Metadata-Version: 2.4
Name: calm-data-generator
Version: 1.2.0
Summary: CALM-Data-Generator: A Python library for synthetic data generation with support for drift injection and clinical data.
Author-email: Alejandro Belda Fernandez <alejandrobeldafernandez@gmail.com>
License: MIT
Project-URL: Homepage, https://github.com/AlejandroBeldaFernandez/Calm-Data_Generator
Project-URL: Bug Tracker, https://github.com/AlejandroBeldaFernandez/Calm-Data_Generator/issues
Keywords: synthetic-data,machine-learning,generative-ai,data-science,drift-detection,clinical-data,privacy
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Operating System :: OS Independent
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy<2.0.0,>=1.26.0
Requires-Dist: pandas>=2.3.0
Requires-Dist: scipy<1.15.0,>=1.10.0
Requires-Dist: tables>=3.10.0
Requires-Dist: h5py>=3.15.0
Requires-Dist: ydata-profiling>=4.18.0
Requires-Dist: synthcity>=0.2.12
Requires-Dist: sdmetrics>=0.27.0
Requires-Dist: numba>=0.60.0
Requires-Dist: llvmlite>=0.43.0
Requires-Dist: scikit-learn>=1.5.0
Requires-Dist: torch<2.4.0,>=2.2.0
Requires-Dist: torchvision<0.19.0,>=0.17.0
Requires-Dist: opacus<1.5
Requires-Dist: pyarrow<15.0.0
Requires-Dist: lightgbm>=4.5.0
Requires-Dist: imbalanced-learn>=0.12.0
Requires-Dist: copulae>=0.7.9
Requires-Dist: anndata>=0.10.0
Requires-Dist: scvi-tools>=1.2.0
Requires-Dist: lightning<2.4.0,>=2.1.0
Requires-Dist: torchmetrics>=1.0.0
Requires-Dist: plotly>=5.18.0
Requires-Dist: cell-gears>=0.1.1
Requires-Dist: torch-geometric>=2.5.0
Requires-Dist: huggingface-hub<1.0,>=0.34.0
Requires-Dist: xgboost<3.0.0,>=2.0.0
Requires-Dist: setuptools<70.0.0
Provides-Extra: stream
Requires-Dist: river>=0.21.0; extra == "stream"
Provides-Extra: full
Requires-Dist: calm-data-generator[stream]; extra == "full"
Dynamic: license-file

# CALM-Data-Generator


[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
[![PyPI version](https://img.shields.io/pypi/v/calm-data-generator.svg)](https://pypi.org/project/calm-data-generator/)
[![Downloads](https://img.shields.io/pypi/dm/calm-data-generator)](https://pypi.org/project/calm-data-generator/)

> 🚀 **Now available on PyPI!** Install with: `pip install calm-data-generator`

> 🇪🇸 **[Versión en Español](README_ES.md)**

**CALM-Data-Generator** is a comprehensive Python library for synthetic data generation with advanced features for:
- **Clinical/Medical Data** - Generate realistic patient demographics, genes, proteins
- **Tabular Data Synthesis** - CTGAN, TVAE, CART, and more
- **Time Series** - TimeGAN, DGAN
- **Single-Cell** - scVI, GEARS (Perturbation Prediction)
- **Drift Injection** - Test ML model robustness with controlled drift
- **Privacy Assessment** - DCR metrics for re-identification risk
- **Scenario Evolution** - Feature evolution and target construction

## Scope & Capabilities

**Calm-Data-Generator** is optimized for **structured tabular data**. It is designed to handle:
- ✅ **Classification** (Binary & Multi-class)
- ✅ **Regression** (Continuous variables)
- ✅ **Multi-label** problems
- ✅ **Clustering** (Preserving natural groupings)
- ✅ **Time Series** (Temporal correlations and patterns)
- ✅ **Single-Cell / Genomics** (scRNA-seq expression data)

> [!IMPORTANT]
> This library is **NOT** designed for unstructured data such as **Images**, **Videos**, or **Audio**. It does not include Computer Vision or Signal Processing models.

---

## What Makes This Library Unique?

**CALM-Data-Generator** is not just another synthetic data tool—it's a **unified ecosystem** that brings together the best open-source libraries under a single, consistent API:

### 🔗 Unified Multi-Library Integration
Instead of learning and managing multiple complex libraries separately, CALM-Data-Generator provides:
- **One API** for 15+ synthesis methods from different sources (Synthcity, scvi-tools, GEARS, imbalanced-learn, etc.)
- **Seamless interoperability** between tabular, time-series, streaming, and genomic data generators
- **Consistent configuration** across all methods with automatic parameter validation
- **Integrated reporting** with YData Profiling for all generation methods

### 🌊 Advanced Drift Injection (Industry-Leading)
The **DriftInjector** module is one of the most comprehensive drift simulation tools available:
- **14+ drift types**: Feature drift (gradual, abrupt, incremental, recurrent), label drift, concept drift, correlation drift, outlier injection, and more
- **Correlation-aware drift**: Propagate realistic drift across correlated features (e.g., increase income → increase spending)
- **Multi-modal drift profiles**: Sigmoid, linear, cosine transitions for gradual drift
- **Conditional drift**: Apply drift only to specific data subsets based on business rules
- **Integrated with generators**: Inject drift directly during synthesis or post-hoc on existing data
- **Perfect for MLOps**: Test data drift monitoring, concept drift detection, and model robustness before production

> **In summary**: While other tools focus on a single approach (e.g., just GANs, just statistical methods), CALM-Data-Generator **unifies the ecosystem** and adds **production-grade drift simulation** that most libraries don't offer.

---

## Core Technologies

This library leverages and unifies best-in-class open-source tools to provide a seamless data generation experience:

- **Synthcity**: The core engine for tabular deep learning models (CTGAN, TVAE) and privacy. **Included by default**.
- **River**: Powers the streaming generation capabilities (`[stream]` extra)..
- **YData Profiling**: Generates comprehensive automated quality reports.

## ⚡ Presets (Templates)

**Calm-Data-Generator** includes a set of **Presets** designed to give you a head start. These are pre-configured settings for common use cases.

> [!TIP]
> **Presets are Baselines**: They are intended to be used as a **starting point**. You should import a preset, modify it to fit your specific data needs (e.g., change columns, tweak thresholds), and then pass it to the generator.

### Available Presets
Located in `calm_data_generator/presets/`, easy to import and iterate upon:

- **`FastPrototypePreset`**: Optimized for speed (fewer epochs, simple models) to test pipelines quickly.
- **`HighFidelityPreset`**: Tuned for maximum quality (CTGAN/TVAE with more training) for production data.
- **`ClinicalDataGenerator`** (and presets): Specialized for healthcare data (demographics + omics).
- **`ImbalancePreset`**: Configured to handle and rebalance highly skewed datasets.
- **`TimeSeriesPreset`**: setup for sequential data generation.

**Example Usage:**
```python
from calm_data_generator.presets import FastPrototypePreset
from calm_data_generator import RealGenerator

# 1. Load the preset config
config = FastPrototypePreset

# 2. Modify it for your specific case
config["epochs"] = 50  # Overwrite default

# 3. Use it
gen = RealGenerator()
gen.generate(data, **config)
```

## Key Libraries & Ecosystem
 
 | Library | Role | Usage in Calm-Data-Generator |
 | :--- | :--- | :--- |
 | **Synthcity** | Deep Learning Engine | Powers `CTGAN`, `TVAE`, `DDPM`, `TimeGAN`. Handling privacy & fidelity. |
 | **scvi-tools** | Single-Cell Analysis | Powers `scvi` method for high-dimensional genomic/transcriptomic data. |
 | **GEARS** | Graph Perturbation | Powers `gears` method for predicting single-cell perturbation effects. |
 | **River** | Streaming ML | Powers `StreamGenerator` for concept drift simulation and real-time data flow. |
 | **YData Profiling**| Reporting | Generates automated quality reports (`QualityReporter`). |
 | **Pydantic** | Validation | Ensures strict type checking and configuration management. |
 | **PyTorch** | Backend | Underlying tensor computation for all deep learning models. |
 | **Copulae** | Statistical Modeling | Powers the `copula` method for multivariate dependence modeling. |

## Safe Data Sharing

A key advantage of **Calm-Data-Generator** is enabling the use of private data in public or collaborative environments:

1.  **Private Origin**: You start with sensitive data (e.g., GDPR/HIPAA restricted) that cannot leave your secure environment.
2.  **Synthetic Twin**: The library generates a synthetic dataset that statistically mirrors the original but contains **no real individuals**.
3.  **Safe Distribution**: Once validated (using `QualityReporter`'s privacy checks), this synthetic dataset allows for **risk-free sharing**, model training, and testing without exposing confidential information.

## Key Use Cases

- **MLOps Monitoring Validation**: Use **StreamGenerator** and **DriftInjector** to simulate data drift (gradual, abrupt) and verify if your monitoring alerts trigger correctly before deployment.
- **Biomedical Research (HealthTech)**: Generate synthetic patient cohorts with **ClinicalDataGenerator** that preserve complex biological correlations (e.g., gene-age relationships) for collaborative studies without compromising patient privacy.
- **Stress Testing ("What-If" Analysis)**: Use **ScenarioInjector** to simulate future scenarios (e.g., "What if the customer age base increases by 10 years?") and measure model performance degradation under stress.
- **Correlation-Aware Drift**: Inject drift that realistically propagates to correlated features (e.g., increasing income also proportionally increases spending) using the `correlations=True` parameter.
- **Development Data**: Provide developers with high-fidelity synthetic replicas of production databases, allowing them to build and test features safely without accessing sensitive real-world data.

---

## Architecture & Design

### Technical Architecture
Minimalist view of the system's core components and data flow.

![Architecture Diagram](calm_data_generator/docs/assets/architecture.png)



---

## Installation
 
 > [!WARNING]
 > The installation might be **heavy (~2-3 GB)** and take a few minutes depending on your internet connection. We strongly recommend using a fresh virtual environment.
 
 ### 🔄 Versioning Strategy
 
 - **GitHub (Recommended for latest features)**: The `main` branch contains the most up-to-date version with the latest bug fixes and features.
 - **PyPI (Stable)**: Releases on PyPI are stable versions updated less frequently for major changes.
 
 ### Standard Installation (PyPI - Stable)
 The library is available on PyPI. For the most stable experience, we recommend using a virtual environment:

```bash
# 1. Create and activate a virtual environment
python3 -m venv venv
source venv/bin/activate

# 2. Upgrade pip, setuptools and wheel (Crucial for successful installation)
pip install --upgrade pip setuptools wheel

# 3. Install the core library (optimized for speed)
pip install calm-data-generator
```

### Installation Extras
Depending on your needs, you can install additional capabilities:
```bash
# For Stream Generator (River)
pip install "calm-data-generator[stream]"



# Full suite
pip install "calm-data-generator[full]"
```

> [!NOTE]
> **Performance & Stability Note**: We have optimized the dependency tree in version 1.0.0 by pinning specific versions such as `scgen==2.1.1` (commit `d79e1f`), `pydantic`, `xgboost`, and `cloudpickle`. This improves compatibility and reduces installation issues. 🚀

**From source (GitHub - Latest Updates):**
Use this method to get the latest bug fixes and features not yet released on PyPI.

```bash
# Option A: Install directly from GitHub
pip install git+https://github.com/AlejandroBeldaFernandez/Calm-Data_Generator.git

# Option B: Clone and install (for development)
git clone https://github.com/AlejandroBeldaFernandez/Calm-Data_Generator.git
cd Calm-Data_Generator
pip install .
```

### Troubleshooting

**Zsh shell (macOS/Linux):** If brackets cause errors, use quotes:
```bash
pip install "calm-data-generator[stream]"
```

**River compilation errors (Linux/macOS):**
```bash
# Ubuntu/Debian
sudo apt install build-essential python3-dev

# macOS
xcode-select --install

# Then retry
pip install calm-data-generator
```

**Windows users:** Install Visual Studio Build Tools first:
1. Download [Visual Studio Build Tools](https://visualstudio.microsoft.com/visual-cpp-build-tools/)
2. Install "Desktop development with C++"
3. Then retry installation

**PyTorch CPU-only (no GPU):**
```bash
pip install torch --index-url https://download.pytorch.org/whl/cpu
pip install calm-data-generator
```

**Dependency conflicts:** Use a clean virtual environment:
```bash
python -m venv venv
source venv/bin/activate  # Linux/macOS
# or: venv\Scripts\activate  # Windows
pip install calm-data-generator
```

---

## Quick Start

### Generate Synthetic Data from Real Dataset

```python
from calm_data_generator import RealGenerator
import pandas as pd

# Your real dataset (can be a DataFrame, path to .csv, .h5, or .h5ad)
data = pd.read_csv("your_data.csv")  # or "your_data.h5ad"

# Initialize generator
gen = RealGenerator()

# Generate 1000 synthetic samples using CTGAN

synthetic = gen.generate(
    data=data,
    n_samples=1000,
    method='ctgan',
    target_col='label',
    epochs=300,
    batch_size=500,
    discriminator_steps=1,
)

print(f"Generated {len(synthetic)} samples")
```

### GPU Acceleration

**Methods with GPU support:**

| Method | GPU Support | Parameter |
|--------|-------------|-----------|
| `ctgan`, `tvae` | ✅ CUDA/MPS | `enable_gpu=True` |
| `diffusion` | ✅ PyTorch | Auto-detected |
| `ddpm` | ✅ PyTorch + Synthcity | Auto-detected |
| `timegan` | ✅ PyTorch + Synthcity | Auto-detected |
| `timevae` | ✅ PyTorch + Synthcity | Auto-detected |
| `fflows` | ✅ PyTorch + Synthcity | Auto-detected |


| `smote`, `adasyn`, `cart`, `rf`, `lgbm`, `gmm`, `copula` | ❌ CPU only | - |

```python
synthetic = gen.generate(
    data=data,
    n_samples=1000,
    method='ctgan',
    epochs=300, 
    enable_gpu=True,
   
)
```

> **Note:** Requires PyTorch with CUDA support:
> ```bash
> pip install torch --index-url https://download.pytorch.org/whl/cu118
> ```

### Generate Clinical Data

```python
from calm_data_generator import ClinicalDataGenerator
from calm_data_generator.generators.configs import DateConfig

gen = ClinicalDataGenerator()

# Generate patient data with genes and proteins
result = gen.generate(
    n_samples=100,
    n_genes=500,
    n_proteins=200,
    date_config=DateConfig(start_date="2024-01-01")
)

demographics = result['demographics']
genes = result['genes']
proteins = result['proteins']
```

### Inject Drift for ML Testing

**Option 1: Directly from `generate()` (recommended)**

```python
from calm_data_generator import RealGenerator

gen = RealGenerator()

# Generate synthetic data WITH drift in one call
synthetic = gen.generate(
    data=real_data,
    n_samples=1000,
    method='ctgan',
    target_col='label',
    drift_injection_config=[
        {
            "method": "inject_drift",
            "params": {
                "columns": ["age", "income", "label"],
                "drift_mode": "gradual", # Auto-detects column types
                "drift_magnitude": 0.3,
                "center": 500,
                "width": 200
            }
        }
    ]
)
```

**Option 2: Standalone DriftInjector**

```python
from calm_data_generator import DriftInjector

injector = DriftInjector()

# Unified drift injection (auto-detects types)
drifted_data = injector.inject_drift(
    df=data,
    columns=['feature1', 'feature2', 'status'],
    drift_mode='gradual',
    drift_magnitude=0.5,
    # Optional specific configs
    numeric_operation='shift',
    categorical_operation='frequency',
    boolean_operation='flip'
)
```
```

**Available drift methods:** `inject_feature_drift`, `inject_feature_drift_gradual`, `inject_feature_drift_incremental`, `inject_feature_drift_recurrent`, `inject_label_drift`, `inject_concept_drift`, `inject_categorical_frequency_drift`, and more. See [DRIFT_INJECTOR_REFERENCE.md](calm_data_generator/docs/DRIFT_INJECTOR_REFERENCE.md).

### Single-Cell / Gene Expression Data

Generate synthetic single-cell RNA-seq-like data using specialized VAE models:

```python
from calm_data_generator import RealGenerator

gen = RealGenerator()

# scVI: Generate new cells from scratch
synthetic = gen.generate(
    data="expression_data.h5ad", # Paths to .h5 or .h5ad are supported directly
    n_samples=1000,
    method='scvi',
    target_col='cell_type',
    epochs=100,
    n_latent=10,
    
)


```

| Method | Use Case |
|--------|----------|
| `scvi` | Generate new cells from learned distribution |


### Stream Data Generation

```python
from calm_data_generator import StreamGenerator

stream_gen = StreamGenerator()

# Generate a data stream with Concept Drift
stream_data = stream_gen.generate(
    n_chunks=10,
    chunk_size=1000,
    concept_drift=True,  # Simulate concept drift over time
    n_features=10
)

print(f"Generated stream with {len(stream_data)} total samples")
```

### Quality Reporting

```python
from calm_data_generator import QualityReporter

# Generate a quality report comparing real vs synthetic data
reporter = QualityReporter()

reporter.generate_report(
    real_data=data,
    synthetic_data=synthetic,
    output_dir="./quality_report",
    target_col="target"
)
# Report saved to ./quality_report/report.html
# Results JSON (including compared_data_files) saved to ./quality_report/report_results.json
```

---

## Modules

| Module | Import | Description |
|--------|--------|-------------|
| **Tabular** | `generators.tabular` | RealGenerator, QualityReporter |
| **Clinical** | `generators.clinical` | ClinicalDataGenerator, ClinicalDataGeneratorBlock |
| **Stream** | \`generators.stream\` | StreamGenerator, StreamBlockGenerator |
| **Blocks** | `generators.tabular` | RealBlockGenerator |
| **Drift** | `generators.drift` | DriftInjector |
| **Dynamics** | `generators.dynamics` | ScenarioInjector |
| **Reports** | `reports` | Visualizer |

---

## Synthesis Methods

| Method | Type | Description | Requirements / Notes |
|--------|------|-------------|----------------------|
| `cart` | ML | CART-based iterative synthesis (fast) | Base installation |
| `rf` | ML | Random Forest synthesis | Base installation |
| `lgbm` | ML | LightGBM-based synthesis | Base installation (Requires `lightgbm`) |
| `ctgan` | DL | Conditional GAN for tabular data | Requires `synthcity` |
| `tvae` | DL | Variational Autoencoder | Requires `synthcity` |
| `diffusion` | DL | Tabular Diffusion (custom, fast) | Base installation (PyTorch) |
| `ddpm` | DL | Synthcity TabDDPM (advanced) | Requires `synthcity` |
| `timegan` | Time Series | TimeGAN for sequential data | Requires `synthcity` |
| `timevae` | Time Series | TimeVAE for sequential data | Requires `synthcity` |
| `fflows` | Time Series | FourierFlows — normalizing flows for temporal data, stable for periodic series | Requires `synthcity` |
| `bn` | DL / Probabilistic | Bayesian Network — models causal dependencies between features | Requires `synthcity` |
| `smote` | Augmentation | SMOTE oversampling | Base installation |
| `adasyn` | Augmentation | ADASYN adaptive sampling | Base installation |


| `copula` | Copula | Copula-based synthesis | Base installation |
| `gmm` | Statistical | Gaussian Mixture Models | Base installation |
| `scvi` | Single-Cell | scVI (Variational Inference) for RNA-seq | Requires `scvi-tools` |


---

## CLI Access

```bash
# List all tutorials
calm-data-generator tutorials

# Show a specific tutorial
calm-data-generator tutorials show 1

# Run a tutorial
calm-data-generator tutorials run 1

# Show version
calm-data-generator version
```

---

## Tutorials

| # | Tutorial | Description |
|---|----------|-------------|
| 1 | Real Generator | Tabular data synthesis |
| 2 | Clinical Generator | Clinical/medical data |
| 3 | Drift Injector | Drift injection for ML |
| 4 | Stream Generator | Stream-based generation |
| 5 | Scenario Injector | Feature evolution |

---

## Documentation Index

Explore the full documentation in the `calm_data_generator/docs/` directory:

| Document | Description |
|----------|-------------|
| **[DOCUMENTATION.md](calm_data_generator/docs/DOCUMENTATION.md)** | **Main User Guide**. Comprehensive manual covering all modules, concepts, and advanced usage. |
| **[REAL_GENERATOR_REFERENCE.md](calm_data_generator/docs/REAL_GENERATOR_REFERENCE.md)** | **API Reference for `RealGenerator`**. Detailed parameters for all synthesis methods (`ctgan`, `lgbm`, `scvi`, etc.). |
| **[DRIFT_INJECTOR_REFERENCE.md](calm_data_generator/docs/DRIFT_INJECTOR_REFERENCE.md)** | **API Reference for `DriftInjector`**. Guide to using `inject_drift` and specialized drift capabilities. |
| **[STREAM_GENERATOR_REFERENCE.md](calm_data_generator/docs/STREAM_GENERATOR_REFERENCE.md)** | **API Reference for `StreamGenerator`**. Details on stream simulation and drift integration. |
| **[CLINICAL_GENERATOR_REFERENCE.md](calm_data_generator/docs/CLINICAL_GENERATOR_REFERENCE.md)** | **API Reference for `ClinicalGenerator`**. Configuration for genes, proteins, and patient data. |
| **[API.md](calm_data_generator/docs/API.md)** | **Technical API Index**. High-level index of classes and functions. |

---

## License

MIT License - see [LICENSE](LICENSE) file

---

## Acknowledgements & Credits

We stand on the shoulders of giants. This library is possible thanks to these amazing open-source projects:

- **[Synthcity](https://github.com/vanderschaarlab/synthcity)** (Apache 2.0) - The engine behind our deep learning models.
- **[River](https://github.com/online-ml/river)** (BSD-3-Clause) - Powering our streaming capabilities.
- **[YData Profiling](https://github.com/ydataai/ydata-profiling)** (MIT) - Providing comprehensive data reporting.
- **[scvi-tools](https://github.com/scverse/scvi-tools)** (BSD-3-Clause) - Enabling single-cell analysis.
- **[GEARS](https://github.com/snap-stanford/GEARS)** (MIT) - Supporting graph-based perturbation prediction.
- **[Imbalanced-learn](https://github.com/scikit-learn-contrib/imbalanced-learn)** (MIT) - Providing SMOTE and ADASYN implementations.
- **[SDMetrics](https://github.com/sdv-dev/SDMetrics)** (MIT) - Powering the standardized metrics in our QualityReporter.
- **[Copulae](https://github.com/DanielBok/copulae)** (MIT) - Enabling multivariate dependence modeling via Gaussian Copulas.
- **[AnnData](https://github.com/scverse/anndata)** (BSD-3-Clause) - Providing the core data structure for single-cell and omics integration.
- **[LightGBM](https://github.com/microsoft/LightGBM)** (MIT) - Powering our gradient boosting synthesis method.
- **[PyTorch](https://github.com/pytorch/pytorch)** (BSD-3-Clause) - The deep learning framework powering our generative models.
- **[PyTorch Geometric](https://github.com/pyg-team/pytorch_geometric)** (MIT) - Enabling Graph Neural Network operations for relational data.
- **[XGBoost](https://github.com/dmlc/xgboost)** (Apache-2.0) - optimized distributed gradient boosting library.
- **[Opacus](https://github.com/pytorch/opacus)** (Apache-2.0) - Enabling differential privacy training for PyTorch models.
- **[Hugging Face Hub](https://github.com/huggingface/huggingface_hub)** (Apache-2.0) - Facilitating model sharing and versioning.
- **[Plotly](https://github.com/plotly/plotly.py)** (MIT) - Enabling interactive data visualizations.
