From a316382ca49063500d1bb7ddc48f167edc47367e Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Mon, 29 Sep 2025 15:56:19 +0200
Subject: [PATCH 1/2] fix: since str arguments in cmd-line, args for Knime must
 be a list

---
 retropath2_wrapper/knime.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/retropath2_wrapper/knime.py b/retropath2_wrapper/knime.py
index ca5c9f4..ac4831f 100644
--- a/retropath2_wrapper/knime.py
+++ b/retropath2_wrapper/knime.py
@@ -1,6 +1,7 @@
 import os
 import requests
 import shutil
+import subprocess
 import sys
 import tempfile
 import urllib.parse
@@ -20,7 +21,6 @@
     download,
     download_and_unzip,
     chown_r,
-    subprocess_call
 )
 from retropath2_wrapper.Args import (
     DEFAULTS,
@@ -526,6 +526,7 @@ def call(
         args += ['-workflow.variable=output.dir,"%s",String' % (self.standardize_path(files['outdir']),)]
         args += ['-workflow.variable=output.solutionfile,"%s",String' % (self.standardize_path(files['results']),)]
         args += ['-workflow.variable=output.sourceinsinkfile,"%s",String' % (self.standardize_path(files['src-in-sk']),)]
+        print("Hydrogen:", params["std_hydrogen"])
         args += ['-workflow.variable=input.std_mode,"%s",String' % (params["std_hydrogen"],)]
         if preference and preference.is_init():
             preference.to_file()
@@ -550,7 +551,8 @@ def call(
                 )
                 is_ld_path_modified = True
 
-            CPE = subprocess_call(cmd=" ".join(args), logger=logger)
+            CPE = subprocess.run(args)
+            logger.debug(CPE)
             if is_ld_path_modified:
                 os.environ['LD_LIBRARY_PATH'] = ':'.join(
                     os.environ['LD_LIBRARY_PATH'].split(':')[:-1]

From c2ef9bde66272defe38a02a1fb3e644b77136957 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Mon, 29 Sep 2025 16:07:46 +0200
Subject: [PATCH 2/2] fix: add import

---
 retropath2_wrapper/knime.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/retropath2_wrapper/knime.py b/retropath2_wrapper/knime.py
index ac4831f..e99fe90 100644
--- a/retropath2_wrapper/knime.py
+++ b/retropath2_wrapper/knime.py
@@ -21,6 +21,7 @@
     download,
     download_and_unzip,
     chown_r,
+    subprocess_call,
 )
 from retropath2_wrapper.Args import (
     DEFAULTS,