masster 0.3.8__py3-none-any.whl → 0.3.9__py3-none-any.whl

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.dist-info → masster-0.3.9.dist-info}/METADATA

@@ -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.dist-info → masster-0.3.9.dist-info}/RECORD

@@ -17,7 +17,7 @@ masster/sample/lib.py,sha256=9r2XlF_BaJ4WNAsQo8hElieRLwsAv0yrbYq4DJ0iVOM,33496
 masster/sample/load.py,sha256=y-KUJ2nCFX_06FHPUOh-CzRRvaTx14xNcXoL19bU8qY,47562
 masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
 masster/sample/plot.py,sha256=uUJAd2qxhVG6Ev2hLuU406zFA2TDkkBz2MG12P9fLik,71449
-masster/sample/processing.py,sha256=Ee0jpu314cLFxhfpARcWTCObm70LWhCCmyNYOFI6hwc,59861
+masster/sample/processing.py,sha256=AZdqEzOu4D_0B-3KCrvEr3wZ67taWpfZqFAIHeslf3s,60265
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
 masster/sample/sample.py,sha256=ekS-qBfzx3_Lb2KLMu-s90owRlk3lK4616mmiAiiHTc,16726
 masster/sample/sample5_schema.json,sha256=3SPFQZH4SooLYUt_lW-PCOE9rHnl56Vhc2XG-r1nyEQ,3586
@@ -52,8 +52,8 @@ masster/study/defaults/integrate_chrom_def.py,sha256=Rih3-vat7fHGVfIvRitjNJJI3zL
 masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgPfMYoPKeWv8,7246
 masster/study/defaults/merge_def.py,sha256=EBsKE3hsAkTEzN9dpdRD5W3_suTKy_WZ_96rwS0uBuE,8572
 masster/study/defaults/study_def.py,sha256=hj8bYtEPwzdowC95yfyoCFt6fZkQePLjpJtmpNz9Z5M,9533
-masster-0.3.8.dist-info/METADATA,sha256=BgeLAnayzxrXBCTRe9MHqt8uB5twHhDOTbLtinIghLQ,44292
-masster-0.3.8.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.3.8.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.3.8.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.3.8.dist-info/RECORD,,
+masster-0.3.9.dist-info/METADATA,sha256=FXWOvACxtEV0Svzws7jY8fKf4v6xmgzZ-Drgc2O_n-0,44292
+masster-0.3.9.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+masster-0.3.9.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.3.9.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+masster-0.3.9.dist-info/RECORD,,