Treat --upgrade-package on the command-line as overriding upgrade = false in configuration (#15395)

## Summary

Right now, if you put `upgrade = false` in a `uv.toml`, then pass
`--upgrade-package numpy` on the CLI, we won't upgrade NumPy. This PR
fixes that interaction by ensuring that when we "combine", we look at
those arguments holistically (i.e., we bundle `upgrade` and
`upgrade-package` into a single struct, which then goes through the
`.combine` logic), rather than combining `upgrade` and `upgrade-package`
independently.

If approved, I then need to add the same thing for `no-build-isolation`,
`reinstall`, `no-build`, and `no-binary`.

crates/uv-settings/src/combine.rs

@@ -5,7 +5,7 @@ use url::Url;
 
 use uv_configuration::{
     ExportFormat, IndexStrategy, KeyringProviderType, RequiredVersion, TargetTriple,
-    TrustedPublishing,
+    TrustedPublishing, UpgradeSelection,
 };
 use uv_distribution_types::{
     ConfigSettings, ExtraBuildVariables, Index, IndexUrl, PackageConfigSettings, PipExtraIndex,
@@ -181,6 +181,15 @@ impl Combine for Option<PackageConfigSettings> {
     }
 }
 
+impl Combine for Option<UpgradeSelection> {
+    fn combine(self, other: Self) -> Self {
+        match (self, other) {
+            (Some(a), Some(b)) => Some(a.combine(b)),
+            (a, b) => a.or(b),
+        }
+    }
+}
+
 impl Combine for serde::de::IgnoredAny {
     fn combine(self, _other: Self) -> Self {
         self

crates/uv-settings/src/lib.rs

@@ -301,7 +301,7 @@ fn warn_uv_toml_masked_fields(options: &Options) {
                 allow_insecure_host,
             },
         top_level:
-            ResolverInstallerOptions {
+            ResolverInstallerSchema {
                 index,
                 index_url,
                 extra_index_url,

crates/uv-settings/src/settings.rs

@@ -5,7 +5,7 @@ use serde::{Deserialize, Serialize};
 use uv_cache_info::CacheKey;
 use uv_configuration::{
     IndexStrategy, KeyringProviderType, PackageNameSpecifier, RequiredVersion, TargetTriple,
-    TrustedHost, TrustedPublishing,
+    TrustedHost, TrustedPublishing, UpgradeSelection,
 };
 use uv_distribution_types::{
     ConfigSettings, ExtraBuildVariables, Index, IndexUrl, IndexUrlError, PackageConfigSettings,
@@ -52,7 +52,7 @@ pub struct Options {
     pub globals: GlobalOptions,
 
     #[serde(flatten)]
-    pub top_level: ResolverInstallerOptions,
+    pub top_level: ResolverInstallerSchema,
 
     #[serde(flatten)]
     pub install_mirrors: PythonInstallMirrors,
@@ -161,7 +161,7 @@ pub struct Options {
 
 impl Options {
     /// Construct an [`Options`] with the given global and top-level settings.
-    pub fn simple(globals: GlobalOptions, top_level: ResolverInstallerOptions) -> Self {
+    pub fn simple(globals: GlobalOptions, top_level: ResolverInstallerSchema) -> Self {
         Self {
             globals,
             top_level,
@@ -369,8 +369,7 @@ pub struct ResolverOptions {
     pub config_settings_package: Option<PackageConfigSettings>,
     pub exclude_newer: ExcludeNewer,
     pub link_mode: Option<LinkMode>,
-    pub upgrade: Option<bool>,
-    pub upgrade_package: Option<Vec<Requirement<VerbatimParsedUrl>>>,
+    pub upgrade: Option<UpgradeSelection>,
     pub no_build: Option<bool>,
     pub no_build_package: Option<Vec<PackageName>>,
     pub no_binary: Option<bool>,
@@ -384,10 +383,159 @@ pub struct ResolverOptions {
 
 /// Shared settings, relevant to all operations that must resolve and install dependencies. The
 /// union of [`InstallerOptions`] and [`ResolverOptions`].
+#[derive(Debug, Clone, Default, CombineOptions)]
+pub struct ResolverInstallerOptions {
+    pub index: Option<Vec<Index>>,
+    pub index_url: Option<PipIndex>,
+    pub extra_index_url: Option<Vec<PipExtraIndex>>,
+    pub no_index: Option<bool>,
+    pub find_links: Option<Vec<PipFindLinks>>,
+    pub index_strategy: Option<IndexStrategy>,
+    pub keyring_provider: Option<KeyringProviderType>,
+    pub resolution: Option<ResolutionMode>,
+    pub prerelease: Option<PrereleaseMode>,
+    pub fork_strategy: Option<ForkStrategy>,
+    pub dependency_metadata: Option<Vec<StaticMetadata>>,
+    pub config_settings: Option<ConfigSettings>,
+    pub config_settings_package: Option<PackageConfigSettings>,
+    pub no_build_isolation: Option<bool>,
+    pub no_build_isolation_package: Option<Vec<PackageName>>,
+    pub extra_build_dependencies: Option<ExtraBuildDependencies>,
+    pub extra_build_variables: Option<ExtraBuildVariables>,
+    pub exclude_newer: Option<ExcludeNewerTimestamp>,
+    pub exclude_newer_package: Option<ExcludeNewerPackage>,
+    pub link_mode: Option<LinkMode>,
+    pub compile_bytecode: Option<bool>,
+    pub no_sources: Option<bool>,
+    pub upgrade: Option<UpgradeSelection>,
+    pub reinstall: Option<bool>,
+    pub reinstall_package: Option<Vec<PackageName>>,
+    pub no_build: Option<bool>,
+    pub no_build_package: Option<Vec<PackageName>>,
+    pub no_binary: Option<bool>,
+    pub no_binary_package: Option<Vec<PackageName>>,
+}
+
+impl From<ResolverInstallerSchema> for ResolverInstallerOptions {
+    fn from(value: ResolverInstallerSchema) -> Self {
+        let ResolverInstallerSchema {
+            index,
+            index_url,
+            extra_index_url,
+            no_index,
+            find_links,
+            index_strategy,
+            keyring_provider,
+            resolution,
+            prerelease,
+            fork_strategy,
+            dependency_metadata,
+            config_settings,
+            config_settings_package,
+            no_build_isolation,
+            no_build_isolation_package,
+            extra_build_dependencies,
+            extra_build_variables,
+            exclude_newer,
+            exclude_newer_package,
+            link_mode,
+            compile_bytecode,
+            no_sources,
+            upgrade,
+            upgrade_package,
+            reinstall,
+            reinstall_package,
+            no_build,
+            no_build_package,
+            no_binary,
+            no_binary_package,
+        } = value;
+        Self {
+            index,
+            index_url,
+            extra_index_url,
+            no_index,
+            find_links,
+            index_strategy,
+            keyring_provider,
+            resolution,
+            prerelease,
+            fork_strategy,
+            dependency_metadata,
+            config_settings,
+            config_settings_package,
+            no_build_isolation,
+            no_build_isolation_package,
+            extra_build_dependencies,
+            extra_build_variables,
+            exclude_newer,
+            exclude_newer_package,
+            link_mode,
+            compile_bytecode,
+            no_sources,
+            upgrade: UpgradeSelection::from_args(
+                upgrade,
+                upgrade_package
+                    .into_iter()
+                    .flatten()
+                    .map(Into::into)
+                    .collect(),
+            ),
+            reinstall,
+            reinstall_package,
+            no_build,
+            no_build_package,
+            no_binary,
+            no_binary_package,
+        }
+    }
+}
+
+impl ResolverInstallerSchema {
+    /// Resolve the [`ResolverInstallerSchema`] relative to the given root directory.
+    pub fn relative_to(self, root_dir: &Path) -> Result<Self, IndexUrlError> {
+        Ok(Self {
+            index: self
+                .index
+                .map(|index| {
+                    index
+                        .into_iter()
+                        .map(|index| index.relative_to(root_dir))
+                        .collect::<Result<Vec<_>, _>>()
+                })
+                .transpose()?,
+            index_url: self
+                .index_url
+                .map(|index_url| index_url.relative_to(root_dir))
+                .transpose()?,
+            extra_index_url: self
+                .extra_index_url
+                .map(|extra_index_url| {
+                    extra_index_url
+                        .into_iter()
+                        .map(|extra_index_url| extra_index_url.relative_to(root_dir))
+                        .collect::<Result<Vec<_>, _>>()
+                })
+                .transpose()?,
+            find_links: self
+                .find_links
+                .map(|find_links| {
+                    find_links
+                        .into_iter()
+                        .map(|find_link| find_link.relative_to(root_dir))
+                        .collect::<Result<Vec<_>, _>>()
+                })
+                .transpose()?,
+            ..self
+        })
+    }
+}
+
+/// The JSON schema for the `[tool.uv]` section of a `pyproject.toml` file.
 #[derive(Debug, Clone, Default, PartialEq, Eq, Deserialize, CombineOptions, OptionsMetadata)]
 #[serde(rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
-pub struct ResolverInstallerOptions {
+pub struct ResolverInstallerSchema {
     /// The package indexes to use when resolving dependencies.
     ///
     /// Accepts either a repository compliant with [PEP 503](https://peps.python.org/pep-0503/)
@@ -814,46 +962,6 @@ pub struct ResolverInstallerOptions {
     pub no_binary_package: Option<Vec<PackageName>>,
 }
 
-impl ResolverInstallerOptions {
-    /// Resolve the [`ResolverInstallerOptions`] relative to the given root directory.
-    pub fn relative_to(self, root_dir: &Path) -> Result<Self, IndexUrlError> {
-        Ok(Self {
-            index: self
-                .index
-                .map(|index| {
-                    index
-                        .into_iter()
-                        .map(|index| index.relative_to(root_dir))
-                        .collect::<Result<Vec<_>, _>>()
-                })
-                .transpose()?,
-            index_url: self
-                .index_url
-                .map(|index_url| index_url.relative_to(root_dir))
-                .transpose()?,
-            extra_index_url: self
-                .extra_index_url
-                .map(|extra_index_url| {
-                    extra_index_url
-                        .into_iter()
-                        .map(|extra_index_url| extra_index_url.relative_to(root_dir))
-                        .collect::<Result<Vec<_>, _>>()
-                })
-                .transpose()?,
-            find_links: self
-                .find_links
-                .map(|find_links| {
-                    find_links
-                        .into_iter()
-                        .map(|find_link| find_link.relative_to(root_dir))
-                        .collect::<Result<Vec<_>, _>>()
-                })
-                .transpose()?,
-            ..self
-        })
-    }
-}
-
 /// Shared settings, relevant to all operations that might create managed python installations.
 #[derive(Debug, Clone, PartialEq, Eq, Deserialize, CombineOptions, OptionsMetadata)]
 #[serde(rename_all = "kebab-case")]
@@ -1752,8 +1860,8 @@ impl PipOptions {
     }
 }
 
-impl From<ResolverInstallerOptions> for ResolverOptions {
-    fn from(value: ResolverInstallerOptions) -> Self {
+impl From<ResolverInstallerSchema> for ResolverOptions {
+    fn from(value: ResolverInstallerSchema) -> Self {
         Self {
             index: value.index,
             index_url: value.index_url,
@@ -1778,8 +1886,15 @@ impl From<ResolverInstallerOptions> for ResolverOptions {
                     .collect(),
             ),
             link_mode: value.link_mode,
-            upgrade: value.upgrade,
-            upgrade_package: value.upgrade_package,
+            upgrade: UpgradeSelection::from_args(
+                value.upgrade,
+                value
+                    .upgrade_package
+                    .into_iter()
+                    .flatten()
+                    .map(Into::into)
+                    .collect(),
+            ),
             no_build: value.no_build,
             no_build_package: value.no_build_package,
             no_binary: value.no_binary,
@@ -1793,8 +1908,8 @@ impl From<ResolverInstallerOptions> for ResolverOptions {
     }
 }
 
-impl From<ResolverInstallerOptions> for InstallerOptions {
-    fn from(value: ResolverInstallerOptions) -> Self {
+impl From<ResolverInstallerSchema> for InstallerOptions {
+    fn from(value: ResolverInstallerSchema) -> Self {
         Self {
             index: value.index,
             index_url: value.index_url,
@@ -1830,7 +1945,7 @@ impl From<ResolverInstallerOptions> for InstallerOptions {
 
 /// The options persisted alongside an installed tool.
 ///
-/// A mirror of [`ResolverInstallerOptions`], without upgrades and reinstalls, which shouldn't be
+/// A mirror of [`ResolverInstallerSchema`], without upgrades and reinstalls, which shouldn't be
 /// persisted in a tool receipt.
 #[derive(
     Debug, Clone, Default, PartialEq, Eq, Serialize, Deserialize, CombineOptions, OptionsMetadata,
@@ -1925,7 +2040,6 @@ impl From<ToolOptions> for ResolverInstallerOptions {
             compile_bytecode: value.compile_bytecode,
             no_sources: value.no_sources,
             upgrade: None,
-            upgrade_package: None,
             reinstall: None,
             reinstall_package: None,
             no_build: value.no_build,
@@ -2120,7 +2234,7 @@ impl From<OptionsWire> for Options {
                 // Used twice for backwards compatibility
                 allow_insecure_host: allow_insecure_host.clone(),
             },
-            top_level: ResolverInstallerOptions {
+            top_level: ResolverInstallerSchema {
                 index,
                 index_url,
                 extra_index_url,