From bf5b534022c683304a29038f0dbb9f41b2276c04 Mon Sep 17 00:00:00 2001
From: Kai Schleicher <kai.schleicher@unibas.ch>
Date: Wed, 28 Oct 2026 17:29:43 +0100
Subject: [PATCH] =?UTF-8?q?=F0=9F=90=9B=20save=5Fscript=5Fparameters:=20sk?=
 =?UTF-8?q?ip=20whole=20names=20only?=
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The skip list ("USERNAME", "SJLOG", "COMMAND", "RM") was matched as a
substring, so e.g. a parameter "fusion_format" (contains "RM") was not
saved. Match the whole name (case insensitive), as documented.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 CHANGELOG.md                |  3 +++
 src/imcflibs/imagej/misc.py |  5 +++--
 tests/test_misc.py          | 18 ++++++++++++++++++
 3 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2647f020..2cae61fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -71,6 +71,9 @@ multiple modules. For detailed information, please refer to the
 * `imcflibs.imagej.misc.run_imarisconvert`:
   * Now allows to select an output folder.
   * Adds pixel calibration to the converted file.
+* `imcflibs.imagej.misc.save_script_parameters` skips only parameters whose
+    whole name is in the skip list (`fusion_format` was skipped because it
+    contains `RM`).
 * `imcflibs.imagej.misc.subtract_images` now validates the slice count is equal
     for both images.
 * `imcflibs.imagej.misc.save_image_with_extension`: fix issue with java path
diff --git a/src/imcflibs/imagej/misc.py b/src/imcflibs/imagej/misc.py
index 045301db..b1771eed 100644
--- a/src/imcflibs/imagej/misc.py
+++ b/src/imcflibs/imagej/misc.py
@@ -843,8 +843,9 @@ def save_script_parameters(
         for item in script_info.inputs():
             key = item.getName()
 
-            # Skip if any keys are in the skip list
-            if any(skip in key.upper() for skip in skip_keys):
+            # Skip if the key is in the skip list (whole name, not a substring:
+            # e.g. "FUSION_FORMAT" contains "RM")
+            if key.upper() in skip_keys:
                 log.info("Skipping parameter from skip-list: %s", key)
                 skipped += 1
                 continue
diff --git a/tests/test_misc.py b/tests/test_misc.py
index 9f137cb7..346fe55f 100644
--- a/tests/test_misc.py
+++ b/tests/test_misc.py
@@ -51,6 +51,24 @@ def _is_password_style(item):
     assert contents == "AAA: aaa\nBBB: bbb\n"
 
 
+def test_save_script_parameters_skip_whole_names(tmp_path, monkeypatch, caplog):
+    """Only whole names are skipped, case insensitive, not substrings."""
+    caplog.set_level(logging.DEBUG)
+    caplog.clear()
+    monkeypatch.setattr(imcflibs.imagej.misc, "_is_password_style", lambda item: False)
+
+    script_module = ScriptModule(
+        input_names=["rm", "fusion_format", "commander"],
+        inputs={"rm": "roimanager", "fusion_format": "TIFF", "commander": "x"},
+    )
+    script_globals = {"org.scijava.script.ScriptModule": script_module}
+    save_script_parameters(script_globals, destination=tmp_path)
+
+    with open(str(tmp_path) + "/script_parameters.txt", "r") as f:
+        contents = f.read()
+    assert contents == "fusion_format: TIFF\ncommander: x\n"
+
+
 def test_bytes_to_human_readable_simple():
     """Ensure common sizes are formatted into human-readable strings."""
     assert bytes_to_human_readable(500) == "500.0 bytes"