masster 0.2.1__tar.gz → 0.2.3__tar.gz

{masster-0.2.1 → masster-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.2.1
+Version: 0.2.3
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -730,18 +730,11 @@ Description-Content-Type: text/markdown
 
 # 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.
+**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. 
 
 Most 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.
 
-## Features
-
-- **Mass spectrometry data processing**: Support for multiple file formats (.wiff, .mzML, .raw, .mzpkl)
-- **Feature detection and alignment**: Automated chromatographic peak detection and retention time alignment
-- **Consensus feature building**: Identification of features across multiple samples
-- **Interactive visualizations**: 2D plots, chromatograms, and statistical dashboards
-- **Batch processing**: Process entire studies with multiple samples
-- **Export capabilities**: MGF export for spectral library searches
+This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab. Novel functionalities will be added based on need and requests.
 
 ## Installation
 
@@ -749,9 +742,7 @@ Most core processing functions are derived from OpenMS. We use the same nomencla
 pip install masster
 ```
 
-## Quick Start
-
-### Basic Workflow
+### Basic Workflow for analyzing LC-MS study with 2-... samples
 
 ```python
 import masster
@@ -769,146 +760,19 @@ study.align(rt_max_diff=2.0)
 study.find_consensus(min_samples=3)
 
 # Retrieve missing data for quantification
-study.fill_chrom_parallel()
+study.fill_chrom(abs_)
 
 # Integrate according to consensus metadata
 study.integrate_chrom()
 
-# link MS2 across the whole study
+# link MS2 across the whole study and export them
 study.find_ms2()
-
-# Export MGF file
 study.export_mgf()
 
-# Save the study
+# Save the study to .study5
 study.save()
 ```
 
-### Single Sample Processing
-
-```python
-from masster.sample import Sample
-
-# Load a single sample (mzML, RAW, WIFF)
-sample = Sample("path/to/your/file.mzML")
-
-# Detect features
-sample.find_features(chrom_peak_snr=10, noise=500, chrom_fwhm=1.0)
-
-# Detect adducts
-sample.find_adducts()
-
-# Find MS2 spectra
-sample.find_ms2()
-
-# Save results
-sample.save()
-```
-
-## Visualization Examples
-
-Masster provides extensive plotting capabilities for data exploration and quality control:
-
-### 2D Data Visualization
-
-```python
-# Plot 2D overview of MS data with detected features
-sample.plot_2d(
-    filename="overview_2d.html",
-    show_features=True,
-    show_ms2=True,
-    title="MS Data Overview"
-)
-
-# Plot with feature filtering
-sample.plot_2d(
-    filename="features_ms2_only.html",
-    show_only_features_with_ms2=True,
-    markersize=8
-)
-```
-
-### Study-Level Plots
-
-```python
-# Plot features from multiple samples
-study.plot_samples_2d(
-    samples=None,  # Use all samples
-    filename="multi_sample_overview.html",
-    markersize=3,
-    alpha_max=0.8
-)
-
-# Plot consensus features
-study.plot_consensus_2d(
-    filename="consensus_features.html",
-    colorby="number_samples",
-    sizeby="inty_mean"
-)
-
-# Plot chromatograms for specific features
-study.plot_chrom(
-    uids=[1, 2, 3],  # Feature UIDs
-    filename="chromatograms.html",
-    aligned=True
-)
-```
-
-### Quality Control Plots
-
-```python
-# Plot DDA acquisition statistics
-sample.plot_dda_stats(filename="dda_stats.html")
-
-# Plot feature statistics
-sample.plot_feature_stats(filename="feature_stats.html")
-
-# Plot total ion chromatogram
-sample.plot_tic(filename="tic.html")
-```
-
-### Advanced Plotting Options
-
-```python
-# Plot with Oracle annotation data
-sample.plot_2d_oracle(
-    oracle_folder="path/to/oracle/results",
-    colorby="hg",  # Color by chemical class
-    filename="annotated_features.html"
-)
-
-# Plot MS2 cycle view
-sample.plot_ms2_cycle(
-    cycle=100,
-    filename="ms2_cycle.html",
-    centroid=True
-)
-
-# Plot extracted ion chromatogram
-sample.plot_eic(
-    feature_uid=123,
-    rt_tol=10,
-    mz_tol=0.005,
-    filename="eic.html"
-)
-```
-
-## File Format Support
-
-- **Input formats**: .wiff, .mzML, .raw files
-- **Intermediate formats**: .sample5 and .study5 (HDF5) for fast loading
-- **Export formats**: .mgf, .csv
-- **Visualization**: .html (interactive), .png, .svg
-
-## Advanced Features
-
-### Batch Processing
-Use the command-line interface for processing multiple files:
-
-```bash
-python -m masster.demo.example_batch_process input_directory --recursive --dest output_directory
-```
-
 ## Requirements
 
 - Python ≥ 3.11
@@ -919,13 +783,6 @@ python -m masster.demo.example_batch_process input_directory --recursive --dest
 
 GNU Affero General Public License v3
 
-## Contributing
-
-Contributions are welcome! Please see our contributing guidelines and code of conduct.
-
 ## Citation
 
-If you use Masster in your research, please cite:
-```
-[Citation details to be added]
-```
+If you use Masster in your research, please cite this repository.

masster-0.2.3/README.md

@@ -0,0 +1,58 @@
+# 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. 
+
+Most 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.
+
+This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab. Novel functionalities will be added based on need and requests.
+
+## Installation
+
+```bash
+pip install masster
+```
+
+### Basic Workflow for analyzing LC-MS study with 2-... samples
+
+```python
+import masster
+
+# Initialize the Study object with the default folder
+study = masster.Study(default_folder=r'D:\...\mylcms')
+
+# Load data from folder with raw data, here: WIFF
+study.add_folder(r'D:\...\...\...\*.wiff')
+
+# Align maps
+study.align(rt_max_diff=2.0)
+
+# Find consensus features
+study.find_consensus(min_samples=3)
+
+# Retrieve missing data for quantification
+study.fill_chrom(abs_)
+
+# Integrate according to consensus metadata
+study.integrate_chrom()
+
+# link MS2 across the whole study and export them
+study.find_ms2()
+study.export_mgf()
+
+# 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 Masster in your research, please cite this repository.

{masster-0.2.1 → masster-0.2.3}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.2.1"
+version = "0.2.3"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.2.1 → masster-0.2.3}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.2.1"
+__version__ = "0.2.3"
 
 
 def get_version():