masster 0.3.18__py3-none-any.whl → 0.3.20__py3-none-any.whl

masster/study/processing.py

@@ -193,9 +193,13 @@ def align(self, **kwargs):
         new_cols = [pl.Series("rt", current_rt)]
 
         # Update rt_original if corresponding updates were collected
-        if 'all_update_rt_original' in locals() and all_update_rt_original:
+        if "all_update_rt_original" in locals() and all_update_rt_original:
             try:
-                current_rt_orig = self.features_df["rt_original"].to_list() if "rt_original" in self.features_df.columns else [None] * self.features_df.height
+                current_rt_orig = (
+                    self.features_df["rt_original"].to_list()
+                    if "rt_original" in self.features_df.columns
+                    else [None] * self.features_df.height
+                )
             except Exception:
                 current_rt_orig = [None] * self.features_df.height
 
@@ -570,15 +574,15 @@ def merge(self, **kwargs):
         min_samples = 1
     if min_samples < 1:
         min_samples = int(min_samples * len(self.samples_df))
-    
+
     # Validate that min_samples doesn't exceed the number of samples
     if min_samples > len(self.samples_df):
         self.logger.warning(
             f"min_samples ({min_samples}) exceeds the number of samples ({len(self.samples_df)}). "
-            f"Setting min_samples to {len(self.samples_df)}."
+            f"Setting min_samples to {len(self.samples_df)}.",
         )
         min_samples = len(self.samples_df)
-    
+
     # filter out consensus features with less than min_samples features
     l1 = len(self.consensus_df)
     self.consensus_df = self.consensus_df.filter(

masster/study/study.py

@@ -50,7 +50,6 @@ import os
 import sys
 
 import polars as pl
-import numpy as np
 
 # Study-specific imports
 from masster.study.h5 import _load_study5
@@ -66,6 +65,8 @@ from masster.study.helpers import compress_ms2
 from masster.study.helpers import compress_chrom
 from masster.study.helpers import restore_features
 from masster.study.helpers import restore_chrom
+from masster.study.helpers import restore_ms2
+from masster.study.helpers import decompress
 from masster.study.helpers import fill_reset
 from masster.study.helpers import get_chrom
 from masster.study.helpers import get_sample
@@ -90,7 +91,6 @@ from masster.study.helpers import features_delete
 from masster.study.helpers import consensus_select
 from masster.study.helpers import consensus_filter
 from masster.study.helpers import consensus_delete
-from masster.study.helpers import migrate_map_id_to_index
 from masster.study.load import add
 from masster.study.load import add_sample
 from masster.study.load import _add_samples_batch
@@ -337,8 +337,6 @@ class Study:
         # cache for Sample instances created/loaded by this Study
         self._samples_cache = {}
 
-
-
     # Attach module functions as class methods
     load = load
     save = save
@@ -377,6 +375,8 @@ class Study:
     compress_chrom = compress_chrom
     restore_features = restore_features
     restore_chrom = restore_chrom
+    restore_ms2 = restore_ms2
+    decompress = decompress
     fill_reset = fill_reset
     align_reset = align_reset
     set_source = set_source
@@ -628,13 +628,13 @@ class Study:
                 try:
                     self.features_df = self.features_df.with_columns(pl.col("feature_uid").cast(pl.Int64))
                     self.consensus_mapping_df = self.consensus_mapping_df.with_columns(
-                        pl.col("feature_uid").cast(pl.Int64)
+                        pl.col("feature_uid").cast(pl.Int64),
                     )
                 except Exception:
                     # If casting to Int64 fails, cast both to string
                     self.features_df = self.features_df.with_columns(pl.col("feature_uid").cast(pl.Utf8))
                     self.consensus_mapping_df = self.consensus_mapping_df.with_columns(
-                        pl.col("feature_uid").cast(pl.Utf8)
+                        pl.col("feature_uid").cast(pl.Utf8),
                     )
 
             # Use more efficient counting - count non-null chroms only for features in consensus mapping

{masster-0.3.18.dist-info → masster-0.3.20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.18
+Version: 0.3.20
 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-0.3.18.dist-info → masster-0.3.20.dist-info}/RECORD

@@ -1,20 +1,26 @@
-masster/__init__.py,sha256=G7hbKO8F_o1wFwQlvO25M8JYGka_YSAVU2_O__2rjlI,697
-masster/_version.py,sha256=qM7C6C6rJ7cm4V4re4y29It0zbZneOVfLrUdlFmrPcs,257
+masster/__init__.py,sha256=8U4cIteNlYyHDrxWSbB_MsDKCX9tds07SJG8-vh8Oa8,738
+masster/_version.py,sha256=vFHeK1lVnRkJ-mBdglb7C3euLIdzNe-vq8ZrZCuimp0,257
 masster/chromatogram.py,sha256=NgPr1uLGJHjRu6PWZZGOrS3pCl7sye1yQCJjlRi9ZSY,19305
 masster/logger.py,sha256=W50V_uh8RSYwGxDrDFhOuj5jpu2tKJyt_16lMw9kQwA,14755
 masster/spectrum.py,sha256=7wKQes97sI-O2lxrkQnYuoroXFyAWgwSzS4TnjUX8RY,47710
-masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.mzML,sha256=3RS_crLN-aoPSacMYaQ45sxszmp_EcQElrg8tiuAQyA,39741920
-masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.timeseries.data,sha256=01vC6m__Qqm2rLvlTMZoeKIKowFvovBTUnrNl8Uav3E,24576
-masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff,sha256=go5N9gAM1rn4PZAVaoCmdteY9f7YGEM9gyPdSmkQ8PE,1447936
-masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff.scan,sha256=ahi1Y3UhAj9Bj4Q2MlbgPekNdkJvMOoMXVOoR6CeIxc,13881220
-masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff2,sha256=TFB0HW4Agkig6yht7FtgjUdbXax8jjKaHpSZSvuU5vs,3252224
+masster/data/libs/README.md,sha256=bjODMSbzAcdKLUFB4tfC3a-yOo-oWwqBfONMMNDYES4,987
+masster/data/libs/ccm.py,sha256=fwkj4gDmsitv_wzcmgk7IcQEBRsbE9E7Nq1nf3VX8P4,18129
+masster/data/libs/central_carbon_README.md,sha256=kse10ijMWdyGv02tK90zQhWzdN6hoXfEjzdezRptt2I,919
+masster/data/libs/central_carbon_metabolites.csv,sha256=heiYADAi6OScPGSp9aX7XhNGOFup6Z97y3phhsPXrzo,10646
+masster/data/libs/urine.py,sha256=HPas5ABPciexFIEM6rV3ok6Lw_eKlqeUTCFA0mebOWk,12873
+masster/data/libs/urine_metabolites.csv,sha256=gdzxTbOxbZTjKlHQDv7aBDgMBJQ9b25TMao9OSgAhKk,1870
+masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.mzML,sha256=3RS_crLN-aoPSacMYaQ45sxszmp_EcQElrg8tiuAQyA,39741920
+masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.timeseries.data,sha256=01vC6m__Qqm2rLvlTMZoeKIKowFvovBTUnrNl8Uav3E,24576
+masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff,sha256=go5N9gAM1rn4PZAVaoCmdteY9f7YGEM9gyPdSmkQ8PE,1447936
+masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff.scan,sha256=ahi1Y3UhAj9Bj4Q2MlbgPekNdkJvMOoMXVOoR6CeIxc,13881220
+masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff2,sha256=TFB0HW4Agkig6yht7FtgjUdbXax8jjKaHpSZSvuU5vs,3252224
 masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
-masster/sample/h5.py,sha256=40H_o2Rno61KZwlWOGuwUmU9YcdVVzecs533fg8uRvI,98042
-masster/sample/helpers.py,sha256=ThmabX_-gXxLFyok-mYMNOr5JErIO_zcrIHwqovXE1c,36541
-masster/sample/lib.py,sha256=l5YdU9TxEWJI0kJxXxrRCxgDDwbzO5zBf1_Qi_HY87w,33556
-masster/sample/load.py,sha256=ZeTB7Rr5c0XEDTt1OfyfjxogWb9TLuiAoBg4loyvnRQ,50013
+masster/sample/h5.py,sha256=ynyHx1SN3F0OYgjhazFfjNseLu48MLV9r-aFIFdfqJE,98038
+masster/sample/helpers.py,sha256=cCla29eTjAhcU5BPQJNr8KZWPD1IKjJj20tx5IrCaWM,36488
+masster/sample/lib.py,sha256=abBEnHjItVCp_20qNT9xGdqBrKX4LL_4z4P6mNQuGRQ,33757
+masster/sample/load.py,sha256=IJTIfg_-UAhBSYRRm2FnZDQv4yqoZCJ3ZQYA0W__iMg,50370
 masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
-masster/sample/plot.py,sha256=mXrQbgBfMhXtfat_xAuliyXNTanW_kezq4hmWQYtFiQ,78445
+masster/sample/plot.py,sha256=ynF4xNs2QPIYGButT-HkrofbYZPeLtyBXo15AOJKH7M,82783
 masster/sample/processing.py,sha256=-H93MEUysA-B9PB4nU31WFjtaU_flqbu2gY35ce4vVs,57827
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
 masster/sample/sample.py,sha256=2Hq3mUZHAN8AVw_-1m5v7Jg1-yqF5Pv7AWWBlhEDSXo,17096
@@ -28,16 +34,16 @@ masster/sample/defaults/find_ms2_def.py,sha256=KTELMAnioGLYbhzAwOgK14TZqboPEvzeB
 masster/sample/defaults/get_spectrum_def.py,sha256=o62p31PhGd-LiIkTOzKQhwPtnO2AtQDHcPu-O-YoQPs,11460
 masster/sample/defaults/sample_def.py,sha256=keoXyMyrm_iLgbYqfIbqCpJ3XHBVlNwCNmb5iMQL0iY,14579
 masster/study/__init__.py,sha256=Zspv6U8jFqjkHGYdNdDy1rfUnCSolCzUdgSSg98PRgE,166
-masster/study/export.py,sha256=E3Ps350T-STFlx-OQc3fU592WvenO1i6Dq7PVH6QUbA,28989
-masster/study/h5.py,sha256=Tl_jdV75yOZ5PH76jvMvTdOJdhiup6uINPC04DhcDX0,71815
-masster/study/helpers.py,sha256=DZKE5H2XdpuUTMAp-9PL7rSCunM59agcweAcFCw5gFg,134692
-masster/study/helpers_optimized.py,sha256=sd87kNPIEPdMijekXzZWSyeZzJ_DTAW8HQjAry-jVyY,13922
-masster/study/load.py,sha256=ywN9AOMatRjSvIdgu5g24_ONkQPd97ToVpSArPWcBI8,65324
+masster/study/export.py,sha256=VywMv0g8Qy_SiWS9V1pw7Q6uYfHGORQ_W9U-iLUciVo,30112
+masster/study/h5.py,sha256=I_yIKWW6zqI_xAq6sJ4uPs3EBWYMTMqiSTdy6VmN04o,72153
+masster/study/helpers.py,sha256=9WuzoNWaTSetkvfFY2y2mK4h8u2L_seAKZfGtBrgFQw,144856
+masster/study/helpers_optimized.py,sha256=5qf6tiLPgsOSna9XVtTrx2B0GJ1wI8ZTrSv8n8MtxNg,13927
+masster/study/load.py,sha256=BhH_dRugsieFvFTZq3jC3W8VHAh2JoGj_swQDnD3gUU,65091
 masster/study/parameters.py,sha256=0elaF7YspTsB7qyajWAbRNL2VfKlGz5GJLifmO8IGkk,3276
-masster/study/plot.py,sha256=ufqrtkd4uPkrRDdnpunU_BrrGu9Pd27WLWwSArj_L44,79623
-masster/study/processing.py,sha256=ZXpeY_vpKs23de4rlvllQegmUrzj2DcH-X6D50MW6YA,53302
+masster/study/plot.py,sha256=Lx9BQz3rEZ6qqLQvUX_YsNA4eX4vIWzFW8hxwJRkGMU,94430
+masster/study/processing.py,sha256=Da__6itJBbW4EwhCMBju4jytxgTLsGS8yWDt8S6V-DU,53379
 masster/study/save.py,sha256=YjFEiuiB4OFLVvW_AX4-kgnsbjCWrYZeqF85VNEtbdw,6560
-masster/study/study.py,sha256=U6_tUk0SD1FaADq6ChwFTBVNYqgOTcva8QDN5Xdp4Ws,31724
+masster/study/study.py,sha256=3ox8wIFlee_R0wUwV7Jmq3Y49pqpyGBM_XwW5rACM8k,31796
 masster/study/study5_schema.json,sha256=Fwt6U6r1J1BQxwR8ArFv1yN_2Cq1tt3tadS2sQCzjhg,5379
 masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
 masster/study/defaults/align_def.py,sha256=K_6xh7B1vf96maYIBTDZGjyA2zBHEgIP5ASzD9--n2Y,20241
@@ -50,8 +56,8 @@ masster/study/defaults/integrate_chrom_def.py,sha256=0MNIWGTjty-Zu-NTQsIweuj3UVq
 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=v2V5i5y288gydhMOM78m8u_GaWC2XdjLM5nJP6e17sI,10476
-masster-0.3.18.dist-info/METADATA,sha256=9b8mIZNrRtJCMs4hip4i9p_ssVvuT5198fvGEDrQVTs,44320
-masster-0.3.18.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.3.18.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.3.18.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.3.18.dist-info/RECORD,,
+masster-0.3.20.dist-info/METADATA,sha256=Kmil3q9BHG7ikwUWKwwEDXuP_3Tw59x3VxpJtkjz5ew,44320
+masster-0.3.20.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+masster-0.3.20.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.3.20.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+masster-0.3.20.dist-info/RECORD,,