sctrial 0.3.0__tar.gz

sctrial-0.3.0/.gitignore

@@ -0,0 +1,57 @@
+# Python bytecode
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+dist/
+/build/
+*.egg-info/
+.eggs/
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+
+# Type checking
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Virtual environments (if created inside this subdirectory)
+venv/
+env/
+ENV/
+
+*.h5ad
+*.gz
+*.txt.gz
+data/
+datasets/
+tutorials/data/
+**/__pycache__/
+.DS_Store
+**/.DS_Store
+.vscode/
+.idea/
+.ruff_cache/
+**/.doctrees/
+docs/build/
+
+# Manuscript figure computation cache
+_cache/
+manuscript_figures/_cache/
+
+# Run scripts (local convenience only)
+run_nb*.sh
+
+# Jupyter notebook artifacts
+*.nbconvert.ipynb
+.ipynb_checkpoints/
+
+# Claude Code
+CLAUDE.md
+.claude/
+.mcp.json

sctrial-0.3.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Mohamed Omar, MD Assistant Professor of Computational Biomedicine and Urology, Cedars-Sinai
+
+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.

sctrial-0.3.0/PKG-INFO

@@ -0,0 +1,236 @@
+Metadata-Version: 2.4
+Name: sctrial
+Version: 0.3.0
+Summary: Participant-level differential analysis for longitudinal single-cell experiments: DiD, paired comparisons, module scoring, pseudobulk, and power analysis.
+Project-URL: Homepage, https://github.com/TheOmarLab/sctrial
+Project-URL: Documentation, https://sctrial.readthedocs.io
+Project-URL: Repository, https://github.com/TheOmarLab/sctrial
+Project-URL: Issues, https://github.com/TheOmarLab/sctrial/issues
+Author: Contributors
+License: MIT
+License-File: LICENSE
+Keywords: anndata,crossover,difference-in-differences,pseudobulk,single-cell,trial
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: >=3.9
+Requires-Dist: anndata>=0.9
+Requires-Dist: joblib>=1.2
+Requires-Dist: numpy>=1.22
+Requires-Dist: pandas>=1.5
+Requires-Dist: scipy>=1.8
+Requires-Dist: statsmodels>=0.13
+Requires-Dist: typing-extensions>=4.0; python_version < '3.11'
+Provides-Extra: all
+Requires-Dist: adjusttext>=1.0; extra == 'all'
+Requires-Dist: gseapy>=1.0; extra == 'all'
+Requires-Dist: lifelines>=0.27; extra == 'all'
+Requires-Dist: matplotlib>=3.6; extra == 'all'
+Requires-Dist: plotly>=5.0; extra == 'all'
+Requires-Dist: pymc>=5.0; extra == 'all'
+Requires-Dist: pyscenic>=0.12; extra == 'all'
+Requires-Dist: scanpy>=1.9; extra == 'all'
+Requires-Dist: seaborn>=0.12; extra == 'all'
+Provides-Extra: aucell
+Requires-Dist: pyscenic>=0.12; extra == 'aucell'
+Provides-Extra: bayes
+Requires-Dist: pymc>=5.0; extra == 'bayes'
+Provides-Extra: dev
+Requires-Dist: build>=1.0; extra == 'dev'
+Requires-Dist: mypy>=1.5; extra == 'dev'
+Requires-Dist: myst-parser>=2.0; extra == 'dev'
+Requires-Dist: nbsphinx>=0.9; extra == 'dev'
+Requires-Dist: pandoc; extra == 'dev'
+Requires-Dist: pre-commit>=3.0; extra == 'dev'
+Requires-Dist: psutil>=5.9; extra == 'dev'
+Requires-Dist: pydata-sphinx-theme>=0.15; extra == 'dev'
+Requires-Dist: pytest-cov>=4.0; extra == 'dev'
+Requires-Dist: pytest>=7.0; extra == 'dev'
+Requires-Dist: ruff>=0.5; extra == 'dev'
+Requires-Dist: sphinx-copybutton>=0.5; extra == 'dev'
+Requires-Dist: sphinx-design>=0.5; extra == 'dev'
+Requires-Dist: sphinx>=7.0; extra == 'dev'
+Requires-Dist: twine>=5.0; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: myst-parser>=2.0; extra == 'docs'
+Requires-Dist: nbsphinx>=0.9; extra == 'docs'
+Requires-Dist: pandoc; extra == 'docs'
+Requires-Dist: pydata-sphinx-theme>=0.15; extra == 'docs'
+Requires-Dist: sphinx-copybutton>=0.5; extra == 'docs'
+Requires-Dist: sphinx-design>=0.5; extra == 'docs'
+Requires-Dist: sphinx>=7.0; extra == 'docs'
+Provides-Extra: gsea
+Requires-Dist: gseapy>=1.0; extra == 'gsea'
+Provides-Extra: plots
+Requires-Dist: adjusttext>=1.0; extra == 'plots'
+Requires-Dist: matplotlib>=3.6; extra == 'plots'
+Requires-Dist: plotly>=5.0; extra == 'plots'
+Requires-Dist: scanpy>=1.9; extra == 'plots'
+Requires-Dist: seaborn>=0.12; extra == 'plots'
+Provides-Extra: survival
+Requires-Dist: lifelines>=0.27; extra == 'survival'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <img src="docs/source/_static/logo.svg" alt="sctrial" width="280">
+</p>
+<p align="center"><strong>Participant-Level Differential Analysis for Longitudinal Single-Cell Experiments</strong></p>
+
+<p align="center">
+  <a href="https://github.com/TheOmarLab/sctrial/actions/workflows/test.yml">
+    <img src="https://github.com/TheOmarLab/sctrial/actions/workflows/test.yml/badge.svg?branch=main" alt="Test Status">
+  </a>
+  <a href="https://github.com/TheOmarLab/sctrial/releases">
+    <img src="https://img.shields.io/github/v/release/TheOmarLab/sctrial?label=version" alt="Release Version">
+  </a>
+  <img src="https://img.shields.io/badge/python-3.9%2B-blue" alt="Python Versions">
+  <a href="https://opensource.org/licenses/MIT">
+    <img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License: MIT">
+  </a>
+  <a href="https://sctrial.readthedocs.io">
+    <img src="https://img.shields.io/badge/docs-latest-brightgreen.svg" alt="Documentation">
+  </a>
+</p>
+
+---
+
+## Overview
+
+**sctrial** is a Python package for performing rigorous statistical inference on single-cell RNA-seq data from clinical trials and longitudinal studies. Built on top of [AnnData](https://anndata.readthedocs.io/) and [Scanpy](https://scanpy.readthedocs.io/), it provides specialized tools for:
+
+- **Difference-in-Differences (DiD)** analysis with participant fixed effects
+- **Paired within-arm** pre→post contrasts
+- **Between-arm** comparisons at fixed timepoints
+- **Cell-type abundance** change testing
+- **Gene set enrichment** analysis (GSEA) on DiD rankings
+- **Power analysis** and sample size calculations
+- **Effect size** estimation with confidence intervals
+
+<p align="center">
+  <img src="docs/source/_static/overview_figure.png" alt="sctrial overview — from scRNA-seq input through trial-aware analysis to statistical outputs" width="100%">
+</p>
+
+## Key Features
+
+| Feature | Description |
+|---------|-------------|
+| **Trial-Aware Design** | Define participant, visit, arm, and cell type columns once |
+| **Robust Statistics** | Wild cluster bootstrap, participant-level aggregation |
+| **Multiple Comparisons** | Built-in FDR correction across features and cell types |
+| **Power Analysis** | Two-arm DiD and single-arm paired power/sample size calculations |
+| **Single-Arm Support** | `arm_col=None` for studies without a control arm |
+| **Publication-Ready Plots** | Forest plots, interaction plots, GSEA heatmaps |
+| **Scalable** | Efficient processing of large single-cell datasets |
+
+## Installation
+
+```bash
+pip install sctrial
+```
+
+For development:
+```bash
+git clone https://github.com/TheOmarLab/sctrial.git
+cd sctrial
+pip install -e ".[dev]"
+```
+
+## Quick Start
+
+```bash
+pip install "sctrial[plots]"   # includes dataset loaders and visualization
+```
+
+```python
+import sctrial as st
+
+# 1. Load a real immunotherapy trial dataset (auto-downloads on first use)
+adata = st.load_sade_feldman()
+adata = st.harmonize_response(adata)  # majority-vote response labels
+
+# 2. Define trial design
+design = st.TrialDesign(
+    participant_col="participant_id",
+    visit_col="visit",
+    arm_col="response_harmonized",
+    arm_treated="Responder",
+    arm_control="Non-responder",
+    celltype_col="cell_type",
+)
+
+# 3. Score gene sets (dataset ships pre-normalized with log1p_tpm layer)
+gene_sets = {
+    "Cytotoxicity": ["GZMA", "GZMB", "PRF1", "GNLY", "NKG7"],
+    "Exhaustion":   ["PDCD1", "CTLA4", "HAVCR2", "LAG3", "TIGIT"],
+}
+adata = st.score_gene_sets(adata, gene_sets, layer="log1p_tpm", method="zmean", prefix="ms_")
+
+# 4. Run Difference-in-Differences on CD8 T cells
+features = [c for c in adata.obs.columns if c.startswith("ms_")]
+results = st.did_table(adata, features, design, visits=("Pre", "Post"), celltype="CD8 T cell")
+print(results[["feature", "beta_DiD", "se_DiD", "p_DiD", "FDR_DiD"]])
+```
+
+Or use the one-liner convenience wrapper for a quick multi-cell-type scan:
+
+```python
+results = st.quick_did(
+    adata,
+    module_scores=gene_sets,
+    visits=("Pre", "Post"),
+    arm_col="response_harmonized",
+    arm_treated="Responder",
+    arm_control="Non-responder",
+    celltype_col="cell_type",
+)
+```
+
+## Supported Study Designs & Datasets
+
+sctrial ships with five real clinical trial datasets, accessible via built-in loaders (`st.load_*()`). Each demonstrates a different study design:
+
+| Design | Description | Dataset | Source | Tutorial |
+|--------|-------------|---------|--------|----------|
+| **Two-arm paired DiD** | Pre/post × treatment/control interaction | Sade-Feldman et al., *Cell* 2018 — melanoma immunotherapy | [GSE120575](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120575) | [Immunotherapy](tutorials/example_immunotherapy_sade_feldman.ipynb) |
+| **Single-arm pre/post** | Paired within-arm contrasts over time | ImmPort GSE171964 — PBMC vaccine response | [GSE171964](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171964) | [Vaccine](tutorials/example_vaccine_immport.ipynb) |
+| **Single-arm pre/post** | Paired within-arm, multi-timepoint | van Galen et al., *Cell* 2019 — AML chemotherapy | [GSE116256](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116256) | — |
+| **Single-arm multi-timepoint** | Longitudinal tracking across 4 visits | GSE290722 — CAR-T cell therapy (ZUMA-1) | [GSE290722](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE290722) | — |
+| **Cross-sectional between-arm** | Between-group comparison at one timepoint | Stephenson et al., *Nature Medicine* 2021 — COVID-19 severity | [E-MTAB-10026](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-10026) | [COVID-19](tutorials/example_covid19_stephenson.ipynb) |
+
+Additional tutorial: [Scalability Benchmark](tutorials/stress_test_real_scale.ipynb) — performance testing on the Sade-Feldman dataset.
+
+## Documentation
+
+Full documentation: [https://sctrial.readthedocs.io](https://sctrial.readthedocs.io)
+
+- [API Reference](https://sctrial.readthedocs.io/en/latest/api.html)
+- [Tutorials](https://sctrial.readthedocs.io/en/latest/tutorials/index.html)
+- [FAQ](https://sctrial.readthedocs.io/en/latest/faq.html)
+
+## Citation
+
+If you use **sctrial** in your research, please cite:
+
+> Vasanthakumari P, Valencia I, Aghmiouni MR, Magana B, Omar MN. **sctrial: Participant-Level Differential Analysis for Longitudinal Single-Cell Experiments.** *bioRxiv* (2026).
+
+```bibtex
+@article{vasanthakumari2026sctrial,
+  title = {sctrial: Participant-Level Differential Analysis for Longitudinal Single-Cell Experiments},
+  author = {Vasanthakumari, Priyanka and Valencia, Itzel and Aghmiouni, Maryam R. and Magana, Bryan and Omar, Mohamed N.},
+  journal = {bioRxiv},
+  year = {2026},
+  url = {https://github.com/TheOmarLab/sctrial}
+}
+```
+
+## License
+
+MIT License - see [LICENSE](LICENSE) for details.

sctrial-0.3.0/README.md

@@ -0,0 +1,155 @@
+<p align="center">
+  <img src="docs/source/_static/logo.svg" alt="sctrial" width="280">
+</p>
+<p align="center"><strong>Participant-Level Differential Analysis for Longitudinal Single-Cell Experiments</strong></p>
+
+<p align="center">
+  <a href="https://github.com/TheOmarLab/sctrial/actions/workflows/test.yml">
+    <img src="https://github.com/TheOmarLab/sctrial/actions/workflows/test.yml/badge.svg?branch=main" alt="Test Status">
+  </a>
+  <a href="https://github.com/TheOmarLab/sctrial/releases">
+    <img src="https://img.shields.io/github/v/release/TheOmarLab/sctrial?label=version" alt="Release Version">
+  </a>
+  <img src="https://img.shields.io/badge/python-3.9%2B-blue" alt="Python Versions">
+  <a href="https://opensource.org/licenses/MIT">
+    <img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License: MIT">
+  </a>
+  <a href="https://sctrial.readthedocs.io">
+    <img src="https://img.shields.io/badge/docs-latest-brightgreen.svg" alt="Documentation">
+  </a>
+</p>
+
+---
+
+## Overview
+
+**sctrial** is a Python package for performing rigorous statistical inference on single-cell RNA-seq data from clinical trials and longitudinal studies. Built on top of [AnnData](https://anndata.readthedocs.io/) and [Scanpy](https://scanpy.readthedocs.io/), it provides specialized tools for:
+
+- **Difference-in-Differences (DiD)** analysis with participant fixed effects
+- **Paired within-arm** pre→post contrasts
+- **Between-arm** comparisons at fixed timepoints
+- **Cell-type abundance** change testing
+- **Gene set enrichment** analysis (GSEA) on DiD rankings
+- **Power analysis** and sample size calculations
+- **Effect size** estimation with confidence intervals
+
+<p align="center">
+  <img src="docs/source/_static/overview_figure.png" alt="sctrial overview — from scRNA-seq input through trial-aware analysis to statistical outputs" width="100%">
+</p>
+
+## Key Features
+
+| Feature | Description |
+|---------|-------------|
+| **Trial-Aware Design** | Define participant, visit, arm, and cell type columns once |
+| **Robust Statistics** | Wild cluster bootstrap, participant-level aggregation |
+| **Multiple Comparisons** | Built-in FDR correction across features and cell types |
+| **Power Analysis** | Two-arm DiD and single-arm paired power/sample size calculations |
+| **Single-Arm Support** | `arm_col=None` for studies without a control arm |
+| **Publication-Ready Plots** | Forest plots, interaction plots, GSEA heatmaps |
+| **Scalable** | Efficient processing of large single-cell datasets |
+
+## Installation
+
+```bash
+pip install sctrial
+```
+
+For development:
+```bash
+git clone https://github.com/TheOmarLab/sctrial.git
+cd sctrial
+pip install -e ".[dev]"
+```
+
+## Quick Start
+
+```bash
+pip install "sctrial[plots]"   # includes dataset loaders and visualization
+```
+
+```python
+import sctrial as st
+
+# 1. Load a real immunotherapy trial dataset (auto-downloads on first use)
+adata = st.load_sade_feldman()
+adata = st.harmonize_response(adata)  # majority-vote response labels
+
+# 2. Define trial design
+design = st.TrialDesign(
+    participant_col="participant_id",
+    visit_col="visit",
+    arm_col="response_harmonized",
+    arm_treated="Responder",
+    arm_control="Non-responder",
+    celltype_col="cell_type",
+)
+
+# 3. Score gene sets (dataset ships pre-normalized with log1p_tpm layer)
+gene_sets = {
+    "Cytotoxicity": ["GZMA", "GZMB", "PRF1", "GNLY", "NKG7"],
+    "Exhaustion":   ["PDCD1", "CTLA4", "HAVCR2", "LAG3", "TIGIT"],
+}
+adata = st.score_gene_sets(adata, gene_sets, layer="log1p_tpm", method="zmean", prefix="ms_")
+
+# 4. Run Difference-in-Differences on CD8 T cells
+features = [c for c in adata.obs.columns if c.startswith("ms_")]
+results = st.did_table(adata, features, design, visits=("Pre", "Post"), celltype="CD8 T cell")
+print(results[["feature", "beta_DiD", "se_DiD", "p_DiD", "FDR_DiD"]])
+```
+
+Or use the one-liner convenience wrapper for a quick multi-cell-type scan:
+
+```python
+results = st.quick_did(
+    adata,
+    module_scores=gene_sets,
+    visits=("Pre", "Post"),
+    arm_col="response_harmonized",
+    arm_treated="Responder",
+    arm_control="Non-responder",
+    celltype_col="cell_type",
+)
+```
+
+## Supported Study Designs & Datasets
+
+sctrial ships with five real clinical trial datasets, accessible via built-in loaders (`st.load_*()`). Each demonstrates a different study design:
+
+| Design | Description | Dataset | Source | Tutorial |
+|--------|-------------|---------|--------|----------|
+| **Two-arm paired DiD** | Pre/post × treatment/control interaction | Sade-Feldman et al., *Cell* 2018 — melanoma immunotherapy | [GSE120575](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120575) | [Immunotherapy](tutorials/example_immunotherapy_sade_feldman.ipynb) |
+| **Single-arm pre/post** | Paired within-arm contrasts over time | ImmPort GSE171964 — PBMC vaccine response | [GSE171964](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171964) | [Vaccine](tutorials/example_vaccine_immport.ipynb) |
+| **Single-arm pre/post** | Paired within-arm, multi-timepoint | van Galen et al., *Cell* 2019 — AML chemotherapy | [GSE116256](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116256) | — |
+| **Single-arm multi-timepoint** | Longitudinal tracking across 4 visits | GSE290722 — CAR-T cell therapy (ZUMA-1) | [GSE290722](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE290722) | — |
+| **Cross-sectional between-arm** | Between-group comparison at one timepoint | Stephenson et al., *Nature Medicine* 2021 — COVID-19 severity | [E-MTAB-10026](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-10026) | [COVID-19](tutorials/example_covid19_stephenson.ipynb) |
+
+Additional tutorial: [Scalability Benchmark](tutorials/stress_test_real_scale.ipynb) — performance testing on the Sade-Feldman dataset.
+
+## Documentation
+
+Full documentation: [https://sctrial.readthedocs.io](https://sctrial.readthedocs.io)
+
+- [API Reference](https://sctrial.readthedocs.io/en/latest/api.html)
+- [Tutorials](https://sctrial.readthedocs.io/en/latest/tutorials/index.html)
+- [FAQ](https://sctrial.readthedocs.io/en/latest/faq.html)
+
+## Citation
+
+If you use **sctrial** in your research, please cite:
+
+> Vasanthakumari P, Valencia I, Aghmiouni MR, Magana B, Omar MN. **sctrial: Participant-Level Differential Analysis for Longitudinal Single-Cell Experiments.** *bioRxiv* (2026).
+
+```bibtex
+@article{vasanthakumari2026sctrial,
+  title = {sctrial: Participant-Level Differential Analysis for Longitudinal Single-Cell Experiments},
+  author = {Vasanthakumari, Priyanka and Valencia, Itzel and Aghmiouni, Maryam R. and Magana, Bryan and Omar, Mohamed N.},
+  journal = {bioRxiv},
+  year = {2026},
+  url = {https://github.com/TheOmarLab/sctrial}
+}
+```
+
+## License
+
+MIT License - see [LICENSE](LICENSE) for details.

sctrial-0.3.0/pyproject.toml

@@ -0,0 +1,123 @@
+[build-system]
+requires = ["hatchling>=1.24.2"]
+build-backend = "hatchling.build"
+
+[project]
+name = "sctrial"
+version = "0.3.0"
+description = "Participant-level differential analysis for longitudinal single-cell experiments: DiD, paired comparisons, module scoring, pseudobulk, and power analysis."
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.9"
+license = {  text = "MIT" }
+authors = [{ name = "Contributors" }]
+keywords = ["single-cell", "anndata", "trial", "difference-in-differences", "crossover", "pseudobulk"]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Typing :: Typed",
+]
+
+dependencies = [
+  "numpy>=1.22",
+  "pandas>=1.5",
+  "scipy>=1.8",
+  "statsmodels>=0.13",
+  "anndata>=0.9",
+  "joblib>=1.2",
+  "typing_extensions>=4.0; python_version < '3.11'",
+]
+
+[project.urls]
+Homepage = "https://github.com/TheOmarLab/sctrial"
+Documentation = "https://sctrial.readthedocs.io"
+Repository = "https://github.com/TheOmarLab/sctrial"
+Issues = "https://github.com/TheOmarLab/sctrial/issues"
+
+[project.optional-dependencies]
+plots = ["matplotlib>=3.6", "seaborn>=0.12", "scanpy>=1.9", "plotly>=5.0", "adjustText>=1.0"]
+gsea = ["gseapy>=1.0"]
+aucell = ["pyscenic>=0.12"]
+survival = ["lifelines>=0.27"]
+bayes = ["pymc>=5.0"]
+all = [
+  "matplotlib>=3.6",
+  "seaborn>=0.12",
+  "scanpy>=1.9",
+  "plotly>=5.0",
+  "adjustText>=1.0",
+  "gseapy>=1.0",
+  "pyscenic>=0.12",
+  "lifelines>=0.27",
+  "pymc>=5.0",
+]
+docs = [
+  "sphinx>=7.0",
+  "pydata-sphinx-theme>=0.15",
+  "sphinx-design>=0.5",
+  "sphinx-copybutton>=0.5",
+  "nbsphinx>=0.9",
+  "myst-parser>=2.0",
+  "pandoc",
+]
+dev = [
+  "pytest>=7.0",
+  "pytest-cov>=4.0",
+  "ruff>=0.5",
+  "mypy>=1.5",
+  "pre-commit>=3.0",
+  "build>=1.0",
+  "twine>=5.0",
+  "psutil>=5.9",
+  "sctrial[docs]",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/sctrial"]
+
+[tool.hatch.build.targets.sdist]
+include = [
+  "src/sctrial",
+  "tests",
+  "README.md",
+  "LICENSE",
+  "pyproject.toml",
+]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-q"
+
+[tool.mypy]
+ignore_missing_imports = true
+check_untyped_defs = true
+
+[tool.ruff]
+line-length = 100
+target-version = "py39"
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I", "UP"]
+ignore = ["E501"]  # Ignore line-too-long errors
+
+[tool.coverage.run]
+branch = true
+source = ["src/sctrial"]
+omit = ["*/tests/*", "*/__pycache__/*", "*/conftest.py"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if TYPE_CHECKING:",
+    "if __name__ == .__main__.:",
+]