Conflicting groups should handle conflicting inclusions automatically (#12005)

This adds support for inferring dependency group conflict sets from the
directly defined conflicts in configuration. For example, if you declare
a conflict between groups `alpha` and `beta` and `dev` includes `beta`,
then we will infer a conflict between `dev` and `alpha`. We will also
handle a conflict between two groups if they transitively include groups
that conflict with each other. See #11232 for more details.

Closes #11232

Cargo.lock

@@ -5391,8 +5391,10 @@ dependencies = [
  "itertools 0.14.0",
  "jiff",
  "mailparse",
+ "petgraph",
  "regex",
  "rkyv",
+ "rustc-hash",
  "schemars",
  "serde",
  "serde-untagged",

crates/uv-pypi-types/Cargo.toml

@@ -29,8 +29,10 @@ indexmap = { workspace = true, features = ["serde"] }
 itertools = { workspace = true }
 jiff = { workspace = true, features = ["serde"] }
 mailparse = { workspace = true }
+petgraph = { workspace = true }
 regex = { workspace = true }
 rkyv = { workspace = true }
+rustc-hash = { workspace = true }
 schemars = { workspace = true, optional = true }
 serde = { workspace = true }
 serde-untagged = { workspace = true }

crates/uv-pypi-types/src/conflicts.rs

@@ -1,11 +1,19 @@
+use petgraph::{
+    algo::toposort,
+    graph::{DiGraph, NodeIndex},
+};
+use rustc_hash::{FxHashMap, FxHashSet};
+use std::{collections::BTreeSet, hash::Hash, rc::Rc};
 use uv_normalize::{ExtraName, GroupName, PackageName};
 
+use crate::dependency_groups::{DependencyGroupSpecifier, DependencyGroups};
+
 /// A list of conflicting sets of extras/groups pre-defined by an end user.
 ///
 /// This is useful to force the resolver to fork according to extras that have
 /// unavoidable conflicts with each other. (The alternative is that resolution
 /// will fail.)
-#[derive(Debug, Default, Clone, Eq, PartialEq, serde::Deserialize, serde::Serialize)]
+#[derive(Debug, Default, Clone, Eq, PartialEq, serde::Deserialize)]
 pub struct Conflicts(Vec<ConflictSet>);
 
 impl Conflicts {
@@ -47,6 +55,157 @@ impl Conflicts {
     pub fn append(&mut self, other: &mut Conflicts) {
         self.0.append(&mut other.0);
     }
+
+    /// Expand [`Conflicts`]s to include all [`ConflictSet`]s that can
+    /// be transitively inferred from group conflicts directly defined
+    /// in configuration.
+    ///
+    /// A directed acyclic graph (DAG) is created representing all
+    /// transitive group includes, with nodes corresponding to group conflict
+    /// items. For every conflict item directly mentioned in configuration,
+    /// its node starts with a set of canonical items with itself as the only
+    /// member.
+    ///
+    /// The graph is traversed one node at a time in topological order and
+    /// canonical items are propagated to each neighbor. We also update our
+    /// substitutions at each neighbor to reflect that this neighbor transitively
+    /// includes all canonical items visited so far to reach it.
+    ///
+    /// Finally, we apply the substitutions to the conflict sets that were
+    /// directly defined in configuration to generate all transitively inferable
+    /// [`ConflictSet`]s.
+    ///
+    /// There is an assumption that inclusion graphs will not be very large
+    /// or complex. This algorithm creates all combinations of substitutions.
+    /// Each resulting [`ConflictSet`] would also later correspond to a separate
+    /// resolver fork during resolution.
+    pub fn expand_transitive_group_includes(
+        &mut self,
+        package: &PackageName,
+        groups: &DependencyGroups,
+    ) {
+        let mut graph = DiGraph::new();
+        let mut group_node_idxs: FxHashMap<&GroupName, NodeIndex> = FxHashMap::default();
+        let mut node_conflict_items: FxHashMap<NodeIndex, Rc<ConflictItem>> = FxHashMap::default();
+        // Used for transitively deriving new conflict sets with substitutions.
+        // The keys are canonical items (mentioned directly in configured conflicts).
+        // The values correspond to groups that transitively include them.
+        let mut substitutions: FxHashMap<Rc<ConflictItem>, FxHashSet<Rc<ConflictItem>>> =
+            FxHashMap::default();
+
+        // Conflict sets that were directly defined in configuration.
+        let mut direct_conflict_sets: FxHashSet<&ConflictSet> = FxHashSet::default();
+        // Conflict sets that we will transitively infer in this method.
+        let mut transitive_conflict_sets: FxHashSet<ConflictSet> = FxHashSet::default();
+
+        // Add groups in directly defined conflict sets to the graph.
+        let mut seen: FxHashSet<&GroupName> = FxHashSet::default();
+
+        for set in &self.0 {
+            direct_conflict_sets.insert(set);
+            for item in set.iter() {
+                let ConflictPackage::Group(group) = &item.conflict else {
+                    // TODO(john): Do we also want to handle extras here?
+                    continue;
+                };
+                if !seen.insert(group) {
+                    continue;
+                }
+                let item = Rc::new(item.clone());
+                let mut canonical_items = FxHashSet::default();
+                canonical_items.insert(item.clone());
+                let node_id = graph.add_node(canonical_items);
+                group_node_idxs.insert(group, node_id);
+                node_conflict_items.insert(node_id, item.clone());
+            }
+        }
+
+        // Create conflict items for remaining groups and add them to the graph.
+        for group in groups.keys() {
+            if !seen.insert(group) {
+                continue;
+            }
+            let group_conflict_item = ConflictItem {
+                package: package.clone(),
+                conflict: ConflictPackage::Group(group.clone()),
+            };
+            let node_id = graph.add_node(FxHashSet::default());
+            group_node_idxs.insert(group, node_id);
+            node_conflict_items.insert(node_id, Rc::new(group_conflict_item));
+        }
+
+        // Create edges representing group inclusion (with edges reversed so that
+        // included groups point to including groups).
+        for (group, specifiers) in groups {
+            if let Some(includer) = group_node_idxs.get(group) {
+                for specifier in specifiers {
+                    if let DependencyGroupSpecifier::IncludeGroup { include_group } = specifier {
+                        if let Some(included) = group_node_idxs.get(include_group) {
+                            graph.add_edge(*included, *includer, ());
+                        }
+                    }
+                }
+            }
+        }
+
+        let Ok(topo_nodes) = toposort(&graph, None) else {
+            // FIXME: If we hit a cycle, we are currently bailing and waiting for
+            // more detailed cycle detection downstream. Is this what we want?
+            return;
+        };
+        // Propagate canonical items through the graph and populate substitutions.
+        for node in topo_nodes {
+            for neighbor_idx in graph.neighbors(node).collect::<Vec<_>>() {
+                let mut neighbor_canonical_items = Vec::new();
+                if let Some(canonical_items) = graph.node_weight(node) {
+                    let neighbor_item = node_conflict_items
+                        .get(&neighbor_idx)
+                        .expect("ConflictItem should already be in graph")
+                        .clone();
+                    for canonical_item in canonical_items {
+                        neighbor_canonical_items.push(canonical_item.clone());
+                        substitutions
+                            .entry(canonical_item.clone())
+                            .or_default()
+                            .insert(neighbor_item.clone());
+                    }
+                }
+                graph
+                    .node_weight_mut(neighbor_idx)
+                    .expect("Graph node should have weight")
+                    .extend(neighbor_canonical_items.into_iter());
+            }
+        }
+
+        // Create new conflict sets for all possible replacements of canonical
+        // items by substitution items.
+        // Note that new sets are (potentially) added to transitive_conflict_sets
+        // at the end of each iteration.
+        for (canonical_item, subs) in substitutions {
+            let mut new_conflict_sets = FxHashSet::default();
+            for conflict_set in direct_conflict_sets
+                .iter()
+                .copied()
+                .chain(transitive_conflict_sets.iter())
+                .filter(|set| set.contains_item(&canonical_item))
+            {
+                for sub in &subs {
+                    let mut new_set = conflict_set
+                        .replaced_item(&canonical_item, (**sub).clone())
+                        .expect("`ConflictItem` should be in `ConflictSet`");
+                    if !direct_conflict_sets.contains(&new_set) {
+                        new_set = new_set.with_inferred_conflict();
+                        if !transitive_conflict_sets.contains(&new_set) {
+                            new_conflict_sets.insert(new_set);
+                        }
+                    }
+                }
+            }
+            transitive_conflict_sets.extend(new_conflict_sets.into_iter());
+        }
+
+        self.0.extend(transitive_conflict_sets);
+    }
 }
 
 /// A single set of package-extra pairs that conflict with one another.
@@ -58,23 +217,24 @@ impl Conflicts {
 ///
 /// A `TryFrom<Vec<ConflictItem>>` impl may be used to build a set from a
 /// sequence. Note though that at least 2 items are required.
-#[derive(Debug, Default, Clone, Eq, PartialEq, serde::Serialize)]
+#[derive(Debug, Default, Clone, Hash, Eq, PartialEq)]
-pub struct ConflictSet(Vec<ConflictItem>);
+pub struct ConflictSet {
+    set: BTreeSet<ConflictItem>,
+    is_inferred_conflict: bool,
+}
 
 impl ConflictSet {
     /// Create a pair of items that conflict with one another.
     pub fn pair(item1: ConflictItem, item2: ConflictItem) -> ConflictSet {
-        ConflictSet(vec![item1, item2])
+        ConflictSet {
-    }
+            set: BTreeSet::from_iter(vec![item1, item2]),
-
+            is_inferred_conflict: false,
-    /// Add a new conflicting item to this set.
+        }
-    pub fn push(&mut self, item: ConflictItem) {
-        self.0.push(item);
     }
 
     /// Returns an iterator over all conflicting items.
     pub fn iter(&self) -> impl Iterator<Item = &'_ ConflictItem> + Clone + '_ {
-        self.0.iter()
+        self.set.iter()
     }
 
     /// Returns true if this conflicting item contains the given package and
@@ -88,6 +248,42 @@ impl ConflictSet {
         self.iter()
             .any(|set| set.package() == package && *set.conflict() == conflict)
     }
+
+    /// Returns true if these conflicts contain any set that contains the given
+    /// [`ConflictItem`].
+    pub fn contains_item(&self, conflict_item: &ConflictItem) -> bool {
+        self.set.contains(conflict_item)
+    }
+
+    /// This [`ConflictSet`] was inferred from directly defined conflicts.
+    pub fn is_inferred_conflict(&self) -> bool {
+        self.is_inferred_conflict
+    }
+
+    /// Replace an old [`ConflictItem`] with a new one.
+    pub fn replaced_item(
+        &self,
+        old: &ConflictItem,
+        new: ConflictItem,
+    ) -> Result<Self, ConflictError> {
+        let mut new_set = self.set.clone();
+        if !new_set.contains(old) {
+            return Err(ConflictError::ReplaceMissingConflictItem);
+        }
+        new_set.remove(old);
+        new_set.insert(new);
+        Ok(Self {
+            set: new_set,
+            is_inferred_conflict: false,
+        })
+    }
+
+    /// Mark this [`ConflictSet`] as being inferred from directly
+    /// defined conflicts.
+    fn with_inferred_conflict(mut self) -> Self {
+        self.is_inferred_conflict = true;
+        self
+    }
 }
 
 impl<'de> serde::Deserialize<'de> for ConflictSet {
@@ -109,14 +305,17 @@ impl TryFrom<Vec<ConflictItem>> for ConflictSet {
             1 => return Err(ConflictError::OneItem),
             _ => {}
         }
-        Ok(ConflictSet(items))
+        Ok(ConflictSet {
+            set: BTreeSet::from_iter(items),
+            is_inferred_conflict: false,
+        })
     }
 }
 
 /// A single item in a conflicting set.
 ///
-/// Each item is a pair of a package and a corresponding extra name for that
+/// Each item is a pair of a package and a corresponding extra or group name
-/// package.
+/// for that package.
 #[derive(
     Debug, Clone, Eq, Hash, PartialEq, PartialOrd, Ord, serde::Deserialize, serde::Serialize,
 )]
@@ -364,6 +563,8 @@ pub enum ConflictError {
     /// An error that occurs when both `extra` and `group` are present.
     #[error("Expected one of `extra` or `group` in conflicting entry, but found both")]
     FoundExtraAndGroup,
+    #[error("Expected `ConflictSet` to contain `ConflictItem` to replace")]
+    ReplaceMissingConflictItem,
 }
 
 /// Like [`Conflicts`], but for deserialization in `pyproject.toml`.

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

@@ -396,7 +396,14 @@ async fn do_lock(
         .collect::<Result<BTreeMap<_, _>, ProjectError>>()?;
 
     // Collect the conflicts.
-    let conflicts = target.conflicts();
+    let mut conflicts = target.conflicts();
+    if let LockTarget::Workspace(workspace) = target {
+        if let Some(groups) = &workspace.pyproject_toml().dependency_groups {
+            if let Some(project) = &workspace.pyproject_toml().project {
+                conflicts.expand_transitive_group_includes(&project.name, groups);
+            }
+        }
+    }
 
     // Collect the list of supported environments.
     let environments = {
@@ -756,7 +763,7 @@ async fn do_lock(
                 None,
                 resolver_env,
                 python_requirement,
-                conflicts,
+                conflicts.clone(),
                 &client,
                 &flat_index,
                 state.index(),
@@ -787,7 +794,7 @@ async fn do_lock(
             let previous = existing_lock.map(ValidatedLock::into_lock);
             let lock = Lock::from_resolution(&resolution, target.install_path())?
                 .with_manifest(manifest)
-                .with_conflicts(target.conflicts())
+                .with_conflicts(conflicts)
                 .with_supported_environments(
                     environments
                         .cloned()

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

@@ -300,9 +300,14 @@ impl std::fmt::Display for ConflictError {
             .iter()
             .all(|conflict| matches!(conflict, ConflictPackage::Group(..)))
         {
+            let conflict_source = if self.set.is_inferred_conflict() {
+                "transitively inferred"
+            } else {
+                "declared"
+            };
             write!(
                 f,
-                "Groups {} are incompatible with the declared conflicts: {{{set}}}",
+                "Groups {} are incompatible with the {conflict_source} conflicts: {{{set}}}",
                 conjunction(
                     self.conflicts
                         .iter()

crates/uv/tests/it/lock_conflict.rs

@@ -2090,13 +2090,13 @@ fn mixed() -> Result<()> {
         filters => context.filters(),
     }, {
         assert_snapshot!(
-            lock, @r###"
+            lock, @r#"
         version = 1
         revision = 1
         requires-python = ">=3.12"
         conflicts = [[
-            { package = "project", group = "group1" },
             { package = "project", extra = "extra1" },
+            { package = "project", group = "group1" },
         ]]
 
         [options]
@@ -2141,7 +2141,7 @@ fn mixed() -> Result<()> {
         wheels = [
             { url = "https://files.pythonhosted.org/packages/32/46/9cb0e58b2deb7f82b84065f37f3bffeb12413f947f9388e4cac22c4621ce/sortedcontainers-2.4.0-py2.py3-none-any.whl", hash = "sha256:a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0", size = 29575 },
         ]
-        "###
+        "#
         );
     });
 
@@ -2189,14 +2189,14 @@ fn mixed() -> Result<()> {
      + sortedcontainers==2.4.0
     "###);
     // And finally, installing both the group and the extra should fail.
-    uv_snapshot!(context.filters(), context.sync().arg("--frozen").arg("--group=group1").arg("--extra=extra1"), @r###"
+    uv_snapshot!(context.filters(), context.sync().arg("--frozen").arg("--group=group1").arg("--extra=extra1"), @r"
     success: false
     exit_code: 2
     ----- stdout -----
 
     ----- stderr -----
-    error: Group `group1` and extra `extra1` are incompatible with the declared conflicts: {`project:group1`, `project[extra1]`}
+    error: Extra `extra1` and group `group1` are incompatible with the declared conflicts: {`project[extra1]`, `project:group1`}
-    "###);
+    ");
 
     Ok(())
 }
@@ -3054,13 +3054,13 @@ fn shared_optional_dependency_extra1() -> Result<()> {
         filters => context.filters(),
     }, {
         assert_snapshot!(
-            lock, @r###"
+            lock, @r#"
         version = 1
         revision = 1
         requires-python = ">=3.12"
         conflicts = [[
-            { package = "project", extra = "foo" },
             { package = "project", extra = "bar" },
+            { package = "project", extra = "foo" },
         ]]
 
         [options]
@@ -3130,7 +3130,7 @@ fn shared_optional_dependency_extra1() -> Result<()> {
         wheels = [
             { url = "https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2", size = 10235 },
         ]
-        "###
+        "#
         );
     });
 
@@ -3194,13 +3194,13 @@ fn shared_optional_dependency_group1() -> Result<()> {
         filters => context.filters(),
     }, {
         assert_snapshot!(
-            lock, @r###"
+            lock, @r#"
         version = 1
         revision = 1
         requires-python = ">=3.12"
         conflicts = [[
-            { package = "project", group = "foo" },
             { package = "project", group = "bar" },
+            { package = "project", group = "foo" },
         ]]
 
         [options]
@@ -3269,7 +3269,7 @@ fn shared_optional_dependency_group1() -> Result<()> {
         wheels = [
             { url = "https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2", size = 10235 },
         ]
-        "###
+        "#
         );
     });
 
@@ -3480,13 +3480,13 @@ fn shared_optional_dependency_extra2() -> Result<()> {
         filters => context.filters(),
     }, {
         assert_snapshot!(
-            lock, @r###"
+            lock, @r#"
         version = 1
         revision = 1
         requires-python = "==3.11.*"
         conflicts = [[
-            { package = "project", extra = "foo" },
             { package = "project", extra = "bar" },
+            { package = "project", extra = "foo" },
         ]]
 
         [options]
@@ -3556,7 +3556,7 @@ fn shared_optional_dependency_extra2() -> Result<()> {
         wheels = [
             { url = "https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2", size = 10235 },
         ]
-        "###
+        "#
         );
     });
 
@@ -3621,13 +3621,13 @@ fn shared_optional_dependency_group2() -> Result<()> {
         filters => context.filters(),
     }, {
         assert_snapshot!(
-            lock, @r###"
+            lock, @r#"
         version = 1
         revision = 1
         requires-python = "==3.11.*"
         conflicts = [[
-            { package = "project", group = "foo" },
             { package = "project", group = "bar" },
+            { package = "project", group = "foo" },
         ]]
 
         [options]
@@ -3700,7 +3700,7 @@ fn shared_optional_dependency_group2() -> Result<()> {
         wheels = [
             { url = "https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2", size = 10235 },
         ]
-        "###
+        "#
         );
     });
 
@@ -3911,13 +3911,13 @@ fn shared_dependency_extra() -> Result<()> {
         filters => context.filters(),
     }, {
         assert_snapshot!(
-            lock, @r###"
+            lock, @r#"
         version = 1
         revision = 1
         requires-python = ">=3.12"
         conflicts = [[
-            { package = "project", extra = "foo" },
             { package = "project", extra = "bar" },
+            { package = "project", extra = "foo" },
         ]]
 
         [options]
@@ -3987,7 +3987,7 @@ fn shared_dependency_extra() -> Result<()> {
         wheels = [
             { url = "https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2", size = 10235 },
         ]
-        "###
+        "#
         );
     });
 
@@ -4086,13 +4086,13 @@ fn shared_dependency_group() -> Result<()> {
         filters => context.filters(),
     }, {
         assert_snapshot!(
-            lock, @r###"
+            lock, @r#"
         version = 1
         revision = 1
         requires-python = ">=3.12"
         conflicts = [[
-            { package = "project", group = "foo" },
             { package = "project", group = "bar" },
+            { package = "project", group = "foo" },
         ]]
 
         [options]
@@ -4161,7 +4161,7 @@ fn shared_dependency_group() -> Result<()> {
         wheels = [
             { url = "https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2", size = 10235 },
         ]
-        "###
+        "#
         );
     });
 
@@ -4988,13 +4988,13 @@ fn collision_extra() -> Result<()> {
     }, {
         assert_snapshot!(
             lock,
-            @r###"
+            @r#"
         version = 1
         revision = 1
         requires-python = ">=3.12"
         conflicts = [[
-            { package = "pkg", extra = "foo" },
             { package = "pkg", extra = "bar" },
+            { package = "pkg", extra = "foo" },
         ]]
 
         [options]
@@ -5077,7 +5077,7 @@ fn collision_extra() -> Result<()> {
         wheels = [
             { url = "https://files.pythonhosted.org/packages/32/46/9cb0e58b2deb7f82b84065f37f3bffeb12413f947f9388e4cac22c4621ce/sortedcontainers-2.4.0-py2.py3-none-any.whl", hash = "sha256:a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0", size = 29575 },
         ]
-        "###
+        "#
         );
     });
 
@@ -10167,14 +10167,14 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
         "#,
     )?;
 
-    uv_snapshot!(context.filters(), context.lock(), @r###"
+    uv_snapshot!(context.filters(), context.lock(), @r"
     success: true
     exit_code: 0
     ----- stdout -----
 
     ----- stderr -----
-    Resolved 133 packages in [TIME]
+    Resolved 132 packages in [TIME]
-    "###);
+    ");
 
     let lock = context.read("uv.lock");
     insta::with_settings!({
@@ -10182,20 +10182,11 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
     }, {
         assert_snapshot!(
             lock,
-            @r###"
+            @r#"
         version = 1
         revision = 1
         requires-python = ">=3.10"
         resolution-markers = [
-            "python_full_version >= '3.12' and sys_platform == 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
-            "python_full_version >= '3.12' and sys_platform != 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
-            "python_full_version == '3.11.*' and sys_platform == 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
-            "python_full_version == '3.11.*' and sys_platform != 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
-            "python_full_version < '3.11' and sys_platform == 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
-            "python_full_version < '3.11' and sys_platform != 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
-            "python_full_version >= '3.12' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
-            "python_full_version == '3.11.*' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
-            "python_full_version < '3.11' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
             "python_full_version >= '3.12' and sys_platform == 'win32' and extra != 'extra-4-test-alignn' and extra == 'extra-4-test-all' and extra == 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
             "python_full_version >= '3.12' and sys_platform != 'win32' and extra != 'extra-4-test-alignn' and extra == 'extra-4-test-all' and extra == 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
             "python_full_version == '3.11.*' and sys_platform == 'win32' and extra != 'extra-4-test-alignn' and extra == 'extra-4-test-all' and extra == 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
@@ -10208,6 +10199,15 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             "python_full_version == '3.11.*' and sys_platform != 'win32' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra == 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
             "python_full_version < '3.11' and sys_platform == 'win32' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra == 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
             "python_full_version < '3.11' and sys_platform != 'win32' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra == 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
+            "python_full_version >= '3.12' and sys_platform == 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
+            "python_full_version >= '3.12' and sys_platform != 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
+            "python_full_version == '3.11.*' and sys_platform == 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
+            "python_full_version == '3.11.*' and sys_platform != 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
+            "python_full_version < '3.11' and sys_platform == 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
+            "python_full_version < '3.11' and sys_platform != 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
+            "python_full_version >= '3.12' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
+            "python_full_version == '3.11.*' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
+            "python_full_version < '3.11' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
             "python_full_version >= '3.12' and sys_platform == 'win32' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
             "python_full_version >= '3.12' and sys_platform != 'win32' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
             "python_full_version == '3.11.*' and sys_platform == 'win32' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
@@ -10225,14 +10225,14 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             "python_full_version < '3.11' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
         ]
         conflicts = [[
-            { package = "test", extra = "chgnet" },
             { package = "test", extra = "alignn" },
+            { package = "test", extra = "chgnet" },
         ], [
             { package = "test", extra = "chgnet" },
             { package = "test", extra = "m3gnet" },
         ], [
-            { package = "test", extra = "all" },
             { package = "test", extra = "alignn" },
+            { package = "test", extra = "all" },
         ], [
             { package = "test", extra = "all" },
             { package = "test", extra = "m3gnet" },
@@ -10368,7 +10368,7 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             { name = "pydantic" },
             { name = "pydantic-settings" },
             { name = "pydocstyle" },
-            { name = "pyparsing" },
+            { name = "pyparsing", version = "2.4.7", source = { registry = "https://pypi.org/simple" } },
             { name = "scikit-learn" },
             { name = "scipy" },
             { name = "spglib" },
@@ -10629,8 +10629,7 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             { name = "numpy" },
             { name = "opt-einsum" },
             { name = "scipy" },
-            { name = "sympy", version = "1.13.1", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
+            { name = "sympy" },
-            { name = "sympy", version = "1.13.3", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
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         wheels = [
@@ -10733,8 +10732,7 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
         dependencies = [
             { name = "opt-einsum-fx" },
             { name = "scipy" },
-            { name = "sympy", version = "1.13.1", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
+            { name = "sympy" },
-            { name = "sympy", version = "1.13.3", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
             { name = "torch", version = "2.2.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
             { name = "torch", version = "2.5.1", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
         ]
@@ -11269,7 +11267,8 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             { name = "numpy" },
             { name = "packaging" },
             { name = "pillow" },
-            { name = "pyparsing" },
+            { name = "pyparsing", version = "2.4.7", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-alignn' or (extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet')" },
+            { name = "pyparsing", version = "3.2.1", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or extra != 'extra-4-test-alignn'" },
             { name = "python-dateutil" },
         ]
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@@ -11754,7 +11753,7 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             "python_full_version < '3.11' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
         ]
         dependencies = [
-            { name = "nvidia-nvjitlink-cu12", version = "12.4.127", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
+            { name = "nvidia-nvjitlink-cu12", marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
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@@ -11824,7 +11823,7 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
         dependencies = [
             { name = "nvidia-cublas-cu12", version = "12.1.3.1", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
             { name = "nvidia-cusparse-cu12", version = "12.1.0.106", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
-            { name = "nvidia-nvjitlink-cu12", version = "12.8.61", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
+            { name = "nvidia-nvjitlink-cu12", marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
         ]
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@@ -11852,7 +11851,7 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
         dependencies = [
             { name = "nvidia-cublas-cu12", version = "12.4.5.8", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
             { name = "nvidia-cusparse-cu12", version = "12.3.1.170", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
-            { name = "nvidia-nvjitlink-cu12", version = "12.4.127", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
+            { name = "nvidia-nvjitlink-cu12", marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
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@@ -11876,7 +11875,7 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             "python_full_version < '3.11' and sys_platform != 'win32' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
         ]
         dependencies = [
-            { name = "nvidia-nvjitlink-cu12", version = "12.8.61", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
+            { name = "nvidia-nvjitlink-cu12", marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
         ]
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@@ -11902,7 +11901,7 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             "python_full_version < '3.11' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
         ]
         dependencies = [
-            { name = "nvidia-nvjitlink-cu12", version = "12.4.127", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
+            { name = "nvidia-nvjitlink-cu12", marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
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@@ -11961,47 +11960,12 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
         name = "nvidia-nvjitlink-cu12"
         version = "12.4.127"
         source = { registry = "https://pypi.org/simple" }
-        resolution-markers = [
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-            "python_full_version == '3.11.*' and sys_platform != 'win32' and extra != 'extra-4-test-alignn' and extra == 'extra-4-test-all' and extra == 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
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@@ -12480,8 +12444,7 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             { name = "ruamel-yaml" },
             { name = "scipy" },
             { name = "spglib" },
-            { name = "sympy", version = "1.13.1", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet'" },
+            { name = "sympy" },
-            { name = "sympy", version = "1.13.3", source = { registry = "https://pypi.org/simple" }, marker = "(extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet') or (extra != 'extra-4-test-alignn' and extra == 'extra-4-test-m3gnet') or (extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet')" },
             { name = "tabulate" },
             { name = "tqdm" },
             { name = "uncertainties" },
@@ -12509,11 +12472,60 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
         name = "pyparsing"
         version = "2.4.7"
         source = { registry = "https://pypi.org/simple" }
+        resolution-markers = [
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+            "python_full_version >= '3.12' and sys_platform != 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
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+            "python_full_version == '3.11.*' and sys_platform != 'win32' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
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+            "python_full_version == '3.11.*' and extra == 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
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+        version = "3.2.1"
+        source = { registry = "https://pypi.org/simple" }
+        resolution-markers = [
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+            "python_full_version < '3.11' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
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+        wheels = [
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+
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         name = "python-dateutil"
         version = "2.9.0.post0"
@@ -12858,66 +12870,14 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
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         version = "1.13.1"
         source = { registry = "https://pypi.org/simple" }
-        resolution-markers = [
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-            "python_full_version == '3.11.*' and sys_platform != 'win32' and extra != 'extra-4-test-alignn' and extra == 'extra-4-test-all' and extra == 'extra-4-test-chgnet' and extra != 'extra-4-test-m3gnet'",
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-            "python_full_version == '3.11.*' and sys_platform != 'win32' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
-            "python_full_version < '3.11' and sys_platform == 'win32' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
-            "python_full_version < '3.11' and sys_platform != 'win32' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-all' and extra != 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet'",
-        ]
-        dependencies = [
-            { name = "mpmath", marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
-        ]
-        sdist = { url = "https://files.pythonhosted.org/packages/11/8a/5a7fd6284fa8caac23a26c9ddf9c30485a48169344b4bd3b0f02fef1890f/sympy-1.13.3.tar.gz", hash = "sha256:b27fd2c6530e0ab39e275fc9b683895367e51d5da91baa8d3d64db2565fec4d9", size = 7533196 }
-        wheels = [
-            { url = "https://files.pythonhosted.org/packages/99/ff/c87e0622b1dadea79d2fb0b25ade9ed98954c9033722eb707053d310d4f3/sympy-1.13.3-py3-none-any.whl", hash = "sha256:54612cf55a62755ee71824ce692986f23c88ffa77207b30c1368eda4a7060f73", size = 6189483 },
-        ]
-
         [[package]]
         name = "tabulate"
         version = "0.9.0"
@@ -13028,7 +12988,7 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             { name = "nvidia-cusparse-cu12", version = "12.1.0.106", source = { registry = "https://pypi.org/simple" }, marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-alignn') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (platform_machine != 'x86_64' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (sys_platform != 'linux' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet') or (sys_platform != 'linux' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet')" },
             { name = "nvidia-nccl-cu12", version = "2.19.3", source = { registry = "https://pypi.org/simple" }, marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-alignn') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (platform_machine != 'x86_64' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (sys_platform != 'linux' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet') or (sys_platform != 'linux' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet')" },
             { name = "nvidia-nvtx-cu12", version = "12.1.105", source = { registry = "https://pypi.org/simple" }, marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-alignn') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (platform_machine != 'x86_64' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (sys_platform != 'linux' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet') or (sys_platform != 'linux' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet')" },
-            { name = "sympy", version = "1.13.3", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
+            { name = "sympy", marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
             { name = "triton", version = "2.2.0", source = { registry = "https://pypi.org/simple" }, marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-alignn') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (platform_machine != 'x86_64' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (sys_platform != 'linux' and extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet') or (sys_platform != 'linux' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet')" },
             { name = "typing-extensions", marker = "extra == 'extra-4-test-alignn' or extra == 'extra-4-test-m3gnet'" },
         ]
@@ -13092,10 +13052,10 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             { name = "nvidia-cusolver-cu12", version = "11.6.1.9", source = { registry = "https://pypi.org/simple" }, marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-all') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-chgnet') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet')" },
             { name = "nvidia-cusparse-cu12", version = "12.3.1.170", source = { registry = "https://pypi.org/simple" }, marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-all') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-chgnet') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet')" },
             { name = "nvidia-nccl-cu12", version = "2.21.5", source = { registry = "https://pypi.org/simple" }, marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-all') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-chgnet') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet')" },
-            { name = "nvidia-nvjitlink-cu12", version = "12.4.127", source = { registry = "https://pypi.org/simple" }, marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-all') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-chgnet') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet')" },
+            { name = "nvidia-nvjitlink-cu12", marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-all') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-chgnet') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet')" },
             { name = "nvidia-nvtx-cu12", version = "12.4.127", source = { registry = "https://pypi.org/simple" }, marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-all') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-chgnet') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet')" },
             { name = "setuptools", marker = "(python_full_version >= '3.12' and extra == 'extra-4-test-all') or (python_full_version >= '3.12' and extra == 'extra-4-test-chgnet') or (python_full_version >= '3.12' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet') or (extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet')" },
-            { name = "sympy", version = "1.13.1", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
+            { name = "sympy", marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
             { name = "triton", version = "3.1.0", source = { registry = "https://pypi.org/simple" }, marker = "(python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-all') or (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'extra-4-test-chgnet') or (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux' and extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet') or (python_full_version >= '3.13' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (python_full_version >= '3.13' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (platform_machine != 'x86_64' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (sys_platform != 'linux' and extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-all') or (extra == 'extra-4-test-alignn' and extra == 'extra-4-test-chgnet')" },
             { name = "typing-extensions", marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or (extra != 'extra-4-test-alignn' and extra != 'extra-4-test-m3gnet')" },
         ]
@@ -13138,7 +13098,8 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             { name = "jinja2" },
             { name = "numpy" },
             { name = "psutil" },
-            { name = "pyparsing" },
+            { name = "pyparsing", version = "2.4.7", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-alignn' or (extra == 'extra-4-test-all' and extra == 'extra-4-test-m3gnet') or (extra == 'extra-4-test-chgnet' and extra == 'extra-4-test-m3gnet')" },
+            { name = "pyparsing", version = "3.2.1", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-4-test-all' or extra == 'extra-4-test-chgnet' or extra != 'extra-4-test-alignn'" },
             { name = "requests" },
             { name = "tqdm" },
         ]
@@ -13378,7 +13339,7 @@ fn duplicate_torch_and_sympy_because_of_wrong_inferences() -> Result<()> {
             { url = "https://files.pythonhosted.org/packages/f5/d5/688db678e987c3e0fb17867970700b92603cadf36c56e5fb08f23e822a0c/yarl-1.18.3-cp313-cp313-win_amd64.whl", hash = "sha256:578e281c393af575879990861823ef19d66e2b1d0098414855dd367e234f5b3c", size = 315723 },
             { url = "https://files.pythonhosted.org/packages/f5/4b/a06e0ec3d155924f77835ed2d167ebd3b211a7b0853da1cf8d8414d784ef/yarl-1.18.3-py3-none-any.whl", hash = "sha256:b57f4f58099328dfb26c6a771d09fb20dbbae81d20cfb66141251ea063bd101b", size = 45109 },
         ]
-        "###
+        "#
         );
     });
 

crates/uv/tests/it/sync.rs

@@ -8019,15 +8019,381 @@ fn multiple_group_conflicts() -> Result<()> {
      + iniconfig==1.1.1
     "###);
 
-    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("foo").arg("--group").arg("bar"), @r###"
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("foo").arg("--group").arg("bar"), @r"
     success: false
     exit_code: 2
     ----- stdout -----
 
     ----- stderr -----
     Resolved 3 packages in [TIME]
-    error: Groups `foo` and `bar` are incompatible with the declared conflicts: {`project:foo`, `project:bar`}
+    error: Groups `bar` and `foo` are incompatible with the declared conflicts: {`project:bar`, `project:foo`}
-    "###);
+    ");
+
+    Ok(())
+}
+
+/// See: <https://github.com/astral-sh/uv/issues/11232>
+#[test]
+fn transitive_group_conflicts_shallow() -> Result<()> {
+    let context = TestContext::new("3.12");
+
+    let pyproject_toml = context.temp_dir.child("pyproject.toml");
+    pyproject_toml.write_str(
+        r#"
+        [project]
+        name = "example"
+        version = "0.1.0"
+        requires-python = ">=3.12"
+        dependencies = []
+
+        [dependency-groups]
+        dev = [
+            { include-group = "test" },
+        ]
+        test = ["anyio>4"]
+        magic = ["anyio<4"]
+
+        [tool.uv]
+        conflicts = [
+            [
+                { group = "test" },
+                { group = "magic" },
+            ],
+        ]
+        "#,
+    )?;
+
+    uv_snapshot!(context.filters(), context.sync(), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 5 packages in [TIME]
+    Prepared 3 packages in [TIME]
+    Installed 3 packages in [TIME]
+     + anyio==4.3.0
+     + idna==3.6
+     + sniffio==1.3.1
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev"), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 5 packages in [TIME]
+    Audited 3 packages in [TIME]
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev").arg("--group").arg("test"), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 5 packages in [TIME]
+    Audited 3 packages in [TIME]
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("test").arg("--group").arg("magic"), @r"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 5 packages in [TIME]
+    error: Groups `magic` and `test` are incompatible with the declared conflicts: {`example:magic`, `example:test`}
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev").arg("--group").arg("magic"), @r"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 5 packages in [TIME]
+    error: Groups `dev` and `magic` are incompatible with the transitively inferred conflicts: {`example:dev`, `example:magic`}
+    ");
+
+    Ok(())
+}
+
+/// See: <https://github.com/astral-sh/uv/issues/11232>
+#[test]
+fn transitive_group_conflicts_deep() -> Result<()> {
+    let context = TestContext::new("3.12");
+
+    let pyproject_toml = context.temp_dir.child("pyproject.toml");
+    pyproject_toml.write_str(
+        r#"
+        [project]
+        name = "example"
+        version = "0.1.0"
+        requires-python = ">=3.12"
+        dependencies = []
+
+        [dependency-groups]
+        dev = [
+            { include-group = "intermediate" },
+        ]
+        intermediate = [
+            { include-group = "test" },
+            { include-group = "other" },
+        ]
+        test = ["iniconfig>=2"]
+        magic = ["iniconfig<2", "anyio<4"]
+        other = ["anyio>4"]
+
+        [tool.uv]
+        conflicts = [
+            [
+                { group = "test" },
+                { group = "magic" },
+            ],
+            [
+                { group = "other" },
+                { group = "magic" },
+            ],
+        ]"#,
+    )?;
+
+    uv_snapshot!(context.filters(), context.sync(), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 7 packages in [TIME]
+    Prepared 4 packages in [TIME]
+    Installed 4 packages in [TIME]
+     + anyio==4.3.0
+     + idna==3.6
+     + iniconfig==2.0.0
+     + sniffio==1.3.1
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev"), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 7 packages in [TIME]
+    Audited 4 packages in [TIME]
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev").arg("--group").arg("test"), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 7 packages in [TIME]
+    Audited 4 packages in [TIME]
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev").arg("--group").arg("magic"), @r"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 7 packages in [TIME]
+    error: Groups `dev` and `magic` are incompatible with the transitively inferred conflicts: {`example:dev`, `example:magic`}
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--no-dev").arg("--group").arg("intermediate").arg("--group").arg("magic"), @r"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 7 packages in [TIME]
+    error: Groups `intermediate` and `magic` are incompatible with the transitively inferred conflicts: {`example:intermediate`, `example:magic`}
+    ");
+
+    Ok(())
+}
+
+/// See: <https://github.com/astral-sh/uv/issues/11232>
+#[test]
+fn transitive_group_conflicts_siblings() -> Result<()> {
+    let context = TestContext::new("3.12");
+
+    let pyproject_toml = context.temp_dir.child("pyproject.toml");
+    pyproject_toml.write_str(
+        r#"
+        [project]
+        name = "example"
+        version = "0.1.0"
+        requires-python = ">=3.12"
+        dependencies = []
+
+        [dependency-groups]
+        dev = [
+            { include-group = "test" },
+        ]
+        dev2 = [
+            { include-group = "magic" },
+        ]
+        test = ["anyio>4"]
+        magic = ["anyio<4"]
+
+        [tool.uv]
+        conflicts = [
+            [
+                { group = "test" },
+                { group = "magic" },
+            ],
+        ]"#,
+    )?;
+
+    uv_snapshot!(context.filters(), context.sync(), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 5 packages in [TIME]
+    Prepared 3 packages in [TIME]
+    Installed 3 packages in [TIME]
+     + anyio==4.3.0
+     + idna==3.6
+     + sniffio==1.3.1
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev"), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 5 packages in [TIME]
+    Audited 3 packages in [TIME]
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--no-dev").arg("--group").arg("dev2"), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 5 packages in [TIME]
+    Prepared 1 package in [TIME]
+    Uninstalled 1 package in [TIME]
+    Installed 1 package in [TIME]
+     - anyio==4.3.0
+     + anyio==3.7.1
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev2"), @r"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 5 packages in [TIME]
+    error: Groups `dev` (enabled by default) and `dev2` are incompatible with the transitively inferred conflicts: {`example:dev`, `example:dev2`}
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev").arg("--group").arg("dev2"), @r"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    Resolved 5 packages in [TIME]
+    error: Groups `dev` and `dev2` are incompatible with the transitively inferred conflicts: {`example:dev`, `example:dev2`}
+    ");
+
+    Ok(())
+}
+
+/// See: <https://github.com/astral-sh/uv/issues/11232>
+#[test]
+fn transitive_group_conflicts_cycle() -> Result<()> {
+    let context = TestContext::new("3.12");
+
+    let pyproject_toml = context.temp_dir.child("pyproject.toml");
+    pyproject_toml.write_str(
+        r#"
+        [project]
+        name = "example"
+        version = "0.1.0"
+        requires-python = ">=3.12"
+        dependencies = []
+
+        [dependency-groups]
+        dev = [
+            { include-group = "test" },
+        ]
+        test = [
+            "anyio>4",
+            { include-group = "dev" },
+        ]
+        magic = ["anyio<4"]
+
+        [tool.uv]
+        conflicts = [
+            [
+                { group = "test" },
+                { group = "magic" },
+            ],
+        ]
+        "#,
+    )?;
+
+    uv_snapshot!(context.filters(), context.sync(), @r"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+
+    ----- stderr -----
+      × Failed to build `example @ file://[TEMP_DIR]/`
+      ╰─▶ Detected a cycle in `dependency-groups`: `dev` -> `test` -> `dev`
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev"), @r"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+
+    ----- stderr -----
+      × Failed to build `example @ file://[TEMP_DIR]/`
+      ╰─▶ Detected a cycle in `dependency-groups`: `dev` -> `test` -> `dev`
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev").arg("--group").arg("test"), @r"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+
+    ----- stderr -----
+      × Failed to build `example @ file://[TEMP_DIR]/`
+      ╰─▶ Detected a cycle in `dependency-groups`: `dev` -> `test` -> `dev`
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("test").arg("--group").arg("magic"), @r"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+
+    ----- stderr -----
+      × Failed to build `example @ file://[TEMP_DIR]/`
+      ╰─▶ Detected a cycle in `dependency-groups`: `dev` -> `test` -> `dev`
+    ");
+
+    uv_snapshot!(context.filters(), context.sync().arg("--group").arg("dev").arg("--group").arg("magic"), @r"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+
+    ----- stderr -----
+      × Failed to build `example @ file://[TEMP_DIR]/`
+      ╰─▶ Detected a cycle in `dependency-groups`: `dev` -> `test` -> `dev`
+    ");
 
     Ok(())
 }