masster 0.4.16__tar.gz → 0.4.18__tar.gz

{masster-0.4.16 → masster-0.4.18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.4.16
+Version: 0.4.18
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -767,7 +767,8 @@ study.integrate()
 # export results
 study.export_mgf()
 study.export_mztab()
-study.export_consensus()
+study.export_xlsx()
+study.export_parquet()
 
 # Save the study to .study5
 study.save()

{masster-0.4.16 → masster-0.4.18}/README.md

@@ -41,7 +41,8 @@ study.integrate()
 # export results
 study.export_mgf()
 study.export_mztab()
-study.export_consensus()
+study.export_xlsx()
+study.export_parquet()
 
 # Save the study to .study5
 study.save()

{masster-0.4.16 → masster-0.4.18}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.4.16"
+version = "0.4.18"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.4.16 → masster-0.4.18}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.4.16"
+__version__ = "0.4.18"
 
 
 def get_version():

{masster-0.4.16 → masster-0.4.18}/src/masster/study/defaults/merge_def.py

@@ -25,24 +25,36 @@ class merge_defaults:
         link_ms2 (bool): Whether to link MS2 spectra to consensus features. Default is True.
     """
 
-    method: str = "kd"
-    min_samples: int = 10
+    method: str = "qt"
+    min_samples: int = 2
     rt_tol: float = 5.0
     mz_tol: float = 0.01
-    chunk_size: int = 300
+    chunk_size: int = 500
     nr_partitions: int = 1000
-    min_rel_cc_size: float = 0.2
+    min_rel_cc_size: float = 0.1
     max_pairwise_log_fc: float = -1.0
     max_nr_conflicts: int = 0
     link_ms2: bool = True
+    
+    # KD-Strict specific parameters
+    optimize_rt_tol: bool = False
+    rt_tol_range: tuple = (0.5, 4.0)  
+    rt_tol_steps: int = 7
+    secondary_merge_rt_tol: float = 1.0
+    secondary_merge_mz_tol: float = 0.005
+    min_sample_overlap: float = 0.8
+    max_rt_spread: float = 2.0  # Will default to 2x rt_tol
+    min_coherence: float = 0.0
 
     _param_metadata: dict[str, dict[str, Any]] = field(
         default_factory=lambda: {
             "method": {
                 "dtype": str,
                 "description": "Merge method (algorithm) to use",
-                "default": "kd",
-                "allowed_values": ["kd", "qt", "kd-nowarp", "chunked"],
+                "default": "quality",
+                "allowed_values": ["sensitivity", "qt", "nowarp", "chunked", "quality", 
+                                 "kd", "kd-nowarp", "kd_nowarp", "kd-strict", "kd_strict",
+                                 "kd_chunked", "kd-chunked", "qt_chunked", "qt-chunked"],
             },
             "min_samples": {
                 "dtype": int,
@@ -103,6 +115,58 @@ class merge_defaults:
                 "description": "Whether to link MS2 spectra to consensus features",
                 "default": True,
             },
+            # KD-Strict specific parameters
+            "optimize_rt_tol": {
+                "dtype": bool,
+                "description": "Enable RT tolerance optimization for kd-strict method",
+                "default": False,
+            },
+            "rt_tol_range": {
+                "dtype": tuple,
+                "description": "RT tolerance range for optimization (min, max) in seconds",
+                "default": (0.8, 2.0),
+            },
+            "rt_tol_steps": {
+                "dtype": int,
+                "description": "Number of steps for RT tolerance optimization",
+                "default": 5,
+                "min_value": 3,
+                "max_value": 20,
+            },
+            "secondary_merge_rt_tol": {
+                "dtype": float,
+                "description": "RT tolerance for secondary clustering in kd-strict (seconds)",
+                "default": 0.5,
+                "min_value": 0.1,
+                "max_value": 5.0,
+            },
+            "secondary_merge_mz_tol": {
+                "dtype": float,
+                "description": "m/z tolerance for secondary clustering in kd-strict (Da)",
+                "default": 0.005,
+                "min_value": 0.001,
+                "max_value": 0.1,
+            },
+            "min_sample_overlap": {
+                "dtype": float,
+                "description": "Minimum sample overlap ratio for merging features (0.0-1.0)",
+                "default": 0.8,
+                "min_value": 0.0,
+                "max_value": 1.0,
+            },
+            "max_rt_spread": {
+                "dtype": float,
+                "description": "Maximum allowed RT spread in seconds (None = 3x rt_tol)",
+                "default": None,
+                "min_value": 0.1,
+            },
+            "min_coherence": {
+                "dtype": float,
+                "description": "Minimum chromatographic coherence score (0.0 = disabled)",
+                "default": 0.0,
+                "min_value": 0.0,
+                "max_value": 1.0,
+            },
         },
         repr=False,
     )