Treat already-installed base environment packages as preferences in uv run --with (#13284)

## Summary

If a script has some requirements, and you provide `--with`, we
currently ignore any constraints from those requirements. We might want
to treat them as hard constraints in the future. For now, though, we
just treat them as preferences -- so we _prefer_ those versions, but
don't require them to match and still run the `--with` resolution in
isolation.

Closes https://github.com/astral-sh/uv/issues/13173.

crates/uv-resolver/src/preferences.rs

@@ -4,7 +4,7 @@ use std::str::FromStr;
 use rustc_hash::FxHashMap;
 use tracing::trace;
 
-use uv_distribution_types::IndexUrl;
+use uv_distribution_types::{IndexUrl, InstalledDist};
 use uv_normalize::PackageName;
 use uv_pep440::{Operator, Version};
 use uv_pep508::{MarkerTree, VerbatimUrl, VersionOrUrl};
@@ -115,6 +115,21 @@ impl Preference {
         }))
     }
 
+    /// Create a [`Preference`] from an installed distribution.
+    pub fn from_installed(dist: &InstalledDist) -> Option<Self> {
+        let InstalledDist::Registry(dist) = dist else {
+            return None;
+        };
+        Some(Self {
+            name: dist.name.clone(),
+            version: dist.version.clone(),
+            marker: MarkerTree::TRUE,
+            index: PreferenceIndex::Any,
+            fork_markers: vec![],
+            hashes: HashDigests::empty(),
+        })
+    }
+
     /// Return the [`PackageName`] of the package for this [`Preference`].
     pub fn name(&self) -> &PackageName {
         &self.name

crates/uv/src/commands/project/mod.rs

@@ -35,8 +35,8 @@ use uv_python::{
 use uv_requirements::upgrade::{read_lock_requirements, LockedRequirements};
 use uv_requirements::{NamedRequirementsResolver, RequirementsSpecification};
 use uv_resolver::{
-    FlatIndex, Lock, OptionsBuilder, PythonRequirement, RequiresPython, ResolverEnvironment,
-    ResolverOutput,
+    FlatIndex, Lock, OptionsBuilder, Preference, PythonRequirement, RequiresPython,
+    ResolverEnvironment, ResolverOutput,
 };
 use uv_scripts::Pep723ItemRef;
 use uv_settings::PythonInstallMirrors;
@@ -1632,27 +1632,42 @@ pub(crate) async fn resolve_names(
     Ok(requirements)
 }
 
+#[derive(Debug, Clone)]
+pub(crate) enum PreferenceSource<'lock> {
+    /// The preferences should be extracted from a lockfile.
+    Lock {
+        lock: &'lock Lock,
+        install_path: &'lock Path,
+    },
+    /// The preferences will be provided directly as [`Preference`] entries.
+    Entries(Vec<Preference>),
+}
+
 #[derive(Debug, Clone)]
 pub(crate) struct EnvironmentSpecification<'lock> {
     /// The requirements to include in the environment.
     requirements: RequirementsSpecification,
-    /// The lockfile from which to extract preferences, along with the install path.
-    lock: Option<(&'lock Lock, &'lock Path)>,
+    /// The preferences to respect when resolving.
+    preferences: Option<PreferenceSource<'lock>>,
 }
 
 impl From<RequirementsSpecification> for EnvironmentSpecification<'_> {
     fn from(requirements: RequirementsSpecification) -> Self {
         Self {
             requirements,
-            lock: None,
+            preferences: None,
         }
     }
 }
 
 impl<'lock> EnvironmentSpecification<'lock> {
+    /// Set the [`PreferenceSource`] for the specification.
     #[must_use]
-    pub(crate) fn with_lock(self, lock: Option<(&'lock Lock, &'lock Path)>) -> Self {
-        Self { lock, ..self }
+    pub(crate) fn with_preferences(self, preferences: PreferenceSource<'lock>) -> Self {
+        Self {
+            preferences: Some(preferences),
+            ..self
+        }
     }
 }
 
@@ -1765,17 +1780,22 @@ pub(crate) async fn resolve_environment(
     let upgrade = Upgrade::default();
 
     // If an existing lockfile exists, build up a set of preferences.
-    let LockedRequirements { preferences, git } = spec
-        .lock
-        .map(|(lock, install_path)| read_lock_requirements(lock, install_path, &upgrade))
-        .transpose()?
-        .unwrap_or_default();
+    let preferences = match spec.preferences {
+        Some(PreferenceSource::Lock { lock, install_path }) => {
+            let LockedRequirements { preferences, git } =
+                read_lock_requirements(lock, install_path, &upgrade)?;
 
-    // Populate the Git resolver.
-    for ResolvedRepositoryReference { reference, sha } in git {
-        debug!("Inserting Git reference into resolver: `{reference:?}` at `{sha}`");
-        state.git().insert(reference, sha);
-    }
+            // Populate the Git resolver.
+            for ResolvedRepositoryReference { reference, sha } in git {
+                debug!("Inserting Git reference into resolver: `{reference:?}` at `{sha}`");
+                state.git().insert(reference, sha);
+            }
+
+            preferences
+        }
+        Some(PreferenceSource::Entries(entries)) => entries,
+        None => vec![],
+    };
 
     // Resolve the flat indexes from `--find-links`.
     let flat_index = {

crates/uv/src/commands/project/run.rs

@@ -31,7 +31,7 @@ use uv_python::{
     VersionFileDiscoveryOptions,
 };
 use uv_requirements::{RequirementsSource, RequirementsSpecification};
-use uv_resolver::{Installable, Lock};
+use uv_resolver::{Installable, Lock, Preference};
 use uv_scripts::Pep723Item;
 use uv_settings::PythonInstallMirrors;
 use uv_shell::runnable::WindowsRunnable;
@@ -49,8 +49,9 @@ use crate::commands::project::lock::LockMode;
 use crate::commands::project::lock_target::LockTarget;
 use crate::commands::project::{
     default_dependency_groups, script_specification, update_environment,
-    validate_project_requires_python, EnvironmentSpecification, ProjectEnvironment, ProjectError,
-    ScriptEnvironment, ScriptInterpreter, UniversalState, WorkspacePython,
+    validate_project_requires_python, EnvironmentSpecification, PreferenceSource,
+    ProjectEnvironment, ProjectError, ScriptEnvironment, ScriptInterpreter, UniversalState,
+    WorkspacePython,
 };
 use crate::commands::reporters::PythonDownloadReporter;
 use crate::commands::run::run_to_completion;
@@ -898,9 +899,14 @@ hint: If you are running a script with `{}` in the shebang, you may need to incl
     };
 
     // If necessary, create an environment for the ephemeral requirements or command.
+    let base_site_packages = SitePackages::from_interpreter(&base_interpreter)?;
     let ephemeral_env = match spec {
         None => None,
-        Some(spec) if can_skip_ephemeral(&spec, &base_interpreter, &settings) => None,
+        Some(spec)
+            if can_skip_ephemeral(&spec, &base_interpreter, &base_site_packages, &settings) =>
+        {
+            None
+        }
         Some(spec) => {
             debug!("Syncing ephemeral requirements");
 
@@ -909,12 +915,24 @@ hint: If you are running a script with `{}` in the shebang, you may need to incl
                 .as_ref()
                 .map(|(lock, path)| lock.build_constraints(path));
 
+            // Read the preferences.
+            let spec = EnvironmentSpecification::from(spec).with_preferences(
+                if let Some((lock, install_path)) = base_lock.as_ref() {
+                    // If we have a lockfile, use the locked versions as preferences.
+                    PreferenceSource::Lock { lock, install_path }
+                } else {
+                    // Otherwise, extract preferences from the base environment.
+                    PreferenceSource::Entries(
+                        base_site_packages
+                            .iter()
+                            .filter_map(Preference::from_installed)
+                            .collect::<Vec<_>>(),
+                    )
+                },
+            );
+
             let result = CachedEnvironment::from_spec(
-                EnvironmentSpecification::from(spec).with_lock(
-                    base_lock
-                        .as_ref()
-                        .map(|(lock, install_path)| (lock, install_path.as_ref())),
-                ),
+                spec,
                 build_constraints.unwrap_or_default(),
                 &base_interpreter,
                 &settings,
@@ -1115,13 +1133,10 @@ hint: If you are running a script with `{}` in the shebang, you may need to incl
 /// Returns `true` if we can skip creating an additional ephemeral environment in `uv run`.
 fn can_skip_ephemeral(
     spec: &RequirementsSpecification,
-    base_interpreter: &Interpreter,
+    interpreter: &Interpreter,
+    site_packages: &SitePackages,
     settings: &ResolverInstallerSettings,
 ) -> bool {
-    let Ok(site_packages) = SitePackages::from_interpreter(base_interpreter) else {
-        return false;
-    };
-
     if !(settings.reinstall.is_none() && settings.reinstall.is_none()) {
         return false;
     }
@@ -1130,7 +1145,7 @@ fn can_skip_ephemeral(
         &spec.requirements,
         &spec.constraints,
         &spec.overrides,
-        &base_interpreter.resolver_marker_environment(),
+        &interpreter.resolver_marker_environment(),
     ) {
         // If the requirements are already satisfied, we're done.
         Ok(SatisfiesResult::Fresh {

crates/uv/tests/it/run.rs

@@ -5078,3 +5078,59 @@ fn run_pep723_script_with_constraints_lock() -> Result<()> {
 
     Ok(())
 }
+
+/// If a `--with` requirement overlaps with a non-locked script requirement, respect the environment
+/// site-packages as preferences.
+///
+/// See: <https://github.com/astral-sh/uv/issues/13173>
+#[test]
+fn run_pep723_script_with_constraints() -> Result<()> {
+    let context = TestContext::new("3.12");
+
+    let test_script = context.temp_dir.child("main.py");
+    test_script.write_str(indoc! { r#"
+        # /// script
+        # requires-python = ">=3.11"
+        # dependencies = [
+        #   "iniconfig<2",
+        # ]
+        # ///
+
+        import iniconfig
+
+        print("Hello, world!")
+       "#
+    })?;
+
+    let pyproject_toml = context.temp_dir.child("pyproject.toml");
+    pyproject_toml.write_str(indoc! { r#"
+        [project]
+        name = "foo"
+        version = "1.0.0"
+        requires-python = ">=3.10"
+        dependencies = [
+          "iniconfig",
+        ]
+        "#
+    })?;
+
+    uv_snapshot!(context.filters(), context.run().arg("--with").arg(".").arg("main.py"), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+    Hello, world!
+
+    ----- stderr -----
+    Resolved 1 package in [TIME]
+    Prepared 1 package in [TIME]
+    Installed 1 package in [TIME]
+     + iniconfig==1.1.1
+    Resolved 2 packages in [TIME]
+    Prepared 1 package in [TIME]
+    Installed 2 packages in [TIME]
+     + foo==1.0.0 (from file://[TEMP_DIR]/)
+     + iniconfig==1.1.1
+    ");
+
+    Ok(())
+}