RF: Pass environment paths to shutil.which()

filemanip.which() took an env dict, used just for an alternative PATH.

Author: effigies

nipype/interfaces/ants/segmentation.py

@@ -996,7 +996,9 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
         if ants_path is None:
             # Check for antsRegistration, which is under bin/ (the $ANTSPATH) instead of
             # checking for antsBrainExtraction.sh which is under script/
-            cmd_path = shutil.which("antsRegistration", env=runtime.environ)
+            cmd_path = shutil.which(
+                "antsRegistration", path=runtime.environ.get("PATH")
+            )
             if not cmd_path:
                 raise RuntimeError(
                     'The environment variable $ANTSPATH is not defined in host "%s", '

nipype/interfaces/base/core.py

@@ -703,7 +703,7 @@ def version_from_command(self, flag="-v", cmd=None):
             cmd = self.cmd.split()[0]
 
         env = dict(os.environ)
-        if shutil.which(cmd, env=env):
+        if shutil.which(cmd):
             out_environ = self._get_environ()
             env.update(out_environ)
             proc = sp.Popen(
@@ -748,7 +748,7 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
 
         # which $cmd
         executable_name = shlex.split(self._cmd_prefix + self.cmd)[0]
-        cmd_path = shutil.which(executable_name, env=runtime.environ)
+        cmd_path = shutil.which(executable_name, path=runtime.environ.get("PATH"))
 
         if cmd_path is None:
             raise IOError(