masster 0.3.5__tar.gz → 0.3.7__tar.gz

{masster-0.3.5 → masster-0.3.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.5
+Version: 0.3.7
 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-0.3.5 → masster-0.3.7}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.3.5"
+version = "0.3.7"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.3.5 → masster-0.3.7}/src/masster/sample/sample.py

@@ -39,8 +39,13 @@ import sys
 import polars as pl
 
 from masster._version import get_version
+from masster.logger import MassterLogger
 
 from masster.sample.defaults.sample_def import sample_defaults
+from masster.sample.defaults.find_features_def import find_features_defaults
+from masster.sample.defaults.find_adducts_def import find_adducts_defaults
+from masster.sample.defaults.find_ms2_def import find_ms2_defaults
+from masster.sample.defaults.get_spectrum_def import get_spectrum_defaults
 
 # Sample-specific imports
 from masster.sample.h5 import _load_sample5
@@ -67,7 +72,6 @@ from masster.sample.load import chrom_extract
 from masster.sample.load import index_file
 from masster.sample.load import load
 from masster.sample.load import sanitize
-from masster.logger import MassterLogger
 from masster.sample.plot import plot_2d
 from masster.sample.plot import plot_2d_oracle
 from masster.sample.plot import plot_dda_stats
@@ -157,7 +161,6 @@ class Sample:
         self.log_sink = params.log_sink
 
         # Initialize independent logger
-        from masster.logger import MassterLogger
         self.logger = MassterLogger(
             instance_type="sample",
             level=params.log_level.upper(),
@@ -256,6 +259,14 @@ class Sample:
     _spec_to_mat = _spec_to_mat
     _save_featureXML = _save_featureXML
 
+    # defaults
+    sample_defaults = sample_defaults
+    find_features_defaults = find_features_defaults
+    merge_defaults = find_features_defaults
+    find_adducts_defaults = find_adducts_defaults
+    find_ms2_defaults = find_ms2_defaults
+    get_spectrum_defaults = get_spectrum_defaults
+
     def logger_update(self, level: str | None = None, label: str | None = None, sink: str | None = None):
         """Update the logging configuration for this Sample instance.
 

{masster-0.3.5 → masster-0.3.7}/src/masster/study/study.py

@@ -116,6 +116,15 @@ from masster.study.export import _get_mgf_df
 
 from masster.logger import MassterLogger
 from masster.study.defaults.study_def import study_defaults
+from masster.study.defaults.align_def import align_defaults
+from masster.study.defaults.export_def import export_mgf_defaults
+from masster.study.defaults.fill_chrom_def import fill_chrom_defaults
+from masster.study.defaults.fill_def import fill_defaults
+from masster.study.defaults.find_consensus_def import find_consensus_defaults
+from masster.study.defaults.find_ms2_def import find_ms2_defaults
+from masster.study.defaults.integrate_chrom_def import integrate_chrom_defaults
+from masster.study.defaults.integrate_def import integrate_defaults
+from masster.study.defaults.merge_def import merge_defaults
 
 
 class Study:
@@ -357,6 +366,17 @@ class Study:
     export_mztab = export_mztab
     _get_mgf_df = _get_mgf_df  # New function for MGF data extraction
 
+    # defaults
+    study_defaults = study_defaults
+    align_defaults = align_defaults
+    export_mgf_defaults = export_mgf_defaults
+    fill_chrom_defaults = fill_chrom_defaults
+    fill_defaults = fill_defaults
+    find_consensus_defaults = find_consensus_defaults
+    find_ms2_defaults = find_ms2_defaults
+    integrate_chrom_defaults = integrate_chrom_defaults
+    integrate_defaults = integrate_defaults
+    merge_defaults = merge_defaults
 
     def _reload(self):
         """

{masster-0.3.5 → masster-0.3.7}/uv.lock

@@ -1315,7 +1315,7 @@ wheels = [
 
 [[package]]
 name = "masster"
-version = "0.3.5"
+version = "0.3.7"
 source = { editable = "." }
 dependencies = [
     { name = "alphabase" },