Prefix the entire setup.py chroot.

src/python/pants/BUILD

@@ -28,7 +28,7 @@ python_distribution(
     # used when creating the wheel, which is a good thing. We should be setting this ABI to ensure
     # consumers of pantsbuild.pants are using a compatible interpreter.
     # TODO(7344): the tuple syntax for ext_modules is deprecated. Use Extension once we support it.
-    ext_modules=[('native_engine', {'sources': ['src/pants/dummy.c']})],
+    ext_modules=[('native_engine', {'sources': ['pants/dummy.c']})],
   ).with_binaries(
     pants='src/python/pants/bin:pants',
   )

src/python/pants/backend/python/goals/setup_py.py

@@ -405,10 +405,6 @@ async def package_python_dist(
         return BuiltPackage(rel_chroot, (BuiltPackageArtifact(dirname),))
 
 
-# We write .py sources into the chroot under this dir.
-CHROOT_SOURCE_ROOT = "src"
-
-
 SETUP_BOILERPLATE = """
 # DO NOT EDIT THIS FILE -- AUTOGENERATED BY PANTS
 # Target: {target_address_spec}
@@ -433,22 +429,40 @@ async def run_setup_py(req: RunSetupPyRequest, setuptools: Setuptools) -> RunSet
             interpreter_constraints=req.interpreter_constraints,
         ),
     )
+
+    # We prefix the entire chroot, and run with this prefix as the cwd, so that we can capture any
+    # changes setup made within it (e.g., when running 'develop') without also capturing other
+    # artifacts of the pex process invocation.
+    chroot_prefix = "chroot"
+
     # The setuptools dist dir, created by it under the chroot (not to be confused with
     # pants's own dist dir, at the buildroot).
-    dist_dir = "dist/"
+    dist_dir = "dist"
+
+    prefixed_chroot = await Get(Digest, AddPrefix(req.chroot.digest, chroot_prefix))
+
+    # setup.py basically always expects to be run with the cwd as its own directory
+    # (e.g., paths in it are relative to that directory). This is true of the setup.py
+    # we generate and is overwhelmingly likely to be true for existing setup.py files,
+    # as there is no robust way to run them otherwise.
+    setup_script_reldir, setup_script_name = os.path.split(req.chroot.setup_script)
+    working_directory = os.path.join(chroot_prefix, setup_script_reldir)
+
     result = await Get(
         ProcessResult,
         VenvPexProcess(
             setuptools_pex,
-            argv=(req.chroot.setup_script, *req.args),
-            input_digest=req.chroot.digest,
+            argv=(setup_script_name, *req.args),
+            input_digest=prefixed_chroot,
+            working_directory=working_directory,
             # setuptools commands that create dists write them to the distdir.
             # TODO: Could there be other useful files to capture?
-            output_directories=(dist_dir,),
+            output_directories=(dist_dir,),  # Relative to the working_directory.
             description=f"Run setuptools for {req.exported_target.target.address}",
             level=LogLevel.DEBUG,
         ),
     )
+    # Note that output_digest paths are relative to the working_directory.
     output_digest = await Get(Digest, RemovePrefix(result.output_digest, dist_dir))
     return RunSetupPyResult(output_digest)
 
@@ -535,7 +549,6 @@ async def generate_chroot(request: SetupPyChrootRequest) -> SetupPyChroot:
     # specified `SetupKwargs(_allow_banned_keys=True)`.
     setup_kwargs.update(
         {
-            "package_dir": {"": CHROOT_SOURCE_ROOT, **setup_kwargs.get("package_dir", {})},
             "packages": (*sources.packages, *(setup_kwargs.get("packages", []))),
             "namespace_packages": (
                 *sources.namespace_packages,
@@ -595,13 +608,8 @@ async def generate_chroot(request: SetupPyChrootRequest) -> SetupPyChroot:
         FileContent("setup.py", setup_py_content),
         FileContent("MANIFEST.in", "include *.py".encode()),
     ]
-    extra_files_digest, src_digest = await MultiGet(
-        Get(Digest, CreateDigest(files_to_create)),
-        # Nest the sources under the src/ prefix.
-        Get(Digest, AddPrefix(sources.digest, CHROOT_SOURCE_ROOT)),
-    )
-
-    chroot_digest = await Get(Digest, MergeDigests((src_digest, extra_files_digest)))
+    extra_files_digest = await Get(Digest, CreateDigest(files_to_create))
+    chroot_digest = await Get(Digest, MergeDigests((sources.digest, extra_files_digest)))
     return SetupPyChroot(
         chroot_digest, "setup.py", FinalizedSetupKwargs(setup_kwargs, address=target.address)
     )

src/python/pants/backend/python/goals/setup_py_test.py

@@ -285,13 +285,13 @@ def test_generate_chroot(chroot_rule_runner: RuleRunner) -> None:
     assert_chroot(
         chroot_rule_runner,
         [
-            "src/files/README.txt",
-            "src/foo/qux/__init__.py",
-            "src/foo/qux/qux.py",
-            "src/foo/qux/qux.pyi",
-            "src/foo/resources/js/code.js",
-            "src/foo/__init__.py",
-            "src/foo/foo.py",
+            "files/README.txt",
+            "foo/qux/__init__.py",
+            "foo/qux/qux.py",
+            "foo/qux/qux.pyi",
+            "foo/resources/js/code.js",
+            "foo/__init__.py",
+            "foo/foo.py",
             "setup.py",
             "MANIFEST.in",
         ],
@@ -300,7 +300,6 @@ def test_generate_chroot(chroot_rule_runner: RuleRunner) -> None:
             "name": "foo",
             "version": "1.2.3",
             "plugin_demo": "hello world",
-            "package_dir": {"": "src"},
             "packages": ("foo", "foo.qux"),
             "namespace_packages": ("foo",),
             "package_data": {"foo": ("resources/js/code.js",)},
@@ -378,13 +377,12 @@ def test_binary_shorthand(chroot_rule_runner: RuleRunner) -> None:
     )
     assert_chroot(
         chroot_rule_runner,
-        ["src/project/app.py", "setup.py", "MANIFEST.in"],
+        ["project/app.py", "setup.py", "MANIFEST.in"],
         "setup.py",
         {
             "name": "bin",
             "version": "1.1.1",
             "plugin_demo": "hello world",
-            "package_dir": {"": "src"},
             "packages": ("project",),
             "namespace_packages": (),
             "install_requires": (),

src/python/pants/engine/process_test.py

@@ -5,7 +5,14 @@
 
 import pytest
 
-from pants.engine.fs import EMPTY_DIGEST, CreateDigest, Digest, DigestContents, FileContent
+from pants.engine.fs import (
+    EMPTY_DIGEST,
+    CreateDigest,
+    Digest,
+    DigestContents,
+    Directory,
+    FileContent,
+)
 from pants.engine.internals.scheduler import ExecutionError
 from pants.engine.process import (
     BinaryPathRequest,
@@ -74,11 +81,24 @@ def test_env(rule_runner: RuleRunner) -> None:
     assert b"VAR2=VAL" in result.stdout
 
 
-def test_output_digest(rule_runner: RuleRunner) -> None:
+@pytest.mark.parametrize("working_directory", ["", "subdir"])
+def test_output_digest(rule_runner: RuleRunner, working_directory) -> None:
+    # Test that the output files are relative to the working directory, both in how
+    # they're specified, and their paths in the output_digest.
+    input_digest = (
+        rule_runner.request(
+            Digest,
+            [CreateDigest([Directory(working_directory)])],
+        )
+        if working_directory
+        else EMPTY_DIGEST
+    )
     process = Process(
+        input_digest=input_digest,
         argv=("/bin/bash", "-c", "echo -n 'European Burmese' > roland"),
         description="echo roland",
         output_files=("roland",),
+        working_directory=working_directory,
     )
     result = rule_runner.request(ProcessResult, [process])
     assert result.output_digest == Digest(