masster 0.4.2__py3-none-any.whl → 0.4.4__py3-none-any.whl

masster/study/helpers.py

@@ -1599,11 +1599,12 @@ def features_select(
     Returns:
         polars.DataFrame: Filtered features DataFrame
     """
+    # Consolidated optimized implementation (previously in helpers_optimized.py)
     if self.features_df is None or self.features_df.is_empty():
         self.logger.warning("No features found in study.")
         return pl.DataFrame()
 
-    # Early return if no filters provided - performance optimization
+    # Early return if no filters provided
     filter_params = [
         mz,
         rt,
@@ -1624,10 +1625,10 @@ def features_select(
 
     initial_count = len(self.features_df)
 
-    # Pre-check available columns once for efficiency
+    # Pre-check available columns once
     available_columns = set(self.features_df.columns)
 
-    # Build all filter conditions first, then apply them all at once
+    # Build all filter conditions
     filter_conditions = []
     warnings = []
 
@@ -1786,18 +1787,18 @@ def features_select(
         else:
             warnings.append("'chrom_height_scaled' column not found in features_df")
 
-    # Log all warnings once at the end for efficiency
+    # Log warnings once at the end
     for warning in warnings:
         self.logger.warning(warning)
 
-    # Apply all filters at once using lazy evaluation for optimal performance
+    # Apply all filters at once if any exist
     if filter_conditions:
         # Combine all conditions with AND
         combined_filter = filter_conditions[0]
         for condition in filter_conditions[1:]:
             combined_filter = combined_filter & condition
 
-        # Apply the combined filter using lazy evaluation
+        # Apply the combined filter using lazy evaluation for better performance
         feats = self.features_df.lazy().filter(combined_filter).collect()
     else:
         feats = self.features_df.clone()
@@ -1807,12 +1808,106 @@ def features_select(
     if final_count == 0:
         self.logger.warning("No features remaining after applying selection criteria.")
     else:
-        # removed_count = initial_count - final_count
-        self.logger.info(f"Features selected: {final_count} (out of {initial_count})")
+        removed_count = initial_count - final_count
+        self.logger.info(f"Features selected: {final_count} (removed: {removed_count})")
 
     return feats
 
 
+def features_select_benchmarked(
+    self,
+    mz=None,
+    rt=None,
+    inty=None,
+    sample_uid=None,
+    sample_name=None,
+    consensus_uid=None,
+    feature_uid=None,
+    filled=None,
+    quality=None,
+    chrom_coherence=None,
+    chrom_prominence=None,
+    chrom_prominence_scaled=None,
+    chrom_height_scaled=None,
+):
+    """
+    Benchmarked version that compares old vs new implementation performance.
+    If an original implementation is available as `features_select_original` on the Study
+    instance, it will be used for comparison; otherwise only the optimized run is timed.
+    """
+    import time
+
+    original_time = None
+    # If an original implementation was stored, call it for comparison
+    original_impl = getattr(self, "features_select_original", None)
+    if callable(original_impl):
+        start_time = time.perf_counter()
+        _ = original_impl(
+            mz=mz,
+            rt=rt,
+            inty=inty,
+            sample_uid=sample_uid,
+            sample_name=sample_name,
+            consensus_uid=consensus_uid,
+            feature_uid=feature_uid,
+            filled=filled,
+            quality=quality,
+            chrom_coherence=chrom_coherence,
+            chrom_prominence=chrom_prominence,
+            chrom_prominence_scaled=chrom_prominence_scaled,
+            chrom_height_scaled=chrom_height_scaled,
+        )
+        original_time = time.perf_counter() - start_time
+
+    # Call the optimized method
+    start_time = time.perf_counter()
+    result_optimized = self.features_select(
+        mz=mz,
+        rt=rt,
+        inty=inty,
+        sample_uid=sample_uid,
+        sample_name=sample_name,
+        consensus_uid=consensus_uid,
+        feature_uid=feature_uid,
+        filled=filled,
+        quality=quality,
+        chrom_coherence=chrom_coherence,
+        chrom_prominence=chrom_prominence,
+        chrom_prominence_scaled=chrom_prominence_scaled,
+        chrom_height_scaled=chrom_height_scaled,
+    )
+    optimized_time = time.perf_counter() - start_time
+
+    # Log performance comparison when possible
+    if original_time is not None:
+        speedup = original_time / optimized_time if optimized_time > 0 else float("inf")
+        self.logger.info(
+            f"Performance comparison - Original: {original_time:.4f}s, Optimized: {optimized_time:.4f}s, Speedup: {speedup:.2f}x",
+        )
+    else:
+        self.logger.info(f"Optimized features_select executed in {optimized_time:.4f}s")
+
+    return result_optimized
+
+
+def monkey_patch_study():
+    """
+    (Optional) Monkey-patch helper for Study. Stores the current Study.features_select
+    as `features_select_original` if not already set, then replaces Study.features_select
+    with the optimized `features_select` defined above. This function is idempotent.
+    """
+    from masster.study.study import Study
+
+    # Only set original if it doesn't exist yet
+    if not hasattr(Study, "features_select_original"):
+        Study.features_select_original = Study.features_select
+
+    Study.features_select = features_select
+    Study.features_select_benchmarked = features_select_benchmarked
+
+    print("Patched Study.features_select with consolidated optimized implementation")
+
+
 def features_filter(self, features):
     """
     Filter features_df by keeping only features that match the given criteria.

masster-0.4.4.dist-info/METADATA

@@ -0,0 +1,129 @@
+Metadata-Version: 2.4
+Name: masster
+Version: 0.4.4
+Summary: Mass spectrometry data analysis package
+Author: Zamboni Lab
+License-Expression: AGPL-3.0-only
+Project-URL: homepage, https://github.com/zamboni-lab/masster
+Project-URL: repository, https://github.com/zamboni-lab/masster
+Project-URL: documentation, https://github.com/zamboni-lab/masster#readme
+Keywords: mass spectrometry,metabolomics,lc-ms,chromatography
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: alpharaw>=0.4.8
+Requires-Dist: bokeh>=3.7.3
+Requires-Dist: datashader>=0.18.1
+Requires-Dist: holoviews>=1.21.0
+Requires-Dist: h5py>=3.14.0
+Requires-Dist: hvplot>=0.11.3
+Requires-Dist: loguru>=0.7.3
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: marimo>=0.14.16
+Requires-Dist: matplotlib>=3.8.0
+Requires-Dist: pandas>=2.2.0
+Requires-Dist: panel>=1.7.0
+Requires-Dist: polars>=1.0.0
+Requires-Dist: pyopenms>=3.3.0
+Requires-Dist: pyteomics>=4.7.0
+Requires-Dist: pythonnet>=3.0.0
+Requires-Dist: scipy>=1.12.0
+Requires-Dist: tqdm>=4.65.0
+Requires-Dist: openpyxl>=3.1.5
+Requires-Dist: cmap>=0.6.2
+Requires-Dist: altair>=5.5.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: pytest-mock>=3.10.0; extra == "dev"
+Requires-Dist: black>=23.0.0; extra == "dev"
+Requires-Dist: flake8>=5.0.0; extra == "dev"
+Requires-Dist: mypy>=1.0.0; extra == "dev"
+Requires-Dist: pre-commit>=3.0.0; extra == "dev"
+Requires-Dist: twine>=4.0.0; extra == "dev"
+Requires-Dist: build>=0.10.0; extra == "dev"
+Requires-Dist: safety>=2.0.0; extra == "dev"
+Requires-Dist: bandit>=1.7.0; extra == "dev"
+Requires-Dist: pyyaml>=6.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=5.0.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=1.2.0; extra == "docs"
+Requires-Dist: sphinxcontrib-napoleon>=0.7; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest>=7.0.0; extra == "test"
+Requires-Dist: pytest-cov>=4.0.0; extra == "test"
+Requires-Dist: pytest-mock>=3.10.0; extra == "test"
+Requires-Dist: coverage>=7.0.0; extra == "test"
+Dynamic: license-file
+
+# MASSter
+
+**MASSter** is a comprehensive Python package for mass spectrometry data analysis, designed for metabolomics and LC-MS data processing. It provides tools for feature detection, alignment, consensus building, and interactive visualization of mass spectrometry datasets. It is designed to deal with DDA, and hides functionalities for DIA and ZTScan DIA data.
+
+This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab.
+
+Some of the core processing functions are derived from OpenMS. We use the same nomenclature and refer to their documentation for an explanation of the parameters. To a large extent, however, you should be able to use the defaults (=no parameters) when calling processing steps.
+
+
+## Installation
+
+```bash
+pip install master
+```
+
+### Basic Workflow for analyzing LC-MS study with 2-... samples
+
+```python
+import master
+
+# Initialize the Study object with the default folder
+study = master.Study(default_folder=r'D:\...\mylcms')
+
+# Load data from folder with raw data, here: WIFF
+study.add(r'D:\...\...\...\*.wiff')
+
+# Perform retention time correction
+study.align(rt_max_diff=2.0)
+study.plot_alignment()
+
+# Find consensus features
+study.merge(min_samples=3)
+study.plot_consensus_2d()
+
+# Retrieve missing data for quantification
+study.fill()
+
+# Integrate according to consensus metadata
+study.integrate()
+
+# export results
+study.export_mgf()
+study.export_mztab()
+study.export_consensus()
+
+# Save the study to .study5
+study.save()
+```
+
+## Requirements
+
+- Python ≥ 3.11
+- Key dependencies: pandas, polars, numpy, scipy, matplotlib, bokeh, holoviews, panel
+- See `pyproject.toml` for complete dependency list
+
+## License
+
+GNU Affero General Public License v3
+
+## Citation
+
+If you use Master in your research, please cite this repository.

{masster-0.4.2.dist-info → masster-0.4.4.dist-info}/RECORD

@@ -1,5 +1,5 @@
 masster/__init__.py,sha256=8U4cIteNlYyHDrxWSbB_MsDKCX9tds07SJG8-vh8Oa8,738
-masster/_version.py,sha256=3PLvtFFtatOSA_8w-RwjzMhdV4Khv39uFcfxtrt2xrE,256
+masster/_version.py,sha256=VO89cZ_6MtW0W_P2yFvZpdGOhoWdoBYiY0efEf1SqsA,256
 masster/chromatogram.py,sha256=NgPr1uLGJHjRu6PWZZGOrS3pCl7sye1yQCJjlRi9ZSY,19305
 masster/logger.py,sha256=W50V_uh8RSYwGxDrDFhOuj5jpu2tKJyt_16lMw9kQwA,14755
 masster/spectrum.py,sha256=7wKQes97sI-O2lxrkQnYuoroXFyAWgwSzS4TnjUX8RY,47710
@@ -10,10 +10,14 @@ masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C017_v5_r99_01.sample5,sha256=h2OOAWWTwKXzTNewhiYeL-cMYdp_JYLPya8Q9Nv9Lvw,12389587
 masster/data/libs/ccm.csv,sha256=Q6nylV1152uTpX-ydqWeGrc6L9kgv45xN_fBZ4f7Tvo,12754
 masster/data/libs/urine.csv,sha256=98L11DolzWzAumTbtKdNNkpDbp-sNDzwAXypgqSZcik,653733
+masster/data/libs/__pycache__/ccm.cpython-312.pyc,sha256=krce-0iqL50kmK1hItP4KWHGCs6M5T10-rgRZynP01w,18597
+masster/data/libs/__pycache__/urine.cpython-312.pyc,sha256=yz16lRCULWE-FDWkkVQCWfJLDKpN6906vm6emeDxu6A,10921
 masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.timeseries.data,sha256=01vC6m__Qqm2rLvlTMZoeKIKowFvovBTUnrNl8Uav3E,24576
 masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff,sha256=go5N9gAM1rn4PZAVaoCmdteY9f7YGEM9gyPdSmkQ8PE,1447936
 masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff.scan,sha256=ahi1Y3UhAj9Bj4Q2MlbgPekNdkJvMOoMXVOoR6CeIxc,13881220
 masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff2,sha256=TFB0HW4Agkig6yht7FtgjUdbXax8jjKaHpSZSvuU5vs,3252224
+masster/lib/__init__.py,sha256=TcePNx3SYZHz6763TL9Sg4gUNXaRWjlrOtyS6vsu-hg,178
+masster/lib/lib.py,sha256=seAOqzat74iF6YnbNakU3rF5MN5t9WABIpcIPTvU1q8,24987
 masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
 masster/sample/adducts.py,sha256=6LvMrrsFjvr4OCuNx6N9qCE1vlvRGEgXtmMz8iwMMQg,31675
 masster/sample/h5.py,sha256=ZAGPJzPXkytmBOlpZXbyRM0K3buzxWd9f4a0hz85NMA,100475
@@ -37,7 +41,7 @@ masster/sample/defaults/sample_def.py,sha256=keoXyMyrm_iLgbYqfIbqCpJ3XHBVlNwCNmb
 masster/study/__init__.py,sha256=Zspv6U8jFqjkHGYdNdDy1rfUnCSolCzUdgSSg98PRgE,166
 masster/study/export.py,sha256=JVsOj-m5aHi4i6M6_Mq1nS_YaukT9E17hdyZtVQJ6FQ,53030
 masster/study/h5.py,sha256=OLSCBfeBrXGibbSogs8YEaqP-3kqcJbP5yIJ4dfPgrc,76339
-masster/study/helpers.py,sha256=tcbDU0QucGA4CyC4ur2MwfInl-cmmehKivVBLw8dInk,144787
+masster/study/helpers.py,sha256=FbHoy2GfArozl1OmxAMsuUjsjhfiobwlOwc1AyEYFaE,148057
 masster/study/helpers_optimized.py,sha256=5qf6tiLPgsOSna9XVtTrx2B0GJ1wI8ZTrSv8n8MtxNg,13927
 masster/study/id.py,sha256=YlrvLhMXQcXAQgkZTYZ6Ih9y2nw0MGIq2on_wx7Oibc,42211
 masster/study/load.py,sha256=V_XHHxPTQaCu1RACliDVpuGoLh7DxQ6gcLTuctRcc6M,69034
@@ -59,8 +63,9 @@ masster/study/defaults/integrate_chrom_def.py,sha256=0MNIWGTjty-Zu-NTQsIweuj3UVq
 masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgPfMYoPKeWv8,7246
 masster/study/defaults/merge_def.py,sha256=EBsKE3hsAkTEzN9dpdRD5W3_suTKy_WZ_96rwS0uBuE,8572
 masster/study/defaults/study_def.py,sha256=5rHxs4rMP2IuBCDEeOoFyjqY8t-Gx54IuQ4Jam3AglM,15510
-masster-0.4.2.dist-info/METADATA,sha256=2LOAc8KioZbeKbp4xFimSmddU7fWceDMfKOdtyqvHyE,44221
-masster-0.4.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.4.2.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.4.2.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.4.2.dist-info/RECORD,,
+masster-0.4.4.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+masster-0.4.4.dist-info/METADATA,sha256=kRUmKm5X-73tccWrIBt5IO1_lBjfgtzelbuL4Ws3ogo,4518
+masster-0.4.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+masster-0.4.4.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.4.4.dist-info/top_level.txt,sha256=MPZokk6zWIP_UhQ_VkKxSTG63eM4WGu9oTcMpQXp7NI,8
+masster-0.4.4.dist-info/RECORD,,

{masster-0.4.2.dist-info → masster-0.4.4.dist-info}/WHEEL

@@ -1,4 +1,5 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
+

masster-0.4.4.dist-info/top_level.txt

@@ -0,0 +1 @@
+masster