masster 0.3.8__tar.gz → 0.3.9__tar.gz

{masster-0.3.8 → masster-0.3.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.8
+Version: 0.3.9
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.3.8 → masster-0.3.9}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.3.8"
+version = "0.3.9"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.3.8 → masster-0.3.9}/src/masster/sample/processing.py

@@ -570,14 +570,20 @@ def find_features(self, **kwargs):
                 self.logger.warning(f"Unknown parameter {key} ignored")
 
     # Set global parameters
-    if params.get('threads') is not None:
-        oms.OpenMSConfig.setNumThreads(params['threads'])
+    if hasattr(params, 'threads') and params.threads is not None:
+        try:
+            # Try setting via OpenMP environment variable first (newer approach)
+            import os
+            os.environ['OMP_NUM_THREADS'] = str(params.threads)
+            self.logger.debug(f"Set thread count to {params.threads} via OMP_NUM_THREADS")
+        except Exception:
+            self.logger.warning(f"Could not set thread count to {params.threads} - using default")
     
     # Set debug mode if enabled
-    if params.get('debug'):
-        oms.OpenMSConfig.setLogLevel(oms.LogType.DEBUG)
-    elif params.get('no_progress', False):
-        oms.OpenMSConfig.setLogLevel(oms.LogType.NONE)
+    if hasattr(params, 'debug') and params.debug:
+        self.logger.debug("Debug mode enabled")
+    elif hasattr(params, 'no_progress') and params.no_progress:
+        self.logger.debug("No progress mode enabled")
     
     self.logger.info("Starting feature detection...")
     self.logger.debug(
@@ -622,7 +628,7 @@ def find_features(self, **kwargs):
     
     # Additional MTD parameters
     mtd_par.setValue("min_sample_rate", float(params.get("min_sample_rate")))
-    mtd_par.setValue("min_trace_length", int(params.get("min_trace_length")))
+    mtd_par.setValue("min_trace_length", float(params.get("min_trace_length")))
     mtd_par.setValue("trace_termination_criterion", params.get("trace_termination_criterion"))
     mtd_par.setValue("reestimate_mt_sd", "true" if params.get("reestimate_mt_sd") else "false")
     mtd_par.setValue("quant_method", params.get("quant_method"))

{masster-0.3.8 → masster-0.3.9}/uv.lock

@@ -1315,7 +1315,7 @@ wheels = [
 
 [[package]]
 name = "masster"
-version = "0.3.8"
+version = "0.3.9"
 source = { editable = "." }
 dependencies = [
     { name = "alphabase" },