calm-data-generator 2.1.0__tar.gz → 2.2.0__tar.gz

{calm_data_generator-2.1.0/calm_data_generator.egg-info → calm_data_generator-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calm-data-generator
-Version: 2.1.0
+Version: 2.2.0
 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
@@ -53,6 +53,7 @@ Requires-Dist: hmmlearn<0.4.0,>=0.3.0
 Requires-Dist: pyarrow<15.0.0,>=14.0.0
 Requires-Dist: setuptools<70.0.0,>=59.0.0
 Requires-Dist: fsspec<2026.0.0,>=2025.12.0
+Requires-Dist: scgft-evaluator<0.2.0,>=0.1.0
 Provides-Extra: stream
 Requires-Dist: river>=0.21.0; extra == "stream"
 Provides-Extra: full
@@ -588,6 +589,26 @@ synthetic = gen.generate(
 |--------|----------|
 | `scvi` | Generate new cells from learned distribution |
 
+Once you have synthetic single-cell data, validate its quality using [scGFT Evaluator](https://github.com/nasim23ea/scgft-evaluator) via `QualityReporter`:
+
+```python
+from calm_data_generator.reports.QualityReporter import QualityReporter
+from calm_data_generator.generators.configs import ReportConfig
+
+reporter = QualityReporter(verbose=True)
+reporter.generate_comprehensive_report(
+    real_df=real_df,
+    synthetic_df=synthetic_df,
+    generator_name="SingleCell_Example",
+    report_config=ReportConfig(
+        output_dir="./sc_report",
+        use_scgft=True,
+        target_column="cell_type",
+    ),
+)
+```
+
+> See [REPORTS_REFERENCE.md](calm_data_generator/docs/REPORTS_REFERENCE.md#single-cell-evaluation-scgft) for full details.
 
 ### Stream Data Generation
 
@@ -625,6 +646,24 @@ reporter.generate_report(
 # Results JSON (including compared_data_files) saved to ./quality_report/report_results.json
 ```
 
+For **single-cell data**, enable [scGFT](https://github.com/nasim23ea/scgft-evaluator) evaluation (Graph Fourier Transform-based manifold preservation metrics):
+
+```python
+from calm_data_generator.generators.configs import ReportConfig
+
+reporter.generate_comprehensive_report(
+    real_df=real_df,
+    synthetic_df=synthetic_df,
+    generator_name="MyGen",
+    report_config=ReportConfig(
+        output_dir="./sc_report",
+        use_scgft=True,
+        target_column="cell_type",
+    ),
+)
+# Generates scgft_report.html with ARI, MMD, Jaccard, Kendall Tau metrics
+```
+
 ---
 
 ## Modules
@@ -760,3 +799,4 @@ We stand on the shoulders of giants. This library is possible thanks to these am
 - **[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.
 - **[hmmlearn](https://github.com/hmmlearn/hmmlearn)** (BSD-3-Clause) - Powering the `hmm` method for drift-aware generation via Hidden Markov Models.
+- **[scgft-evaluator](https://github.com/nasim23ea/scgft-evaluator)** - Providing Graph Fourier Transform-based evaluation for single-cell synthetic data quality assessment.

{calm_data_generator-2.1.0 → calm_data_generator-2.2.0}/README.md

@@ -527,6 +527,26 @@ synthetic = gen.generate(
 |--------|----------|
 | `scvi` | Generate new cells from learned distribution |
 
+Once you have synthetic single-cell data, validate its quality using [scGFT Evaluator](https://github.com/nasim23ea/scgft-evaluator) via `QualityReporter`:
+
+```python
+from calm_data_generator.reports.QualityReporter import QualityReporter
+from calm_data_generator.generators.configs import ReportConfig
+
+reporter = QualityReporter(verbose=True)
+reporter.generate_comprehensive_report(
+    real_df=real_df,
+    synthetic_df=synthetic_df,
+    generator_name="SingleCell_Example",
+    report_config=ReportConfig(
+        output_dir="./sc_report",
+        use_scgft=True,
+        target_column="cell_type",
+    ),
+)
+```
+
+> See [REPORTS_REFERENCE.md](calm_data_generator/docs/REPORTS_REFERENCE.md#single-cell-evaluation-scgft) for full details.
 
 ### Stream Data Generation
 
@@ -564,6 +584,24 @@ reporter.generate_report(
 # Results JSON (including compared_data_files) saved to ./quality_report/report_results.json
 ```
 
+For **single-cell data**, enable [scGFT](https://github.com/nasim23ea/scgft-evaluator) evaluation (Graph Fourier Transform-based manifold preservation metrics):
+
+```python
+from calm_data_generator.generators.configs import ReportConfig
+
+reporter.generate_comprehensive_report(
+    real_df=real_df,
+    synthetic_df=synthetic_df,
+    generator_name="MyGen",
+    report_config=ReportConfig(
+        output_dir="./sc_report",
+        use_scgft=True,
+        target_column="cell_type",
+    ),
+)
+# Generates scgft_report.html with ARI, MMD, Jaccard, Kendall Tau metrics
+```
+
 ---
 
 ## Modules
@@ -699,3 +737,4 @@ We stand on the shoulders of giants. This library is possible thanks to these am
 - **[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.
 - **[hmmlearn](https://github.com/hmmlearn/hmmlearn)** (BSD-3-Clause) - Powering the `hmm` method for drift-aware generation via Hidden Markov Models.
+- **[scgft-evaluator](https://github.com/nasim23ea/scgft-evaluator)** - Providing Graph Fourier Transform-based evaluation for single-cell synthetic data quality assessment.

{calm_data_generator-2.1.0 → calm_data_generator-2.2.0}/calm_data_generator/docs/PRESETS_REFERENCE.md

@@ -521,6 +521,27 @@ preset = SingleCellQualityPreset(random_state=42)
 synthetic_cells = preset.generate(data=adata_df, n_samples=500)
 ```
 
+To validate the generated data quality, use `QualityReporter` with scGFT enabled:
+
+```python
+from calm_data_generator.reports.QualityReporter import QualityReporter
+from calm_data_generator.generators.configs import ReportConfig
+
+reporter = QualityReporter(verbose=True)
+reporter.generate_comprehensive_report(
+    real_df=adata_df,
+    synthetic_df=synthetic_cells,
+    generator_name="SingleCellQualityPreset",
+    report_config=ReportConfig(
+        output_dir="./sc_report",
+        use_scgft=True,
+        target_column="cell_type",
+    ),
+)
+```
+
+> See [REPORTS_REFERENCE.md](REPORTS_REFERENCE.md#single-cell-evaluation-scgft) for full scGFT documentation.
+
 ---
 
 ## Import Summary

{calm_data_generator-2.1.0 → calm_data_generator-2.2.0}/calm_data_generator/docs/PRESETS_REFERENCE_ES.md

@@ -521,6 +521,27 @@ preset = SingleCellQualityPreset(random_state=42)
 synthetic_cells = preset.generate(data=adata_df, n_samples=500)
 ```
 
+Para validar la calidad de los datos generados, usa `QualityReporter` con scGFT activado:
+
+```python
+from calm_data_generator.reports.QualityReporter import QualityReporter
+from calm_data_generator.generators.configs import ReportConfig
+
+reporter = QualityReporter(verbose=True)
+reporter.generate_comprehensive_report(
+    real_df=adata_df,
+    synthetic_df=synthetic_cells,
+    generator_name="SingleCellQualityPreset",
+    report_config=ReportConfig(
+        output_dir="./sc_report",
+        use_scgft=True,
+        target_column="cell_type",
+    ),
+)
+```
+
+> Ver [REPORTS_REFERENCE_ES.md](REPORTS_REFERENCE_ES.md#evaluación-single-cell-scgft) para documentación completa de scGFT.
+
 ---
 
 ## Resumen de Imports

{calm_data_generator-2.1.0 → calm_data_generator-2.2.0}/calm_data_generator/docs/REAL_GENERATOR_REFERENCE.md

@@ -600,6 +600,30 @@ sc.pp.pca(synthetic_adata)
 sc.pl.pca(synthetic_adata, color="cell_type")
 ```
 
+**Validating single-cell quality with scGFT:**
+
+After generating synthetic single-cell data, validate its fidelity using [scgft-evaluator](https://github.com/nasim23ea/scgft-evaluator):
+
+```python
+from calm_data_generator.reports.QualityReporter import QualityReporter
+from calm_data_generator.generators.configs import ReportConfig
+
+reporter = QualityReporter(verbose=True)
+reporter.generate_comprehensive_report(
+    real_df=real_df,
+    synthetic_df=synthetic_df,
+    generator_name="scVI_SingleCell",
+    report_config=ReportConfig(
+        output_dir="./sc_report",
+        use_scgft=True,
+        target_column="cell_type",
+    ),
+)
+# Generates scgft_report.html with ARI, MMD, Jaccard, Kendall Tau metrics
+```
+
+> See [REPORTS_REFERENCE.md](REPORTS_REFERENCE.md#single-cell-evaluation-scgft) for full details.
+
 ---
 
 ---

{calm_data_generator-2.1.0 → calm_data_generator-2.2.0}/calm_data_generator/docs/REAL_GENERATOR_REFERENCE_ES.md

@@ -235,6 +235,30 @@ sc.pp.pca(synthetic_adata)
 sc.pl.pca(synthetic_adata, color="cell_type")
 ```
 
+**Validación de calidad single-cell con scGFT:**
+
+Tras generar datos sintéticos de célula única, valida su fidelidad usando [scgft-evaluator](https://github.com/nasim23ea/scgft-evaluator):
+
+```python
+from calm_data_generator.reports.QualityReporter import QualityReporter
+from calm_data_generator.generators.configs import ReportConfig
+
+reporter = QualityReporter(verbose=True)
+reporter.generate_comprehensive_report(
+    real_df=real_df,
+    synthetic_df=synthetic_df,
+    generator_name="scVI_SingleCell",
+    report_config=ReportConfig(
+        output_dir="./sc_report",
+        use_scgft=True,
+        target_column="cell_type",
+    ),
+)
+# Genera scgft_report.html con métricas ARI, MMD, Jaccard, Kendall Tau
+```
+
+> Ver [REPORTS_REFERENCE_ES.md](REPORTS_REFERENCE_ES.md#evaluación-single-cell-scgft) para documentación completa.
+
 ---
 
 ## Características Avanzadas