Fix rmg_env_command dropping PYTHONPATH needed for source-tree RMG-Py

arc/job/env_run.py

@@ -196,7 +196,10 @@ def rmg_env_command(py_args: str | list[str],
     Resolution order, preserved from the call sites this replaced:
     ``MAMBA_EXE`` (exported by setup-micromamba in CI) → ``RMG_PYTHON`` from
     ARC's settings (needed on conda/mambaforge installs where micromamba's
-    ``conda`` shim is broken) → a launcher found on PATH, hunted for under a
+    ``conda`` shim is broken; this branch invokes the interpreter directly,
+    so it also re-exports ``PYTHONPATH`` from ``RMG_PATH`` after scrubbing
+    ARC's leaked activation vars, restoring visibility of a source-tree
+    RMG-Py/Arkane checkout) → a launcher found on PATH, hunted for under a
     login shell so that a conda initialization block in the user's profile is
     still honoured.
 
@@ -240,11 +243,21 @@ def rmg_env_command(py_args: str | list[str],
         ])
 
     if rmg_python and os.path.isfile(rmg_python):
-        return '\n'.join(preamble + [
+        rmg_path = settings.get('RMG_PATH')
+        lines = preamble + [
             f'unset {" ".join(_ARC_ENV_ACTIVATION_VARS)}',
             f'export PATH={shlex.quote(os.path.dirname(rmg_python))}:"$PATH"',
-            f'{shlex.quote(rmg_python)} {py_args}{suffix}',
-        ])
+        ]
+        if rmg_path:
+            # Restore PYTHONPATH to RMG_PATH after scrubbing ARC's leakage above.
+            # rmg_python is invoked directly (no launcher, no activation hooks), so
+            # on a source-tree RMG-Py/Arkane checkout reachable only via
+            # PYTHONPATH -- rather than pip-installed into rmg_env -- unsetting
+            # PYTHONPATH and stopping there leaves the child unable to import
+            # rmgpy/arkane at all.
+            lines.append(f'export PYTHONPATH={shlex.quote(rmg_path)}')
+        lines.append(f'{shlex.quote(rmg_python)} {py_args}{suffix}')
+        return '\n'.join(lines)
 
     # No launcher pinned by an env var and no configured interpreter: hunt for a
     # launcher on PATH. This runs under ``bash -l`` so the user's profile (where

arc/job/env_run_test.py

@@ -384,5 +384,42 @@ def test_py_args_list_arkane_module_invocation_three_tokens(self):
         self.assertIn('python -m arkane input.py', script)
 
 
+class TestRmgEnvCommandPythonPath(unittest.TestCase):
+    """The RMG_PYTHON (direct-interpreter) branch unsets PYTHONPATH along
+    with the rest of ARC's leaked activation vars, then must re-export it
+    from RMG_PATH -- otherwise a source-tree RMG-Py/Arkane checkout that is
+    only reachable via PYTHONPATH (not pip-installed into rmg_env) can never
+    be imported by the child interpreter."""
+
+    def setUp(self):
+        # Force the RMG_PYTHON branch: no MAMBA_EXE, and RMG_PYTHON resolves
+        # to a real file (RMG_PATH/RMG_PYTHON come from the patched settings
+        # dict below; os.path.isfile still needs a real path on disk, so
+        # point it at this test file itself).
+        self.env_patch = patch.dict(os.environ, {}, clear=False)
+        self.env_patch.start()
+        self.addCleanup(self.env_patch.stop)
+        os.environ.pop('MAMBA_EXE', None)
+        self.fake_rmg_python = __file__
+
+    def test_pythonpath_reexported_from_rmg_path(self):
+        settings_overrides = {'RMG_ENV_NAME': 'rmg_env', 'RMG_PYTHON': self.fake_rmg_python,
+                               'RMG_PATH': '/opt/RMG-Py'}
+        with patch.dict('arc.job.env_run.settings', settings_overrides):
+            script = rmg_env_command("-c 'pass'")
+        self.assertIn(f'export PYTHONPATH={shlex.quote("/opt/RMG-Py")}', script)
+        # The re-export must come after the unset, so it is not clobbered.
+        unset_idx = script.index('unset ')
+        export_idx = script.index('export PYTHONPATH=')
+        self.assertLess(unset_idx, export_idx)
+
+    def test_no_pythonpath_export_when_rmg_path_falsy(self):
+        settings_overrides = {'RMG_ENV_NAME': 'rmg_env', 'RMG_PYTHON': self.fake_rmg_python,
+                               'RMG_PATH': None}
+        with patch.dict('arc.job.env_run.settings', settings_overrides):
+            script = rmg_env_command("-c 'pass'")
+        self.assertNotIn('export PYTHONPATH=', script)
+
+
 if __name__ == '__main__':
     unittest.main()