Add support for configuring knot in pyproject.toml files

This PR adds support for configuring Red Knot in the `tool.knot` section of the project's
`pyproject.toml` section. Options specified on the CLI take precedence over the
options in the configuration file.

For now, this PR only adds support for the `environment` and the `src.root` options.
Other options will be added as separate PRs.

There are also a few concerns that I intentionally ignored as part of this PR:

* Handling of relative paths: We need to anchor paths relative to the current working directory (CLI), or the project (`pyproject.toml` or `knot.toml`)
* Tracking the source of a value. It would be nice for diagnostics to know from which configuration a value comes so that we can point the user to the right configuration file (or CLI) if the configuration is invalid.
* Schema generation, and there's a lot more, see #15491

crates/red_knot/Cargo.toml

@@ -34,6 +34,7 @@ tracing-tree = { workspace = true }
 [dev-dependencies]
 filetime = { workspace = true }
 tempfile = { workspace = true }
+toml = { workspace = true }
 ruff_db = { workspace = true, features = ["testing"] }
 
 [lints]

crates/red_knot/src/main.rs

@@ -6,10 +6,10 @@ 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_python_semantic::PythonPath;
 use red_knot_server::run_server;
 use red_knot_workspace::db::ProjectDatabase;
-use red_knot_workspace::project::settings::Configuration;
+use red_knot_workspace::project::options::{EnvironmentOptions, Options};
 use red_knot_workspace::project::ProjectMetadata;
 use red_knot_workspace::watch;
 use red_knot_workspace::watch::ProjectWatcher;
@@ -43,12 +43,12 @@ struct Args {
     #[arg(long, value_name = "PROJECT")]
     project: Option<SystemPathBuf>,
 
-    /// Path to the virtual environment the project uses.
+    /// Specifies the path to the python installation or the virtual environment.
     ///
-    /// If provided, red-knot will use the `site-packages` directory of this virtual environment
+    /// If provided, red-knot will use the `site-packages` directory from this python installation
     /// to resolve type information for the project's third-party dependencies.
     #[arg(long, value_name = "PATH")]
-    venv_path: Option<SystemPathBuf>,
+    python: Option<SystemPathBuf>,
 
     /// Custom directory to use for stdlib typeshed stubs.
     #[arg(long, value_name = "PATH", alias = "custom-typeshed-dir")]
@@ -71,31 +71,27 @@ 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());
-        }
-
-        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();
+    fn to_options(&self, cli_cwd: &SystemPath) -> Options {
+        Options {
+            environment: Some(EnvironmentOptions {
+                python_version: self.python_version.map(Into::into),
+                python: self.python.as_ref().map(|venv_path| PythonPath::Derived {
+                    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()
         }
-
-        configuration
     }
 }
 
@@ -164,18 +160,15 @@ 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));
@@ -228,19 +221,19 @@ 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);
 
         (
             Self {
                 sender: sender.clone(),
                 receiver,
                 watcher: None,
-                cli_configuration,
+                cli_options,
             },
             MainLoopCancellationToken { sender },
         )
@@ -324,7 +317,7 @@ 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);
                     }