masster 0.4.0__py3-none-any.whl → 0.4.1__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 +3 -9
  4. masster/data/libs/README.md +1 -1
  5. masster/data/libs/ccm.csv +120 -120
  6. masster/data/libs/ccm.py +116 -62
  7. masster/data/libs/central_carbon_README.md +1 -1
  8. masster/data/libs/urine.py +161 -65
  9. masster/data/libs/urine_metabolites.csv +4693 -4693
  10. masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.mzML +2 -2
  11. masster/logger.py +43 -78
  12. masster/sample/__init__.py +1 -1
  13. masster/sample/adducts.py +264 -338
  14. masster/sample/defaults/find_adducts_def.py +8 -21
  15. masster/sample/defaults/find_features_def.py +1 -6
  16. masster/sample/defaults/get_spectrum_def.py +1 -5
  17. masster/sample/defaults/sample_def.py +1 -5
  18. masster/sample/h5.py +282 -561
  19. masster/sample/helpers.py +75 -131
  20. masster/sample/lib.py +17 -42
  21. masster/sample/load.py +17 -31
  22. masster/sample/parameters.py +2 -6
  23. masster/sample/plot.py +27 -88
  24. masster/sample/processing.py +87 -117
  25. masster/sample/quant.py +51 -57
  26. masster/sample/sample.py +90 -103
  27. masster/sample/sample5_schema.json +44 -44
  28. masster/sample/save.py +12 -35
  29. masster/sample/sciex.py +19 -66
  30. masster/spectrum.py +20 -58
  31. masster/study/__init__.py +1 -1
  32. masster/study/defaults/align_def.py +1 -5
  33. masster/study/defaults/fill_chrom_def.py +1 -5
  34. masster/study/defaults/fill_def.py +1 -5
  35. masster/study/defaults/integrate_chrom_def.py +1 -5
  36. masster/study/defaults/integrate_def.py +1 -5
  37. masster/study/defaults/study_def.py +25 -58
  38. masster/study/export.py +207 -233
  39. masster/study/h5.py +136 -470
  40. masster/study/helpers.py +202 -495
  41. masster/study/helpers_optimized.py +13 -40
  42. masster/study/id.py +110 -213
  43. masster/study/load.py +143 -230
  44. masster/study/plot.py +257 -518
  45. masster/study/processing.py +257 -469
  46. masster/study/save.py +5 -15
  47. masster/study/study.py +276 -379
  48. masster/study/study5_schema.json +96 -96
  49. {masster-0.4.0.dist-info → masster-0.4.1.dist-info}/METADATA +1 -1
  50. masster-0.4.1.dist-info/RECORD +67 -0
  51. masster-0.4.0.dist-info/RECORD +0 -67
  52. {masster-0.4.0.dist-info → masster-0.4.1.dist-info}/WHEEL +0 -0
  53. {masster-0.4.0.dist-info → masster-0.4.1.dist-info}/entry_points.txt +0 -0
  54. {masster-0.4.0.dist-info → masster-0.4.1.dist-info}/licenses/LICENSE +0 -0
masster/sample/defaults/find_adducts_def.py CHANGED
@@ -54,15 +54,13 @@ class find_adducts_defaults:
54
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  charge_span_max: int = 2
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  # Retention time constraints (in seconds - final confirmed unit)
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- retention_max_diff: float = 1.0 # 1 second - precise RT grouping
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+ retention_max_diff: float = 1.0 # 1 second - precise RT grouping
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  retention_max_diff_local: float = 1.0 # 1 second - precise RT grouping
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-
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+
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  # Mass tolerance constraints
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- mass_max_diff: float = (
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- 0.01 # 0.01 Da - strict mass tolerance for chemical specificity
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- )
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+ mass_max_diff: float = 0.01 # 0.01 Da - strict mass tolerance for chemical specificity
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  unit: str = "Da" # Mass tolerance unit: "Da" or "ppm"
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-
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+
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  # Probability filtering
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  min_probability: float = 0.03 # Minimum probability to consider adducts (filters low-probability adducts)
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@@ -183,7 +181,7 @@ class find_adducts_defaults:
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  return all(isinstance(item, str) for item in value)
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  else:
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  return False
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-
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+
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  # Handle unit parameter
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  if param_name == "unit":
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  if isinstance(value, str):
@@ -350,27 +348,16 @@ class find_adducts_defaults:
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  if adducts is None or adducts in ["pos", "positive"]:
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  return [
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- "+H:1:0.65",
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- "+Na:1:0.15",
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- "+NH4:1:0.15",
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- "+K:1:0.05",
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- "-H2O:0:0.15",
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+ "+H:1:0.65", "+Na:1:0.15", "+NH4:1:0.15", "+K:1:0.05", "-H2O:0:0.15"
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  ]
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  elif adducts in ["neg", "negative"]:
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  return [
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- "-H:-1:0.9",
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- "+Cl:-1:0.1",
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- "+CH2O2:0:0.15",
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- "-H2O:0:0.15",
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+ "-H:-1:0.9", "+Cl:-1:0.1", "+CH2O2:0:0.15", "-H2O:0:0.15"
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  ]
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  elif isinstance(adducts, list):
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  return adducts
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  else:
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  # Fallback to positive mode if unexpected format
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  return [
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- "+H:1:0.65",
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- "+Na:1:0.15",
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- "+NH4:1:0.15",
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- "+K:1:0.05",
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- "-H2O:0:0.2",
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+ "+H:1:0.65", "+Na:1:0.15", "+NH4:1:0.15", "+K:1:0.05", "-H2O:0:0.2"
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  ]
masster/sample/defaults/find_features_def.py CHANGED
@@ -210,12 +210,7 @@ class find_features_defaults:
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  "dtype": str,
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  "description": "Isotope filtering model",
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  "default": "metabolites (5% RMS)",
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- "allowed_values": [
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- "metabolites (2% RMS)",
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- "metabolites (5% RMS)",
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- "peptides",
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- "none",
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- ],
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+ "allowed_values": ["metabolites (2% RMS)", "metabolites (5% RMS)", "peptides", "none"],
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  },
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  "threads": {
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  "dtype": int,
masster/sample/defaults/get_spectrum_def.py CHANGED
@@ -222,11 +222,7 @@ class get_spectrum_defaults:
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  expected_dtype = self._param_metadata[param_name]["dtype"]
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  # Handle optional types
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- if (
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- isinstance(expected_dtype, str)
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- and expected_dtype.startswith("Optional")
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- and value is not None
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- ):
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+ if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional") and value is not None:
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  if "int" in expected_dtype and not isinstance(value, int):
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  try:
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  value = int(value)
masster/sample/defaults/sample_def.py CHANGED
@@ -297,11 +297,7 @@ class sample_defaults:
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  expected_dtype = self._param_metadata[param_name]["dtype"]
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  # Handle optional types
300
- if (
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- isinstance(expected_dtype, str)
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- and expected_dtype.startswith("Optional")
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- and value is not None
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- ):
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+ if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional") and value is not None:
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  if "int" in expected_dtype and not isinstance(value, int):
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  try:
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  value = int(value)