masster 0.5.23__tar.gz → 0.5.24__tar.gz

{masster-0.5.23 → masster-0.5.24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.23
+Version: 0.5.24
 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-0.5.23 → masster-0.5.24}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.5.23"
+version = "0.5.24"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.5.23 → masster-0.5.24}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.5.23"
+__version__ = "0.5.24"
 
 
 def get_version():

{masster-0.5.23 → masster-0.5.24}/src/masster/study/h5.py

@@ -717,11 +717,33 @@ def _reconstruct_object_column(data_col, col_name: str):
                 # Handle isotope patterns (numpy arrays with [mz, intensity] data)
                 try:
                     import numpy as np
-
-                    iso_data = json.loads(item)
-                    # Convert back to numpy array
-                    reconstructed_data.append(np.array(iso_data) if iso_data else None)
-                except (json.JSONDecodeError, ValueError, ImportError):
+                    
+                    # Try JSON parsing first (new format)
+                    try:
+                        iso_data = json.loads(item)
+                        # Convert back to numpy array
+                        reconstructed_data.append(np.array(iso_data) if iso_data else None)
+                    except json.JSONDecodeError:
+                        # Handle numpy array string representation (old format)
+                        # This handles strings like "[[   875.7865 447675.    ]\n [   876.7902 168819.    ]]"
+                        try:
+                            # Use numpy's string representation parser
+                            iso_array = np.fromstring(item.replace('[', '').replace(']', '').replace('\n', ' '), sep=' ')
+                            # Reshape to 2D array (pairs of mz, intensity)
+                            if len(iso_array) % 2 == 0:
+                                iso_array = iso_array.reshape(-1, 2)
+                                reconstructed_data.append(iso_array)
+                            else:
+                                reconstructed_data.append(None)
+                        except (ValueError, AttributeError):
+                            # If all else fails, try to evaluate the string as a literal
+                            try:
+                                import ast
+                                iso_data = ast.literal_eval(item)
+                                reconstructed_data.append(np.array(iso_data) if iso_data else None)
+                            except (ValueError, SyntaxError):
+                                reconstructed_data.append(None)
+                except (ValueError, ImportError):
                     reconstructed_data.append(None)
             elif col_name == "ms1_spec":
                 # Handle MS1 spectra patterns (numpy arrays with [mz, intensity] data)
@@ -1952,10 +1974,15 @@ def _load_study5(self, filename=None):
                 f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]} | INFO     | {self.log_label}Loading consensus",
             )
             if "consensus" in f and len(f["consensus"].keys()) > 0:
-                # Only include adducts in object_columns if it actually exists in the file
+                # Only include object columns if they actually exist in the file
                 object_columns = []
-                if "adducts" in f["consensus"]:
-                    object_columns.append("adducts")
+                try:
+                    if "adducts" in f["consensus"]:
+                        object_columns.append("adducts")
+                    if "iso" in f["consensus"]:
+                        object_columns.append("iso")
+                except (KeyError, TypeError):
+                    pass
 
                 self.consensus_df = _load_dataframe_from_group(
                     f["consensus"],

{masster-0.5.23 → masster-0.5.24}/src/masster/wizard/wizard.py

@@ -526,7 +526,7 @@ class Wizard:
             "    # === Processing Parameters ===",
             f'    "adducts": {self.params.adducts!r},  # Adduct specifications for feature detection and annotation',
             f'    "noise": {noise},  # Noise threshold for feature detection',
-            f'    "chrom_fwhm": {self.params.chrom_fwhm},  # Chromatographic peak full width at half maximum (seconds)',
+            f'    "chrom_fwhm": {chrom_fwhm},  # Chromatographic peak full width at half maximum (seconds)',
             f'    "chrom_peak_snr": {self.params.chrom_peak_snr},  # Minimum signal-to-noise ratio for chromatographic peaks',
             "",
             "    # === Alignment & Merging ===",
@@ -1267,7 +1267,7 @@ class Wizard:
             "        )",
             "        sample.find_adducts(adducts=PARAMS['adducts'])",
             "        sample.find_ms2()",
-            "        # sample.find_iso()",
+            "        sample.find_iso()",
             "        # sample.export_mgf()",
             "        # sample.export_mztab()",
             '        # sample.plot_2d(filename="{sample_name}.html")',

{masster-0.5.23 → masster-0.5.24}/uv.lock

@@ -1473,7 +1473,7 @@ wheels = [
 
 [[package]]
 name = "masster"
-version = "0.5.23"
+version = "0.5.24"
 source = { editable = "." }
 dependencies = [
     { name = "alpharaw" },