masster 0.4.5__py3-none-any.whl → 0.4.9__py3-none-any.whl

masster/study/id.py

@@ -36,7 +36,7 @@ def lib_load(
     """
     # Lazy import to avoid circular imports at module import time
     try:
-        from master.lib.lib import Lib
+        from masster.lib.lib import Lib
     except Exception:
         Lib = None
 
@@ -58,7 +58,7 @@ def lib_load(
     if isinstance(lib_source, str):
         if Lib is None:
             raise ImportError(
-                "Could not import master.lib.lib.Lib - required for CSV loading",
+                "Could not import masster.lib.lib.Lib - required for CSV loading",
             )
 
         lib_obj = Lib()
@@ -74,7 +74,7 @@ def lib_load(
 
     else:
         raise TypeError(
-            "lib_source must be a CSV file path (str), a master.lib.Lib instance, or have a 'lib_df' attribute",
+            "lib_source must be a CSV file path (str), a masster.lib.Lib instance, or have a 'lib_df' attribute",
         )
 
     # Ensure lib_df is populated
@@ -159,7 +159,7 @@ def identify(study, features=None, params=None, **kwargs):
     """
     # Import defaults class
     try:
-        from master.study.defaults.identify_def import identify_defaults
+        from masster.study.defaults.identify_def import identify_defaults
     except ImportError:
         identify_defaults = None
 

masster/study/load.py

@@ -10,10 +10,10 @@ import pyopenms as oms
 
 from tqdm import tqdm
 
-from master.chromatogram import Chromatogram
-from master.study.defaults import fill_defaults
-from master.sample.sample import Sample
-from master.spectrum import Spectrum
+from masster.chromatogram import Chromatogram
+from masster.study.defaults import fill_defaults
+from masster.sample.sample import Sample
+from masster.spectrum import Spectrum
 
 
 # Pre-import heavy modules to avoid repeated loading in add_sample()
@@ -144,7 +144,7 @@ def add(
         )
     else:
         self.logger.debug(f"Successfully added {counter} samples to the study.")
-    
+
     # Return a simple summary to suppress marimo's automatic object display
     return f"Added {counter} samples to study"
 
@@ -533,7 +533,7 @@ def fill_single(self, **kwargs):
         min_samples_abs: Absolute minimum sample threshold (default: 2)
     """
     # parameters initialization
-    from master.study.defaults import fill_defaults
+    from masster.study.defaults import fill_defaults
 
     params = fill_defaults()
 

masster/study/plot.py

@@ -1132,7 +1132,7 @@ def plot_bpc(
     from bokeh.plotting import figure, show, output_file
     from bokeh.models import ColumnDataSource, HoverTool
     from bokeh.io.export import export_png
-    from master.study.helpers import get_bpc
+    from masster.study.helpers import get_bpc
 
     sample_uids = self._get_sample_uids(samples)
     if not sample_uids:
@@ -1309,7 +1309,7 @@ def plot_eic(
     from bokeh.plotting import figure, show, output_file
     from bokeh.models import ColumnDataSource, HoverTool
     from bokeh.io.export import export_png
-    from master.study.helpers import get_eic
+    from masster.study.helpers import get_eic
 
     # Use study's eic_mz_tol parameter as default if not provided
     if mz_tol is None:
@@ -2325,7 +2325,7 @@ def plot_tic(
     from bokeh.plotting import figure, show, output_file
     from bokeh.models import ColumnDataSource, HoverTool
     from bokeh.io.export import export_png
-    from master.study.helpers import get_tic
+    from masster.study.helpers import get_tic
 
     sample_uids = self._get_sample_uids(samples)
     if not sample_uids:

masster/study/processing.py

@@ -8,7 +8,7 @@ import pyopenms as oms
 
 from tqdm import tqdm
 
-from master.study.defaults import (
+from masster.study.defaults import (
     align_defaults,
     find_ms2_defaults,
     integrate_defaults,
@@ -152,7 +152,7 @@ def align(self, **kwargs):
     all_update_rt = []
     all_update_rt_original = []
 
-    tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
+    tdqm_disable = self.log_level not in ["TRACE", "DEBUG"]
 
     for index, fm in tqdm(
         list(enumerate(fmaps)),
@@ -1754,7 +1754,7 @@ def _align_kd_algorithm(study_obj, fmaps, params):
             study_obj.logger.warning(f"Map {i}: failed applying transformation ({e})")
 
     study_obj.logger.info(
-        f"Custom KD alignment completed. Reference index {ref_index}. Applied {len(transformations)} transformations.",
+        f"Alignment completed. Reference index {ref_index}.",
     )
 
 

masster/study/save.py

@@ -9,7 +9,7 @@ import pyopenms as oms
 
 from tqdm import tqdm
 
-from master.sample.sample import Sample
+from masster.sample.sample import Sample
 
 
 def save(self, filename=None, add_timestamp=True, compress=False):

masster/study/study.py

@@ -52,111 +52,111 @@ import sys
 import polars as pl
 
 # Study-specific imports
-from master.study.h5 import _load_study5
-from master.study.h5 import _save_study5
-from master.study.h5 import _save_study5_compressed
-from master.study.helpers import _get_consensus_uids
-from master.study.helpers import _get_feature_uids
-from master.study.helpers import _get_sample_uids
-from master.study.helpers import _ensure_features_df_schema_order
-from master.study.helpers import compress
-from master.study.helpers import compress_features
-from master.study.helpers import compress_ms2
-from master.study.helpers import compress_chrom
-from master.study.helpers import restore_features
-from master.study.helpers import restore_chrom
-from master.study.helpers import restore_ms2
-from master.study.helpers import decompress
-from master.study.helpers import fill_reset
-from master.study.helpers import get_chrom
-from master.study.helpers import get_sample
-from master.study.helpers import get_consensus
-from master.study.helpers import get_consensus_matches
-from master.study.helpers import get_consensus_matrix
-from master.study.helpers import get_orphans
-from master.study.helpers import get_gaps_matrix
-from master.study.helpers import get_gaps_stats
-from master.study.helpers import align_reset
-from master.study.helpers import set_folder
-from master.study.helpers import set_source
-from master.study.helpers import sample_color
-from master.study.helpers import sample_color_reset
-from master.study.helpers import sample_name_replace
-from master.study.helpers import sample_name_reset
-from master.study.helpers import samples_select
-from master.study.helpers import samples_delete
-from master.study.helpers import features_select
-from master.study.helpers import features_filter
-from master.study.helpers import features_delete
-from master.study.helpers import consensus_select
-from master.study.helpers import consensus_filter
-from master.study.helpers import consensus_delete
-from master.study.load import add
-from master.study.load import add_sample
-from master.study.load import _add_samples_batch
-from master.study.load import _add_sample_optimized
-from master.study.load import _add_sample_standard
-from master.study.load import _sample_color_reset_optimized
-from master.study.load import fill_single
-from master.study.load import fill
-from master.study.load import _process_sample_for_parallel_fill
-from master.study.load import _get_missing_consensus_sample_combinations
-from master.study.load import load
-from master.study.load import _load_consensusXML
-from master.study.load import load_features
-from master.study.load import sanitize
-from master.study.plot import plot_alignment
-from master.study.plot import plot_consensus_2d
-from master.study.plot import plot_samples_2d
-from master.study.plot import plot_consensus_stats
-from master.study.plot import plot_chrom
-from master.study.plot import plot_pca
-from master.study.plot import plot_bpc
-from master.study.plot import plot_tic
-from master.study.plot import plot_eic
-from master.study.plot import plot_rt_correction
-from master.study.processing import align
-from master.study.processing import merge
-from master.study.processing import integrate
-from master.study.processing import find_ms2
-from master.study.parameters import store_history
-from master.study.parameters import get_parameters
-from master.study.parameters import update_parameters
-from master.study.parameters import get_parameters_property
-from master.study.parameters import set_parameters_property
-from master.study.save import save, save_consensus, _save_consensusXML, save_samples
-from master.study.export import (
+from masster.study.h5 import _load_study5
+from masster.study.h5 import _save_study5
+from masster.study.h5 import _save_study5_compressed
+from masster.study.helpers import _get_consensus_uids
+from masster.study.helpers import _get_feature_uids
+from masster.study.helpers import _get_sample_uids
+from masster.study.helpers import _ensure_features_df_schema_order
+from masster.study.helpers import compress
+from masster.study.helpers import compress_features
+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
+from masster.study.helpers import get_consensus
+from masster.study.helpers import get_consensus_matches
+from masster.study.helpers import get_consensus_matrix
+from masster.study.helpers import get_orphans
+from masster.study.helpers import get_gaps_matrix
+from masster.study.helpers import get_gaps_stats
+from masster.study.helpers import align_reset
+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 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.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
+from masster.study.load import _get_missing_consensus_sample_combinations
+from masster.study.load import load
+from masster.study.load import _load_consensusXML
+from masster.study.load import load_features
+from masster.study.load import sanitize
+from masster.study.plot import plot_alignment
+from masster.study.plot import plot_consensus_2d
+from masster.study.plot import plot_samples_2d
+from masster.study.plot import plot_consensus_stats
+from masster.study.plot import plot_chrom
+from masster.study.plot import plot_pca
+from masster.study.plot import plot_bpc
+from masster.study.plot import plot_tic
+from masster.study.plot import plot_eic
+from masster.study.plot import plot_rt_correction
+from masster.study.processing import align
+from masster.study.processing import merge
+from masster.study.processing import integrate
+from masster.study.processing import find_ms2
+from masster.study.parameters import store_history
+from masster.study.parameters import get_parameters
+from masster.study.parameters import update_parameters
+from masster.study.parameters import get_parameters_property
+from masster.study.parameters import set_parameters_property
+from masster.study.save import save, save_consensus, _save_consensusXML, save_samples
+from masster.study.export import (
     export_mgf,
     export_mztab,
     export_xlsx,
     export_parquet,
     _get_mgf_df,
 )
-from master.study.id import lib_load, identify, get_id, id_reset, lib_reset
-from master.study.id import (
+from masster.study.id import lib_load, identify, get_id, id_reset, lib_reset
+from masster.study.id import (
     _get_adducts,
     _calculate_formula_mass_shift,
     _format_adduct_name,
     _parse_element_counts,
 )
 
-from master.logger import MasterLogger
-from master.study.defaults.study_def import study_defaults
-from master.study.defaults.align_def import align_defaults
-from master.study.defaults.export_def import export_mgf_defaults
-from master.study.defaults.fill_chrom_def import fill_chrom_defaults
-from master.study.defaults.fill_def import fill_defaults
-from master.study.defaults.find_consensus_def import find_consensus_defaults
-from master.study.defaults.find_ms2_def import find_ms2_defaults
-from master.study.defaults.integrate_chrom_def import integrate_chrom_defaults
-from master.study.defaults.integrate_def import integrate_defaults
-from master.study.defaults.merge_def import merge_defaults
+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
 
 # Import sample defaults
-from master.sample.defaults.sample_def import sample_defaults
-from master.sample.defaults.find_features_def import find_features_defaults
-from master.sample.defaults.find_adducts_def import find_adducts_defaults
-from master.sample.defaults.get_spectrum_def import get_spectrum_defaults
+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.get_spectrum_def import get_spectrum_defaults
 
 # Warning symbols for info display
 _WARNING_SYMBOL = "⚠️"  # Yellow warning triangle
@@ -188,8 +188,8 @@ class Study:
         - `export_consensus()`: Export consensus features for downstream analysis.
 
     Example Usage:
-        >>> from master import study
-        >>> study_obj = study(folder="./data")
+        >>> from masster import Study
+        >>> study_obj = Study(folder="./data")
         >>> study_obj.load_folder("./mzml_files")
         >>> study_obj.process_all()
         >>> study_obj.align()
@@ -342,7 +342,7 @@ class Study:
         self.id_df = pl.DataFrame()
 
         # Initialize independent logger
-        self.logger = MasterLogger(
+        self.logger = MassterLogger(
             instance_type="study",
             level=self.log_level.upper(),
             label=self.log_label,
@@ -479,20 +479,20 @@ class Study:
 
     def _reload(self):
         """
-        Reloads all master modules to pick up any changes to their source code,
+        Reloads all masster modules to pick up any changes to their source code,
         and updates the instance's class reference to the newly reloaded class version.
         This ensures that the instance uses the latest implementation without restarting the interpreter.
         """
         # Reset logger configuration flags to allow proper reconfiguration after reload
         """        try:
-            import master.sample.logger as logger_module
+            import masster.sample.logger as logger_module
 
             if hasattr(logger_module, "_STUDY_LOGGER_CONFIGURED"):
                 logger_module._STUDY_LOGGER_CONFIGURED = False
         except Exception:
             pass"""
 
-        # Get the base module name (master)
+        # Get the base module name (masster)
         base_modname = self.__class__.__module__.split(".")[0]
         current_module = self.__class__.__module__
 
@@ -508,7 +508,7 @@ class Study:
             ):
                 study_modules.append(module_name)
 
-        # Add core master modules
+        # Add core masster modules
         core_modules = [
             f"{base_modname}._version",
             f"{base_modname}.chromatogram",