Fix pypi release

* Fix pypi release * Improve docs --------- Co-authored-by: Philipp A. <[email protected]>
theislab · Nov 11, 2024 · 3658b88 · 3658b88
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diff --git 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
 
 <h1 align="center">
     <picture>
-        <source srcset=".github/misc/concept.svg">
-        <img width="800" src=".github/misc/concept.svg" alt="DRVI concept">
+        <source srcset="https://raw.githubusercontent.com/theislab/DRVI/main/.github/misc/concept.svg">
+        <img width="800" src="https://raw.githubusercontent.com/theislab/DRVI/main/.github/misc/concept.svg" alt="DRVI concept">
     </picture>
 </h1>
 
@@ -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 release of `drvi-py` from [PyPI][link-pypi]:
 
 ```bash
 pip install drvi-py
 ```
--->
 
 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
@@ -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
@@ -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
@@ -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
@@ -1,7 +1,7 @@
 # Tutorials
 
 ```{toctree}
-:maxdepth: 2
+:maxdepth: 1
 
 notebooks/general_pipeline
 ```
diff --git 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
@@ -2,7 +2,7 @@
 
 from . import model, nn_modules, scvi_tools_based, utils
 
-__version__ = version("drvi")
+__version__ = version("drvi-py")
 
 __all__ = [
     "__version__",