masster 0.4.3__py3-none-any.whl → 0.4.5__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Potentially problematic release.
This version of masster might be problematic. Click here for more details.
- masster/__init__.py +8 -8
- masster/_version.py +1 -1
- masster/chromatogram.py +1 -1
- masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil2_01_20250602151849.sample5 +0 -0
- masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil3_01_20250602150634.sample5 +0 -0
- masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008_v6_r38_01.sample5 +0 -0
- masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008_v7_r37_01.sample5 +0 -0
- masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C017_v5_r99_01.sample5 +0 -0
- masster/data/libs/__pycache__/ccm.cpython-312.pyc +0 -0
- masster/data/libs/__pycache__/urine.cpython-312.pyc +0 -0
- masster/data/libs/ccm.csv +120 -0
- masster/data/libs/urine.csv +4693 -0
- masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.timeseries.data +0 -0
- masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff +0 -0
- masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff.scan +0 -0
- masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff2 +0 -0
- masster/logger.py +11 -11
- masster/sample/__init__.py +1 -1
- masster/sample/adducts.py +338 -264
- masster/sample/defaults/find_adducts_def.py +21 -8
- masster/sample/h5.py +561 -282
- masster/sample/helpers.py +131 -75
- masster/sample/lib.py +4 -4
- masster/sample/load.py +31 -17
- masster/sample/parameters.py +1 -1
- masster/sample/plot.py +7 -7
- masster/sample/processing.py +117 -87
- masster/sample/sample.py +103 -90
- masster/sample/sample5_schema.json +196 -0
- masster/sample/save.py +35 -12
- masster/spectrum.py +1 -1
- masster/study/__init__.py +1 -1
- masster/study/defaults/align_def.py +5 -1
- masster/study/defaults/identify_def.py +3 -1
- masster/study/defaults/study_def.py +58 -25
- masster/study/export.py +360 -210
- masster/study/h5.py +560 -158
- masster/study/helpers.py +496 -203
- masster/study/helpers_optimized.py +1 -1
- masster/study/id.py +538 -349
- masster/study/load.py +233 -143
- masster/study/plot.py +71 -71
- masster/study/processing.py +456 -254
- masster/study/save.py +15 -5
- masster/study/study.py +213 -131
- masster/study/study5_schema.json +360 -0
- masster-0.4.5.dist-info/METADATA +131 -0
- masster-0.4.5.dist-info/RECORD +71 -0
- masster-0.4.3.dist-info/METADATA +0 -791
- masster-0.4.3.dist-info/RECORD +0 -56
- {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/WHEEL +0 -0
- {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/entry_points.txt +0 -0
- {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/licenses/LICENSE +0 -0
- {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/top_level.txt +0 -0
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
masster/logger.py
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
# masster/logger.py
|
|
2
2
|
"""
|
|
3
|
-
Simple logger system for
|
|
3
|
+
Simple logger system for master Study and Sample instances.
|
|
4
4
|
Uses basic Python logging timestamp = dt.strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]
|
|
5
5
|
|
|
6
6
|
# Loguru-style colors for different log levels
|
|
@@ -25,7 +25,7 @@ import datetime
|
|
|
25
25
|
from typing import Any
|
|
26
26
|
|
|
27
27
|
|
|
28
|
-
class
|
|
28
|
+
class MasterLogger:
|
|
29
29
|
"""Simple logger wrapper for Study/Sample instances.
|
|
30
30
|
Each instance gets its own Python logger to avoid conflicts.
|
|
31
31
|
|
|
@@ -59,7 +59,7 @@ class MassterLogger:
|
|
|
59
59
|
self.sink = sink
|
|
60
60
|
|
|
61
61
|
# Create a unique logger name for this instance
|
|
62
|
-
self.logger_name = f"
|
|
62
|
+
self.logger_name = f"master.{self.instance_type}.{self.instance_id}"
|
|
63
63
|
|
|
64
64
|
# Get a Python logger instance
|
|
65
65
|
self.logger_instance = logging.getLogger(self.logger_name)
|
|
@@ -73,8 +73,8 @@ class MassterLogger:
|
|
|
73
73
|
# Create a stream handler
|
|
74
74
|
self.handler = logging.StreamHandler(self.sink)
|
|
75
75
|
|
|
76
|
-
# Create formatter that matches the original
|
|
77
|
-
class
|
|
76
|
+
# Create formatter that matches the original master style
|
|
77
|
+
class masterFormatter(logging.Formatter):
|
|
78
78
|
def __init__(self, label):
|
|
79
79
|
super().__init__()
|
|
80
80
|
self.label = label
|
|
@@ -124,7 +124,7 @@ class MassterLogger:
|
|
|
124
124
|
f"{level_color}{record.getMessage()}\x1b[0m"
|
|
125
125
|
) # colored message
|
|
126
126
|
|
|
127
|
-
self.handler.setFormatter(
|
|
127
|
+
self.handler.setFormatter(masterFormatter(self.label))
|
|
128
128
|
self.logger_instance.addHandler(self.handler)
|
|
129
129
|
|
|
130
130
|
# Prevent propagation to avoid duplicate messages
|
|
@@ -143,7 +143,7 @@ class MassterLogger:
|
|
|
143
143
|
self.label = label
|
|
144
144
|
|
|
145
145
|
# Update formatter with new label
|
|
146
|
-
class
|
|
146
|
+
class masterFormatter(logging.Formatter):
|
|
147
147
|
def __init__(self, label):
|
|
148
148
|
super().__init__()
|
|
149
149
|
self.label = label
|
|
@@ -192,7 +192,7 @@ class MassterLogger:
|
|
|
192
192
|
f"{level_color}{record.getMessage()}\x1b[0m"
|
|
193
193
|
) # colored message
|
|
194
194
|
|
|
195
|
-
self.handler.setFormatter(
|
|
195
|
+
self.handler.setFormatter(masterFormatter(self.label))
|
|
196
196
|
|
|
197
197
|
def update_sink(self, sink: Any):
|
|
198
198
|
"""Update the output sink for log messages."""
|
|
@@ -207,7 +207,7 @@ class MassterLogger:
|
|
|
207
207
|
self.handler = logging.StreamHandler(self.sink)
|
|
208
208
|
|
|
209
209
|
# Apply formatter
|
|
210
|
-
class
|
|
210
|
+
class masterFormatter(logging.Formatter):
|
|
211
211
|
def __init__(self, label):
|
|
212
212
|
super().__init__()
|
|
213
213
|
self.label = label
|
|
@@ -256,7 +256,7 @@ class MassterLogger:
|
|
|
256
256
|
f"{level_color}{record.getMessage()}\x1b[0m"
|
|
257
257
|
) # colored message
|
|
258
258
|
|
|
259
|
-
self.handler.setFormatter(
|
|
259
|
+
self.handler.setFormatter(masterFormatter(self.label))
|
|
260
260
|
self.logger_instance.addHandler(self.handler)
|
|
261
261
|
|
|
262
262
|
# Logger method delegates
|
|
@@ -329,4 +329,4 @@ class MassterLogger:
|
|
|
329
329
|
self.handler = None
|
|
330
330
|
|
|
331
331
|
def __repr__(self):
|
|
332
|
-
return f"
|
|
332
|
+
return f"MasterLogger(type={self.instance_type}, id={self.instance_id}, level={self.level})"
|
masster/sample/__init__.py
CHANGED