masster 0.4.3__tar.gz → 0.4.5__tar.gz

masster-0.4.5/MANIFEST.in

@@ -0,0 +1,8 @@
+# Exclude tests from source distribution
+recursive-exclude tests *
+recursive-exclude src/masster/tests *
+
+# Include the package data files we want
+include src/masster/sample/*.json
+include src/masster/study/*.json
+recursive-include src/masster/data *

masster-0.4.5/PKG-INFO

@@ -0,0 +1,131 @@
+Metadata-Version: 2.4
+Name: masster
+Version: 0.4.5
+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
+Requires-Dist: scikit-learn>=1.7.1
+Requires-Dist: ipython>=9.4.0
+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-0.4.3 → masster-0.4.5}/pyproject.toml

@@ -1,19 +1,20 @@
 
 [project]
 name = "masster"
-version = "0.4.3"
+version = "0.4.5"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }
 ]
-license = { file = "LICENSE" }
+# Use SPDX expression for license (replaces deprecated TOML table form)
+license = "AGPL-3.0-only"
+license-files = ["LICENSE"]
 readme = "README.md"
 requires-python = ">=3.11"
 keywords = ["mass spectrometry", "metabolomics", "lc-ms", "chromatography"]
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: GNU Affero General Public License v3",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.11",
@@ -47,6 +48,8 @@ dependencies = [
     "openpyxl>=3.1.5",
     "cmap>=0.6.2",
     "altair>=5.5.0",
+    "scikit-learn>=1.7.1",
+    "ipython>=9.4.0",
 ]
 
 [project.optional-dependencies]
@@ -88,6 +91,20 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools.packages.find]
 where = ["src"]
 include = ["masster*"]
+exclude = ["tests*", "tests.*"]
+
+[tool.setuptools]
+# Do not automatically include files from MANIFEST.in as package data; we declare package-data explicitly
+include-package-data = false
+
+# Include JSON schema files and other non-Python resources packaged under masster
+[tool.setuptools.package-data]
+"masster" = [
+    "sample/*.json",
+    "study/*.json",
+    # include data files (recursive)
+    "data/**",
+]
 
 # Testing configuration
 [tool.pytest.ini_options]

{masster-0.4.3 → masster-0.4.5}/src/masster/__init__.py

@@ -1,5 +1,5 @@
 """
-masster - Mass Spectrometry Analysis Assistant
+master - Mass Spectrometry Analysis Assistant
 
 A comprehensive Python package for processing and analyzing untargeted metabolomics data,
 supporting both DDA (Data-Dependent Acquisition) and DIA (Data-Independent Acquisition)
@@ -8,14 +8,14 @@ mass spectrometry workflows.
 
 from __future__ import annotations
 
-from masster._version import __version__
+from master._version import __version__
 
-# from masster._version import get_version
-from masster.chromatogram import Chromatogram
-from masster.lib import Lib
-from masster.sample.sample import Sample
-from masster.spectrum import Spectrum
-from masster.study.study import Study
+# from master._version import get_version
+from master.chromatogram import Chromatogram
+from master.lib import Lib
+from master.sample.sample import Sample
+from master.spectrum import Spectrum
+from master.study.study import Study
 
 
 __all__ = [

{masster-0.4.3 → masster-0.4.5}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.4.3"
+__version__ = "0.4.4"
 
 
 def get_version():

{masster-0.4.3 → masster-0.4.5}/src/masster/chromatogram.py

@@ -88,7 +88,7 @@ class Chromatogram:
 
     Example Usage:
         >>> import numpy as np
-        >>> from masster import chrom
+        >>> from master import chrom
         >>> rt = np.linspace(0, 300, 1000)
         >>> intensity = np.random.normal(1000, 100, 1000)
         >>> chromatogram = chrom(rt=rt, inty=intensity, label="EIC m/z 150")

masster-0.4.5/src/masster/data/libs/ccm.csv

@@ -0,0 +1,120 @@
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