masster 0.4.3__py3-none-any.whl → 0.4.5__py3-none-any.whl

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Files changed (54) hide show
  1. masster/__init__.py +8 -8
  2. masster/_version.py +1 -1
  3. masster/chromatogram.py +1 -1
  4. masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil2_01_20250602151849.sample5 +0 -0
  5. masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil3_01_20250602150634.sample5 +0 -0
  6. masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008_v6_r38_01.sample5 +0 -0
  7. masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008_v7_r37_01.sample5 +0 -0
  8. masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C017_v5_r99_01.sample5 +0 -0
  9. masster/data/libs/__pycache__/ccm.cpython-312.pyc +0 -0
  10. masster/data/libs/__pycache__/urine.cpython-312.pyc +0 -0
  11. masster/data/libs/ccm.csv +120 -0
  12. masster/data/libs/urine.csv +4693 -0
  13. masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.timeseries.data +0 -0
  14. masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff +0 -0
  15. masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff.scan +0 -0
  16. masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff2 +0 -0
  17. masster/logger.py +11 -11
  18. masster/sample/__init__.py +1 -1
  19. masster/sample/adducts.py +338 -264
  20. masster/sample/defaults/find_adducts_def.py +21 -8
  21. masster/sample/h5.py +561 -282
  22. masster/sample/helpers.py +131 -75
  23. masster/sample/lib.py +4 -4
  24. masster/sample/load.py +31 -17
  25. masster/sample/parameters.py +1 -1
  26. masster/sample/plot.py +7 -7
  27. masster/sample/processing.py +117 -87
  28. masster/sample/sample.py +103 -90
  29. masster/sample/sample5_schema.json +196 -0
  30. masster/sample/save.py +35 -12
  31. masster/spectrum.py +1 -1
  32. masster/study/__init__.py +1 -1
  33. masster/study/defaults/align_def.py +5 -1
  34. masster/study/defaults/identify_def.py +3 -1
  35. masster/study/defaults/study_def.py +58 -25
  36. masster/study/export.py +360 -210
  37. masster/study/h5.py +560 -158
  38. masster/study/helpers.py +496 -203
  39. masster/study/helpers_optimized.py +1 -1
  40. masster/study/id.py +538 -349
  41. masster/study/load.py +233 -143
  42. masster/study/plot.py +71 -71
  43. masster/study/processing.py +456 -254
  44. masster/study/save.py +15 -5
  45. masster/study/study.py +213 -131
  46. masster/study/study5_schema.json +360 -0
  47. masster-0.4.5.dist-info/METADATA +131 -0
  48. masster-0.4.5.dist-info/RECORD +71 -0
  49. masster-0.4.3.dist-info/METADATA +0 -791
  50. masster-0.4.3.dist-info/RECORD +0 -56
  51. {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/WHEEL +0 -0
  52. {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/entry_points.txt +0 -0
  53. {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/licenses/LICENSE +0 -0
  54. {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/top_level.txt +0 -0
masster/logger.py CHANGED
@@ -1,6 +1,6 @@
1
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  # masster/logger.py
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  """
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- Simple logger system for masster Study and Sample instances.
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+ Simple logger system for master Study and Sample instances.
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  Uses basic Python logging timestamp = dt.strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]
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  # Loguru-style colors for different log levels
@@ -25,7 +25,7 @@ import datetime
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  from typing import Any
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- class MassterLogger:
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+ class MasterLogger:
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  """Simple logger wrapper for Study/Sample instances.
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  Each instance gets its own Python logger to avoid conflicts.
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@@ -59,7 +59,7 @@ class MassterLogger:
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  self.sink = sink
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  # Create a unique logger name for this instance
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- self.logger_name = f"masster.{self.instance_type}.{self.instance_id}"
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+ self.logger_name = f"master.{self.instance_type}.{self.instance_id}"
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  # Get a Python logger instance
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  self.logger_instance = logging.getLogger(self.logger_name)
@@ -73,8 +73,8 @@ class MassterLogger:
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  # Create a stream handler
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  self.handler = logging.StreamHandler(self.sink)
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- # Create formatter that matches the original masster style
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- class massterFormatter(logging.Formatter):
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+ # Create formatter that matches the original master style
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+ class masterFormatter(logging.Formatter):
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  def __init__(self, label):
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  super().__init__()
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  self.label = label
@@ -124,7 +124,7 @@ class MassterLogger:
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  f"{level_color}{record.getMessage()}\x1b[0m"
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  ) # colored message
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- self.handler.setFormatter(massterFormatter(self.label))
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+ self.handler.setFormatter(masterFormatter(self.label))
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  self.logger_instance.addHandler(self.handler)
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  # Prevent propagation to avoid duplicate messages
@@ -143,7 +143,7 @@ class MassterLogger:
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  self.label = label
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  # Update formatter with new label
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- class massterFormatter(logging.Formatter):
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+ class masterFormatter(logging.Formatter):
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  def __init__(self, label):
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  super().__init__()
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  self.label = label
@@ -192,7 +192,7 @@ class MassterLogger:
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  f"{level_color}{record.getMessage()}\x1b[0m"
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  ) # colored message
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- self.handler.setFormatter(massterFormatter(self.label))
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+ self.handler.setFormatter(masterFormatter(self.label))
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  def update_sink(self, sink: Any):
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  """Update the output sink for log messages."""
@@ -207,7 +207,7 @@ class MassterLogger:
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  self.handler = logging.StreamHandler(self.sink)
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  # Apply formatter
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- class massterFormatter(logging.Formatter):
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+ class masterFormatter(logging.Formatter):
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  def __init__(self, label):
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  super().__init__()
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  self.label = label
@@ -256,7 +256,7 @@ class MassterLogger:
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  f"{level_color}{record.getMessage()}\x1b[0m"
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  ) # colored message
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- self.handler.setFormatter(massterFormatter(self.label))
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+ self.handler.setFormatter(masterFormatter(self.label))
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  self.logger_instance.addHandler(self.handler)
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  # Logger method delegates
@@ -329,4 +329,4 @@ class MassterLogger:
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  self.handler = None
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  def __repr__(self):
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- return f"MassterLogger(type={self.instance_type}, id={self.instance_id}, level={self.level})"
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+ return f"MasterLogger(type={self.instance_type}, id={self.instance_id}, level={self.level})"
@@ -1,5 +1,5 @@
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  """
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- Sample module for masster.
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+ Sample module for master.
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  This module provides the Sample class for handling mass spectrometry data.
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  """