From 7bfc864fa312ff7a5ed516853c9669dc2c3260ce Mon Sep 17 00:00:00 2001
From: Alyssa Coghlan <ncoghlan@gmail.com>
Date: Fri, 1 Nov 2024 19:51:55 +1000
Subject: [PATCH 01/12] Fix automated layer versioning

Closes #24
---
 src/venvstacks/pack_venv.py          |  20 ++-
 src/venvstacks/stacks.py             | 176 +++++++++++++++++----------
 tests/sample_project/venvstacks.toml |   8 +-
 3 files changed, 130 insertions(+), 74 deletions(-)

diff --git a/src/venvstacks/pack_venv.py b/src/venvstacks/pack_venv.py
index d60c282..b95a091 100755
--- a/src/venvstacks/pack_venv.py
+++ b/src/venvstacks/pack_venv.py
@@ -196,12 +196,15 @@ def _supports_symlinks(target_path: Path) -> bool:
 def export_venv(
     source_dir: StrPath,
     target_dir: StrPath,
+    sitecustomize_source: StrPath | None = None,
     run_postinstall: Callable[[Path, Path], None] | None = None,
 ) -> Path:
     """Export the given build environment, skipping archive creation and unpacking
 
     * injects a suitable `postinstall.py` script for the environment being exported
-    * excludes __pycache__ folders and package metadata RECORD files
+    * excludes `__pycache__` folders and package metadata `RECORD` files
+    * allows build environment `sitecustomize.py` to be replaced with a deployed variant
+    * excludes `*sitecustomize.py` files from the tree copy if a specific source is given
     * replaces symlinks with copies on Windows or if the target doesn't support symlinks
 
     If supplied, *run_postinstall* is called with the path to the environment's Python
@@ -213,7 +216,15 @@ def export_venv(
     """
     source_path = as_normalized_path(source_dir)
     target_path = as_normalized_path(target_dir)
-    excluded = shutil.ignore_patterns("__pycache__", "RECORD")
+    patterns_to_ignore = ["__pycache__", "RECORD"]
+    if sitecustomize_source is not None:
+        # The deployed `sitecustomize.py` should be saved alongside the
+        # build version with a name like `_deployed_sitecustomize.py`
+        sc_source_path = as_normalized_path(sitecustomize_source)
+        sc_relative_path = sc_source_path.relative_to(source_path)
+        sc_target_path = target_path / sc_relative_path.with_name("sitecustomize.py")
+        patterns_to_ignore.append("*sitecustomize.py")
+    excluded = shutil.ignore_patterns(*patterns_to_ignore)
     # Avoid symlinks on Windows, as they need elevated privileges to create
     # Also avoid them if the target folder doesn't support symlink creation
     # (that way exports to FAT/FAT32/VFAT file systems should work, even if
@@ -228,6 +239,8 @@ def export_venv(
         symlinks=publish_symlinks,
         dirs_exist_ok=True,
     )
+    if sitecustomize_source is not None:
+        shutil.copy2(sc_source_path, sc_target_path)
     postinstall_path = _inject_postinstall_script(target_path)
     if run_postinstall is not None:
         run_postinstall(target_path, postinstall_path)
@@ -237,6 +250,7 @@ def export_venv(
 def create_archive(
     source_dir: StrPath,
     archive_base_name: StrPath,
+    sitecustomize_source: StrPath | None = None,
     *,
     install_target: str | None = None,
     clamp_mtime: datetime | None = None,
@@ -261,7 +275,7 @@ def create_archive(
         install_target = source_path.name
     with tempfile.TemporaryDirectory(dir=work_dir) as tmp_dir:
         target_path = Path(tmp_dir) / install_target
-        env_path = export_venv(source_path, target_path)
+        env_path = export_venv(source_path, target_path, sitecustomize_source)
         if not show_progress:
 
             def report_progress(_: Any) -> None:
diff --git a/src/venvstacks/stacks.py b/src/venvstacks/stacks.py
index 5ba244b..fe4c939 100755
--- a/src/venvstacks/stacks.py
+++ b/src/venvstacks/stacks.py
@@ -27,6 +27,7 @@
     Any,
     ClassVar,
     Iterable,
+    Iterator,
     Literal,
     Mapping,
     MutableMapping,
@@ -645,6 +646,7 @@ def create_archive(
         self,
         env_path: Path,
         previous_metadata: ArchiveMetadata | None = None,
+        sitecustomize_source_path: Path | None = None,
         work_path: Path | None = None,
     ) -> tuple[ArchiveMetadata, Path]:
         if env_path.name != self.env_name:
@@ -669,6 +671,7 @@ def create_archive(
             pack_venv.create_archive(
                 env_path,
                 archive_base_path,
+                sitecustomize_source_path,
                 clamp_mtime=last_locked,
                 work_dir=work_path,
                 install_target=build_metadata["install_target"],
@@ -798,6 +801,7 @@ def export_environment(
         self,
         env_path: Path,
         previous_metadata: ExportMetadata | None = None,
+        sitecustomize_source_path: Path | None = None,
     ) -> tuple[ExportMetadata, Path]:
         if env_path.name != self.env_name:
             err_msg = (
@@ -822,6 +826,7 @@ def _run_postinstall(export_path: Path, postinstall_path: Path) -> None:
         exported_path = pack_venv.export_venv(
             env_path,
             export_path,
+            sitecustomize_source_path,
             _run_postinstall,
         )
         assert self.export_path == exported_path  # pack_venv ensures this is true
@@ -990,6 +995,7 @@ class _PythonEnvironment(ABC):
     base_python_path: Path | None = field(init=False, repr=False)
     tools_python_path: Path | None = field(init=False, repr=False)
     py_version: str = field(init=False, repr=False)
+    sitecustomize_source_path: Path | None = field(default=None, init=False, repr=False)
 
     # Operation flags allow for requested commands to be applied only to selected layers
     # Notes:
@@ -1023,6 +1029,11 @@ def env_name(self) -> EnvNameBuild:
     def install_target(self) -> EnvNameDeploy:
         return self.env_lock.get_deployed_name(self.env_spec.env_name)
 
+    def get_deployed_path(self, build_path: Path) -> Path:
+        env_deployed_path = Path(self.install_target)
+        relative_path = build_path.relative_to(self.env_path)
+        return env_deployed_path / relative_path
+
     def __post_init__(self) -> None:
         self.env_path = self.build_path / self.env_name
         self.pylib_path = self._get_py_scheme_path("purelib")
@@ -1313,7 +1324,9 @@ def create_archive(
             output_path, target_platform, tag_output, previous_metadata, force
         )
         work_path = self.build_path  # /tmp is likely too small for ML environments
-        return build_request.create_archive(env_path, previous_metadata, work_path)
+        return build_request.create_archive(
+            env_path, previous_metadata, self.sitecustomize_source_path, work_path
+        )
 
     def request_export(
         self,
@@ -1339,7 +1352,9 @@ def export_environment(
 
         # Define the input metadata that gets published in the export manifest
         export_request = self.request_export(output_path, previous_metadata, force)
-        return export_request.export_environment(env_path, previous_metadata)
+        return export_request.export_environment(
+            env_path, previous_metadata, self.sitecustomize_source_path
+        )
 
 
 class RuntimeEnv(_PythonEnvironment):
@@ -1417,11 +1432,13 @@ def create_build_environment(self, *, clean: bool = False) -> None:
 class _VirtualEnvironment(_PythonEnvironment):
     _include_system_site_packages = False
 
+    base_runtime: RuntimeEnv | None = field(init=False, repr=False)
     linked_constraints_paths: list[Path] = field(init=False, repr=False)
 
     def __post_init__(self) -> None:
         self.py_version = self.env_spec.runtime.py_version
         super().__post_init__()
+        self.base_runtime = None
         self.linked_constraints_paths = []
 
     @property
@@ -1430,13 +1447,17 @@ def env_spec(self) -> _VirtualEnvironmentSpec:
         assert isinstance(self._env_spec, _VirtualEnvironmentSpec)
         return self._env_spec
 
-    def link_base_runtime_paths(self, runtime: RuntimeEnv) -> None:
+    def link_base_runtime(self, runtime: RuntimeEnv) -> None:
+        if self.base_runtime is not None:
+            raise BuildEnvError(f"Layered environment base runtime already linked {self}")
+        # Link the runtime environment
+        self.base_runtime = runtime
         # Link executable paths
         self.base_python_path = runtime.python_path
         self.tools_python_path = runtime.tools_python_path
-        if self.linked_constraints_paths:
-            raise BuildEnvError("Layered environment base runtime already linked")
+        # Link runtime layer dependency constraints
         self.linked_constraints_paths[:] = [runtime.requirements_path]
+        print(f"Linked {self}")
 
     def get_constraint_paths(self) -> list[Path]:
         return self.linked_constraints_paths
@@ -1464,12 +1485,12 @@ def _ensure_virtual_environment(self) -> subprocess.CompletedProcess[str]:
             str(self.env_path),
         ]
         result = run_python_command(command)
-        self._link_layered_environment()
+        self._generate_sitecustomize()
         fs_sync()
         print(f"Virtual environment configured in {str(self.env_path)!r}")
         return result
 
-    def _link_layered_environment(self) -> None:
+    def _generate_sitecustomize(self) -> None:
         pass  # Nothing to do by default, subclasses override if necessary
 
     def _update_existing_environment(self, *, lock_only: bool = False) -> None:
@@ -1515,8 +1536,6 @@ class ApplicationEnv(_VirtualEnvironment):
     category = LayerCategories.APPLICATIONS
 
     launch_module_name: str = field(init=False, repr=False)
-    linked_pylib_paths: list[Path] = field(init=False, repr=False)
-    linked_dynlib_paths: list[Path] = field(init=False, repr=False)
     linked_frameworks: list[FrameworkEnv] = field(init=False, repr=False)
 
     @property
@@ -1527,65 +1546,69 @@ def env_spec(self) -> ApplicationSpec:
 
     def __post_init__(self) -> None:
         super().__post_init__()
+        self.sitecustomize_source_path = self.pylib_path / "_deployed_sitecustomize.py"
         self.launch_module_name = self.env_spec.launch_module_path.stem
-        self.linked_pylib_paths = []
-        self.linked_dynlib_paths = []
         self.linked_frameworks = []
 
+    def _linked_environments(self) -> Iterator[_PythonEnvironment]:
+        for fw_env in self.linked_frameworks:
+            yield fw_env
+        runtime_env = self.base_runtime
+        assert runtime_env is not None
+        yield runtime_env
+
+    def _linked_pylib_build_paths(self) -> Iterator[Path]:
+        for env in self._linked_environments():
+            yield env.pylib_path
+
+    def _linked_dynlib_build_paths(self) -> Iterator[Path]:
+        for env in self._linked_environments():
+            dynlib_path = env.dynlib_path
+            if dynlib_path is not None:
+                yield dynlib_path
+
+    def _linked_pylib_deployed_paths(self) -> Iterator[Path]:
+        for env in self._linked_environments():
+            yield env.get_deployed_path(env.pylib_path)
+
+    def _linked_dynlib_deployed_paths(self) -> Iterator[Path]:
+        for env in self._linked_environments():
+            dynlib_path = env.dynlib_path
+            if dynlib_path is not None:
+                yield env.get_deployed_path(dynlib_path)
+
     def link_layered_environments(
         self, runtime: RuntimeEnv, frameworks: Mapping[LayerBaseName, FrameworkEnv]
     ) -> None:
-        self.link_base_runtime_paths(runtime)
+        self.link_base_runtime(runtime)
         constraints_paths = self.linked_constraints_paths
         if not constraints_paths:
             raise BuildEnvError("Failed to add base environment constraints path")
         # The runtime site-packages folder is added here rather than via pyvenv.cfg
         # to ensure it appears in sys.path after the framework site-packages folders
-        pylib_paths = self.linked_pylib_paths
-        dynlib_paths = self.linked_dynlib_paths
         fw_envs = self.linked_frameworks
-        if pylib_paths or dynlib_paths or fw_envs:
+        if fw_envs:
             raise BuildEnvError("Layered application environment already linked")
-        for env_spec in self.env_spec.frameworks:
-            env = frameworks[env_spec.name]
-            fw_envs.append(env)
-            constraints_paths.append(env.requirements_path)
-            install_target_path = Path(env.install_target)
-
-            def _fw_env_path(build_path: Path) -> Path:
-                relative_path = build_path.relative_to(env.env_path)
-                return install_target_path / relative_path
-
-            pylib_paths.append(_fw_env_path(env.pylib_path))
-            if env.dynlib_path is not None:
-                dynlib_paths.append(_fw_env_path(env.pylib_path))
-        runtime_target_path = Path(runtime.install_target)
-
-        def _runtime_path(build_path: Path) -> Path:
-            relative_path = build_path.relative_to(runtime.env_path)
-            return runtime_target_path / relative_path
-
-        pylib_paths.append(_runtime_path(runtime.pylib_path))
-        if runtime.dynlib_path is not None:
-            dynlib_paths.append(_runtime_path(runtime.dynlib_path))
-
-    def _link_layered_environment(self) -> None:
-        # Create sitecustomize file
-        sc_dir_path = self.pylib_path
+        for fw_env_spec in self.env_spec.frameworks:
+            fw_env = frameworks[fw_env_spec.name]
+            fw_envs.append(fw_env)
+            constraints_paths.append(fw_env.requirements_path)
+
+    @staticmethod
+    def _render_sitecustomize(
+        relative_prefix: Path,
+        pylib_paths: Iterable[Path],
+        dynlib_paths: Iterable[Path],
+    ) -> str:
         sc_contents = [
             "# Automatically generated by venvstacks",
             "import site",
             "import os",
             "from os.path import abspath, dirname, join as joinpath",
-            "# Allow loading modules and packages from framework environments",
+            "# Allow loading modules and packages from linked environments",
             "this_dir = dirname(abspath(__file__))",
         ]
-        # Add framework and runtime folders to sys.path
-        parent_path = self.env_path.parent
-        relative_prefix = Path(
-            os.path.relpath(str(parent_path), start=str(sc_dir_path))
-        )
-        for pylib_path in self.linked_pylib_paths:
+        for pylib_path in pylib_paths:
             relative_path = relative_prefix / pylib_path
             sc_contents.extend(
                 [
@@ -1593,31 +1616,54 @@ def _link_layered_environment(self) -> None:
                     "site.addsitedir(path_entry)",
                 ]
             )
-        # Add DLL search folders if needed
-        dynlib_paths = self.linked_dynlib_paths
-        if _WINDOWS_BUILD and dynlib_paths:
+        dynlib_entries: list[str] = []
+        for dynlib_path in dynlib_paths:
+            if not dynlib_path.exists():
+                # Nothing added DLLs to this folder at build time, so skip it
+                continue
+            relative_path = relative_prefix / dynlib_path
+            dynlib_entries.extend(
+                [
+                    f"dll_dir = abspath(joinpath(this_dir, {str(relative_path)!r}))",
+                    "os.add_dll_directory(dll_dir)",
+                ]
+            )
+        if dynlib_entries:
             sc_contents.extend(
                 [
                     "",
                     "# Allow loading misplaced DLLs on Windows",
+                    *dynlib_entries,
                 ]
             )
-            for dynlib_path in dynlib_paths:
-                if not dynlib_path.exists():
-                    # Nothing added DLLs to this folder at build time, so skip it
-                    continue
-                relative_path = relative_prefix / dynlib_path
-                sc_contents.extend(
-                    [
-                        f"dll_dir = abspath(joinpath(this_dir, {str(relative_path)!r}))",
-                        "os.add_dll_directory(dll_dir)",
-                    ]
-                )
         sc_contents.append("")
+        return "\n".join(sc_contents)
+
+    def _generate_sitecustomize(self) -> None:
+        # Create build & deployment sitecustomize files
+        sc_dir_path = self.pylib_path
+        # Add framework and runtime folders to sys.path
+        parent_path = self.env_path.parent
+        relative_prefix = Path(
+            os.path.relpath(str(parent_path), start=str(sc_dir_path))
+        )
+        sc_contents = self._render_sitecustomize(
+            relative_prefix,
+            self._linked_pylib_build_paths(),
+            self._linked_dynlib_build_paths(),
+        )
+        deployed_sc_contents = self._render_sitecustomize(
+            relative_prefix,
+            self._linked_pylib_deployed_paths(),
+            self._linked_dynlib_deployed_paths(),
+        )
         sc_path = self.pylib_path / "sitecustomize.py"
         print(f"Generating {sc_path!r}...")
-        with open(sc_path, "w", encoding="utf-8") as f:
-            f.write("\n".join(sc_contents))
+        sc_path.write_text(sc_contents)
+        deployed_sc_path = self.sitecustomize_source_path
+        assert deployed_sc_path is not None
+        print(f"Generating {deployed_sc_path!r}...")
+        deployed_sc_path.write_text(deployed_sc_contents)
 
     def _update_existing_environment(self, *, lock_only: bool = False) -> None:
         super()._update_existing_environment(lock_only=lock_only)
@@ -1805,7 +1851,7 @@ def define_build_environment(
         )
         for fw_env in frameworks.values():
             runtime = runtimes[fw_env.env_spec.runtime.name]
-            fw_env.link_base_runtime_paths(runtime)
+            fw_env.link_base_runtime(runtime)
         print("Defining application environments:")
         applications = self._define_envs(
             build_path, index_config, ApplicationEnv, self.applications
diff --git a/tests/sample_project/venvstacks.toml b/tests/sample_project/venvstacks.toml
index 9ceb843..17cb920 100644
--- a/tests/sample_project/venvstacks.toml
+++ b/tests/sample_project/venvstacks.toml
@@ -65,9 +65,7 @@ requirements = [
 
 [[frameworks]]
 name = "scipy"
-# Automatic versioning currently breaks venv layering
-# https://github.com/lmstudio-ai/venvstacks/issues/24
-# versioned = true
+versioned = true
 runtime = "cpython@3.11"
 requirements = [
     "scipy",
@@ -96,9 +94,7 @@ requirements = [
 
 [[applications]]
 name = "scipy-import"
-# Automatic versioning currently breaks venv layering
-# https://github.com/lmstudio-ai/venvstacks/issues/24
-# versioned = true
+versioned = true
 launch_module = "launch_modules/scipy_import.py"
 frameworks = ["scipy"]
 requirements = [

From 90cf3ec502c111c23504cb06d94391d11398e626 Mon Sep 17 00:00:00 2001
From: Alyssa Coghlan <ncoghlan@gmail.com>
Date: Mon, 4 Nov 2024 14:26:53 +1000
Subject: [PATCH 02/12] Force site customization encoding and newlines

---
 src/venvstacks/stacks.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/venvstacks/stacks.py b/src/venvstacks/stacks.py
index fe4c939..f9da726 100755
--- a/src/venvstacks/stacks.py
+++ b/src/venvstacks/stacks.py
@@ -1659,11 +1659,11 @@ def _generate_sitecustomize(self) -> None:
         )
         sc_path = self.pylib_path / "sitecustomize.py"
         print(f"Generating {sc_path!r}...")
-        sc_path.write_text(sc_contents)
+        sc_path.write_text(sc_contents, encoding="utf-8", newline="\n")
         deployed_sc_path = self.sitecustomize_source_path
         assert deployed_sc_path is not None
         print(f"Generating {deployed_sc_path!r}...")
-        deployed_sc_path.write_text(deployed_sc_contents)
+        deployed_sc_path.write_text(deployed_sc_contents, encoding="utf-8", newline="\n")
 
     def _update_existing_environment(self, *, lock_only: bool = False) -> None:
         super()._update_existing_environment(lock_only=lock_only)

From e4df1c33e4988916ae686a9b9875dc1572303e2e Mon Sep 17 00:00:00 2001
From: Alyssa Coghlan <ncoghlan@gmail.com>
Date: Mon, 4 Nov 2024 14:28:18 +1000
Subject: [PATCH 03/12] Force newlines in postinstall scripts

---
 src/venvstacks/pack_venv.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/venvstacks/pack_venv.py b/src/venvstacks/pack_venv.py
index b95a091..07762ce 100755
--- a/src/venvstacks/pack_venv.py
+++ b/src/venvstacks/pack_venv.py
@@ -176,7 +176,7 @@ def _inject_postinstall_script(
     else:
         script_contents = _BASE_RUNTIME_POST_INSTALL_SCRIPT
     script_path = env_path / script_name
-    script_path.write_text(script_contents, encoding="utf-8")
+    script_path.write_text(script_contents, encoding="utf-8", newline="\n")
     return script_path
 
 

From a0ad20c51dfc839ec541368aeb56fa6cddee93f3 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 4 Nov 2024 15:09:25 +1000
Subject: [PATCH 04/12] Update expected output (2024-11-04 04:58:20+00:00)
 (#65)

Update expected test output files from automated/expected-output/20241104-045820-e4df1c3 (source PR: #64)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 .../env_metadata/app-scipy-client.json        |  6 +--
 .../env_metadata/app-scipy-import.json        | 10 ++---
 .../env_metadata/app-sklearn-import.json      |  2 +-
 .../env_metadata/framework-scipy.json         |  8 ++--
 .../linux_x86_64/venvstacks.json              | 26 ++++++------
 .../env_metadata/app-scipy-client.json        |  6 +--
 .../env_metadata/app-scipy-import.json        |  8 ++--
 .../env_metadata/framework-scipy.json         |  8 ++--
 .../macosx_arm64/venvstacks.json              | 22 +++++-----
 .../env_metadata/app-scipy-client.json        |  6 +--
 .../env_metadata/app-scipy-import.json        | 10 ++---
 .../win_amd64/env_metadata/cpython@3.11.json  |  4 +-
 .../win_amd64/env_metadata/cpython@3.12.json  |  4 +-
 .../env_metadata/framework-http-client.json   |  4 +-
 .../env_metadata/framework-scipy.json         |  8 ++--
 .../env_metadata/framework-sklearn.json       |  4 +-
 .../win_amd64/venvstacks.json                 | 40 +++++++++----------
 17 files changed, 88 insertions(+), 88 deletions(-)

diff --git a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json
index 6636940..efc5c26 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "84c38c5717c3ff4e5fc9a13b22045b8c7fa2a96682648e419e22983e9023f554"
+    "sha256": "a2352d92b495315ac2fb5d011d7527fd8d7ad018e5feacf4aeddfd87d61251d0"
   },
   "archive_name": "app-scipy-client.tar.xz",
-  "archive_size": 1504,
+  "archive_size": 1508,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:43.205589+00:00",
   "required_layers": [
-    "framework-scipy",
+    "framework-scipy@1",
     "framework-http-client"
   ],
   "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
diff --git a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json
index 36b7bde..c5bcebd 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "4c30fb1472a1905d0369b700bd922f317f8ab4875e7b02a9c997dedf5cb0b175"
+    "sha256": "30169e6d298e1fc3d4cba0d9b07da0e835ab4e0dfd82ab4b4eabd28e79432d9c"
   },
-  "archive_name": "app-scipy-import.tar.xz",
-  "archive_size": 1412,
-  "install_target": "app-scipy-import",
+  "archive_name": "app-scipy-import@1.tar.xz",
+  "archive_size": 1416,
+  "install_target": "app-scipy-import@1",
   "layer_name": "app-scipy-import",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:43.173589+00:00",
   "required_layers": [
-    "framework-scipy"
+    "framework-scipy@1"
   ],
   "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
   "runtime_name": "cpython@3.11",
diff --git a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-sklearn-import.json b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-sklearn-import.json
index 76a2b85..863350c 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-sklearn-import.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-sklearn-import.json
@@ -3,7 +3,7 @@
   "app_launch_module_hash": "sha256:f66c01bbcca47cd31d79d2fb5377de0de18631ffc3c904629d46f6cad2918694",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "ba0b38bb3c8539b9882bdfd752f1407961f26fe8a2c1af3d1bed62d83478b8e7"
+    "sha256": "b08bfd48cc54bfb3123f64bda0c023e7d82c2d31ea310c258da7ef761165d49e"
   },
   "archive_name": "app-sklearn-import.tar.xz",
   "archive_size": 1420,
diff --git a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json
index b22ca25..84030b0 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json
@@ -1,11 +1,11 @@
 {
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "bd8bf5b409d03d78e878f3a5d7e350daea0e94cc983a6146997a1bd0d1834bf5"
+    "sha256": "a66860607012b4ddd1855abbca4e3dea80681ae42d49a5f2ea76bf93bcd1084a"
   },
-  "archive_name": "framework-scipy.tar.xz",
-  "archive_size": 23956040,
-  "install_target": "framework-scipy",
+  "archive_name": "framework-scipy@1.tar.xz",
+  "archive_size": 23959992,
+  "install_target": "framework-scipy@1",
   "layer_name": "framework-scipy",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:42.825586+00:00",
diff --git a/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json b/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json
index f1bd931..b72452e 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json
@@ -6,16 +6,16 @@
         "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "4c30fb1472a1905d0369b700bd922f317f8ab4875e7b02a9c997dedf5cb0b175"
+          "sha256": "30169e6d298e1fc3d4cba0d9b07da0e835ab4e0dfd82ab4b4eabd28e79432d9c"
         },
-        "archive_name": "app-scipy-import.tar.xz",
-        "archive_size": 1412,
-        "install_target": "app-scipy-import",
+        "archive_name": "app-scipy-import@1.tar.xz",
+        "archive_size": 1416,
+        "install_target": "app-scipy-import@1",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:43.173589+00:00",
         "required_layers": [
-          "framework-scipy"
+          "framework-scipy@1"
         ],
         "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
         "runtime_name": "cpython@3.11",
@@ -26,16 +26,16 @@
         "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "84c38c5717c3ff4e5fc9a13b22045b8c7fa2a96682648e419e22983e9023f554"
+          "sha256": "a2352d92b495315ac2fb5d011d7527fd8d7ad018e5feacf4aeddfd87d61251d0"
         },
         "archive_name": "app-scipy-client.tar.xz",
-        "archive_size": 1504,
+        "archive_size": 1508,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:43.205589+00:00",
         "required_layers": [
-          "framework-scipy",
+          "framework-scipy@1",
           "framework-http-client"
         ],
         "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
@@ -47,7 +47,7 @@
         "app_launch_module_hash": "sha256:f66c01bbcca47cd31d79d2fb5377de0de18631ffc3c904629d46f6cad2918694",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "ba0b38bb3c8539b9882bdfd752f1407961f26fe8a2c1af3d1bed62d83478b8e7"
+          "sha256": "b08bfd48cc54bfb3123f64bda0c023e7d82c2d31ea310c258da7ef761165d49e"
         },
         "archive_name": "app-sklearn-import.tar.xz",
         "archive_size": 1420,
@@ -67,11 +67,11 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "bd8bf5b409d03d78e878f3a5d7e350daea0e94cc983a6146997a1bd0d1834bf5"
+          "sha256": "a66860607012b4ddd1855abbca4e3dea80681ae42d49a5f2ea76bf93bcd1084a"
         },
-        "archive_name": "framework-scipy.tar.xz",
-        "archive_size": 23956040,
-        "install_target": "framework-scipy",
+        "archive_name": "framework-scipy@1.tar.xz",
+        "archive_size": 23959992,
+        "install_target": "framework-scipy@1",
         "layer_name": "framework-scipy",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:42.825586+00:00",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json
index a9a8af9..ebc6f13 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "2cdf88d7a5ed2dca88d7a59e2b5d9744503cf824218371948000f1b08486df4e"
+    "sha256": "1c47823146319078f9f7fc5d27605205c9d99449d85b7719fe9e21ec39dea457"
   },
   "archive_name": "app-scipy-client.tar.xz",
-  "archive_size": 1484,
+  "archive_size": 1488,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:33.147967+00:00",
   "required_layers": [
-    "framework-scipy",
+    "framework-scipy@1",
     "framework-http-client"
   ],
   "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json
index 2cbf816..73b7e21 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "5034f1fa0a0731af9e88699519a508e72662b003c30e14814ce72e00ef8a6223"
+    "sha256": "066c98a2355bf314ebdd66c9eaf5d01514cf9b738d761aefaefe6dd57154b6b3"
   },
-  "archive_name": "app-scipy-import.tar.xz",
+  "archive_name": "app-scipy-import@1.tar.xz",
   "archive_size": 1392,
-  "install_target": "app-scipy-import",
+  "install_target": "app-scipy-import@1",
   "layer_name": "app-scipy-import",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:33.121208+00:00",
   "required_layers": [
-    "framework-scipy"
+    "framework-scipy@1"
   ],
   "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
   "runtime_name": "cpython@3.11",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json
index 331a486..b19a6fb 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json
@@ -1,11 +1,11 @@
 {
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "45d6b5abeddedc12978b54d8ff4a29db76495bd5ab7b7a051ed45b8aa8fc76b9"
+    "sha256": "b201312705774dc3b748e71ac27fefbf54d750c11618b8048303cf84ea43713b"
   },
-  "archive_name": "framework-scipy.tar.xz",
-  "archive_size": 15077296,
-  "install_target": "framework-scipy",
+  "archive_name": "framework-scipy@1.tar.xz",
+  "archive_size": 15074628,
+  "install_target": "framework-scipy@1",
   "layer_name": "framework-scipy",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:32.960668+00:00",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json b/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json
index 86778c7..998b4f9 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json
@@ -6,16 +6,16 @@
         "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "5034f1fa0a0731af9e88699519a508e72662b003c30e14814ce72e00ef8a6223"
+          "sha256": "066c98a2355bf314ebdd66c9eaf5d01514cf9b738d761aefaefe6dd57154b6b3"
         },
-        "archive_name": "app-scipy-import.tar.xz",
+        "archive_name": "app-scipy-import@1.tar.xz",
         "archive_size": 1392,
-        "install_target": "app-scipy-import",
+        "install_target": "app-scipy-import@1",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:33.121208+00:00",
         "required_layers": [
-          "framework-scipy"
+          "framework-scipy@1"
         ],
         "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
         "runtime_name": "cpython@3.11",
@@ -26,16 +26,16 @@
         "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "2cdf88d7a5ed2dca88d7a59e2b5d9744503cf824218371948000f1b08486df4e"
+          "sha256": "1c47823146319078f9f7fc5d27605205c9d99449d85b7719fe9e21ec39dea457"
         },
         "archive_name": "app-scipy-client.tar.xz",
-        "archive_size": 1484,
+        "archive_size": 1488,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:33.147967+00:00",
         "required_layers": [
-          "framework-scipy",
+          "framework-scipy@1",
           "framework-http-client"
         ],
         "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
@@ -47,11 +47,11 @@
       {
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         "archive_hashes": {
-          "sha256": "45d6b5abeddedc12978b54d8ff4a29db76495bd5ab7b7a051ed45b8aa8fc76b9"
+          "sha256": "b201312705774dc3b748e71ac27fefbf54d750c11618b8048303cf84ea43713b"
         },
-        "archive_name": "framework-scipy.tar.xz",
-        "archive_size": 15077296,
-        "install_target": "framework-scipy",
+        "archive_name": "framework-scipy@1.tar.xz",
+        "archive_size": 15074628,
+        "install_target": "framework-scipy@1",
         "layer_name": "framework-scipy",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:32.960668+00:00",
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json
index a32e876..98e8bd7 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "69060c0e0a74290723c5e65a343e463112a249da960d8bf29997933cd1565787"
+    "sha256": "ca18363cd4b9cc9a567ee2a1624ae61f413297bd00595ddbe7cb4b5aaa3f7e52"
   },
   "archive_name": "app-scipy-client.zip",
-  "archive_size": 255147,
+  "archive_size": 255109,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:24:36.468633+00:00",
   "required_layers": [
-    "framework-scipy",
+    "framework-scipy@1",
     "framework-http-client"
   ],
   "requirements_hash": "sha256:3bff0428616a2f1724732e78e7788e753dd5f1aa10aa5d3b87707b8dbde121de",
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json
index be1e7d7..36b698a 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "1907700fc74c6a0bc62d851dce87bfed6a0ad52d0fec5863c9eadd1e26c029ff"
+    "sha256": "e987f9c43f8df61602699686e28f5178e7547c509e3d838285d7c22d995974b3"
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-  "archive_name": "app-scipy-import.zip",
-  "archive_size": 254658,
-  "install_target": "app-scipy-import",
+  "archive_name": "app-scipy-import@1.zip",
+  "archive_size": 254660,
+  "install_target": "app-scipy-import@1",
   "layer_name": "app-scipy-import",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:24:36.386938+00:00",
   "required_layers": [
-    "framework-scipy"
+    "framework-scipy@1"
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   "requirements_hash": "sha256:9aba38b5efe287f35d58825dce6b1c47ed556b930056e6edc00ca9e1a165796b",
   "runtime_name": "cpython@3.11.10",
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/cpython@3.11.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/cpython@3.11.json
index 5346397..b543ee2 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/cpython@3.11.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/cpython@3.11.json
@@ -1,10 +1,10 @@
 {
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   "archive_hashes": {
-    "sha256": "70a00f1e469d6c4ab82e0d74946ca6da0fb97ee480b294d93e6b217d8a9f3cd0"
+    "sha256": "96810b28fc38dfd207fe6d3ff30b89f3fbf34f519fbe3a1337c035abdfed714b"
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   "archive_name": "cpython@3.11.zip",
-  "archive_size": 46592259,
+  "archive_size": 46592251,
   "install_target": "cpython@3.11",
   "layer_name": "cpython@3.11",
   "lock_version": 1,
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/cpython@3.12.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/cpython@3.12.json
index 508e5a9..09cc807 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/cpython@3.12.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/cpython@3.12.json
@@ -1,10 +1,10 @@
 {
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+    "sha256": "ff79b5b4d9c7546d2c3c05313877c66c501c38eb1d48eed148237a65fc54bbbf"
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   "archive_name": "cpython@3.12.zip",
-  "archive_size": 45864491,
+  "archive_size": 45864483,
   "install_target": "cpython@3.12",
   "layer_name": "cpython@3.12",
   "lock_version": 1,
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-http-client.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-http-client.json
index 6af3112..9763d44 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-http-client.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-http-client.json
@@ -1,10 +1,10 @@
 {
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   "archive_hashes": {
-    "sha256": "b0193afc9d1f4a51b9fcb60903d335696804d2b35115986c68e4ebf5aaf1b621"
+    "sha256": "050eca5f2fa105b2750cd2a6b3de51310ca8e5ac453f843d2198629e5aa8f13d"
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   "archive_name": "framework-http-client.zip",
-  "archive_size": 817522,
+  "archive_size": 817511,
   "install_target": "framework-http-client",
   "layer_name": "framework-http-client",
   "lock_version": 1,
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json
index c86bc68..b94c31b 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json
@@ -1,11 +1,11 @@
 {
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "132cd5e29dae8d082c453b276e5e207e5f82f29458db62d6c7df2a01b8225f92"
+    "sha256": "643389d3e7f7c37fdf768ca02377f7e2ab019e7c0f6a448e6f61d40c390ce572"
   },
-  "archive_name": "framework-scipy.zip",
-  "archive_size": 45078361,
-  "install_target": "framework-scipy",
+  "archive_name": "framework-scipy@1.zip",
+  "archive_size": 45084834,
+  "install_target": "framework-scipy@1",
   "layer_name": "framework-scipy",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:24:35.999197+00:00",
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-sklearn.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-sklearn.json
index 6bb7c4f..d50c2d4 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-sklearn.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-sklearn.json
@@ -1,10 +1,10 @@
 {
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "eaaa57b8f636eb0258bf4b4ac11a7a76a4691b1659d9a14bd8b908129f75e936"
+    "sha256": "dd67aa8431b52d526fdb1eeb6109a30f44d36d1b56356590e9bb96ad474d71be"
   },
   "archive_name": "framework-sklearn.zip",
-  "archive_size": 56185753,
+  "archive_size": 56185742,
   "install_target": "framework-sklearn",
   "layer_name": "framework-sklearn",
   "lock_version": 1,
diff --git a/tests/sample_project/expected_manifests/win_amd64/venvstacks.json b/tests/sample_project/expected_manifests/win_amd64/venvstacks.json
index d06983c..910a6c9 100644
--- a/tests/sample_project/expected_manifests/win_amd64/venvstacks.json
+++ b/tests/sample_project/expected_manifests/win_amd64/venvstacks.json
@@ -6,16 +6,16 @@
         "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "1907700fc74c6a0bc62d851dce87bfed6a0ad52d0fec5863c9eadd1e26c029ff"
+          "sha256": "e987f9c43f8df61602699686e28f5178e7547c509e3d838285d7c22d995974b3"
         },
-        "archive_name": "app-scipy-import.zip",
-        "archive_size": 254658,
-        "install_target": "app-scipy-import",
+        "archive_name": "app-scipy-import@1.zip",
+        "archive_size": 254660,
+        "install_target": "app-scipy-import@1",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:24:36.386938+00:00",
         "required_layers": [
-          "framework-scipy"
+          "framework-scipy@1"
         ],
         "requirements_hash": "sha256:9aba38b5efe287f35d58825dce6b1c47ed556b930056e6edc00ca9e1a165796b",
         "runtime_name": "cpython@3.11.10",
@@ -26,16 +26,16 @@
         "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "69060c0e0a74290723c5e65a343e463112a249da960d8bf29997933cd1565787"
+          "sha256": "ca18363cd4b9cc9a567ee2a1624ae61f413297bd00595ddbe7cb4b5aaa3f7e52"
         },
         "archive_name": "app-scipy-client.zip",
-        "archive_size": 255147,
+        "archive_size": 255109,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:24:36.468633+00:00",
         "required_layers": [
-          "framework-scipy",
+          "framework-scipy@1",
           "framework-http-client"
         ],
         "requirements_hash": "sha256:3bff0428616a2f1724732e78e7788e753dd5f1aa10aa5d3b87707b8dbde121de",
@@ -47,11 +47,11 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "132cd5e29dae8d082c453b276e5e207e5f82f29458db62d6c7df2a01b8225f92"
+          "sha256": "643389d3e7f7c37fdf768ca02377f7e2ab019e7c0f6a448e6f61d40c390ce572"
         },
-        "archive_name": "framework-scipy.zip",
-        "archive_size": 45078361,
-        "install_target": "framework-scipy",
+        "archive_name": "framework-scipy@1.zip",
+        "archive_size": 45084834,
+        "install_target": "framework-scipy@1",
         "layer_name": "framework-scipy",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:24:35.999197+00:00",
@@ -62,10 +62,10 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "eaaa57b8f636eb0258bf4b4ac11a7a76a4691b1659d9a14bd8b908129f75e936"
+          "sha256": "dd67aa8431b52d526fdb1eeb6109a30f44d36d1b56356590e9bb96ad474d71be"
         },
         "archive_name": "framework-sklearn.zip",
-        "archive_size": 56185753,
+        "archive_size": 56185742,
         "install_target": "framework-sklearn",
         "layer_name": "framework-sklearn",
         "lock_version": 1,
@@ -77,10 +77,10 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "b0193afc9d1f4a51b9fcb60903d335696804d2b35115986c68e4ebf5aaf1b621"
+          "sha256": "050eca5f2fa105b2750cd2a6b3de51310ca8e5ac453f843d2198629e5aa8f13d"
         },
         "archive_name": "framework-http-client.zip",
-        "archive_size": 817522,
+        "archive_size": 817511,
         "install_target": "framework-http-client",
         "layer_name": "framework-http-client",
         "lock_version": 1,
@@ -94,10 +94,10 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "70a00f1e469d6c4ab82e0d74946ca6da0fb97ee480b294d93e6b217d8a9f3cd0"
+          "sha256": "96810b28fc38dfd207fe6d3ff30b89f3fbf34f519fbe3a1337c035abdfed714b"
         },
         "archive_name": "cpython@3.11.zip",
-        "archive_size": 46592259,
+        "archive_size": 46592251,
         "install_target": "cpython@3.11",
         "layer_name": "cpython@3.11",
         "lock_version": 1,
@@ -109,10 +109,10 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "ab8860e56b834ff4b9eacd11e8a0c705c83edac6b1627990f5317e1514314d76"
+          "sha256": "ff79b5b4d9c7546d2c3c05313877c66c501c38eb1d48eed148237a65fc54bbbf"
         },
         "archive_name": "cpython@3.12.zip",
-        "archive_size": 45864491,
+        "archive_size": 45864483,
         "install_target": "cpython@3.12",
         "layer_name": "cpython@3.12",
         "lock_version": 1,

From c98717869aaad5b1710d862da317519dc14b5963 Mon Sep 17 00:00:00 2001
From: Alyssa Coghlan <ncoghlan@gmail.com>
Date: Mon, 4 Nov 2024 16:11:58 +1000
Subject: [PATCH 05/12] Strengthen export path checks

---
 src/venvstacks/stacks.py      |  8 ++++++--
 tests/test_minimal_project.py | 20 +++++++++++---------
 tests/test_sample_project.py  |  8 +++++---
 3 files changed, 22 insertions(+), 14 deletions(-)

diff --git a/src/venvstacks/stacks.py b/src/venvstacks/stacks.py
index f9da726..d0b8ce7 100755
--- a/src/venvstacks/stacks.py
+++ b/src/venvstacks/stacks.py
@@ -1449,7 +1449,9 @@ def env_spec(self) -> _VirtualEnvironmentSpec:
 
     def link_base_runtime(self, runtime: RuntimeEnv) -> None:
         if self.base_runtime is not None:
-            raise BuildEnvError(f"Layered environment base runtime already linked {self}")
+            raise BuildEnvError(
+                f"Layered environment base runtime already linked {self}"
+            )
         # Link the runtime environment
         self.base_runtime = runtime
         # Link executable paths
@@ -1663,7 +1665,9 @@ def _generate_sitecustomize(self) -> None:
         deployed_sc_path = self.sitecustomize_source_path
         assert deployed_sc_path is not None
         print(f"Generating {deployed_sc_path!r}...")
-        deployed_sc_path.write_text(deployed_sc_contents, encoding="utf-8", newline="\n")
+        deployed_sc_path.write_text(
+            deployed_sc_contents, encoding="utf-8", newline="\n"
+        )
 
     def _update_existing_environment(self, *, lock_only: bool = False) -> None:
         super()._update_existing_environment(lock_only=lock_only)
diff --git a/tests/test_minimal_project.py b/tests/test_minimal_project.py
index 3aefa28..a68670e 100644
--- a/tests/test_minimal_project.py
+++ b/tests/test_minimal_project.py
@@ -532,26 +532,28 @@ def get_exported_python(
 
             self.check_deployed_environments(layered_metadata, get_exported_python)
 
-    def check_environment_exports(self, export_paths: ExportedEnvironmentPaths) -> None:
+    def check_environment_exports(
+        self, export_path: Path, export_paths: ExportedEnvironmentPaths
+    ) -> None:
         metadata_path, snippet_paths, env_paths = export_paths
         exported_manifests = ManifestData(metadata_path, snippet_paths)
-        env_name_to_path: dict[str, Path] = {}
+        deployed_name_to_path: dict[str, Path] = {}
         for env_metadata, env_path in zip(exported_manifests.snippet_data, env_paths):
             # TODO: Check more details regarding expected metadata contents
             self.assertTrue(env_path.exists())
-            env_name = EnvNameDeploy(env_metadata["install_target"])
-            self.assertEqual(env_path.name, env_name)
-            env_name_to_path[env_name] = env_path
+            deployed_name = EnvNameDeploy(env_metadata["install_target"])
+            self.assertEqual(env_path, export_path / deployed_name)
+            deployed_name_to_path[deployed_name] = env_path
         layered_metadata = exported_manifests.combined_data["layers"]
 
         def get_exported_python(
             env: ExportMetadata,
         ) -> tuple[EnvNameDeploy, Path, list[str]]:
-            env_name = env["install_target"]
-            env_path = env_name_to_path[env_name]
+            deployed_name = env["install_target"]
+            env_path = deployed_name_to_path[deployed_name]
             env_python = get_env_python(env_path)
             env_sys_path = get_sys_path(env_python)
-            return env_name, env_python, env_sys_path
+            return deployed_name, env_python, env_sys_path
 
         self.check_deployed_environments(layered_metadata, get_exported_python)
 
@@ -654,7 +656,7 @@ def test_locking_and_publishing(self) -> None:
         with self.subTest("Check environment export"):
             export_path = self.working_path / "_export🦎"
             export_result = build_env.export_environments(export_path)
-            self.check_environment_exports(export_result)
+            self.check_environment_exports(export_path, export_result)
             subtests_passed += 1
         # Test stage: ensure published archives and manifests have the expected name
         #             and that unpacking them allows launch module execution
diff --git a/tests/test_sample_project.py b/tests/test_sample_project.py
index ff4487d..9c56640 100644
--- a/tests/test_sample_project.py
+++ b/tests/test_sample_project.py
@@ -322,14 +322,16 @@ def check_deployed_environments(
             )
             self.assertEqual(launch_result.stderr, "")
 
-    def check_environment_exports(self, export_paths: ExportedEnvironmentPaths) -> None:
+    def check_environment_exports(
+        self, export_path: Path, export_paths: ExportedEnvironmentPaths
+    ) -> None:
         metadata_path, snippet_paths, env_paths = export_paths
         exported_manifests = ManifestData(metadata_path, snippet_paths)
         deployed_name_to_path: dict[str, Path] = {}
         for env_metadata, env_path in zip(exported_manifests.snippet_data, env_paths):
             self.assertTrue(env_path.exists())
             deployed_name = EnvNameDeploy(env_metadata["install_target"])
-            self.assertEqual(env_path.name, deployed_name)
+            self.assertEqual(env_path, export_path / deployed_name)
             deployed_name_to_path[deployed_name] = env_path
         layered_metadata = exported_manifests.combined_data["layers"]
 
@@ -450,7 +452,7 @@ def test_build_is_reproducible(self) -> None:
         with self.subTest("Check environment export"):
             export_path = self.working_path / "_export🦎"
             export_result = build_env.export_environments(export_path)
-            self.check_environment_exports(export_result)
+            self.check_environment_exports(export_path, export_result)
             subtests_passed += 1
 
         # Work aroung pytest-subtests not failing the test case when subtests fail

From 88518101070d0e53e5a86951f6d78cabc3d782c1 Mon Sep 17 00:00:00 2001
From: Alyssa Coghlan <ncoghlan@gmail.com>
Date: Thu, 7 Nov 2024 22:16:14 +1000
Subject: [PATCH 06/12] Remove now obsolete API additions

---
 src/venvstacks/stacks.py | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/src/venvstacks/stacks.py b/src/venvstacks/stacks.py
index 0a4124a..e8a0ee2 100755
--- a/src/venvstacks/stacks.py
+++ b/src/venvstacks/stacks.py
@@ -647,7 +647,6 @@ def create_archive(
         self,
         env_path: Path,
         previous_metadata: ArchiveMetadata | None = None,
-        sitecustomize_source_path: Path | None = None,
         work_path: Path | None = None,
     ) -> tuple[ArchiveMetadata, Path]:
         if env_path.name != self.env_name:
@@ -672,7 +671,6 @@ def create_archive(
             pack_venv.create_archive(
                 env_path,
                 archive_base_path,
-                sitecustomize_source_path,
                 clamp_mtime=last_locked,
                 work_dir=work_path,
                 install_target=build_metadata["install_target"],
@@ -788,7 +786,6 @@ def export_environment(
         self,
         env_path: Path,
         previous_metadata: ExportMetadata | None = None,
-        sitecustomize_source_path: Path | None = None,
     ) -> tuple[ExportMetadata, Path]:
         if env_path.name != self.env_name:
             err_msg = (
@@ -813,7 +810,6 @@ def _run_postinstall(_export_path: Path, postinstall_path: Path) -> None:
         exported_path = pack_venv.export_venv(
             env_path,
             export_path,
-            sitecustomize_source_path,
             _run_postinstall,
         )
         assert self.export_path == exported_path  # pack_venv ensures this is true
@@ -982,7 +978,6 @@ class _PythonEnvironment(ABC):
     base_python_path: Path | None = field(init=False, repr=False)
     tools_python_path: Path | None = field(init=False, repr=False)
     py_version: str = field(init=False, repr=False)
-    sitecustomize_source_path: Path | None = field(default=None, init=False, repr=False)
 
     # Operation flags allow for requested commands to be applied only to selected layers
     # Notes:
@@ -1387,7 +1382,7 @@ def create_archive(
         )
         work_path = self.build_path  # /tmp is likely too small for ML environments
         return build_request.create_archive(
-            env_path, previous_metadata, self.sitecustomize_source_path, work_path
+            env_path, previous_metadata, work_path
         )
 
     def request_export(
@@ -1415,7 +1410,7 @@ def export_environment(
         # Define the input metadata that gets published in the export manifest
         export_request = self.request_export(output_path, previous_metadata, force)
         return export_request.export_environment(
-            env_path, previous_metadata, self.sitecustomize_source_path
+            env_path, previous_metadata,
         )
 
 
@@ -1632,7 +1627,6 @@ def env_spec(self) -> ApplicationSpec:
 
     def __post_init__(self) -> None:
         super().__post_init__()
-        self.sitecustomize_source_path = self.pylib_path / "_deployed_sitecustomize.py"
         self.launch_module_name = self.env_spec.launch_module_path.stem
         self.linked_frameworks = []
 

From 2e474c8413ac5f5e4296f24f66899c06b6bc355a Mon Sep 17 00:00:00 2001
From: Alyssa Coghlan <ncoghlan@gmail.com>
Date: Fri, 8 Nov 2024 13:17:13 +1000
Subject: [PATCH 07/12] Tidy up env base Python config

---
 src/venvstacks/stacks.py | 39 +++++++++++++++++++--------------------
 1 file changed, 19 insertions(+), 20 deletions(-)

diff --git a/src/venvstacks/stacks.py b/src/venvstacks/stacks.py
index e8a0ee2..f83ce2a 100755
--- a/src/venvstacks/stacks.py
+++ b/src/venvstacks/stacks.py
@@ -956,6 +956,10 @@ def get_build_platform() -> TargetPlatform:
 
 @dataclass
 class _PythonEnvironment(ABC):
+
+    # Python environment used to run tools like `uv` and `pip`
+    tools_python_path: ClassVar[Path] = Path(sys.executable)
+
     # Specified in concrete subclasses
     kind: ClassVar[LayerVariants]
     category: ClassVar[LayerCategories]
@@ -974,11 +978,12 @@ class _PythonEnvironment(ABC):
     python_path: Path = field(init=False, repr=False)
     env_lock: EnvironmentLock = field(init=False)
 
-    # Set in subclass or externally after creation
-    base_python_path: Path | None = field(init=False, repr=False)
-    tools_python_path: Path | None = field(init=False, repr=False)
+    # Derived from layer spec in subclass __post_init__
     py_version: str = field(init=False, repr=False)
 
+    # Set in subclass __post_init__, or when build environments are created
+    base_python_path: Path | None = field(init=False, repr=False)
+
     # Operation flags allow for requested commands to be applied only to selected layers
     # Notes:
     #   - the "build if needed" (want_build=None) option is fairly ineffective, since
@@ -1017,6 +1022,9 @@ def get_deployed_path(self, build_path: Path) -> Path:
         return env_deployed_path / relative_path
 
     def __post_init__(self) -> None:
+        # Concrete subclasses must set the version before finishing the base initialisation
+        # Assert its existence here to make failures to do so easier to diagnose
+        assert self.py_version is not None, "Subclass failed to set 'py_version'"
         self.env_path = self.build_path / self.env_name
         self.pylib_path = self._get_py_scheme_path("purelib")
         self.executables_path = self._get_py_scheme_path("scripts")
@@ -1089,9 +1097,8 @@ def from_external_path(target_build_path: Path) -> str:
         if link_external_base:
             base_python = from_external_path(base_python_path)
         else:
-            # "base_python" in the runtime layer refers solely to
-            # the external environment used to set up the base
-            # runtime layer, rather than being a linked environment
+            # "base_python" in a runtime layer refers to the layer itself
+            assert layer_python == from_internal_path(base_python_path)
             base_python = layer_python
 
         return postinstall.LayerConfig(
@@ -1427,20 +1434,11 @@ def _get_python_dir_path(self) -> Path:
         return super()._get_python_dir_path()
 
     def __post_init__(self) -> None:
-        self.py_version = py_version = self.env_spec.py_version
+        # Ensure Python version is set before finishing base class initialisation
+        self.py_version = self.env_spec.py_version
         super().__post_init__()
-        tools_env_path = self.build_path / "build-tools"
-        if tools_env_path.exists():
-            tools_bin_path = Path(
-                _get_py_scheme_path("scripts", tools_env_path, py_version)
-            )
-            tools_python_path = tools_bin_path / _binary_with_extension("python")
-        else:
-            # No build tools environment created by wrapper script, so use the running Python
-            tools_python_path = Path(sys.executable)
-        # Runtimes have no base Python other than the build tools Python
-        self.base_python_path = tools_python_path
-        self.tools_python_path = tools_python_path
+        # Runtimes are their own base Python
+        self.base_python_path = self.python_path
 
     @property
     def env_spec(self) -> RuntimeSpec:
@@ -1495,8 +1493,10 @@ class _VirtualEnvironment(_PythonEnvironment):
     linked_constraints_paths: list[Path] = field(init=False, repr=False)
 
     def __post_init__(self) -> None:
+        # Ensure Python version is set before finishing base class initialisation
         self.py_version = self.env_spec.runtime.py_version
         super().__post_init__()
+        # Base runtime env will be linked when creating the build environments
         self.base_runtime = None
         self.linked_constraints_paths = []
 
@@ -1517,7 +1517,6 @@ def link_base_runtime(self, runtime: RuntimeEnv) -> None:
         self.base_runtime = runtime
         # Link executable paths
         self.base_python_path = runtime.python_path
-        self.tools_python_path = runtime.tools_python_path
         # Link runtime layer dependency constraints
         if self.linked_constraints_paths:
             self._fail_build("Layered environment base runtime already linked")

From 2d6d69bc6ead7363f518dccfd995f7734a6cce41 Mon Sep 17 00:00:00 2001
From: Alyssa Coghlan <ncoghlan@gmail.com>
Date: Fri, 8 Nov 2024 13:52:36 +1000
Subject: [PATCH 08/12] Adjust for post-install changes

---
 src/venvstacks/stacks.py      | 93 ++++++++++++++++++-----------------
 tests/support.py              | 13 ++++-
 tests/test_minimal_project.py |  2 +-
 tests/test_sample_project.py  |  2 +-
 4 files changed, 60 insertions(+), 50 deletions(-)

diff --git a/src/venvstacks/stacks.py b/src/venvstacks/stacks.py
index f83ce2a..17b5b8f 100755
--- a/src/venvstacks/stacks.py
+++ b/src/venvstacks/stacks.py
@@ -956,7 +956,6 @@ def get_build_platform() -> TargetPlatform:
 
 @dataclass
 class _PythonEnvironment(ABC):
-
     # Python environment used to run tools like `uv` and `pip`
     tools_python_path: ClassVar[Path] = Path(sys.executable)
 
@@ -1016,10 +1015,11 @@ def env_name(self) -> EnvNameBuild:
     def install_target(self) -> EnvNameDeploy:
         return self.env_lock.get_deployed_name(self.env_spec.env_name)
 
-    def get_deployed_path(self, build_path: Path) -> Path:
+    def get_deployed_path(self, build_path: Path) -> str:
+        """Get relative deployment location for a build env path"""
         env_deployed_path = Path(self.install_target)
         relative_path = build_path.relative_to(self.env_path)
-        return env_deployed_path / relative_path
+        return str(env_deployed_path / relative_path)
 
     def __post_init__(self) -> None:
         # Concrete subclasses must set the version before finishing the base initialisation
@@ -1055,8 +1055,8 @@ def get_deployed_config(self) -> postinstall.LayerConfig:
 
     def _get_deployed_config(
         self,
-        pylib_paths: Iterable[Path],
-        dynlib_paths: Iterable[Path],
+        pylib_dirs: Iterable[str],
+        dynlib_dirs: Iterable[str],
         link_external_base: bool = True,
     ) -> postinstall.LayerConfig:
         # Helper for subclass get_deployed_config implementations
@@ -1067,18 +1067,13 @@ def _get_deployed_config(
         build_env_name = build_env_path.name
         build_path = build_env_path.parent
 
-        def from_internal_path(target_build_path: Path) -> str:
-            # Input path is an absolute path inside the environment
-            # Output path is relative to the base of the environment
-            return str(target_build_path.relative_to(build_env_path))
-
-        def from_relative_path(relative_build_path: Path) -> str:
+        def relative_to_env(relative_build_path: Path) -> str:
             # Input path is relative to the base of the build directory
             # Output path is relative to the base of the environment
             # Note: we avoid `walk_up=True` here, firstly to maintain
             #       Python 3.11 compatibility, but also to limit the
             #       the relative paths to *peer* environments, rather
-            #       than all potentially value relative path calculations
+            #       than all potentially valid relative path calculations
             if relative_build_path.is_absolute():
                 self._fail_build(f"{relative_build_path} is not a relative path")
             if relative_build_path.parts[0] == build_env_name:
@@ -1087,11 +1082,16 @@ def from_relative_path(relative_build_path: Path) -> str:
             # Emit relative reference to peer environment
             return str(Path("..", *relative_build_path.parts))
 
+        def from_internal_path(target_build_path: Path) -> str:
+            # Input path is an absolute path inside the environment
+            # Output path is relative to the base of the environment
+            return str(target_build_path.relative_to(build_env_path))
+
         def from_external_path(target_build_path: Path) -> str:
             # Input path is an absolute path, potentially from a peer environment
             # Output path is relative to the base of the environment
             relative_build_path = target_build_path.relative_to(build_path)
-            return from_relative_path(relative_build_path)
+            return relative_to_env(relative_build_path)
 
         layer_python = from_internal_path(self.python_path)
         if link_external_base:
@@ -1106,8 +1106,8 @@ def from_external_path(target_build_path: Path) -> str:
             py_version=self.py_version,
             base_python=base_python,
             site_dir=from_internal_path(self.pylib_path),
-            pylib_dirs=[from_relative_path(p) for p in pylib_paths],
-            dynlib_dirs=[from_relative_path(p) for p in dynlib_paths],
+            pylib_dirs=[relative_to_env(Path(d)) for d in pylib_dirs],
+            dynlib_dirs=[relative_to_env(Path(d)) for d in dynlib_dirs],
         )
 
     def _write_deployed_config(self) -> None:
@@ -1388,9 +1388,7 @@ def create_archive(
             output_path, target_platform, tag_output, previous_metadata, force
         )
         work_path = self.build_path  # /tmp is likely too small for ML environments
-        return build_request.create_archive(
-            env_path, previous_metadata, work_path
-        )
+        return build_request.create_archive(env_path, previous_metadata, work_path)
 
     def request_export(
         self,
@@ -1417,7 +1415,8 @@ def export_environment(
         # Define the input metadata that gets published in the export manifest
         export_request = self.request_export(output_path, previous_metadata, force)
         return export_request.export_environment(
-            env_path, previous_metadata,
+            env_path,
+            previous_metadata,
         )
 
 
@@ -1506,7 +1505,31 @@ def env_spec(self) -> _VirtualEnvironmentSpec:
         assert isinstance(self._env_spec, _VirtualEnvironmentSpec)
         return self._env_spec
 
-    # TODO: define interfaces for get_linked_pylib_paths and get_linked_dynlib_paths
+    def _linked_environments(self) -> Iterator[_PythonEnvironment]:
+        runtime_env = self.base_runtime
+        # This is only ever invoked *after* the environment has been linked
+        assert runtime_env is not None
+        yield runtime_env
+
+    def _iter_build_pylib_dirs(self) -> Iterator[str]:
+        for env in self._linked_environments():
+            yield str(env.pylib_path.relative_to(self.build_path))
+
+    def _iter_build_dynlib_dirs(self) -> Iterator[str]:
+        for env in self._linked_environments():
+            dynlib_path = env.dynlib_path
+            if dynlib_path is not None:
+                yield str(dynlib_path.relative_to(self.build_path))
+
+    def _iter_deployed_pylib_dirs(self) -> Iterator[str]:
+        for env in self._linked_environments():
+            yield env.get_deployed_path(env.pylib_path)
+
+    def _iter_deployed_dynlib_dirs(self) -> Iterator[str]:
+        for env in self._linked_environments():
+            dynlib_path = env.dynlib_path
+            if dynlib_path is not None:
+                yield env.get_deployed_path(dynlib_path)
 
     def link_base_runtime(self, runtime: RuntimeEnv) -> None:
         if self.base_runtime is not None:
@@ -1526,7 +1549,7 @@ def link_base_runtime(self, runtime: RuntimeEnv) -> None:
     def get_deployed_config(self) -> postinstall.LayerConfig:
         """Layer config to be published in `venvstacks_layer.json`"""
         return self._get_deployed_config(
-            self.get_linked_pylib_paths(), self.get_linked_dynlib_paths()
+            self._iter_deployed_pylib_dirs(), self._iter_deployed_dynlib_dirs()
         )
 
     def get_constraint_paths(self) -> list[Path]:
@@ -1561,8 +1584,8 @@ def _ensure_virtual_environment(self) -> subprocess.CompletedProcess[str]:
     def _link_build_environment(self) -> None:
         # Create sitecustomize file for the build environment
         build_path = self.build_path
-        build_pylib_paths = [build_path / p for p in self.get_linked_pylib_paths()]
-        build_dynlib_paths = [build_path / p for p in self.get_linked_dynlib_paths()]
+        build_pylib_paths = [build_path / p for p in self._iter_build_pylib_dirs()]
+        build_dynlib_paths = [build_path / p for p in self._iter_build_dynlib_dirs()]
         sc_contents = postinstall.generate_sitecustomize(
             build_pylib_paths, build_dynlib_paths
         )
@@ -1632,29 +1655,7 @@ def __post_init__(self) -> None:
     def _linked_environments(self) -> Iterator[_PythonEnvironment]:
         for fw_env in self.linked_frameworks:
             yield fw_env
-        runtime_env = self.base_runtime
-        assert runtime_env is not None
-        yield runtime_env
-
-    def _linked_pylib_build_paths(self) -> Iterator[Path]:
-        for env in self._linked_environments():
-            yield env.pylib_path
-
-    def _linked_dynlib_build_paths(self) -> Iterator[Path]:
-        for env in self._linked_environments():
-            dynlib_path = env.dynlib_path
-            if dynlib_path is not None:
-                yield dynlib_path
-
-    def _linked_pylib_deployed_paths(self) -> Iterator[Path]:
-        for env in self._linked_environments():
-            yield env.get_deployed_path(env.pylib_path)
-
-    def _linked_dynlib_deployed_paths(self) -> Iterator[Path]:
-        for env in self._linked_environments():
-            dynlib_path = env.dynlib_path
-            if dynlib_path is not None:
-                yield env.get_deployed_path(dynlib_path)
+        yield from super()._linked_environments()
 
     def link_layered_environments(
         self, runtime: RuntimeEnv, frameworks: Mapping[LayerBaseName, FrameworkEnv]
diff --git a/tests/support.py b/tests/support.py
index 8b790f6..d26fc25 100644
--- a/tests/support.py
+++ b/tests/support.py
@@ -243,6 +243,12 @@ class DeploymentTestCase(unittest.TestCase):
     def assertPathExists(self, expected_path: Path) -> None:
         self.assertTrue(expected_path.exists(), f"No such path: {str(expected_path)}")
 
+    def assertPathContains(self, containing_path: Path, contained_path: Path) -> None:
+        self.assertTrue(
+            contained_path.is_relative_to(containing_path),
+            f"{str(containing_path)!r} is not a parent folder of {str(contained_path)!r}",
+        )
+
     def assertSysPathEntry(self, expected: str, env_sys_path: Sequence[str]) -> None:
         self.assertTrue(
             any(expected in path_entry for path_entry in env_sys_path),
@@ -364,13 +370,16 @@ def check_deployed_environments(
             # Nothing at all should be emitted on stderr
             self.assertEqual(launch_result.stderr, "")
 
-    def check_environment_exports(self, export_paths: ExportedEnvironmentPaths) -> None:
+    def check_environment_exports(
+        self, export_path: Path, export_paths: ExportedEnvironmentPaths
+    ) -> None:
         metadata_path, snippet_paths, env_paths = export_paths
         exported_manifests = ManifestData(metadata_path, snippet_paths)
         env_name_to_path: dict[str, Path] = {}
         for env_metadata, env_path in zip(exported_manifests.snippet_data, env_paths):
             # TODO: Check more details regarding expected metadata contents
-            self.assertTrue(env_path.exists())
+            self.assertPathExists(env_path)
+            self.assertPathContains(export_path, env_path)
             env_name = EnvNameDeploy(env_metadata["install_target"])
             self.assertEqual(env_path.name, env_name)
             env_name_to_path[env_name] = env_path
diff --git a/tests/test_minimal_project.py b/tests/test_minimal_project.py
index 30932e1..7bd2160 100644
--- a/tests/test_minimal_project.py
+++ b/tests/test_minimal_project.py
@@ -489,7 +489,7 @@ def get_deployed_env_details(
 
     def test_create_environments(self) -> None:
         # Fast test to check the links between build envs are set up correctly
-        # (if this fails, there's no point even trying to full slow test case)
+        # (if this fails, there's no point even trying the full slow test case)
         build_env = self.build_env
         build_env.create_environments()
         self.check_build_environments(self.build_env.all_environments())
diff --git a/tests/test_sample_project.py b/tests/test_sample_project.py
index 4755b2e..1e3b184 100644
--- a/tests/test_sample_project.py
+++ b/tests/test_sample_project.py
@@ -267,7 +267,7 @@ def setUp(self) -> None:
 
     def test_create_environments(self) -> None:
         # Fast test to check the links between build envs are set up correctly
-        # (if this fails, there's no point even trying to full slow test case)
+        # (if this fails, there's no point even trying the full slow test case)
         build_env = self.build_env
         build_env.create_environments()
         self.check_build_environments(self.build_env.all_environments())

From 594bf97f3fb9960e4d3323b30e057279ddf4b828 Mon Sep 17 00:00:00 2001
From: Alyssa Coghlan <ncoghlan@gmail.com>
Date: Fri, 8 Nov 2024 13:58:19 +1000
Subject: [PATCH 09/12] Minor cleanup tweaks

---
 src/venvstacks/stacks.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/venvstacks/stacks.py b/src/venvstacks/stacks.py
index 17b5b8f..82a68fe 100755
--- a/src/venvstacks/stacks.py
+++ b/src/venvstacks/stacks.py
@@ -1584,8 +1584,8 @@ def _ensure_virtual_environment(self) -> subprocess.CompletedProcess[str]:
     def _link_build_environment(self) -> None:
         # Create sitecustomize file for the build environment
         build_path = self.build_path
-        build_pylib_paths = [build_path / p for p in self._iter_build_pylib_dirs()]
-        build_dynlib_paths = [build_path / p for p in self._iter_build_dynlib_dirs()]
+        build_pylib_paths = [build_path / d for d in self._iter_build_pylib_dirs()]
+        build_dynlib_paths = [build_path / d for d in self._iter_build_dynlib_dirs()]
         sc_contents = postinstall.generate_sitecustomize(
             build_pylib_paths, build_dynlib_paths
         )
@@ -1653,6 +1653,7 @@ def __post_init__(self) -> None:
         self.linked_frameworks = []
 
     def _linked_environments(self) -> Iterator[_PythonEnvironment]:
+        # Linked frameworks are emitted before the base runtime layer
         for fw_env in self.linked_frameworks:
             yield fw_env
         yield from super()._linked_environments()

From 152524ad1f810cb84b06da1df824889a1fab92f9 Mon Sep 17 00:00:00 2001
From: Alyssa Coghlan <ncoghlan@gmail.com>
Date: Fri, 8 Nov 2024 14:05:49 +1000
Subject: [PATCH 10/12] Trigger output updates when draft PRs are marked as
 ready

---
 .github/workflows/update-expected-output.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/update-expected-output.yml b/.github/workflows/update-expected-output.yml
index b3b2672..71bef16 100644
--- a/.github/workflows/update-expected-output.yml
+++ b/.github/workflows/update-expected-output.yml
@@ -2,9 +2,10 @@ name: Update expected output
 
 on:
   pull_request:
-    # Don't update PRs on every push. PRs can be closed and
-    # reopened if the update action should be run again.
-    types: [opened, reopened]
+    # Don't update PRs on every push. PRs can be switched
+    # to draft status and back (or closed and reopened),
+    # if the update action should be run again.
+    types: [opened, reopened, ready_for_review]
     branches:
       - "**"
     paths:

From e4b61278e384c46caf3a1517fe95185cf1459237 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 8 Nov 2024 15:21:12 +1000
Subject: [PATCH 11/12] Update expected output (2024-11-08 04:06:31+00:00)
 (#76)

Update expected test output files from automated/expected-output/20241108-040631-152524a (source PR: #64)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 .../env_metadata/app-scipy-client.json        |  6 ++---
 .../env_metadata/app-scipy-import.json        |  8 +++----
 .../env_metadata/framework-scipy.json         |  8 +++----
 .../linux_x86_64/venvstacks.json              | 22 ++++++++---------
 .../env_metadata/app-scipy-client.json        |  6 ++---
 .../env_metadata/app-scipy-import.json        |  8 +++----
 .../env_metadata/framework-scipy.json         |  8 +++----
 .../macosx_arm64/venvstacks.json              | 22 ++++++++---------
 .../env_metadata/app-scipy-client.json        |  6 ++---
 .../env_metadata/app-scipy-import.json        | 10 ++++----
 .../env_metadata/framework-scipy.json         |  8 +++----
 .../win_amd64/venvstacks.json                 | 24 +++++++++----------
 12 files changed, 68 insertions(+), 68 deletions(-)

diff --git a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json
index 8a70e77..351ad8f 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "bb594ea66705fe5a122e930e2c48f1aaf6f720d568e37e0b590db95fb7261dea"
+    "sha256": "d932e554c35c9ce2cd1d594cb20e8a37c0195a5b82ffcb50627a96fc122e79a2"
   },
   "archive_name": "app-scipy-client.tar.xz",
-  "archive_size": 3004,
+  "archive_size": 3008,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:43.205589+00:00",
   "required_layers": [
-    "framework-scipy",
+    "framework-scipy@1",
     "framework-http-client"
   ],
   "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
diff --git a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json
index 64b962f..91213b7 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "8d69cfe0f408ba396dde664cd58c18b4541e6937f470e6e4f06a03d6ec069e46"
+    "sha256": "ec5be5ebc608e24bf32642cf0e071ce975f4650dac69c233c36124e53f4c10f9"
   },
-  "archive_name": "app-scipy-import.tar.xz",
+  "archive_name": "app-scipy-import@1.tar.xz",
   "archive_size": 2912,
-  "install_target": "app-scipy-import",
+  "install_target": "app-scipy-import@1",
   "layer_name": "app-scipy-import",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:43.173589+00:00",
   "required_layers": [
-    "framework-scipy"
+    "framework-scipy@1"
   ],
   "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
   "runtime_name": "cpython@3.11",
diff --git a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json
index ae73caf..91978f2 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json
@@ -1,11 +1,11 @@
 {
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "e8ef68225cfa6a016539a4db3c5dc1b984f53de0df51181eefeb0e9449771ea9"
+    "sha256": "622e3056ccf54d8723bf983c92f35bf4138d2fee5da3cdd56d25391f18906aab"
   },
-  "archive_name": "framework-scipy.tar.xz",
-  "archive_size": 23957800,
-  "install_target": "framework-scipy",
+  "archive_name": "framework-scipy@1.tar.xz",
+  "archive_size": 23961760,
+  "install_target": "framework-scipy@1",
   "layer_name": "framework-scipy",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:42.825586+00:00",
diff --git a/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json b/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json
index c9818e3..973d2e5 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json
@@ -6,16 +6,16 @@
         "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "8d69cfe0f408ba396dde664cd58c18b4541e6937f470e6e4f06a03d6ec069e46"
+          "sha256": "ec5be5ebc608e24bf32642cf0e071ce975f4650dac69c233c36124e53f4c10f9"
         },
-        "archive_name": "app-scipy-import.tar.xz",
+        "archive_name": "app-scipy-import@1.tar.xz",
         "archive_size": 2912,
-        "install_target": "app-scipy-import",
+        "install_target": "app-scipy-import@1",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:43.173589+00:00",
         "required_layers": [
-          "framework-scipy"
+          "framework-scipy@1"
         ],
         "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
         "runtime_name": "cpython@3.11",
@@ -26,16 +26,16 @@
         "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "bb594ea66705fe5a122e930e2c48f1aaf6f720d568e37e0b590db95fb7261dea"
+          "sha256": "d932e554c35c9ce2cd1d594cb20e8a37c0195a5b82ffcb50627a96fc122e79a2"
         },
         "archive_name": "app-scipy-client.tar.xz",
-        "archive_size": 3004,
+        "archive_size": 3008,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:43.205589+00:00",
         "required_layers": [
-          "framework-scipy",
+          "framework-scipy@1",
           "framework-http-client"
         ],
         "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
@@ -67,11 +67,11 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "e8ef68225cfa6a016539a4db3c5dc1b984f53de0df51181eefeb0e9449771ea9"
+          "sha256": "622e3056ccf54d8723bf983c92f35bf4138d2fee5da3cdd56d25391f18906aab"
         },
-        "archive_name": "framework-scipy.tar.xz",
-        "archive_size": 23957800,
-        "install_target": "framework-scipy",
+        "archive_name": "framework-scipy@1.tar.xz",
+        "archive_size": 23961760,
+        "install_target": "framework-scipy@1",
         "layer_name": "framework-scipy",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:42.825586+00:00",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json
index 2282818..290b09b 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "bf065fe724e53e03886117ff0a7d61e29910da9c46b4a14799581cfc1238c77f"
+    "sha256": "f0338c45382c53320d30dc99e4370075de52593adb46a969f0692e772dcfb3ca"
   },
   "archive_name": "app-scipy-client.tar.xz",
-  "archive_size": 2980,
+  "archive_size": 2984,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:33.147967+00:00",
   "required_layers": [
-    "framework-scipy",
+    "framework-scipy@1",
     "framework-http-client"
   ],
   "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json
index 40a1486..cd4588b 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "3ab7e8458a233e96790809ad0437209bcbf1823d7883220a44554b1c3fd51afa"
+    "sha256": "3ef2198496159dca41b2fa5cdea6ec0afb40b6060f95f23dc3da02e99e2d435f"
   },
-  "archive_name": "app-scipy-import.tar.xz",
+  "archive_name": "app-scipy-import@1.tar.xz",
   "archive_size": 2896,
-  "install_target": "app-scipy-import",
+  "install_target": "app-scipy-import@1",
   "layer_name": "app-scipy-import",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:33.121208+00:00",
   "required_layers": [
-    "framework-scipy"
+    "framework-scipy@1"
   ],
   "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
   "runtime_name": "cpython@3.11",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json
index 996c5bd..0735cfd 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json
@@ -1,11 +1,11 @@
 {
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "6872599275f0b5448926033968ba5f3467b07bf09ac19af8538975a39bf7b712"
+    "sha256": "32f6135ea3b938e47c8897b0da7a51c6992397edbefe2b27358665b1c83d29aa"
   },
-  "archive_name": "framework-scipy.tar.xz",
-  "archive_size": 15078848,
-  "install_target": "framework-scipy",
+  "archive_name": "framework-scipy@1.tar.xz",
+  "archive_size": 15076180,
+  "install_target": "framework-scipy@1",
   "layer_name": "framework-scipy",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:32.960668+00:00",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json b/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json
index 1006d12..08d663a 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json
@@ -6,16 +6,16 @@
         "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "3ab7e8458a233e96790809ad0437209bcbf1823d7883220a44554b1c3fd51afa"
+          "sha256": "3ef2198496159dca41b2fa5cdea6ec0afb40b6060f95f23dc3da02e99e2d435f"
         },
-        "archive_name": "app-scipy-import.tar.xz",
+        "archive_name": "app-scipy-import@1.tar.xz",
         "archive_size": 2896,
-        "install_target": "app-scipy-import",
+        "install_target": "app-scipy-import@1",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:33.121208+00:00",
         "required_layers": [
-          "framework-scipy"
+          "framework-scipy@1"
         ],
         "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
         "runtime_name": "cpython@3.11",
@@ -26,16 +26,16 @@
         "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "bf065fe724e53e03886117ff0a7d61e29910da9c46b4a14799581cfc1238c77f"
+          "sha256": "f0338c45382c53320d30dc99e4370075de52593adb46a969f0692e772dcfb3ca"
         },
         "archive_name": "app-scipy-client.tar.xz",
-        "archive_size": 2980,
+        "archive_size": 2984,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:33.147967+00:00",
         "required_layers": [
-          "framework-scipy",
+          "framework-scipy@1",
           "framework-http-client"
         ],
         "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
@@ -47,11 +47,11 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "6872599275f0b5448926033968ba5f3467b07bf09ac19af8538975a39bf7b712"
+          "sha256": "32f6135ea3b938e47c8897b0da7a51c6992397edbefe2b27358665b1c83d29aa"
         },
-        "archive_name": "framework-scipy.tar.xz",
-        "archive_size": 15078848,
-        "install_target": "framework-scipy",
+        "archive_name": "framework-scipy@1.tar.xz",
+        "archive_size": 15076180,
+        "install_target": "framework-scipy@1",
         "layer_name": "framework-scipy",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:32.960668+00:00",
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json
index 0c350fb..4bf772b 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "9f3de2bf483797a9a93629feca94756de57d82e62b157a4836b96fa14a289180"
+    "sha256": "ca15fb796933f031340de069d53f6d3a821e481b1372eb4ff001368ac92a214c"
   },
   "archive_name": "app-scipy-client.zip",
-  "archive_size": 257112,
+  "archive_size": 257117,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:24:36.468633+00:00",
   "required_layers": [
-    "framework-scipy",
+    "framework-scipy@1",
     "framework-http-client"
   ],
   "requirements_hash": "sha256:3bff0428616a2f1724732e78e7788e753dd5f1aa10aa5d3b87707b8dbde121de",
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json
index f679796..b68d0a2 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "3f4e2a19a1611db1139f9e68a268a963dd30139690ee6d8325896265007bf823"
+    "sha256": "9eae1f6e63422d58ccef53ae199ac55884c50f19e1faf5ecd98c2dfc651ce723"
   },
-  "archive_name": "app-scipy-import.zip",
-  "archive_size": 256621,
-  "install_target": "app-scipy-import",
+  "archive_name": "app-scipy-import@1.zip",
+  "archive_size": 256677,
+  "install_target": "app-scipy-import@1",
   "layer_name": "app-scipy-import",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:24:36.386938+00:00",
   "required_layers": [
-    "framework-scipy"
+    "framework-scipy@1"
   ],
   "requirements_hash": "sha256:9aba38b5efe287f35d58825dce6b1c47ed556b930056e6edc00ca9e1a165796b",
   "runtime_name": "cpython@3.11.10",
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json
index 34fa1a6..827d795 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json
@@ -1,11 +1,11 @@
 {
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "71146182f2bcf36ed9af674ac146ee32228e8d0a2890fb9c51ebd87e7fe58b45"
+    "sha256": "ac2c6a48192ac3657c5cbec001aeddf48ddd45881ac86a0cfa9eb5b839d2e3d4"
   },
-  "archive_name": "framework-scipy.zip",
-  "archive_size": 45080726,
-  "install_target": "framework-scipy",
+  "archive_name": "framework-scipy@1.zip",
+  "archive_size": 45087226,
+  "install_target": "framework-scipy@1",
   "layer_name": "framework-scipy",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:24:35.999197+00:00",
diff --git a/tests/sample_project/expected_manifests/win_amd64/venvstacks.json b/tests/sample_project/expected_manifests/win_amd64/venvstacks.json
index b21d903..73a7469 100644
--- a/tests/sample_project/expected_manifests/win_amd64/venvstacks.json
+++ b/tests/sample_project/expected_manifests/win_amd64/venvstacks.json
@@ -6,16 +6,16 @@
         "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "3f4e2a19a1611db1139f9e68a268a963dd30139690ee6d8325896265007bf823"
+          "sha256": "9eae1f6e63422d58ccef53ae199ac55884c50f19e1faf5ecd98c2dfc651ce723"
         },
-        "archive_name": "app-scipy-import.zip",
-        "archive_size": 256621,
-        "install_target": "app-scipy-import",
+        "archive_name": "app-scipy-import@1.zip",
+        "archive_size": 256677,
+        "install_target": "app-scipy-import@1",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:24:36.386938+00:00",
         "required_layers": [
-          "framework-scipy"
+          "framework-scipy@1"
         ],
         "requirements_hash": "sha256:9aba38b5efe287f35d58825dce6b1c47ed556b930056e6edc00ca9e1a165796b",
         "runtime_name": "cpython@3.11.10",
@@ -26,16 +26,16 @@
         "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "9f3de2bf483797a9a93629feca94756de57d82e62b157a4836b96fa14a289180"
+          "sha256": "ca15fb796933f031340de069d53f6d3a821e481b1372eb4ff001368ac92a214c"
         },
         "archive_name": "app-scipy-client.zip",
-        "archive_size": 257112,
+        "archive_size": 257117,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:24:36.468633+00:00",
         "required_layers": [
-          "framework-scipy",
+          "framework-scipy@1",
           "framework-http-client"
         ],
         "requirements_hash": "sha256:3bff0428616a2f1724732e78e7788e753dd5f1aa10aa5d3b87707b8dbde121de",
@@ -47,11 +47,11 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "71146182f2bcf36ed9af674ac146ee32228e8d0a2890fb9c51ebd87e7fe58b45"
+          "sha256": "ac2c6a48192ac3657c5cbec001aeddf48ddd45881ac86a0cfa9eb5b839d2e3d4"
         },
-        "archive_name": "framework-scipy.zip",
-        "archive_size": 45080726,
-        "install_target": "framework-scipy",
+        "archive_name": "framework-scipy@1.zip",
+        "archive_size": 45087226,
+        "install_target": "framework-scipy@1",
         "layer_name": "framework-scipy",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:24:35.999197+00:00",

From bc00964f3dc84a8c543ae723112a8ca6b00b8cee Mon Sep 17 00:00:00 2001
From: Alyssa Coghlan <ncoghlan@gmail.com>
Date: Fri, 8 Nov 2024 16:55:03 +1000
Subject: [PATCH 12/12] Docs fixes, add release note

---
 ...08_162952_ncoghlan_fix_automatic_layer_versioning.rst | 9 +++++++++
 docs/api/stacks/venvstacks.stacks.ApplicationEnv.rst     | 5 ++---
 docs/api/stacks/venvstacks.stacks.FrameworkEnv.rst       | 3 ++-
 3 files changed, 13 insertions(+), 4 deletions(-)
 create mode 100644 changelog.d/20241108_162952_ncoghlan_fix_automatic_layer_versioning.rst

diff --git a/changelog.d/20241108_162952_ncoghlan_fix_automatic_layer_versioning.rst b/changelog.d/20241108_162952_ncoghlan_fix_automatic_layer_versioning.rst
new file mode 100644
index 0000000..55d7fbf
--- /dev/null
+++ b/changelog.d/20241108_162952_ncoghlan_fix_automatic_layer_versioning.rst
@@ -0,0 +1,9 @@
+Added
+-----
+
+- Setting ``versioned = True`` in a layer definition will append a
+  lock version number to the layer name that automatically increments
+  each time the locked requirements change for that layer (``layer@1``,
+  ``layer@2``, etc). Layer dependency declarations and build environments,
+  use the unversioned name, but deployed environments and their metadata
+  will use the versioned name (implemented in :issue:`24`).
diff --git a/docs/api/stacks/venvstacks.stacks.ApplicationEnv.rst b/docs/api/stacks/venvstacks.stacks.ApplicationEnv.rst
index 8fa92f4..dca1c1e 100644
--- a/docs/api/stacks/venvstacks.stacks.ApplicationEnv.rst
+++ b/docs/api/stacks/venvstacks.stacks.ApplicationEnv.rst
@@ -15,7 +15,7 @@ venvstacks.stacks.ApplicationEnv
       ~ApplicationEnv.export_environment
       ~ApplicationEnv.get_constraint_paths
       ~ApplicationEnv.install_requirements
-      ~ApplicationEnv.link_base_runtime_paths
+      ~ApplicationEnv.link_base_runtime
       ~ApplicationEnv.link_layered_environments
       ~ApplicationEnv.lock_requirements
       ~ApplicationEnv.report_python_site_details
@@ -26,6 +26,7 @@ venvstacks.stacks.ApplicationEnv
 
    .. autosummary::
 
+      ~FrameworkEnv.base_runtime
       ~ApplicationEnv.category
       ~ApplicationEnv.env_name
       ~ApplicationEnv.env_spec
@@ -33,9 +34,7 @@ venvstacks.stacks.ApplicationEnv
       ~ApplicationEnv.kind
       ~ApplicationEnv.launch_module_name
       ~ApplicationEnv.linked_constraints_paths
-      ~ApplicationEnv.linked_dynlib_paths
       ~ApplicationEnv.linked_frameworks
-      ~ApplicationEnv.linked_pylib_paths
       ~ApplicationEnv.want_build
       ~ApplicationEnv.want_lock
       ~ApplicationEnv.want_publish
diff --git a/docs/api/stacks/venvstacks.stacks.FrameworkEnv.rst b/docs/api/stacks/venvstacks.stacks.FrameworkEnv.rst
index 14e21ee..d0aa889 100644
--- a/docs/api/stacks/venvstacks.stacks.FrameworkEnv.rst
+++ b/docs/api/stacks/venvstacks.stacks.FrameworkEnv.rst
@@ -16,7 +16,7 @@ venvstacks.stacks.FrameworkEnv
       ~FrameworkEnv.export_environment
       ~FrameworkEnv.get_constraint_paths
       ~FrameworkEnv.install_requirements
-      ~FrameworkEnv.link_base_runtime_paths
+      ~FrameworkEnv.link_base_runtime
       ~FrameworkEnv.lock_requirements
       ~FrameworkEnv.report_python_site_details
       ~FrameworkEnv.request_export
@@ -26,6 +26,7 @@ venvstacks.stacks.FrameworkEnv
 
    .. autosummary::
 
+      ~FrameworkEnv.base_runtime
       ~FrameworkEnv.category
       ~FrameworkEnv.env_name
       ~FrameworkEnv.env_spec