Installation

Choose the installation path that matches how you will use REVISE. For a normal analysis workflow, install the PyPI package. For documentation, refactoring, or route development, use an editable checkout.

Prerequisites

  • Python environment with the scientific stack required by your selected route.

  • Local access to input .h5ad files under raw_data/.

  • A writable output location such as output/ or results_unified/.

Stable Release

Install the latest release from PyPI:

pip install revise-svc

Optional annotation support installs tacco:

pip install "revise-svc[annotation]"

Development Install

Clone the repository and install with development tooling:

git clone https://github.com/wuys13/REVISE.git
cd REVISE
pip install -e ".[dev]"

The source distribution and wheel include revise/revise.yaml. Installed Python code can therefore use REVISEPipeline() without passing a config path. Source-tree scripts still default to --config revise/revise.yaml for backward compatibility.

Useful development checks:

ruff check revise/
black revise/
python revise/validate_refactor.py

After installation, run one of the commands in Quick Start to validate that your data layout and route selection are correct.

Documentation Build

ReadTheDocs uses the repository-level .readthedocs.yaml file. Local docs builds use docs/conf.py as the Sphinx configuration:

pip install -r docs/requirements.txt
cd docs
make html

The documentation build imports revise from the repository checkout and mocks heavy scientific dependencies. ReadTheDocs therefore does not install the full runtime package during docs builds.

docs/source/api/generated/ is produced by Sphinx autosummary during the build and is intentionally not tracked by Git. Notebook pages under docs/benchmark and docs/case are tracked symbolic links to the maintained notebooks in reproduce/.

Data Layout

Download Sim2Real-ST benchmark data, generated results, and real application data from Zenodo. Place downloaded inputs under raw_data/:

raw_data/
├── Sim2Real-ST/
│   ├── segmentation/
│   ├── bin2cell/
│   ├── batch_effect/
│   ├── spot_size/
│   ├── gene_panel/
│   └── gene_dropout/
└── Real_application/

Generated outputs should go under output/ or results_unified/. These directories are intentionally ignored by Git.