fix: manually exposed executables are removed after `pixi global upda…

…te` (#3109)

src/cli/global/install.rs

@@ -210,7 +210,13 @@ async fn setup_environment(
         .collect::<miette::Result<Vec<_>>>()?;
 
     // Sync exposed binaries
-    let expose_type = ExposedType::new(args.expose.clone(), with_package_names);
+    let expose_type = if !args.expose.is_empty() {
+        ExposedType::Mappings(args.expose.clone())
+    } else if with_package_names.is_empty() {
+        ExposedType::All
+    } else {
+        ExposedType::Ignore(with_package_names)
+    };
 
     project.sync_exposed_names(env_name, expose_type).await?;
 

src/cli/global/update.rs

@@ -28,7 +28,7 @@ pub async fn execute(args: Args) -> miette::Result<()> {
         project: &mut Project,
     ) -> miette::Result<StateChanges> {
         // See what executables were installed prior to update
-        let env_binaries = project.executables(env_name).await?;
+        let env_binaries = project.executables_of_direct_dependencies(env_name).await?;
 
         // Get the exposed binaries from mapping
         let exposed_mapping_binaries = project
@@ -38,9 +38,9 @@ pub async fn execute(args: Args) -> miette::Result<()> {
 
         // Check if they were all auto-exposed, or if the user manually exposed a subset of them
         let expose_type = if check_all_exposed(&env_binaries, exposed_mapping_binaries) {
-            ExposedType::default()
+            ExposedType::All
         } else {
-            ExposedType::subset()
+            ExposedType::Nothing
         };
 
         // Reinstall the environment

src/global/project/manifest.rs

@@ -515,32 +515,17 @@ impl FromStr for Mapping {
     }
 }
 
+/// Describes which executables should be (additionally) exposed
+/// Only executables by direct dependencies are taken into account
 #[derive(Default)]
 pub enum ExposedType {
     #[default]
     All,
-    Filter(Vec<PackageName>),
+    Nothing,
+    Ignore(Vec<PackageName>),
     Mappings(Vec<Mapping>),
 }
 
-impl ExposedType {
-    pub fn new(mappings: Vec<Mapping>, filter: Vec<PackageName>) -> Self {
-        if !mappings.is_empty() {
-            return Self::Mappings(mappings);
-        }
-
-        if filter.is_empty() {
-            Self::All
-        } else {
-            Self::Filter(filter)
-        }
-    }
-
-    pub fn subset() -> Self {
-        Self::Mappings(Default::default())
-    }
-}
-
 #[cfg(test)]
 mod tests {
     use std::str::FromStr;

src/global/project/mod.rs

@@ -662,8 +662,23 @@ impl Project {
         Ok(state_changes)
     }
 
-    /// Get all installed executables for specific environment.
-    pub async fn executables(
+    /// Gets all installed executables of a specific environment.
+    pub async fn executables_of_all_dependencies(
+        &self,
+        env_name: &EnvironmentName,
+    ) -> miette::Result<Vec<Executable>> {
+        let env_dir = EnvDir::from_env_root(self.env_root.clone(), env_name).await?;
+        let prefix = Prefix::new(env_dir.path());
+
+        let prefix_records = &prefix.find_installed_packages()?;
+
+        let all_executables = find_executables_for_many_records(&prefix, prefix_records);
+
+        Ok(all_executables)
+    }
+
+    /// Get installed executables of direct dependencies of a specific environment.
+    pub async fn executables_of_direct_dependencies(
         &self,
         env_name: &EnvironmentName,
     ) -> miette::Result<IndexMap<PackageName, Vec<Executable>>> {
@@ -698,7 +713,7 @@ impl Project {
 
     /// Sync the `exposed` field in manifest based on the executables in the
     /// environment and the expose type. Expose type can be either:
-    /// * If the user initially chooses to auto-exposed everything, we will add
+    /// * If the user initially chooses to auto-expose everything, we will add
     ///   new binaries that are not exposed in the `exposed` field.
     ///
     /// * If the use chose to expose only a subset of binaries, we will remove
@@ -710,7 +725,7 @@ impl Project {
         expose_type: ExposedType,
     ) -> miette::Result<()> {
         // Get env executables
-        let env_executables = self.executables(env_name).await?;
+        let execs_all = self.executables_of_all_dependencies(env_name).await?;
 
         // Get the parsed environment
         let environment = self
@@ -722,15 +737,14 @@ impl Project {
             .exposed
             .iter()
             .filter_map(|mapping| {
-                // If the executable is still requested, do not remove the mapping
-                if env_executables.values().flatten().any(|executable| {
-                    executable_from_path(&executable.path) == mapping.executable_relname()
+                // If the executable isn't requested, remove the mapping
+                if execs_all.iter().all(|executable| {
+                    executable_from_path(&executable.path) != mapping.executable_relname()
                 }) {
-                    tracing::debug!("Not removing mapping to: {}", mapping.executable_relname());
-                    return None;
+                    Some(mapping.exposed_name().clone())
+                } else {
+                    None
                 }
-                // Else do remove the mapping
-                Some(mapping.exposed_name().clone())
             })
             .collect_vec();
 
@@ -739,11 +753,12 @@ impl Project {
             self.manifest.remove_exposed_name(env_name, exposed_name)?;
         }
 
-        // auto-expose the executables if necessary
+        let execs_direct_deps = self.executables_of_direct_dependencies(env_name).await?;
+
         match expose_type {
             ExposedType::All => {
                 // Add new binaries that are not yet exposed
-                let executable_names = env_executables
+                let executable_names = execs_direct_deps
                     .into_iter()
                     .flat_map(|(_, executables)| executables)
                     .map(|executable| executable.name);
@@ -755,13 +770,14 @@ impl Project {
                     self.manifest.add_exposed_mapping(env_name, &mapping)?;
                 }
             }
-            ExposedType::Filter(filter) => {
+            ExposedType::Nothing => {}
+            ExposedType::Ignore(ignore) => {
                 // Add new binaries that are not yet exposed and that don't come from one of the
-                // packages we filter on
-                let executable_names = env_executables
+                // packages we ignore
+                let executable_names = execs_direct_deps
                     .into_iter()
                     .filter_map(|(package_name, executable)| {
-                        if filter.contains(&package_name) {
+                        if ignore.contains(&package_name) {
                             None
                         } else {
                             Some(executable)
@@ -856,6 +872,7 @@ impl Project {
         }
         Ok(in_sync)
     }
+
     /// Expose executables from the environment to the global bin directory.
     ///
     /// This function will first remove all binaries that are not listed as
@@ -870,17 +887,15 @@ impl Project {
         // First clean up binaries that are not listed as exposed
         state_changes |= self.prune_exposed(env_name).await?;
 
+        let all_executables = self.executables_of_all_dependencies(env_name).await?;
+
         let env_dir = EnvDir::from_env_root(self.env_root.clone(), env_name).await?;
         let prefix = Prefix::new(env_dir.path());
 
         let environment = self
             .environment(env_name)
             .ok_or_else(|| miette::miette!("Environment {} not found", env_name.fancy_display()))?;
 
-        let prefix_records = &prefix.find_installed_packages()?;
-
-        let all_executables = find_executables_for_many_records(&prefix, prefix_records);
-
         let exposed: HashSet<&str> = environment
             .exposed
             .iter()

tests/data/channels/channels/multiple_versions_channel_1/linux-64/repodata.json

@@ -9,83 +9,115 @@
       "build": "hb0f4dca_0",
       "build_number": 0,
       "depends": [],
-      "md5": "eda5e13e034ed30fabbb49d6adec78af",
+      "md5": "144f427a6558be168bacdde2508ea273",
       "name": "package",
       "platform": "linux",
-      "sha256": "cd7e704f3a54e76a9a2f386d695e388039a63b4d5ed2e57f9c13c30dd6978cd1",
-      "size": 1253,
+      "sha256": "adf942ef40fb044ae0928bc84d5088b6531d34970bfd2accd9880987d1e21bb4",
+      "size": 1238,
       "subdir": "linux-64",
-      "timestamp": 1731504816716,
+      "timestamp": 1739269679287,
       "version": "0.1.0"
     },
     "package-0.2.0-hb0f4dca_0.conda": {
       "arch": "x86_64",
       "build": "hb0f4dca_0",
       "build_number": 0,
       "depends": [],
-      "md5": "cead91f7d9e6bbd014b5781c63684fef",
+      "md5": "80619e064f2c06acf5b99df874578ebd",
       "name": "package",
       "platform": "linux",
-      "sha256": "7588a51e818dc716df8d0748db902c37d170102360bc2464e8edafdef40a28d5",
-      "size": 1252,
+      "sha256": "c072bd1c96be574675cfadf9e4fe6bb77e41a8d6e1d33142edd9ca1dd1a3dfef",
+      "size": 1239,
       "subdir": "linux-64",
-      "timestamp": 1731504816943,
+      "timestamp": 1739269679532,
       "version": "0.2.0"
     },
     "package2-0.1.0-hb0f4dca_0.conda": {
       "arch": "x86_64",
       "build": "hb0f4dca_0",
       "build_number": 0,
       "depends": [],
-      "md5": "4f840c89f3a644a666b529d58084c320",
+      "md5": "784c289c066248051a5028d8cc7e813e",
       "name": "package2",
       "platform": "linux",
-      "sha256": "1ebbb8ff9b7018a3363074b1d8536a2ca5d658153368458a9c129cd6edd38cc2",
-      "size": 1181,
+      "sha256": "86f0d8afeedbd1ee47b4509d50e8dfc88533fabbccbae6752a8092d8d0c263cf",
+      "size": 1161,
       "subdir": "linux-64",
-      "timestamp": 1731504816715,
+      "timestamp": 1739269679287,
       "version": "0.1.0"
     },
     "package2-0.2.0-hb0f4dca_0.conda": {
       "arch": "x86_64",
       "build": "hb0f4dca_0",
       "build_number": 0,
       "depends": [],
-      "md5": "ebef22cf4f0313a21065ae4856e335e5",
+      "md5": "00522ddb341ba86371a7707cfa6a509d",
       "name": "package2",
       "platform": "linux",
-      "sha256": "20c4af256078236462b16f329b71f6c89818f72174482f5cf02fd3a536aab494",
-      "size": 1179,
+      "sha256": "9dc249de8f8286a5709f39b9474bb95d4a52f41ba008ef3dd60880517219929f",
+      "size": 1159,
       "subdir": "linux-64",
-      "timestamp": 1731504816942,
+      "timestamp": 1739269679532,
       "version": "0.2.0"
     },
     "package3-0.1.0-abc.conda": {
       "arch": "x86_64",
       "build": "abc",
       "build_number": 1,
       "depends": [],
-      "md5": "1b94f7d0d9813fb55d9d60dcbb096219",
+      "md5": "18035c0a801986364117f9e85fa0ad03",
       "name": "package3",
       "platform": "linux",
-      "sha256": "61ffb579d1f2e5d1c6423e97f0c9def9501d17ea5d012dc2fcf55e86ed139aba",
-      "size": 1149,
+      "sha256": "2ee7d1413b7d00cc24f34d4c207c74b65266b0f66fa4662b998e32987a985a9b",
+      "size": 1129,
       "subdir": "linux-64",
-      "timestamp": 1731504816716,
+      "timestamp": 1739269679287,
       "version": "0.1.0"
     },
     "package3-0.2.0-abc.conda": {
       "arch": "x86_64",
       "build": "abc",
       "build_number": 1,
       "depends": [],
-      "md5": "686ce11c0f47d1d39dd015219d62b1ce",
+      "md5": "aef4795be1d1acdc7f22c6fd294d2e68",
       "name": "package3",
       "platform": "linux",
-      "sha256": "919f961cfe8fa046f487ef07e20a736efcd57ac0a4966b1f26a29fc6bfa420ba",
-      "size": 1148,
+      "sha256": "ab8d65916e9c9c70523e34d848db4491ad4a7836b963b80d601fe37cd39ccd22",
+      "size": 1128,
       "subdir": "linux-64",
-      "timestamp": 1731504816942,
+      "timestamp": 1739269679532,
+      "version": "0.2.0"
+    },
+    "package4-0.1.0-hb0f4dca_0.conda": {
+      "arch": "x86_64",
+      "build": "hb0f4dca_0",
+      "build_number": 0,
+      "depends": [
+        "package3 ==0.1.0"
+      ],
+      "md5": "c173658fffadb227f4761e0c9beb7458",
+      "name": "package4",
+      "platform": "linux",
+      "sha256": "7a98b2f977cf7d3092d9e58d2be21299f4c087c3b1fba28bd874ef604fc00ea4",
+      "size": 1177,
+      "subdir": "linux-64",
+      "timestamp": 1739269679287,
+      "version": "0.1.0"
+    },
+    "package4-0.2.0-hb0f4dca_0.conda": {
+      "arch": "x86_64",
+      "build": "hb0f4dca_0",
+      "build_number": 0,
+      "depends": [
+        "package3 ==0.2.0"
+      ],
+      "md5": "d6fee16be3f5d94f8eda564103949f0c",
+      "name": "package4",
+      "platform": "linux",
+      "sha256": "97ffe4fcf185202a0379b7622c436c1ec6e1c417edab1ec5f8dcc967ac0891b5",
+      "size": 1177,
+      "subdir": "linux-64",
+      "timestamp": 1739269679532,
       "version": "0.2.0"
     }
   },