masster 0.5.8__tar.gz → 0.5.10__tar.gz

{masster-0.5.8 → masster-0.5.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.8
+Version: 0.5.10
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -685,6 +685,7 @@ Requires-Dist: altair>=5.5.0
 Requires-Dist: bokeh>=3.7.3
 Requires-Dist: cmap>=0.6.2
 Requires-Dist: datashader>=0.18.1
+Requires-Dist: get-gecko-driver>=1.4
 Requires-Dist: h5py>=3.14.0
 Requires-Dist: hdbscan>=0.8.40
 Requires-Dist: holoviews>=1.21.0
@@ -703,6 +704,7 @@ Requires-Dist: scikit-learn>=1.7.1
 Requires-Dist: scipy>=1.12.0
 Requires-Dist: tqdm>=4.65.0
 Requires-Dist: umap-learn>=0.5.9.post2
+Requires-Dist: webdriver-manager>=4.0.2
 Provides-Extra: dev
 Requires-Dist: bandit>=1.7.0; extra == 'dev'
 Requires-Dist: black>=23.0.0; extra == 'dev'

{masster-0.5.8 → masster-0.5.10}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.5.8"
+version = "0.5.10"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }
@@ -49,6 +49,8 @@ dependencies = [
     "scikit-learn>=1.7.1",
     "umap-learn>=0.5.9.post2",
     "hdbscan>=0.8.40",
+    "get-gecko-driver>=1.4",
+    "webdriver-manager>=4.0.2",
 ]
 
 [project.optional-dependencies]

{masster-0.5.8 → masster-0.5.10}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.5.8"
+__version__ = "0.5.10"
 
 
 def get_version():

{masster-0.5.8 → masster-0.5.10}/src/masster/logger.py

@@ -3,15 +3,15 @@
 Simple logger system for masster Study and Sample instances.
 Uses basic Python logging                timestamp = dt.strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]
 
-                # Loguru-style colors for different log levels
+                # Universal colors compatible with both dark and light themes
                 level_colors = {
-                    'TRACE': '\x1b[34m',      # blue
-                    'DEBUG': '\x1b[36m',      # cyan
-                    'INFO': '\x1b[37m',       # white
-                    'SUCCESS': '\x1b[32m',    # green
-                    'WARNING': '\x1b[33m',    # yellow
-                    'ERROR': '\x1b[31m',      # red
-                    'CRITICAL': '\x1b[35m',   # magenta
+                    'TRACE': '\x1b[94m',      # bright blue (readable on both dark/light)
+                    'DEBUG': '\x1b[96m',      # bright cyan (readable on both dark/light)  
+                    'INFO': '\x1b[90m',       # bright black/gray (readable on both dark/light)
+                    'SUCCESS': '\x1b[92m',    # bright green (readable on both dark/light)
+                    'WARNING': '\x1b[93m',    # bright yellow (readable on both dark/light)
+                    'ERROR': '\x1b[91m',      # bright red (readable on both dark/light)
+                    'CRITICAL': '\x1b[95m',   # bright magenta (readable on both dark/light)
                 }
 
                 level_str = record.levelname.ljust(8)complex loguru filtering.
@@ -102,19 +102,19 @@ class MassterLogger:
                 dt = datetime.datetime.fromtimestamp(record.created)
                 timestamp = dt.strftime("%Y-%m-%d %H:%M:%S.%f")[:-3]  # Remove last 3 digits for milliseconds
 
-                # Loguru-style colors for different log levels
+                # Universal colors compatible with both dark and light themes
                 level_colors = {
-                    "TRACE": "\x1b[34m",  # blue
-                    "DEBUG": "\x1b[36m",  # cyan
-                    "INFO": "\x1b[37m",  # white
-                    "SUCCESS": "\x1b[32m",  # green
-                    "WARNING": "\x1b[33m",  # yellow
-                    "ERROR": "\x1b[31m",  # red
-                    "CRITICAL": "\x1b[35m",  # magenta
+                    "TRACE": "\x1b[94m",  # bright blue (readable on both dark/light)
+                    "DEBUG": "\x1b[96m",  # bright cyan (readable on both dark/light)
+                    "INFO": "\x1b[90m",   # bright black/gray (readable on both dark/light)
+                    "SUCCESS": "\x1b[92m",  # bright green (readable on both dark/light)
+                    "WARNING": "\x1b[93m",  # bright yellow (readable on both dark/light)
+                    "ERROR": "\x1b[91m",    # bright red (readable on both dark/light)
+                    "CRITICAL": "\x1b[95m", # bright magenta (readable on both dark/light)
                 }
 
                 level_str = record.levelname.ljust(8)
-                level_color = level_colors.get(record.levelname, "\x1b[37m")  # default white
+                level_color = level_colors.get(record.levelname, "\x1b[90m")  # default to gray instead of white
                 label_part = self.label + " | " if self.label else ""
 
                 # For DEBUG and TRACE levels, add module/location information
@@ -133,9 +133,9 @@ class MassterLogger:
                         f"\x1b[90m{module_name}:{func_name}:{line_no}\x1b[0m | "  # dim gray for location info
                     )
 
-                # Loguru-style format: <white>timestamp</white> | <level>LEVEL</level> | <location> | <cyan>label</cyan> - <level>message</level>
+                # Universal format: timestamp | level | location | label - message
                 return (
-                    f"\x1b[37m{timestamp}\x1b[0m | "  # white timestamp
+                    f"\x1b[90m{timestamp}\x1b[0m | "  # gray timestamp (universal for both themes)
                     f"{level_color}{level_str}\x1b[0m | "  # colored level
                     f"{location_info}"  # location info for DEBUG/TRACE
                     f"{level_color}{label_part}\x1b[0m"  # colored label
@@ -181,19 +181,19 @@ class MassterLogger:
                 dt = datetime.datetime.fromtimestamp(record.created)
                 timestamp = dt.strftime("%Y-%m-%d %H:%M:%S.%f")[:-3]
 
-                # Loguru-style colors for different log levels
+                # Universal colors compatible with both dark and light themes
                 level_colors = {
-                    "TRACE": "\x1b[34m",  # blue
-                    "DEBUG": "\x1b[36m",  # cyan
-                    "INFO": "\x1b[37m",  # white
-                    "SUCCESS": "\x1b[32m",  # green
-                    "WARNING": "\x1b[33m",  # yellow
-                    "ERROR": "\x1b[31m",  # red
-                    "CRITICAL": "\x1b[35m",  # magenta
+                    "TRACE": "\x1b[94m",  # bright blue (readable on both dark/light)
+                    "DEBUG": "\x1b[96m",  # bright cyan (readable on both dark/light)
+                    "INFO": "\x1b[90m",   # bright black/gray (readable on both dark/light)
+                    "SUCCESS": "\x1b[92m",  # bright green (readable on both dark/light)
+                    "WARNING": "\x1b[93m",  # bright yellow (readable on both dark/light)
+                    "ERROR": "\x1b[91m",    # bright red (readable on both dark/light)
+                    "CRITICAL": "\x1b[95m", # bright magenta (readable on both dark/light)
                 }
 
                 level_str = record.levelname.ljust(8)
-                level_color = level_colors.get(record.levelname, "\x1b[37m")  # default white
+                level_color = level_colors.get(record.levelname, "\x1b[90m")  # default to gray instead of white
                 label_part = self.label + " | " if self.label else ""
 
                 # For DEBUG and TRACE levels, add module/location information
@@ -212,9 +212,9 @@ class MassterLogger:
                         f"\x1b[90m{module_name}:{func_name}:{line_no}\x1b[0m | "  # dim gray for location info
                     )
 
-                # Loguru-style format: <white>timestamp</white> | <level>LEVEL</level> | <location> | <cyan>label</cyan> - <level>message</level>
+                # Universal format: timestamp | level | location | label - message  
                 return (
-                    f"\x1b[37m{timestamp}\x1b[0m | "  # white timestamp
+                    f"\x1b[90m{timestamp}\x1b[0m | "  # gray timestamp (universal for both themes)
                     f"{level_color}{level_str}\x1b[0m | "  # colored level
                     f"{location_info}"  # location info for DEBUG/TRACE
                     f"{level_color}{label_part}\x1b[0m"  # colored label
@@ -245,19 +245,19 @@ class MassterLogger:
                 dt = datetime.datetime.fromtimestamp(record.created)
                 timestamp = dt.strftime("%Y-%m-%d %H:%M:%S.%f")[:-3]
 
-                # Loguru-style colors for different log levels
+                # Universal colors compatible with both dark and light themes
                 level_colors = {
-                    "TRACE": "\x1b[34m",  # blue
-                    "DEBUG": "\x1b[36m",  # cyan
-                    "INFO": "\x1b[37m",  # white
-                    "SUCCESS": "\x1b[32m",  # green
-                    "WARNING": "\x1b[33m",  # yellow
-                    "ERROR": "\x1b[31m",  # red
-                    "CRITICAL": "\x1b[35m",  # magenta
+                    "TRACE": "\x1b[94m",  # bright blue (readable on both dark/light)
+                    "DEBUG": "\x1b[96m",  # bright cyan (readable on both dark/light)
+                    "INFO": "\x1b[90m",   # bright black/gray (readable on both dark/light)
+                    "SUCCESS": "\x1b[92m",  # bright green (readable on both dark/light)
+                    "WARNING": "\x1b[93m",  # bright yellow (readable on both dark/light)
+                    "ERROR": "\x1b[91m",    # bright red (readable on both dark/light)
+                    "CRITICAL": "\x1b[95m", # bright magenta (readable on both dark/light)
                 }
 
                 level_str = record.levelname.ljust(8)
-                level_color = level_colors.get(record.levelname, "\x1b[37m")  # default white
+                level_color = level_colors.get(record.levelname, "\x1b[90m")  # default to gray instead of white
                 label_part = self.label + " | " if self.label else ""
 
                 # For DEBUG and TRACE levels, add module/location information
@@ -276,9 +276,9 @@ class MassterLogger:
                         f"\x1b[90m{module_name}:{func_name}:{line_no}\x1b[0m | "  # dim gray for location info
                     )
 
-                # Loguru-style format: <white>timestamp</white> | <level>LEVEL</level> | <location> | <cyan>label</cyan> - <level>message</level>
+                # Universal format: timestamp | level | location | label - message  
                 return (
-                    f"\x1b[37m{timestamp}\x1b[0m | "  # white timestamp
+                    f"\x1b[90m{timestamp}\x1b[0m | "  # gray timestamp (universal for both themes)
                     f"{level_color}{level_str}\x1b[0m | "  # colored level
                     f"{location_info}"  # location info for DEBUG/TRACE
                     f"{level_color}{label_part}\x1b[0m"  # colored label
@@ -332,8 +332,22 @@ class MassterLogger:
         self.logger_instance.info(message, *args, **kwargs)
 
     def success(self, message: str, *args, **kwargs):
-        """Log a SUCCESS level message (mapped to INFO)."""
-        self.info(message, *args, **kwargs)
+        """Log a SUCCESS level message (custom level)."""
+        # Create a custom log record with SUCCESS level
+        import logging
+        
+        # Create a LogRecord manually with SUCCESS level
+        record = self.logger_instance.makeRecord(
+            self.logger_instance.name,
+            logging.INFO,  # Use INFO level for Python's filtering
+            "", 0, message, args, None, func="success"
+        )
+        # Override the levelname for display
+        record.levelname = "SUCCESS"
+        
+        # Handle the record directly through our handler
+        if self.handler:
+            self.handler.handle(record)
 
     def warning(self, message: str, *args, **kwargs):
         """Log a WARNING level message."""
@@ -372,3 +386,4 @@ class MassterLogger:
 
     def __repr__(self):
         return f"MassterLogger(type={self.instance_type}, id={self.instance_id}, level={self.level})"
+

{masster-0.5.8 → masster-0.5.10}/src/masster/sample/adducts.py

@@ -798,8 +798,8 @@ def find_adducts(self, **kwargs):
     total_with_adducts = sum(1 for x in final_adducts if x is not None)
     total_groups = max(final_groups) if final_groups else 0
 
-    self.logger.info(
-        f"Adduct detection completed: {total_with_adducts} features with adducts in {total_groups} groups",
+    self.logger.success(
+        f"Adduct detection completed. Features with adducts: {total_with_adducts}. Adduct groups: {total_groups}.",
     )
 
     # Store parameters including the actual processed adducts list

{masster-0.5.8 → masster-0.5.10}/src/masster/sample/h5.py

@@ -295,7 +295,7 @@ def _save_sample5(
 
         # Store lib and lib_match - removed (no longer saving lib data)
 
-    self.logger.info(f"Sample saved to {filename}")
+    self.logger.success(f"Sample saved to {filename}")
     if save_featurexml:
         # Get or recreate the feature map if needed
         feature_map = self._get_feature_map()

{masster-0.5.8 → masster-0.5.10}/src/masster/sample/helpers.py

@@ -360,6 +360,7 @@ def get_eic(self, mz, mz_tol=None):
 
 def features_select(
     self,
+    uid=None,
     mz=None,
     rt=None,
     coherence=None,
@@ -369,15 +370,16 @@ def features_select(
     iso_of=None,
     has_MS2=None,
     prominence_scaled=None,
-    height_scaled=None,
     prominence=None,
+    height_scaled=None,
     height=None,
-    uids=None,
+    adduct_group=None,
 ):
     """
     Select features based on specified criteria and return the filtered DataFrame.
 
     Parameters:
+        uid: feature UID filter (list of feature UIDs, tuple for range of feature UIDs, polars/pandas DataFrame with feature_uid/feature_id column, or None for all features)
         mz: m/z range filter (tuple for range, single value for minimum)
         rt: retention time range filter (tuple for range, single value for minimum)
         coherence: chromatogram coherence filter (tuple for range, single value for minimum)
@@ -390,8 +392,7 @@ def features_select(
         height_scaled: scaled height filter (tuple for range, single value for minimum)
         prominence: prominence filter (tuple for range, single value for minimum)
         height: height filter (tuple for range, single value for minimum)
-        uids: feature UID filter (list of feature UIDs, polars/pandas DataFrame with feature_uid/feature_id column, or None for all features)
-
+        adduct_group: adduct group filter (single value for exact match, list of values for multiple groups, tuple for range, or None for all)
     Returns:
         polars.DataFrame: Filtered features DataFrame
     """
@@ -402,17 +403,29 @@ def features_select(
     feats = self.features_df.clone()
     
     # Filter by feature UIDs if provided
-    if uids is not None:
-        feature_uids_to_keep = self._get_feature_uids(features=uids, verbose=True)
-        if not feature_uids_to_keep:
-            self.logger.warning("No valid feature UIDs provided.")
-            return feats.limit(0)  # Return empty DataFrame with same structure
-        
-        feats_len_before_filter = len(feats)
-        feats = feats.filter(pl.col("feature_uid").is_in(feature_uids_to_keep))
-        self.logger.debug(
-            f"Selected features by UIDs. Features removed: {feats_len_before_filter - len(feats)}",
-        )
+    if uid is not None:
+        if isinstance(uid, tuple) and len(uid) == 2:
+            # Handle tuple as range of feature UIDs
+            min_uid, max_uid = uid
+            feats_len_before_filter = len(feats)
+            feats = feats.filter(
+                (pl.col("feature_uid") >= min_uid) & (pl.col("feature_uid") <= max_uid)
+            )
+            self.logger.debug(
+                f"Selected features by UID range ({min_uid}-{max_uid}). Features removed: {feats_len_before_filter - len(feats)}",
+            )
+        else:
+            # Handle list or DataFrame input
+            feature_uids_to_keep = self._get_feature_uids(features=uid, verbose=True)
+            if not feature_uids_to_keep:
+                self.logger.warning("No valid feature UIDs provided.")
+                return feats.limit(0)  # Return empty DataFrame with same structure
+            
+            feats_len_before_filter = len(feats)
+            feats = feats.filter(pl.col("feature_uid").is_in(feature_uids_to_keep))
+            self.logger.debug(
+                f"Selected features by UIDs. Features removed: {feats_len_before_filter - len(feats)}",
+            )
     
     if coherence is not None:
         has_coherence = "chrom_coherence" in self.features_df.columns
@@ -579,6 +592,25 @@ def features_select(
         self.logger.debug(
             f"Selected features by {height_col}. Features removed: {feats_len_before_filter - len(feats)}",
         )
+
+    if adduct_group is not None:
+        feats_len_before_filter = len(feats)
+        if "adduct_group" not in feats.columns:
+            self.logger.warning("No adduct_group data found in features.")
+        else:
+            if isinstance(adduct_group, tuple) and len(adduct_group) == 2:
+                min_adduct_group, max_adduct_group = adduct_group
+                feats = feats.filter(
+                    (pl.col("adduct_group") >= min_adduct_group) & (pl.col("adduct_group") <= max_adduct_group)
+                )
+            elif isinstance(adduct_group, list):
+                feats = feats.filter(pl.col("adduct_group").is_in(adduct_group))
+            else:
+                feats = feats.filter(pl.col("adduct_group") == adduct_group)
+            self.logger.debug(
+                f"Selected features by adduct_group. Features removed: {feats_len_before_filter - len(feats)}",
+            )
+
     if len(feats) == 0:
         self.logger.warning("No features remaining after applying selection criteria.")
     else: