hic-sca 0.0.0__py3-none-any.whl

hic_sca-0.0.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: hic-sca
+Version: 0.0.0
+Summary: HiC-SCA: Hi-C Spectral Compartment Assignment for predicting A-B chromosomal compartments
+Author-email: Justin Chan <chan.waisoon@qst.go.jp>, Hidetoshi Kono <kono.hidetoshi@qst.go.jp>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/iQLS-MMS/hic-sca
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.19.0
+Requires-Dist: scipy>=1.15.0
+Requires-Dist: hic-straw>=1.3.0
+Requires-Dist: h5py>=3.0.0
+Requires-Dist: matplotlib>=3.0.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: openpyxl>=3.0.0
+Requires-Dist: h5typer>=0.1.0
+Provides-Extra: tests
+Requires-Dist: pytest>=6.0; extra == "tests"
+Requires-Dist: pytest-cov>=2.0; extra == "tests"
+Dynamic: license-file
+
+# HiC-SCA: Hi-C Spectral Compartment Analysis
+
+A Python package for predicting A-B chromosomal compartments from Hi-C (chromosome conformation capture) data using spectral decomposition and observed/expected normalization.
+
+## Overview
+
+HiC-SCA implements a complete pipeline for analyzing Hi-C contact matrices to identify chromatin compartmentalization patterns. It uses spectral decomposition with adaptive tolerance adjustment and an advanced eigenvector selection algorithm to predict A and B chromosomal compartments.
+
+**Key capabilities:**
+- Process .hic files at single or multiple resolutions
+- Automatic genome-wide O/E normalization with smoothing
+- Quality-based eigenvector selection
+- Cross-resolution evaluation to identify suitable resolutions
+- Multiple output formats (HDF5, Excel, BED, BedGraph, plots)
+
+## Table of Contents
+
+- [Installation](#installation)
+  - [Requirements](#requirements)
+  - [Install from Source](#install-from-source)
+  - [Dependencies](#dependencies)
+- [Quick Start](#quick-start)
+  - [Command-Line Interface](#command-line-interface)
+  - [Python API](#python-api)
+- [Command-Line Interface](#command-line-interface-1)
+  - [Arguments](#arguments)
+  - [Usage Examples](#usage-examples)
+  - [Output Files](#output-files)
+  - [Troubleshooting CLI](#troubleshooting-cli)
+- [Python API](#python-api-1)
+  - [Core Classes](#core-classes)
+  - [Results Dictionary Structure](#results-dictionary-structure)
+  - [Evaluation Tools](#evaluation-tools)
+- [Testing](#testing)
+- [Other Documentation](#other-documentation)
+- [Citation](#citation)
+- [License](#license)
+- [Contributing](#contributing)
+- [Acknowledgments](#acknowledgments)
+
+## Installation
+
+### Requirements
+
+- Python >= 3.10
+- pip >= 21.0
+
+### Install from Source
+
+HiC-SCA requires the [h5typer](https://github.com/iQLS-MMS/h5typer) package as a dependency.
+
+```bash
+# Clone repositories
+git clone https://github.com/iQLS-MMS/h5typer.git
+git clone https://github.com/iQLS-MMS/hic-sca.git
+
+# Install h5typer first (required dependency)
+cd h5typer
+pip install .
+
+# Install HiC-SCA
+cd ../hicsca
+pip install .
+
+# Or install with test dependencies
+pip install ".[tests]"
+```
+
+### Dependencies
+
+The package automatically installs:
+- hicstraw >= 1.3.0 (reading .hic files)
+- numpy >= 1.19.0 (numerical computations)
+- scipy >= 1.15.0 (sparse matrices, eigendecomposition)
+- h5py >= 3.0.0 (HDF5 I/O)
+- pandas >= 1.0.0 (Excel export)
+- openpyxl >= 3.0.0 (Excel I/O)
+- matplotlib >= 3.0.0 (plotting)
+- h5typer >= 0.1.0 (HDF5 type mapping)
+
+## Quick Start
+
+### Command-Line Interface
+
+The easiest way to use HiC-SCA is through the command-line interface:
+
+```bash
+# Process single resolution
+hic-sca -f hic-sca/tests/test_data/ENCFF216ZNY_Intra_Only.hic -r 100000 -p my_sample
+
+# Process with BED and BedGraph output
+hic-sca -f hic-sca/tests/test_data/ENCFF216ZNY_Intra_Only.hic -r 100000 -p my_sample --bed --bedgraph
+
+# Process multiple resolutions
+hic-sca -f hic-sca/tests/test_data/ENCFF216ZNY_Intra_Only.hic -r 100000 50000 25000 -p my_sample
+
+# Process all available resolutions with verbose output
+hic-sca -f hic-sca/tests/test_data/ENCFF216ZNY_Intra_Only.hic -p my_sample -v
+
+# Specify output directory
+hic-sca -f hic-sca/tests/test_data/ENCFF216ZNY_Intra_Only.hic -r 100000 -p my_sample -o results/
+
+# Process specific chromosomes
+hic-sca -f hic-sca/tests/test_data/ENCFF216ZNY_Intra_Only.hic -r 100000 -c chr1 chr2 chr3 -p my_sample
+```
+
+**Output files:**
+- `my_sample_results.h5` - HDF5 file with complete results
+- `my_sample_100000bp.xlsx` - Excel file (mandatory)
+- `my_sample_100000bp.bed` - BED file (if `--bed` specified)
+- `my_sample_100000bp.bedgraph` - BedGraph file (if `--bedgraph` specified)
+- `my_sample_chr1_100000bp.png` - Compartment plot for chr1
+- `my_sample_cross_resolution_mcc.png` - Cross-resolution MCC heatmap (if multiple resolutions)
+
+### Python API
+
+```python
+from hicsca import HiCSCA
+
+# Initialize pipeline with Hi-C file
+hicsca = HiCSCA(
+    hic_file_path="hic-sca/tests/test_data/ENCFF216ZNY_Intra_Only.hic",
+    resolutions=[100000],  # or None for auto-detect all
+    chr_names=None  # None = all autosomal chromosomes
+)
+
+# Process all chromosomes
+hicsca.process_all_chromosomes(verbose=True)
+
+# Access results
+result = hicsca.results[100000]['chr1']
+if result['Success']:
+    compartment = result['assigned_AB_compartment']
+    eig_idx = result['selected_eig_idx']
+    score = result['modified_inter_eigval_score']
+    print(f"chr1: Selected Eig{eig_idx}, Score: {score:.4f}")
+
+# Export results using convenience methods
+hicsca.to_bed(100000, "compartments_100kb.bed")
+hicsca.to_bedgraph(100000, "compartments_100kb.bedgraph")
+hicsca.to_excel(100000, "compartments_100kb.xlsx")
+hicsca.to_hdf5("saved_analysis.h5")
+
+# Plot compartments (saves to files)
+hicsca.plot_compartments(100000, output_dir="plots", output_prefix="sample")
+
+# Plot cross-resolution MCC correlation
+hicsca.plot_cross_resolution_mcc(save_path="cross_res_mcc.png")
+```
+
+## Command-Line Interface
+
+### Arguments
+
+**Required (one of):**
+- `-f, --hic-file PATH` - Path to input .hic file
+- `--load-hdf5 PATH` - Load existing HDF5 results file
+
+**Optional:**
+- `-r, --resolutions BP [BP ...]` - Space-separated resolutions in bp (default: auto-detect all)
+- `-p, --output-prefix PREFIX` - Prefix for output files (required)
+- `-o, --output-dir DIR` - Output directory (default: current directory)
+- `-c, --chromosomes CHR [CHR ...]` - Space-separated chromosome names (default: chr1-chr22)
+- `-t, --data-type TYPE` - Data type: "observed" or "oe" (default: "observed")
+- `-v, --verbose` - Enable verbose output
+- `--bed` - Generate BED files for each resolution
+- `--bedgraph` - Generate BedGraph files for each resolution
+
+### Usage Examples
+
+```bash
+# Basic usage
+hic-sca -f data.hic -r 100000 -p my_sample
+
+# With BED and BedGraph output
+hic-sca -f data.hic -r 100000 -p my_sample --bed --bedgraph
+
+# Multiple resolutions
+hic-sca -f data.hic -r 500000 250000 100000 50000 -p my_sample
+
+# All available resolutions
+hic-sca -f data.hic -p my_sample -v
+
+# Custom output directory
+hic-sca -f data.hic -r 100000 -p my_sample -o results/
+
+# Specific chromosomes
+hic-sca -f data.hic -r 100000 -c chr1 chr2 chr3 -p my_sample
+
+# Use pre-normalized O/E data (skip background normalization)
+hic-sca -f data.hic -r 100000 -p my_sample -t oe
+
+# Load existing HDF5 and export to BED/BedGraph
+hic-sca --load-hdf5 results.h5 -p output --bed --bedgraph
+
+# Load HDF5 with .hic file (enables processing additional data)
+hic-sca --load-hdf5 results.h5 -f data.hic -p output
+
+# Load HDF5 and export filtered data (specific resolutions/chromosomes)
+hic-sca --load-hdf5 results.h5 -r 100000 -c chr1 chr2 -p output --bed
+```
+
+### Output Files
+
+The CLI generates the following output files:
+
+#### 1. HDF5 Results File (always generated)
+**Filename:** `{prefix}_results.h5`
+
+Complete analysis results for all resolutions and chromosomes:
+- All compartment predictions
+- Pre-computed background normalizations (for fast reloading)
+- Eigendecomposition results
+- Quality control metrics
+- Self-contained: stores chromosome lengths, no .hic file path stored
+- Can be loaded with or without .hic file for export or further processing
+
+**Loading HDF5 files:**
+```python
+from hicsca import HiCSCA
+
+# Load for export only
+hicsca = HiCSCA.from_hdf5("results.h5")
+hicsca.to_bed(100000, "compartments.bed")
+
+# Load with .hic file to enable processing additional data
+hicsca = HiCSCA.from_hdf5("results.h5", hic_file_path="data.hic")
+hicsca.process_chromosome("chr1")  # Can process more chromosomes
+```
+
+#### 2. Excel Files (always generated)
+**Filename:** `{prefix}_{resolution}bp.xlsx`
+
+One file per resolution with:
+- **Per-chromosome worksheets** containing:
+  - `Start`: Bin start position (1-indexed, in bp)
+  - `End`: Bin end position (in bp)
+  - `Value`: Compartment eigenvector value
+  - `Compartment`: "A" (positive values), "B" (negative values), or "" (excluded bins)
+- **Summary worksheet "Inter-AB Scores"** containing:
+  - `Chromosome`: Chromosome name
+  - `Inter-AB Score`: Quality metric (numeric value or "N/A" if processing failed)
+  - `Confidence`: "High Confidence" if 1.75 ≤ score ≤ 3.20, else "Low Confidence"
+
+#### 3. BED Files (optional, with `--bed`)
+**Filename:** `{prefix}_{resolution}bp.bed`
+
+BED9 format with RGB colors:
+- Consecutive bins of same compartment are merged
+- A compartments: red (255,0,0)
+- B compartments: blue (0,0,255)
+- Zero values (excluded regions) are skipped
+- Track header included for genome browser compatibility
+
+**Format:**
+```
+track name=AB_Compartments_100000bp description="..." itemRgb="On"
+chr1    0       300000  A   0   .   0       300000  255,0,0
+chr1    400000  800000  B   0   .   400000  800000  0,0,255
+```
+
+#### 4. BedGraph Files (optional, with `--bedgraph`)
+**Filename:** `{prefix}_{resolution}bp.bedgraph`
+
+Continuous compartment scores for genome browser visualization:
+- One value per bin (not merged)
+- Zero values (excluded regions) are skipped
+- Track header included
+
+**Format:**
+```
+track type=bedGraph name="AB_Compartments_100000bp"
+chr1    0       100000  0.123456
+chr1    100000  200000  -0.098765
+```
+
+#### 5. Compartment Plots (always generated)
+**Filename:** `{prefix}_{chr_name}_{resolution}bp.png`
+
+Publication-quality plots (300 DPI) for each chromosome:
+- Red line: A compartment (positive values)
+- Blue line: B compartment (negative values)
+- Automatic unit scaling (bp, Kbp, Mbp)
+- 5 evenly-spaced x-axis ticks
+
+#### 6. Cross-Resolution MCC Plot (if multiple resolutions)
+**Filename:** `{prefix}_cross_resolution_mcc.png` and `{prefix}_cross_resolution_mcc_colorbar.png`
+
+Heatmap showing Matthews Correlation Coefficient between resolutions:
+- Assesses consistency across different resolutions
+- Main heatmap and separate colorbar figure
+- Gray cells indicate incompatible resolution pairs (not round multiples)
+- Red-white-blue colormap for MCC values (0-1)
+
+### Troubleshooting CLI
+
+**"Error: Must provide either --load-hdf5 or -f/--hic-file"**
+- Provide at least one input source: `-f` for new .hic file, or `--load-hdf5` for existing results
+
+**"Error: Hi-C file not found"**
+- Verify path to .hic file
+- Use absolute paths if relative paths cause issues
+
+**"Error: HDF5 file not found"**
+- Verify path to HDF5 results file
+- Ensure correct file name with `.h5` extension
+
+**"No resolutions available"**
+- Check that .hic file contains data at specified resolutions
+- Use auto-detection (omit `-r` flag) to see available resolutions
+
+**Memory errors**
+- Process fewer resolutions at once
+- Use higher resolutions (e.g., 100kb instead of 10kb)
+- Close other applications to free up RAM
+
+## Python API
+
+### Core Classes
+
+#### HiCSCA - Main Pipeline Class
+
+Complete pipeline for A-B compartment prediction from Hi-C data.
+
+**Initialization:**
+```python
+from hicsca import HiCSCA
+
+hicsca = HiCSCA(
+    hic_file_path="data/sample.hic",
+    chr_names=None,  # None = all autosomal chromosomes (chr1-chr22)
+    resolutions=None,  # None = all available resolutions
+    data_type="observed",  # "observed" or "oe"
+    norm_type="NONE",
+    smoothing_cutoff=400
+)
+```
+
+**Parameters:**
+- `hic_file_path` (str): Path to .hic file
+- `chr_names` (list or None): Chromosome names to process (default: all autosomal)
+- `resolutions` (list or None): Resolutions in bp (default: auto-detect all)
+- `data_type` (str): "observed" (raw contacts with O/E normalization) or "oe" (pre-normalized, skip O/E)
+- `norm_type` (str): Normalization type for hicstraw (default: "NONE")
+- `smoothing_cutoff` (int): Smoothing parameter for O/E normalization (default: 400, only used when data_type="observed")
+
+**Key Methods:**
+```python
+# Compute background normalization (automatic when processing, can be called explicitly)
+hicsca.compute_background_normalization(resolutions=None)
+
+# Process single chromosome at specified resolutions
+hicsca.process_chromosome(chr_name, resolutions=None, verbose=True)
+
+# Process all chromosomes at specified resolutions
+hicsca.process_all_chromosomes(resolutions=None, verbose=True)
+
+# Load saved HiCSCA instance
+hicsca = HiCSCA.from_hdf5(hdf5_path, hic_file_path=None)
+```
+
+**Export Methods:**
+```python
+# Save complete instance to HDF5
+hicsca.to_hdf5(output_path, update=False)
+
+# Generate BED file
+hicsca.to_bed(resolution, output_path, chr_names=None, dataset_id=None)
+
+# Generate BedGraph file
+hicsca.to_bedgraph(resolution, output_path, chr_names=None, dataset_id=None, track_name=None)
+
+# Generate Excel file
+hicsca.to_excel(resolution, output_path, chr_names=None, dataset_id=None)
+
+# Plot compartments (saves to files and/or displays in Jupyter)
+hicsca.plot_compartments(
+    resolution,
+    chr_names=None,
+    output_dir=None,  # Specify to save files
+    output_prefix=None,
+    display=True,  # Set False to disable Jupyter display
+    dpi=300,
+    figsize=(3.595, 2)
+)
+
+# Plot cross-resolution MCC correlation heatmap
+hicsca.plot_cross_resolution_mcc(
+    chr_name='all',  # 'all' or specific chromosome
+    resolutions=None,  # None = all resolutions
+    chr_names=None,  # For genome-wide ('all') calculation
+    figsize=(2.8, 2.8),
+    dpi=300,
+    background_alpha=1,  # 0=transparent, 1=opaque
+    plot_colorbar=True,  # Generate separate colorbar figure
+    save_path=None  # Path to save main figure
+)
+```
+
+**Usage:**
+```python
+# Example 1: Using observed data (default - with O/E normalization)
+hicsca = HiCSCA(
+    "data/sample.hic",
+    resolutions=[100000, 50000],
+    data_type="observed",
+    norm_type="NONE"
+)
+
+# Process all chromosomes (results stored in hicsca.results)
+hicsca.process_all_chromosomes(verbose=True)
+
+# Access results
+result = hicsca.results[100000]["chr1"]
+if result['Success']:
+    compartment = result['assigned_AB_compartment']
+    eig_idx = result['selected_eig_idx']
+    score = result['modified_inter_eigval_score']
+
+# Export results
+hicsca.to_bed(100000, "compartments_100kb.bed")
+hicsca.to_excel(100000, "compartments_100kb.xlsx")
+hicsca.to_hdf5("saved_analysis.h5")
+
+# Example 2: Using pre-normalized O/E data (skips background normalization)
+hicsca_oe = HiCSCA(
+    "data/sample.hic",
+    resolutions=[100000],
+    data_type="oe",  # Data already O/E normalized
+    norm_type="KR"   # Can use normalized data if available
+)
+hicsca_oe.process_all_chromosomes(verbose=True)
+
+# Example 3: Load previously saved HiCSCA instance
+hicsca_loaded = HiCSCA.from_hdf5("saved_analysis.h5")
+# All results and normalizations already loaded - no processing needed
+result = hicsca_loaded.results[100000]['chr1']
+```
+
+### Results Dictionary Structure
+
+Results are stored in: `hicsca.results[resolution][chr_name]`
+
+Each result dictionary contains:
+
+**Core Fields (always present):**
+- `Success` (bool): Whether processing succeeded
+- `Eig Converged` (bool): Whether eigendecomposition converged
+
+**Compartment Prediction (when Success=True):**
+- `assigned_AB_compartment` (ndarray): Normalized compartment eigenvector (positive=A, negative=B, zero=excluded)
+- `selected_eig_idx` (int): Index of selected eigenvector (1-10)
+- `modified_inter_eigval_score` (float): Eigenvalue-weighted eigenvector selection score
+- `unmodified_inter_AB_score` (float): Raw inter-compartment contact score
+
+**Eigendecomposition Results:**
+- `eigvals` (ndarray): All eigenvalues (11 values: trivial + 10 non-trivial)
+- `eigenvects` (ndarray): All eigenvectors (11 × N matrix, row-major format)
+
+**Quality Control:**
+- `cutoff` (float): Low-coverage filter cutoff value
+- `include_bool` (ndarray): Boolean array indicating bins included in analysis
+- `non_zero_not_included_bool` (ndarray): Boolean array for excluded non-zero bins
+- `deg` (ndarray): Degree (column sums) of filtered O/E matrix
+- `OE_normed_diag` (ndarray): Diagonal of O/E matrix for included bins
+
+**See RESULTS_STRUCTURE.md for complete documentation.**
+
+### Evaluation Tools
+
+#### CrossResolutionAnalyzer
+
+Analyzes agreement between different resolutions within the same Hi-C dataset.
+
+```python
+from hicsca.evals import CrossResolutionAnalyzer
+
+# Initialize with HiCSCA results (auto-detects resolutions and chromosomes)
+analyzer = CrossResolutionAnalyzer(hicsca.results)
+
+# Or specify custom resolutions/chromosomes
+analyzer = CrossResolutionAnalyzer(
+    hicsca.results,
+    resolutions=[500000, 250000, 100000, 50000],
+    chr_names=['chr1', 'chr2', ..., 'chr22']
+)
+
+# Analyze (results stored internally, cached)
+analyzer.analyze()
+
+# Plot genome-wide cross-resolution MCC with colorbar
+fig, ax, cbar_fig, cbar_ax = analyzer.plot_cross_resolution_mcc()
+
+# Plot specific chromosome with transparent background
+fig, ax, cbar_fig, cbar_ax = analyzer.plot_cross_resolution_mcc(
+    chr_name='chr1',
+    save_path='chr1_mcc.png',
+    background_alpha=0
+)
+# Saves: chr1_mcc.png and chr1_mcc_colorbar.png
+
+# Access MCC matrices directly
+genome_wide_mcc = analyzer.mcc_matrices['all']
+chr1_mcc = analyzer.mcc_matrices['chr1']
+```
+
+#### CrossDatasetAnalyzer
+
+Analyzes agreement between different Hi-C datasets at the same resolution(s).
+
+```python
+from hicsca.evals import CrossDatasetAnalyzer
+
+# Create dataset dictionary (dataset_id -> HiCSCA results)
+dataset_dict = {
+    'dataset1': hicsca_inst1.results,
+    'dataset2': hicsca_inst2.results,
+    'dataset3': hicsca_inst3.results
+}
+
+# Initialize (auto-detects resolutions, dataset_ids, and chromosomes)
+analyzer = CrossDatasetAnalyzer(dataset_dict)
+
+# Analyze all resolutions
+analyzer.analyze()
+
+# Plot genome-wide MCC correlation at 100kb with colorbar
+fig1, ax1, cbar_fig1, cbar_ax1 = analyzer.plot_mcc_correlation(
+    100000,
+    tick_labels=['A', 'B', 'C'],
+    save_path='mcc_100kb.png'
+)
+# Saves: mcc_100kb.png and mcc_100kb_colorbar.png
+
+# Plot chr1 orientation agreement
+fig2, ax2, cbar_fig2, cbar_ax2 = analyzer.plot_orientation_agreement(
+    100000,
+    chr_name='chr1',
+    save_path='orient_chr1_100kb.png'
+)
+
+# Access matrices directly
+mcc_genome_wide = analyzer.mcc_matrices[100000]['all']
+```
+
+#### MCCCalculator
+
+Compute Matthews Correlation Coefficient between compartment predictions.
+
+```python
+from hicsca.evals import MCCCalculator
+
+mcc, tp, fp, tn, fn, zeroed, reversed = MCCCalculator.compute_AB_MCC(
+    reference_compartments,
+    predicted_compartments,
+    auto_flip=True  # Automatically handle orientation
+)
+
+print(f"MCC: {mcc:.4f}")
+```
+
+## Testing
+
+The package includes a comprehensive test suite:
+
+```bash
+# Run all tests (including regression tests)
+pytest tests/
+
+# Run with coverage
+pytest tests/ --cov=hicsca --cov-report=html
+
+# Specific test classes
+pytest tests/test_hicsca.py::TestResultStructure
+pytest tests/test_hicsca.py::TestRegressionComparison
+```
+
+**Test Coverage:**
+- Data availability checks
+- Result structure validation
+- Regression tests (compartment vectors, scores, eigenvalues)
+- Cross-resolution analysis validation
+
+**Note**: Regression tests require test data files in `tests/test_data/` (ENCFF216ZNY_Intra_Only.hic and reference.h5).
+
+### Test Data
+The test .hic dataset contains only the intra-chromosomal contacts of [ENCFF216ZNY](https://www.encodeproject.org/files/ENCFF216ZNY/). The file is located at [tests/test_data/ENCFF216ZNY_Intra_Only.hic](./tests/test_data/ENCFF216ZNY_Intra_Only.hic)
+
+## Other Documentation
+
+- **RESULTS_STRUCTURE.md**: Complete documentation of results dictionary structure
+
+## Citation
+
+If you use this software in your research, please cite:
+
+Chan, J. & Kono, H. HiC-SCA: A Spectral Clustering Method for Reliable A/B Compartment Assignment From Hi-C Data. Preprint at https://doi.org/10.1101/2025.09.22.677711 (2025).
+
+## License
+
+MIT License
+
+## Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request.
+
+## Acknowledgments
+
+This package uses:
+- [hicstraw](https://github.com/aidenlab/straw) for reading .hic files
+- NumPy and SciPy for numerical computations and sparse matrix operations
+- matplotlib for visualization
+- h5py for HDF5 file I/O
+- h5typer for automatic HDF5 type mapping
+- LOBPCG algorithm (SciPy) for efficient eigenvalue decomposition

hic_sca-0.0.0.dist-info/RECORD

@@ -0,0 +1,11 @@
+hic_sca-0.0.0.dist-info/licenses/LICENSE,sha256=58XdpW1w9bAYTrokz315fY90xhh-SMsFh55EUiZL0V0,1106
+hicsca/__init__.py,sha256=Vy3g10k9TB_UGddxetJDnPLamcH_yKAxBQcsiplvuGk,658
+hicsca/evals.py,sha256=WEigUOJfsDpRmd7vZSDL30A6M6iBLdMQOCcm3Rt2kQo,38430
+hicsca/formats.py,sha256=gHwkfriG_6DPGdhhU2pCcL_9xRq39UmMOcn8VKATots,33456
+hicsca/hicsca.py,sha256=CD-TVcE1zkZE7dtKi2CzLwGMHqa8JBBRCLptxqfD9rI,61712
+hicsca/hicsca_cli.py,sha256=pbH9IE483P0OauclzHFj66wM0vqOMurofR3mrZsLtKU,13372
+hic_sca-0.0.0.dist-info/METADATA,sha256=wa5VH7KeU2d19yEiemLU99n6ke-4fodDpGih1VInCUU,21129
+hic_sca-0.0.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+hic_sca-0.0.0.dist-info/entry_points.txt,sha256=BpVzJuv3jw_Od-Ynv6FWL5ZtbKXLJUmzUtGYECmjDnY,51
+hic_sca-0.0.0.dist-info/top_level.txt,sha256=zM9i5ME2rNPKqhthAXC0oyezf_r5yiMcEbO8m3wIuH8,7
+hic_sca-0.0.0.dist-info/RECORD,,

hic_sca-0.0.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

hic_sca-0.0.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+hic-sca = hicsca.hicsca_cli:main

hic_sca-0.0.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Molecular Modelling and Simulation Team, iQLS, QST
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

hic_sca-0.0.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+hicsca