fix: pypi dependencies not being removed

src/install_pypi.rs

@@ -50,6 +50,7 @@ fn elapsed(duration: Duration) -> String {
 }
 
 /// Derived from uv [`uv_installer::Plan`]
+#[derive(Debug)]
 struct PixiInstallPlan {
     /// The distributions that are not already installed in the current environment, but are
     /// available in the local cache.

src/lock_file/update.rs

@@ -107,35 +107,33 @@ impl<'p> LockFileDerivedData<'p> {
             .unwrap_or_default();
         let pypi_records = self.pypi_records(environment, platform).unwrap_or_default();
 
-        if environment.has_pypi_dependencies() {
-            let uv_context = match &self.uv_context {
-                None => {
-                    let context = UvResolutionContext::from_project(self.project)?;
-                    self.uv_context = Some(context.clone());
-                    context
-                }
-                Some(context) => context.clone(),
-            };
+        let uv_context = match &self.uv_context {
+            None => {
+                let context = UvResolutionContext::from_project(self.project)?;
+                self.uv_context = Some(context.clone());
+                context
+            }
+            Some(context) => context.clone(),
+        };
 
-            let env_variables = environment.project().get_env_variables(environment).await?;
-            // Update the prefix with Pypi records
-            environment::update_prefix_pypi(
-                environment.name(),
-                &prefix,
-                platform,
-                &repodata_records,
-                &pypi_records,
-                &python_status,
-                &environment.system_requirements(),
-                uv_context,
-                env_variables,
-            )
-            .await?;
+        let env_variables = environment.project().get_env_variables(environment).await?;
+        // Update the prefix with Pypi records
+        environment::update_prefix_pypi(
+            environment.name(),
+            &prefix,
+            platform,
+            &repodata_records,
+            &pypi_records,
+            &python_status,
+            &environment.system_requirements(),
+            uv_context,
+            env_variables,
+        )
+        .await?;
 
-            // Store that we updated the environment, so we won't have to do it again.
-            self.updated_pypi_prefixes
-                .insert(environment.clone(), prefix.clone());
-        }
+        // Store that we updated the environment, so we won't have to do it again.
+        self.updated_pypi_prefixes
+            .insert(environment.clone(), prefix.clone());
 
         Ok(prefix)
     }

tests/common/builders.rs

@@ -24,6 +24,7 @@
 //! ```
 
 use futures::FutureExt;
+use pixi::cli::remove;
 use pixi::task::TaskName;
 use pixi::{
     cli::{add, init, install, project, task},
@@ -143,6 +144,53 @@ impl IntoFuture for AddBuilder {
     }
 }
 
+/// Contains the arguments to pass to [`remove::execute()`]. Call `.await` to call the CLI execute method
+/// and await the result at the same time.
+pub struct RemoveBuilder {
+    pub args: remove::Args,
+}
+
+impl RemoveBuilder {
+    pub fn with_spec(mut self, spec: &str) -> Self {
+        self.args.deps.push(spec.to_string());
+        self
+    }
+
+    /// Set as a host
+    pub fn set_type(mut self, t: DependencyType) -> Self {
+        match t {
+            DependencyType::CondaDependency(spec_type) => match spec_type {
+                SpecType::Host => {
+                    self.args.host = true;
+                    self.args.build = false;
+                }
+                SpecType::Build => {
+                    self.args.host = false;
+                    self.args.build = true;
+                }
+                SpecType::Run => {
+                    self.args.host = false;
+                    self.args.build = false;
+                }
+            },
+            DependencyType::PypiDependency => {
+                self.args.host = false;
+                self.args.build = false;
+                self.args.pypi = true;
+            }
+        }
+        self
+    }
+}
+
+impl IntoFuture for RemoveBuilder {
+    type Output = miette::Result<()>;
+    type IntoFuture = Pin<Box<dyn Future<Output = Self::Output> + 'static>>;
+
+    fn into_future(self) -> Self::IntoFuture {
+        remove::execute(self.args).boxed_local()
+    }
+}
 pub struct TaskAddBuilder {
     pub manifest_path: Option<PathBuf>,
     pub args: task::AddArgs,

tests/common/mod.rs

@@ -11,7 +11,7 @@ use pixi::{
     cli::{
         add, init,
         install::Args,
-        project, run,
+        project, remove, run,
         task::{self, AddArgs, AliasArgs},
     },
     consts, EnvironmentName, ExecutableTask, Project, RunOutput, SearchEnvironments, TaskGraph,
@@ -35,6 +35,8 @@ use std::{
 use tempfile::TempDir;
 use thiserror::Error;
 
+use self::builders::RemoveBuilder;
+
 /// To control the pixi process
 pub struct PixiControl {
     /// The path to the project working file
@@ -229,6 +231,21 @@ impl PixiControl {
         }
     }
 
+    /// Remove dependencies from the project. Returns a [`RemoveBuilder`].
+    pub fn remove(&self, spec: &str) -> RemoveBuilder {
+        RemoveBuilder {
+            args: remove::Args {
+                deps: vec![spec.to_string()],
+                manifest_path: Some(self.manifest_path()),
+                host: false,
+                build: false,
+                pypi: false,
+                platform: Default::default(),
+                feature: None,
+            },
+        }
+    }
+
     /// Add a new channel to the project.
     pub fn project_channel_add(&self) -> ProjectChannelAddBuilder {
         ProjectChannelAddBuilder {

tests/install_tests.rs

@@ -250,6 +250,41 @@ async fn pypi_reinstall_python() {
     }
 }
 
+#[tokio::test(flavor = "multi_thread", worker_threads = 1)]
+#[serial]
+#[cfg_attr(not(feature = "slow_integration_tests"), ignore)]
+// Check if we add and remove a pypi package that the site-packages is cleared
+async fn pypi_add_remove() {
+    let pixi = PixiControl::new().unwrap();
+    pixi.init().await.unwrap();
+    // Add and update lockfile with this version of python
+    pixi.add("python==3.11").with_install(true).await.unwrap();
+
+    // Add flask from pypi
+    pixi.add("flask")
+        .with_install(true)
+        .set_type(pixi::DependencyType::PypiDependency)
+        .await
+        .unwrap();
+
+    let prefix = pixi.project().unwrap().root().join(".pixi/envs/default");
+
+    let cache = uv_cache::Cache::temp().unwrap();
+
+    // Check if site-packages has entries
+    let env = create_uv_environment(&prefix, &cache);
+    let installed_311 = uv_installer::SitePackages::from_executable(&env).unwrap();
+    assert!(installed_311.iter().count() > 0);
+
+    pixi.remove("flask")
+        .set_type(pixi::DependencyType::PypiDependency)
+        .await
+        .unwrap();
+
+    let installed_311 = uv_installer::SitePackages::from_executable(&env).unwrap();
+    assert!(installed_311.iter().count() == 0);
+}
+
 #[tokio::test]
 async fn test_channels_changed() {
     // Write a channel with a package `bar` with only one version