Use Preferences struct in Manifest API (#4496)

## Summary

This is just a bit more consistent with `Overrides` and `Constraints`.

crates/uv-resolver/src/lib.rs

@@ -6,7 +6,7 @@ pub use flat_index::FlatIndex;
 pub use lock::{Lock, LockError};
 pub use manifest::Manifest;
 pub use options::{Options, OptionsBuilder};
-pub use preferences::{Preference, PreferenceError};
+pub use preferences::{Preference, PreferenceError, Preferences};
 pub use prerelease_mode::PreReleaseMode;
 pub use pubgrub::{PubGrubSpecifier, PubGrubSpecifierError};
 pub use python_requirement::PythonRequirement;

crates/uv-resolver/src/manifest.rs

@@ -6,7 +6,8 @@ use uv_configuration::{Constraints, Overrides};
 use uv_normalize::{GroupName, PackageName};
 use uv_types::RequestedRequirements;
 
-use crate::{preferences::Preference, DependencyMode, Exclusions};
+use crate::preferences::Preferences;
+use crate::{DependencyMode, Exclusions};
 
 /// A manifest of requirements, constraints, and preferences.
 #[derive(Clone, Debug)]
@@ -29,7 +30,7 @@ pub struct Manifest {
     /// These represent "preferred" versions of a given package. For example, they may be the
     /// versions that are already installed in the environment, or already pinned in an existing
     /// lockfile.
-    pub(crate) preferences: Vec<Preference>,
+    pub(crate) preferences: Preferences,
 
     /// The name of the project.
     pub(crate) project: Option<PackageName>,
@@ -55,7 +56,7 @@ impl Manifest {
         constraints: Constraints,
         overrides: Overrides,
         dev: Vec<GroupName>,
-        preferences: Vec<Preference>,
+        preferences: Preferences,
         project: Option<PackageName>,
         exclusions: Exclusions,
         lookaheads: Vec<RequestedRequirements>,
@@ -78,7 +79,7 @@ impl Manifest {
             constraints: Constraints::default(),
             overrides: Overrides::default(),
             dev: Vec::new(),
-            preferences: Vec::new(),
+            preferences: Preferences::default(),
             project: None,
             exclusions: Exclusions::default(),
             lookaheads: Vec::new(),

crates/uv-resolver/src/preferences.rs

@@ -98,8 +98,8 @@ impl Preference {
 }
 
 /// A set of pinned packages that should be preserved during resolution, if possible.
-#[derive(Debug, Clone)]
-pub(crate) struct Preferences(Arc<FxHashMap<PackageName, Pin>>);
+#[derive(Debug, Clone, Default)]
+pub struct Preferences(Arc<FxHashMap<PackageName, Pin>>);
 
 impl Preferences {
     /// Create a map of pinned packages from an iterator of [`Preference`] entries.
@@ -107,7 +107,7 @@ impl Preferences {
     ///
     /// The provided [`MarkerEnvironment`] will be used to filter  the preferences
     /// to an applicable subset.
-    pub(crate) fn from_iter<PreferenceIterator: IntoIterator<Item = Preference>>(
+    pub fn from_iter<PreferenceIterator: IntoIterator<Item = Preference>>(
         preferences: PreferenceIterator,
         markers: Option<&MarkerEnvironment>,
     ) -> Self {
@@ -137,6 +137,11 @@ impl Preferences {
         Self(Arc::new(preferences))
     }
 
+    /// Returns an iterator over the preferences.
+    pub fn iter(&self) -> impl Iterator<Item = (&PackageName, &Version)> {
+        self.0.iter().map(|(name, pin)| (name, pin.version()))
+    }
+
     /// Return the pinned version for a package, if any.
     pub(crate) fn version(&self, package_name: &PackageName) -> Option<&Version> {
         self.0.get(package_name).map(Pin::version)

crates/uv-resolver/src/resolver/mod.rs

@@ -213,7 +213,7 @@ impl<Provider: ResolverProvider, InstalledPackages: InstalledPackagesProvider>
             constraints: manifest.constraints,
             overrides: manifest.overrides,
             dev: manifest.dev,
-            preferences: Preferences::from_iter(manifest.preferences, markers),
+            preferences: manifest.preferences,
             exclusions: manifest.exclusions,
             hasher: hasher.clone(),
             markers: markers.cloned(),

crates/uv-resolver/src/yanks.rs

@@ -40,11 +40,11 @@ impl AllowedYanks {
         }
 
         // Allow yanks for any packages that are already pinned in the lockfile.
-        for preference in &manifest.preferences {
+        for (name, version) in manifest.preferences.iter() {
             allowed_yanks
-                .entry(preference.name().clone())
+                .entry(name.clone())
                 .or_default()
-                .insert(preference.version().clone());
+                .insert(version.clone());
         }
 
         Self(allowed_yanks)

crates/uv/src/commands/pip/operations.rs

@@ -35,7 +35,7 @@ use uv_requirements::{
 };
 use uv_resolver::{
     DependencyMode, Exclusions, FlatIndex, InMemoryIndex, Manifest, Options, Preference,
-    PythonRequirement, ResolutionGraph, Resolver,
+    Preferences, PythonRequirement, ResolutionGraph, Resolver,
 };
 use uv_toolchain::{Interpreter, PythonEnvironment};
 use uv_types::{HashStrategy, InFlight, InstalledPackagesProvider};
@@ -184,6 +184,7 @@ pub(crate) async fn resolve<InstalledPackages: InstalledPackagesProvider>(
     // Collect constraints and overrides.
     let constraints = Constraints::from_requirements(constraints);
     let overrides = Overrides::from_requirements(overrides);
+    let preferences = Preferences::from_iter(preferences, markers);
 
     // Determine the Python requirement, defaulting to that of the interpreter.
     let python_requirement =