oceanproc 1.3.4__tar.gz → 1.3.5__tar.gz

{oceanproc-1.3.4 → oceanproc-1.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oceanproc
-Version: 1.3.4
+Version: 1.3.5
 Summary: MRI preprocessing for WUSTL Ocean labs
 Author-Email: Ramone Agard <rhagard@wustl.edu>, Joey Scanga <joeyscanga92@gmail.com>
 Requires-Python: <3.13,>=3.10

{oceanproc-1.3.4 → oceanproc-1.3.5}/oceanproc/ocean_proc.py

@@ -103,7 +103,7 @@ def main():
         epilog="An arguments file can be accepted with @FILEPATH.\nAny additional arguments not listed in the help message will be passed to the preprocessing subprocess.",
         allow_abbrev=False
     )
-    parser.add_argument("--version", action="version", version='%(prog)s v1.3.3')
+    parser.add_argument("--version", action="version", version='%(prog)s v1.3.5')
     session_args = parser.add_argument_group("Session Specific")
     config_args = parser.add_argument_group("Configuration Arguments", "These arguments are saved to a file if the '--export_args' option is used")
 

{oceanproc-1.3.4 → oceanproc-1.3.5}/oceanproc/utils.py

@@ -2,7 +2,7 @@ import sys
 import logging
 from pathlib import Path
 import json
-from subprocess import Popen, PIPE
+from subprocess import DEVNULL, STDOUT, Popen, PIPE
 import shlex
 from types import SimpleNamespace
 import nibabel as nib
@@ -243,19 +243,26 @@ def run_subprocess(cmd: str, title: str, log_output=True, quiet=False):
     split_cmd = shlex.split(cmd)
     logger.info(f"running '{title}' with the following command: \n{' '.join(split_cmd)}\n")
     prepare_subprocess_logging(logger)
-    ecode = 0
-    with Popen(split_cmd, stdout=PIPE, stderr=PIPE) as p:
-        while p.poll() == None:
-            if log_output:
-                for line in p.stdout:
-                    logger.info(line.decode("utf-8", "ignore"))
-                for line in p.stderr:
-                    logger.info(line.decode("utf-8", "ignore"))
+    ecode=0
+    try:
+        with Popen(
+            split_cmd, 
+            stdin=DEVNULL, 
+            stdout=PIPE, 
+            stderr=STDOUT, 
+            text=True, 
+            errors="ignore"
+        ) as p:
+            for line in p.stdout:
+                if log_output:
+                    logger.info(line)
+        ecode = p.returncode
+    finally:
         prepare_subprocess_logging(logger, stop=True)
-        ecode = p.poll()
-        p.kill()
-        if (ecode != 0) and (not quiet):
-            raise RuntimeError(f"process -'{title}'- has ended with a non-zero exit code <{ecode}>.")
+
+    if (ecode != 0) and (not quiet):
+        raise RuntimeError(f"process -'{title}'- has ended with a non-zero exit code <{ecode}>.")
+    
     return ecode
 
 

{oceanproc-1.3.4 → oceanproc-1.3.5}/pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "pybids>=0.16.3",
 ]
 name = "oceanproc"
-version = "1.3.4"
+version = "1.3.5"
 description = "MRI preprocessing for WUSTL Ocean labs"
 readme = "README.md"