masster 0.3.14__py3-none-any.whl → 0.3.16__py3-none-any.whl

masster/study/plot.py

@@ -375,7 +375,7 @@ def plot_consensus_2d(
         ])
 
     if cmap is None:
-        cmap = "vi"
+        cmap = "viridis"
     elif cmap == "grey":
         cmap = "Greys256"
 
@@ -898,7 +898,7 @@ def plot_bpc(
 def plot_eic(
     self,
     mz,
-    mz_tol=0.01,
+    mz_tol=None,
     samples=None,
     title: str | None = None,
     filename: str | None = None,
@@ -912,6 +912,9 @@ def plot_eic(
     Parameters mirror `plot_bpc` with additional `mz` and `mz_tol` arguments. The function
     retrieves a Sample object for each sample UID, calls `sample.get_eic(mz, mz_tol)`, and
     overlays the resulting chromatograms.
+
+    Args:
+        mz_tol: m/z tolerance in Da. If None, uses study.parameters.eic_mz_tol as default.
     """
     # Local imports to avoid heavy top-level deps / circular imports
     from bokeh.plotting import figure, show, output_file
@@ -919,6 +922,10 @@ def plot_eic(
     from bokeh.io.export import export_png
     from masster.study.helpers import get_eic
 
+    # Use study's eic_mz_tol parameter as default if not provided
+    if mz_tol is None:
+        mz_tol = self.parameters.eic_mz_tol
+
     if mz is None:
         self.logger.error("mz must be provided for EIC plotting")
         return

masster/study/study.py

@@ -80,16 +80,23 @@ from masster.study.helpers import set_folder
 from masster.study.helpers import set_source
 from masster.study.helpers import sample_color
 from masster.study.helpers import sample_color_reset
-from masster.study.helpers import name_replace
-from masster.study.helpers import name_reset
+from masster.study.helpers import sample_name_replace
+from masster.study.helpers import sample_name_reset
+from masster.study.helpers import samples_select
+from masster.study.helpers import samples_delete
 from masster.study.helpers import features_select
 from masster.study.helpers import features_filter
 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
+from masster.study.load import _add_sample_optimized
+from masster.study.load import _add_sample_standard
+from masster.study.load import _sample_color_reset_optimized
 from masster.study.load import fill_single
 from masster.study.load import fill
 from masster.study.load import _process_sample_for_parallel_fill
@@ -279,24 +286,30 @@ class Study:
                 "sample_name": [],
                 "sample_path": [],
                 "sample_type": [],
-                "size": [],
                 "map_id": [],
-                "file_source": [],
-                "ms1": [],
-                "ms2": [],
+                "sample_source": [],
                 "sample_color": [],
+                "sample_group": [],
+                "sample_batch": [],
+                "sample_sequence": [],
+                "num_features": [],
+                "num_ms1": [],
+                "num_ms2": [],
             },
             schema={
                 "sample_uid": pl.Int64,
                 "sample_name": pl.Utf8,
                 "sample_path": pl.Utf8,
                 "sample_type": pl.Utf8,
-                "size": pl.Int64,
-                "map_id": pl.Utf8,
-                "file_source": pl.Utf8,
-                "ms1": pl.Int64,
-                "ms2": pl.Int64,
+                "map_id": pl.Int64,
+                "sample_source": pl.Utf8,
                 "sample_color": pl.Utf8,
+                "sample_group": pl.Utf8,
+                "sample_batch": pl.Int64,
+                "sample_sequence": pl.Int64,
+                "num_features": pl.Int64,
+                "num_ms1": pl.Int64,
+                "num_ms2": pl.Int64,
             },
         )
         self.features_maps = []
@@ -369,8 +382,10 @@ class Study:
     set_source = set_source
     sample_color = sample_color
     sample_color_reset = sample_color_reset
-    name_replace = name_replace
-    name_reset = name_reset
+    name_replace = sample_name_replace
+    name_reset = sample_name_reset
+    samples_select = samples_select
+    samples_delete = samples_delete
     features_select = features_select
     features_filter = features_filter
     features_delete = features_delete
@@ -388,6 +403,10 @@ class Study:
     add_folder = add  # backward compatibility alias
     add = add
     add_sample = add_sample
+    _add_samples_batch = _add_samples_batch
+    _add_sample_optimized = _add_sample_optimized
+    _add_sample_standard = _add_sample_standard
+    _sample_color_reset_optimized = _sample_color_reset_optimized
     _load_study5 = _load_study5
     _save_study5 = _save_study5
     _save_study5_compressed = _save_study5_compressed

masster/study/study5_schema.json

@@ -225,9 +225,9 @@
         "dtype": "pl.Int64"
       },
       "map_id": {
-        "dtype": "pl.Utf8"
+        "dtype": "pl.Int64"
       },
-      "file_source": {
+      "sample_source": {
         "dtype": "pl.Utf8"
       },
       "sample_name": {
@@ -239,13 +239,25 @@
       "sample_type": {
         "dtype": "pl.Utf8"
       },
-      "size": {
+      "sample_group": {
+        "dtype": "pl.Utf8"
+      },
+      "sample_batch": {
+        "dtype": "pl.Int64"
+      },
+      "sample_sequence": {
+        "dtype": "pl.Int64"
+      },
+      "sample_color": {
+        "dtype": "pl.Utf8"
+      },
+      "num_features": {
         "dtype": "pl.Int64"
       },
-      "ms1": {
+      "num_ms1": {
         "dtype": "pl.Int64"
       },
-      "ms2": {
+      "num_ms2": {
         "dtype": "pl.Int64"
       }
     }

{masster-0.3.14.dist-info → masster-0.3.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.14
+Version: 0.3.16
 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-0.3.14.dist-info → masster-0.3.16.dist-info}/RECORD

@@ -1,23 +1,23 @@
 masster/__init__.py,sha256=G7hbKO8F_o1wFwQlvO25M8JYGka_YSAVU2_O__2rjlI,697
-masster/_version.py,sha256=ginlJdJgdMh1rp81NNhKs0fwmLr17IZA4S9-6W_glZw,257
+masster/_version.py,sha256=HDf6S1ynXvmSKXApEpj2twR-B_GqBMtsnLl5qQe7mBU,257
 masster/chromatogram.py,sha256=NgPr1uLGJHjRu6PWZZGOrS3pCl7sye1yQCJjlRi9ZSY,19305
 masster/logger.py,sha256=W50V_uh8RSYwGxDrDFhOuj5jpu2tKJyt_16lMw9kQwA,14755
-masster/spectrum.py,sha256=LuDa7qP_JInctzkmxC9c5468opHOholy321KpUgyW2U,47550
+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/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
-masster/sample/h5.py,sha256=IdfbdkDgKcij-jMQTxnjW-gsBhb6vwi8w1XXL795yEs,63793
-masster/sample/helpers.py,sha256=U2VyboRdTsQbOefCy7VXh6PlSQtEsR6BK5QF2jGUd94,36208
+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=5Ig94gEWBfdxR86yNwaPj9mdNvPI1nVCp0LXcFJt05U,47577
+masster/sample/load.py,sha256=ZeTB7Rr5c0XEDTt1OfyfjxogWb9TLuiAoBg4loyvnRQ,50013
 masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
-masster/sample/plot.py,sha256=C8Y2DLLHw3Bo_U0MPhKMI3AKOkqj0zMUQxasRVWp26U,77964
+masster/sample/plot.py,sha256=mXrQbgBfMhXtfat_xAuliyXNTanW_kezq4hmWQYtFiQ,78445
 masster/sample/processing.py,sha256=-H93MEUysA-B9PB4nU31WFjtaU_flqbu2gY35ce4vVs,57827
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
-masster/sample/sample.py,sha256=QxKjXPO5lWRrIq5eDsYzNQPjp0zI_vuPdPlRQe1y3uI,16925
+masster/sample/sample.py,sha256=2Hq3mUZHAN8AVw_-1m5v7Jg1-yqF5Pv7AWWBlhEDSXo,17096
 masster/sample/sample5_schema.json,sha256=4g_uBMODLvxnhZU6iCK61W3fbaT6sTgOvBhEFc3U1nI,3772
 masster/sample/save.py,sha256=kQULZkuhx2ED8jMlQsi5yK98dRKlQKvQf5uJDvI01ZA,31896
 masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
@@ -28,30 +28,30 @@ 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=9Bhz8wpO3ZHdwV0iWSX0E38GS3UfqfAFlW9VN8ht2-Y,28845
-masster/study/h5.py,sha256=UOc4tbeWr8Xa_5Aescz7rMMnkzpu8PSTsOAnTfPv0-E,67109
-masster/study/helpers.py,sha256=O5aTbbELc_zCOPHg0YO4PXrVjWE_gKQuDxjdVfaDKwU,112710
+masster/study/export.py,sha256=E3Ps350T-STFlx-OQc3fU592WvenO1i6Dq7PVH6QUbA,28989
+masster/study/h5.py,sha256=Tl_jdV75yOZ5PH76jvMvTdOJdhiup6uINPC04DhcDX0,71815
+masster/study/helpers.py,sha256=PZ0Lb3eFSnEmPQ3sFzHn-cYr_OehHGzTOogfo3r5K-0,133432
 masster/study/helpers_optimized.py,sha256=sd87kNPIEPdMijekXzZWSyeZzJ_DTAW8HQjAry-jVyY,13922
-masster/study/load.py,sha256=1wRIIB-n8H1d9vUtb7GTaJLIS4AHrujAafGs4tvJrcs,49647
+masster/study/load.py,sha256=WwQ52rzjWeL2JqdA7b7NfMy4hmBws_iFATpn32r0ANg,63100
 masster/study/parameters.py,sha256=0elaF7YspTsB7qyajWAbRNL2VfKlGz5GJLifmO8IGkk,3276
-masster/study/plot.py,sha256=-WYiR-tmXP9x2YKn6fxy6UyJnAxptuvPw9g-13zo6WY,75899
+masster/study/plot.py,sha256=RZ-ko0ocsXzaPtsa5QzBDX4FIwQkx4lYf5RPLJAH5Ss,76147
 masster/study/processing.py,sha256=ijLaVKZlPJQpcQh_u-Cj6acrSEOaB3vKMNzS9alXdzg,52661
 masster/study/save.py,sha256=YjFEiuiB4OFLVvW_AX4-kgnsbjCWrYZeqF85VNEtbdw,6560
-masster/study/study.py,sha256=2ReH0w6-oIAypQZVxSe3IKFAbHPIJSC9JyuDRhaOSOc,30749
-masster/study/study5_schema.json,sha256=Grm2vfi2NnfNfcqKndz3IX9JNyhgwh92T8x-IofLay4,5103
+masster/study/study.py,sha256=U6_tUk0SD1FaADq6ChwFTBVNYqgOTcva8QDN5Xdp4Ws,31724
+masster/study/study5_schema.json,sha256=Fwt6U6r1J1BQxwR8ArFv1yN_2Cq1tt3tadS2sQCzjhg,5379
 masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
 masster/study/defaults/align_def.py,sha256=QSJXfe5kAtYp_IN8LUuXjq61IkxT74ml84k5kmmRjqM,19846
 masster/study/defaults/export_def.py,sha256=eXl3h4aoLX88XkHTpqahLd-QZ2gjUqrmjq8IJULXeWo,1203
 masster/study/defaults/fill_chrom_def.py,sha256=hB6-tyC9bhx-IpGj2HC8FinQdW4VLYj_pn5t1rlj-Ew,8887
-masster/study/defaults/fill_def.py,sha256=5B7-iNCngdwHPbf0146LzrqxKCi7_g5OC1XtkxvckeQ,8869
+masster/study/defaults/fill_def.py,sha256=TdDqOt-fva44JptLvxOy7GNUCR5isOKz1jR2xj_V8sQ,8869
 masster/study/defaults/find_consensus_def.py,sha256=uWB4NKCXDMQgNp4BaQUExkDofnXz0ZDffsxH1tvH2_Q,8599
 masster/study/defaults/find_ms2_def.py,sha256=RL0DFG41wQ05U8UQKUGr3vzSl3mU0m0knQus8DpSoJE,5070
 masster/study/defaults/integrate_chrom_def.py,sha256=0MNIWGTjty-Zu-NTQsIweuj3UVqEY3x1x8pK0mPwYak,7264
 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=d8mQWIpvWEWI8grPTAcQa4jKTG7QrM98RRgHZVoh134,9519
-masster-0.3.14.dist-info/METADATA,sha256=ekvyajONIIV7y6Ma8rFE6U0EnPgq07XpXB8ox1e-Ld4,44320
-masster-0.3.14.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.3.14.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.3.14.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.3.14.dist-info/RECORD,,
+masster/study/defaults/study_def.py,sha256=v2V5i5y288gydhMOM78m8u_GaWC2XdjLM5nJP6e17sI,10476
+masster-0.3.16.dist-info/METADATA,sha256=Ix7nQy8uh4Rp4wiA85TEyjCeXrn8vtx02X49kticgjM,44320
+masster-0.3.16.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+masster-0.3.16.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.3.16.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+masster-0.3.16.dist-info/RECORD,,