fix: Don't remove project.dependencies when deps groups are present

docs/uv.md

@@ -103,9 +103,14 @@ uv.override_package(
 use_repo(uv, "pypi")
 ```
 
-We can configure a default dependency group by setting the `dep_group` flag on our hub as part of the `.bazelrc`.
-Each `[dependency-group]` of the `pyproject.toml` is registered as a named dependency group.
-If no dependency groups are listed, an implicit default group with the name of the project itself is created.
+We can configure a default dependency group by setting the `dep_group` flag on
+our hub as part of the `.bazelrc`. Each entry in `[dependency-groups]` of the
+`pyproject.toml` is registered as a named dependency group. Requirements in
+`project.dependencies` remain available in every named group; each dependency
+group adds its own requirements to that shared base. Set
+`include_project_dependencies = False` on `uv.project()` when named groups
+should expose only their own requirements. If no dependency groups are listed,
+an implicit default group with the name of the project itself is created.
 
 ```
 # .bazelrc

examples/dev_deps/README.md

@@ -30,8 +30,9 @@ dev  = [
 ```
 
 The `dev` group composes `prod` (the runtime deps) with dev-only tools using
-PEP 735's `include-group` syntax. `uv lock` resolves all groups into a
-single lockfile.
+PEP 735's `include-group` syntax. The project's default `build` and
+`setuptools` dependencies remain available in both groups. `uv lock` resolves
+all groups into a single lockfile.
 
 ### 2. Venv selection via `.bazelrc`
 
@@ -46,8 +47,9 @@ common:release --stamp
 ```
 
 The `--@pypi//dep_group=` flag controls which dependency group the hub makes
-available. The default is `dev` (everything importable). `--config=release`
-switches to `prod` (runtime deps only).
+available in addition to the project's default dependencies. The default is
+`dev` (everything importable); `--config=release` switches to `prod` (the
+runtime group, without dev-only tools).
 
 ### 3. A `string_flag` to control dep inclusion
 
@@ -112,8 +114,8 @@ The venv flag and the mode flag work together:
 
 | `.bazelrc` config  | `--@pypi//dep_group=` | `--//:mode=` | Effect                                                       |
 | ------------------ | ---------------- | ------------ | ------------------------------------------------------------ |
-| _(default)_        | `dev`            | `dev`        | Hub exposes all packages; `select()` includes dev_deps       |
-| `--config=release` | `prod`           | `prod`       | Hub exposes only prod packages; `select()` excludes dev_deps |
+| _(default)_        | `dev`            | `dev`        | Default + prod + dev; `select()` includes dev_deps                |
+| `--config=release` | `prod`           | `prod`       | Default + prod; `select()` excludes dev_deps                      |
 
 The venv flag controls which packages the hub _makes available_ (which wheels
 are fetched and linked). The mode flag controls which packages the target

uv/private/extension/defs.bzl

@@ -344,7 +344,16 @@ def _parse_projects(module_ctx, hub_specs):
 
             whl_configurations.update(collect_configurations(lock_data))
 
-            configuration_names, activated_extras = collect_activated_extras(project.lock, project_id, project_data, lock_data, default_versions, marker_graph, package_versions)
+            configuration_names, activated_extras = collect_activated_extras(
+                project.lock,
+                project_id,
+                project_data,
+                lock_data,
+                default_versions,
+                marker_graph,
+                package_versions,
+                include_project_dependencies = project.include_project_dependencies,
+            )
             version_activations = collate_versions_by_name(activated_extras)
 
             # Mapping from SCC ID to marked SCC members
@@ -791,6 +800,12 @@ _project_tag = tag_class(
                 "build",
             ],
         ),
+        "include_project_dependencies": attr.bool(
+            default = True,
+            doc = "Whether `project.dependencies` remain available in every explicit " +
+                  "dependency group. Set to false to make selected groups expose only " +
+                  "their own requirements.",
+        ),
         "unstable_configure_command": attr.string_list(
             mandatory = False,
             doc = "Command to run as the sdist configure tool. Each element is either " +

uv/private/extension/projectfile.bzl

@@ -149,7 +149,15 @@ def _extract_lockfile_group_versions(lock_id, lock_data):
                     result.setdefault(group_name, {})[pkg_name] = (lock_id, pkg_name, dep["version"], "__base__")
     return result
 
-def collect_activated_extras(projectfile, lock_id, project_data, lock_data, default_versions, graph, package_versions = {}):
+def collect_activated_extras(
+        projectfile,
+        lock_id,
+        project_data,
+        lock_data,
+        default_versions,
+        graph,
+        package_versions = {},
+        include_project_dependencies = True):
     """Collects the set of transitively activated extras for each configuration.
 
     This function determines the full set of extras that are activated for each
@@ -162,6 +170,10 @@ def collect_activated_extras(projectfile, lock_id, project_data, lock_data, defa
         default_versions: A dictionary mapping package names to their default
             version dependency tuples.
         graph: The dependency graph, as returned by `build_marker_graph`.
+        include_project_dependencies: Whether requirements from
+            `project.dependencies` are included in every explicit dependency
+            group. Set to false to make named groups expose only their own
+            resolved requirements.
 
     Returns:
         A tuple containing:
@@ -172,12 +184,19 @@ def collect_activated_extras(projectfile, lock_id, project_data, lock_data, defa
           `{dep: {cfg: {extra_dep: {marker: 1}}}}`.
     """
 
-    # If no dependency-groups are specified, use the lock members manifest, or just the self-list
+    # If no dependency-groups are specified, use the lock members manifest, or just the self-list.
+    # Otherwise, project dependencies are the common base of every explicit group
+    # unless the project explicitly opts out.
+    # PEP 735 groups add requirements to a project; they do not replace
+    # `project.dependencies`.
     dep_groups = project_data.get("dependency-groups", {
         project_data["project"]["name"]: lock_data.get("manifest", {}).get("members", [
             project_data["project"]["name"],
         ]),
     })
+    default_specs = project_data["project"].get("dependencies", []) if (
+        include_project_dependencies and "dependency-groups" in project_data
+    ) else []
 
     # Normalize dep groups to our dependency triples (graph keys)
     normalized_dep_groups = {}
@@ -190,7 +209,7 @@ def collect_activated_extras(projectfile, lock_id, project_data, lock_data, defa
     lockfile_group_versions = _extract_lockfile_group_versions(lock_id, lock_data)
 
     for group_name in dep_groups.keys():
-        resolved_specs = resolve_dependency_group_specs(dep_groups, group_name)
+        resolved_specs = default_specs + resolve_dependency_group_specs(dep_groups, group_name)
 
         group_preferences = dict(lockfile_group_versions.get(group_name, {}))
 

uv/private/extension/test_projectfile.bzl

@@ -200,6 +200,74 @@ collect_activated_extras_transitive_remap_test = unittest.make(
     _collect_activated_extras_transitive_remap_test_impl,
 )
 
+def _collect_activated_extras_keeps_project_dependencies_in_groups_test_impl(ctx):
+    """Dependency groups don't replace project dependencies through their existence."""
+    env = unittest.begin(ctx)
+    project_data = {
+        "project": {
+            "name": "test_project",
+            "dependencies": ["base"],
+        },
+        "dependency-groups": {
+            "prod": ["runtime"],
+            "dev": [
+                {"include-group": "prod"},
+                "devtool",
+            ],
+        },
+    }
+    default_versions = {
+        name: ("lock", name, "1.0.0", "__base__")
+        for name in ["base", "runtime", "devtool"]
+    }
+    graph = {
+        ("lock", name, "1.0.0", "__base__"): {}
+        for name in ["base", "runtime", "devtool"]
+    }
+
+    configuration_names, activated_extras = collect_activated_extras(
+        "//:pyproject.toml",
+        "lock",
+        project_data,
+        {"package": []},
+        default_versions,
+        graph,
+    )
+
+    base = ("lock", "base", "1.0.0", "__base__")
+    runtime = ("lock", "runtime", "1.0.0", "__base__")
+    devtool = ("lock", "devtool", "1.0.0", "__base__")
+
+    asserts.equals(env, {"prod": 1, "dev": 1}, configuration_names)
+    asserts.true(env, "prod" in activated_extras[base])
+    asserts.true(env, "dev" in activated_extras[base])
+    asserts.true(env, "prod" in activated_extras[runtime])
+    asserts.true(env, "dev" in activated_extras[runtime])
+    asserts.false(env, "prod" in activated_extras[devtool])
+    asserts.true(env, "dev" in activated_extras[devtool])
+
+    _configuration_names, group_only_extras = collect_activated_extras(
+        "//:pyproject.toml",
+        "lock",
+        project_data,
+        {"package": []},
+        default_versions,
+        graph,
+        include_project_dependencies = False,
+    )
+
+    asserts.false(env, base in group_only_extras)
+    asserts.true(env, "prod" in group_only_extras[runtime])
+    asserts.true(env, "dev" in group_only_extras[runtime])
+    asserts.false(env, "prod" in group_only_extras[devtool])
+    asserts.true(env, "dev" in group_only_extras[devtool])
+
+    return unittest.end(env)
+
+collect_activated_extras_keeps_project_dependencies_in_groups_test = unittest.make(
+    _collect_activated_extras_keeps_project_dependencies_in_groups_test_impl,
+)
+
 def projectfile_test_suite():
     unittest.suite(
         "extract_requirement_marker_pairs_tests",
@@ -210,4 +278,5 @@ def projectfile_test_suite():
         extract_requirement_marker_pairs_preferred_overrides_version_map_test,
         extract_requirement_marker_pairs_preferred_overrides_multi_version_test,
         collect_activated_extras_transitive_remap_test,
+        collect_activated_extras_keeps_project_dependencies_in_groups_test,
     )