Unix only
+        [(
+            "bar.py",
+            r#"
+import sys
+import os
+print(sys.last_exc, os.getegid())
+"#,
+        )],
+        |_root_path, _project_path| {
+            Some(Options {
+                environment: Some(EnvironmentOptions {
+                    python_version: Some(PythonVersion::PY311),
+                    python_platform: Some(PythonPlatform::Identifier("win32".to_string())),
+                    ..EnvironmentOptions::default()
+                }),
+                ..Options::default()
+            })
+        },
+    )?;
+
+    let diagnostics = case.db.check().context("Failed to check project.")?;
+
+    assert_eq!(diagnostics.len(), 2);
+    assert_eq!(
+        diagnostics[0].message(),
+        "Type `<module 'sys'>` has no attribute `last_exc`"
+    );
+    assert_eq!(
+        diagnostics[1].message(),
+        "Type `<module 'os'>` has no attribute `getegid`"
+    );
+
+    // Change the python version
+    case.update_options(Options {
+        environment: Some(EnvironmentOptions {
+            python_version: Some(PythonVersion::PY312),
+            python_platform: Some(PythonPlatform::Identifier("linux".to_string())),
+            ..EnvironmentOptions::default()
+        }),
+        ..Options::default()
+    })
+    .expect("Search path settings to be valid");
+
+    let diagnostics = case.db.check().context("Failed to check project.")?;
+    assert!(diagnostics.is_empty());
+
+    Ok(())
+}
+
 #[test]
 fn changed_versions_file() -> anyhow::Result<()> {
-    let mut case = setup_with_search_paths(
+    let mut case = setup_with_options(
         |root_path: &SystemPath, project_path: &SystemPath| {
             std::fs::write(project_path.join("bar.py").as_std_path(), "import sub.a")?;
             std::fs::create_dir_all(root_path.join("typeshed/stdlib").as_std_path())?;
@@ -860,9 +948,14 @@ fn changed_versions_file() -> anyhow::Result<()> {
 
             Ok(())
         },
-        |root_path, _project_path| SearchPathConfiguration {
-            typeshed: Some(root_path.join("typeshed")),
-            ..SearchPathConfiguration::default()
+        |root_path, _project_path| {
+            Some(Options {
+                environment: Some(EnvironmentOptions {
+                    typeshed: Some(root_path.join("typeshed")),
+                    ..EnvironmentOptions::default()
+                }),
+                ..Options::default()
+            })
         },
     )?;
 
@@ -1127,7 +1220,7 @@ mod unix {
         update_file(baz_original, "def baz(): print('Version 2')")
             .context("Failed to update bar/baz.py")?;
 
-        let changes = case.take_watch_changes();
+        let changes = case.take_watch_changes(event_for_file("baz.py"));
 
         case.apply_changes(changes);
 
@@ -1259,7 +1352,7 @@ mod unix {
     /// ```
     #[test]
     fn symlinked_module_search_path() -> anyhow::Result<()> {
-        let mut case = setup_with_search_paths(
+        let mut case = setup_with_options(
             |root: &SystemPath, project: &SystemPath| {
                 // Set up the symlink target.
                 let site_packages = root.join("site-packages");
@@ -1282,11 +1375,15 @@ mod unix {
 
                 Ok(())
             },
-            |_root, project| SearchPathConfiguration {
-                site_packages: Some(SitePackages::Known(vec![
-                    project.join(".venv/lib/python3.12/site-packages")
-                ])),
-                ..SearchPathConfiguration::default()
+            |_root, project| {
+                Some(Options {
+                    environment: Some(EnvironmentOptions {
+                        extra_paths: Some(vec![project.join(".venv/lib/python3.12/site-packages")]),
+                        python_version: Some(PythonVersion::PY312),
+                        ..EnvironmentOptions::default()
+                    }),
+                    ..Options::default()
+                })
             },
         )?;
 

crates/red_knot_project/Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-name = "red_knot_workspace"
+name = "red_knot_project"
 version = "0.0.0"
 edition.workspace = true
 rust-version.workspace = true
@@ -12,12 +12,12 @@ license.workspace = true
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-red_knot_python_semantic = { workspace = true }
-
 ruff_cache = { workspace = true }
 ruff_db = { workspace = true, features = ["os", "cache", "serde"] }
+ruff_macros = { workspace = true }
 ruff_python_ast = { workspace = true, features = ["serde"] }
 ruff_text_size = { workspace = true }
+red_knot_python_semantic = { workspace = true, features = ["serde"] }
 red_knot_vendored = { workspace = true }
 
 anyhow = { workspace = true }
@@ -34,7 +34,6 @@ toml = { workspace = true }
 tracing = { workspace = true }
 
 [dev-dependencies]
-red_knot_python_semantic = { workspace = true, features = ["serde"] }
 ruff_db = { workspace = true, features = ["testing"] }
 glob = { workspace = true }
 insta = { workspace = true, features = ["redactions", "ron"] }