diff --git a/README.md b/README.md index 19c3522..a03a972 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,23 @@ # DRVI +[![Build][badge-build]][link-build] [![Tests][badge-tests]][link-tests] [![Documentation][badge-docs]][link-docs] +[![Python Version][badge-pyver]][link-pypi] -[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/drvi/test.yaml?branch=main +[badge-build]: https://github.com/theislab/drvi/actions/workflows/build.yaml/badge.svg +[badge-tests]: https://github.com/theislab/drvi/actions/workflows/test.yaml/badge.svg +[link-build]: https://github.com/theislab/drvi/actions/workflows/build.yml [link-tests]: https://github.com/theislab/drvi/actions/workflows/test.yml -[badge-docs]: https://img.shields.io/readthedocs/drvi +[badge-docs]: https://img.shields.io/readthedocs/drvi/latest.svg?label=Read%20the%20Docs +[badge-pyver]: https://img.shields.io/pypi/pyversions/drvi Unsupervised Deep Disentangled Representation of Single-Cell Omics

- - DRVI concept + + DRVI concept

@@ -30,13 +35,11 @@ Python installed, we recommend installing [Mambaforge](https://github.com/conda- There are several options to install drvi: - 1. Install the latest development version: @@ -59,11 +62,13 @@ If you found a bug, please use the [issue tracker][issue-tracker]. If DRVI is helpful in your research, please consider citing the following paper: -> t.b.a +> Moinfar, A. A. & Theis, F. J. +> **Unsupervised deep disentangled representation of single-cell omics.** +> bioRxiv 2024.11.06.622266 (2024) [doi:10.1101/2024.11.06.622266](https://doi.org/10.1101/2024.11.06.622266). [issue-tracker]: https://github.com/theislab/drvi/issues [changelog]: https://drvi.readthedocs.io/latest/changelog.html [link-docs]: https://drvi.readthedocs.io -[link-api]: https://drvi.readthedocs.io/latest/api.html +[link-api]: https://drvi.readthedocs.io/latest/api/index.html [link-tutorials]: https://drvi.readthedocs.io/latest/tutorials.html [link-pypi]: https://pypi.org/project/drvi-py diff --git a/docs/conf.py b/docs/conf.py index 7c99d90..5b53d64 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -18,7 +18,7 @@ # NOTE: If you installed your project in editable mode, this might be stale. # If this is the case, reinstall it to refresh the metadata -info = metadata("drvi") +info = metadata("drvi-py") project_name = info["Name"] author = info["Author"] copyright = f"{datetime.now():%Y}, {author}." diff --git a/docs/references.bib b/docs/references.bib index 9f5bed4..7387b1b 100644 --- a/docs/references.bib +++ b/docs/references.bib @@ -8,3 +8,15 @@ @article{Virshup_2023 title = {The scverse project provides a computational ecosystem for single-cell omics data analysis}, journal = {Nature Biotechnology} } + +@ARTICLE{Moinfar2024-cx, + doi = {10.1101/2024.11.06.622266}, + url = {https://doi.org/10.1101/2024.11.06.622266}, + title = "Unsupervised deep disentangled representation of single-cell omics", + author = "Moinfar, Amir Ali and Theis, Fabian J", + journal = "bioRxiv", + pages = "2024.11.06.622266", + month = nov, + year = 2024, + language = "en" +} diff --git a/docs/references.md b/docs/references.md index e7c7548..2cd9128 100644 --- a/docs/references.md +++ b/docs/references.md @@ -1,6 +1,7 @@ # References -If DRVI is helpful in your research, please consider citing the following paper: +If DRVI is helpful in your research, please consider citing {cite:p}`Moinfar2024-cx`. +For other references used in the documentation see below: ```{bibliography} :cited: diff --git a/docs/tutorials.md b/docs/tutorials.md index d071e94..1c8798a 100644 --- a/docs/tutorials.md +++ b/docs/tutorials.md @@ -1,7 +1,7 @@ # Tutorials ```{toctree} -:maxdepth: 2 +:maxdepth: 1 notebooks/general_pipeline ``` diff --git a/pyproject.toml b/pyproject.toml index c6f4a3d..fb1bd4a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,8 +3,8 @@ build-backend = "hatchling.build" requires = ["hatchling"] [project] -name = "drvi" -version = "0.1.0" +name = "drvi-py" +version = "0.1.2" description = "Disentangled Generative Representation of Single Cell Omics" readme = "README.md" requires-python = ">=3.10,<3.13" @@ -19,6 +19,23 @@ urls.Documentation = "https://drvi.readthedocs.io/" urls.Source = "https://github.com/theislab/drvi" urls.Home-page = "https://github.com/theislab/drvi" +# PyPI classifiers +classifiers = [ + "License :: OSI Approved :: BSD License", + "Development Status :: 4 - Beta", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "Natural Language :: English", + "Operating System :: MacOS :: MacOS X", + "Operating System :: POSIX :: Linux", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Topic :: Scientific/Engineering :: Artificial Intelligence", + "Topic :: Scientific/Engineering :: Bio-Informatics", +] + # Please make an issue if you need wider range of versions dependencies = [ "torch>=2.1.0,<2.4", @@ -42,6 +59,9 @@ dependencies = [ "session-info", ] +[tool.hatch.build.targets.wheel] +packages = ["src/drvi"] + [project.optional-dependencies] dev = [ "pre-commit", diff --git a/src/drvi/__init__.py b/src/drvi/__init__.py index c78b3af..e41a63c 100644 --- a/src/drvi/__init__.py +++ b/src/drvi/__init__.py @@ -2,7 +2,7 @@ from . import model, nn_modules, scvi_tools_based, utils -__version__ = version("drvi") +__version__ = version("drvi-py") __all__ = [ "__version__",