masster 0.4.10__tar.gz → 0.4.11__tar.gz

{masster-0.4.10 → masster-0.4.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.4.10
+Version: 0.4.11
 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-0.4.10 → masster-0.4.11}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.4.10"
+version = "0.4.11"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.4.10 → masster-0.4.11}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.4.10"
+__version__ = "0.4.11"
 
 
 def get_version():

{masster-0.4.10 → masster-0.4.11}/src/masster/sample/sample5_schema.json

@@ -1,95 +1,95 @@
 {
   "features_df": {
     "columns": {
-      "adduct": {
-        "dtype": "pl.Utf8"
-      },
-      "adduct_charge": {
-        "dtype": "pl.Int64"
-      },
-      "adduct_group": {
+      "feature_uid": {
         "dtype": "pl.Int64"
       },
-      "adduct_mass_neutral": {
-        "dtype": "pl.Float64"
-      },
-      "adduct_mass_shift": {
-        "dtype": "pl.Float64"
+      "feature_id": {
+        "dtype": "pl.Utf8"
       },
-      "charge": {
+      "sample_uid": {
         "dtype": "pl.Int32"
       },
-      "chrom": {
-        "dtype": "pl.Object"
-      },
-      "chrom_area": {
+      "mz": {
         "dtype": "pl.Float64"
       },
-      "chrom_coherence": {
+      "rt": {
         "dtype": "pl.Float64"
       },
-      "chrom_height_scaled": {
+      "rt_original": {
         "dtype": "pl.Float64"
       },
-      "chrom_prominence": {
+      "rt_start": {
         "dtype": "pl.Float64"
       },
-      "chrom_prominence_scaled": {
+      "rt_end": {
         "dtype": "pl.Float64"
       },
-      "feature_id": {
-        "dtype": "pl.Utf8"
+      "rt_delta": {
+        "dtype": "pl.Float64"
       },
-      "feature_uid": {
-        "dtype": "pl.Int64"
+      "mz_start": {
+        "dtype": "pl.Float64"
       },
-      "filled": {
-        "dtype": "pl.Boolean"
+      "mz_end": {
+        "dtype": "pl.Float64"
       },
       "inty": {
         "dtype": "pl.Float64"
       },
+      "quality": {
+        "dtype": "pl.Float64"
+      },
+      "charge": {
+        "dtype": "pl.Int32"
+      },
       "iso": {
         "dtype": "pl.Int64"
       },
       "iso_of": {
         "dtype": "pl.Int64"
       },
-      "ms2_scans": {
-        "dtype": "pl.Object"
+      "adduct": {
+        "dtype": "pl.Utf8"
       },
-      "ms2_specs": {
-        "dtype": "pl.Object"
+      "adduct_charge": {
+        "dtype": "pl.Int64"
       },
-      "mz": {
+      "adduct_mass_shift": {
         "dtype": "pl.Float64"
       },
-      "mz_end": {
+      "adduct_mass_neutral": {
         "dtype": "pl.Float64"
       },
-      "mz_start": {
-        "dtype": "pl.Float64"
+      "adduct_group": {
+        "dtype": "pl.Int64"
       },
-      "quality": {
-        "dtype": "pl.Float64"
+      "chrom": {
+        "dtype": "pl.Object"
       },
-      "rt": {
+      "filled": {
+        "dtype": "pl.Boolean"
+      },
+      "chrom_area": {
         "dtype": "pl.Float64"
       },
-      "rt_delta": {
+      "chrom_coherence": {
         "dtype": "pl.Float64"
       },
-      "rt_end": {
+      "chrom_prominence": {
         "dtype": "pl.Float64"
       },
-      "rt_original": {
+      "chrom_prominence_scaled": {
         "dtype": "pl.Float64"
       },
-      "rt_start": {
+      "chrom_height_scaled": {
         "dtype": "pl.Float64"
       },
-      "sample_uid": {
-        "dtype": "pl.Int32"
+      "ms2_scans": {
+        "dtype": "pl.Object"
+      },
+      "ms2_specs": {
+        "dtype": "pl.Object"
       }
     }
   },

{masster-0.4.10 → masster-0.4.11}/src/masster/study/h5.py

@@ -1686,19 +1686,6 @@ def _load_study5(self, filename=None):
     # Check if progress bar should be disabled based on log level
     tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
 
-    # Define loading steps for progress tracking
-    loading_steps = [
-        "metadata",
-        "samples_df",
-        "features_df",
-        "consensus_df",
-        "consensus_mapping_df",
-        "consensus_ms2",
-    ]
-
-    # Check if progress bar should be disabled based on log level
-    tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
-
     with h5py.File(filename, "r") as f:
         # Use progress bar to show loading progress
         with tqdm(

{masster-0.4.10 → masster-0.4.11}/src/masster/study/helpers.py

@@ -780,6 +780,7 @@ def _get_sample_uids(self, samples=None, seed=42):
         # choose a random sample of sample_uids
         if len(self.samples_df) > samples:
             np.random.seed(seed)  # for reproducibility
+            self.logger.info(f"Randomly selected {samples} samples")
             return np.random.choice(
                 self.samples_df["sample_uid"].to_list(),
                 samples,