Merge pull request #24 from quadbio/feature/docs

Update the README

Author: Marius1311

README.md

@@ -4,11 +4,13 @@
 [![Coverage][badge-coverage]][coverage]
 [![Documentation][badge-docs]][documentation]
 [![Pre-commit.ci][badge-pre-commit]][pre-commit]
+[![PyPI][badge-pypi]][pypi]
 
 [badge-tests]: https://img.shields.io/github/actions/workflow/status/quadbio/cell-annotator/test.yaml?branch=main
 [badge-coverage]: https://codecov.io/gh/quadbio/cell-annotator/branch/main/graph/badge.svg
 [badge-docs]: https://img.shields.io/readthedocs/cell-annotator
 [badge-pre-commit]: https://results.pre-commit.ci/badge/github/quadbio/cell-annotator/main.svg
+[badge-pypi]: https://img.shields.io/pypi/v/cell-annotator.svg
 
 A tool to annotate cell types in scRNA-seq data based on marker genes using OpenAI models.
 
@@ -20,6 +22,8 @@ A tool to annotate cell types in scRNA-seq data based on marker genes using Open
 - Retrieve reliable results thanks to [OpenAI structured outputs](https://platform.openai.com/docs/guides/structured-outputs)
 - Use this tool to quickly generate pre-integration cell type labels to either score your integration quality (e.g. [scIB metrics](https://scib-metrics.readthedocs.io/en/stable/)) or to guide your integration effort (e.g. [scPoli](https://docs.scarches.org/en/latest/), [scANVI](https://docs.scvi-tools.org/en/stable/api/reference/scvi.model.SCANVI.html)).
 
+Note that this package is based on output generated by large language models and might **sometimes make mistakes**. We use some safeguards, like anchoring the tool in a multi-step process, and using structured output predictions, but mistakes are still possible. We recommend using this tool as a first step in an annotation workflow to generate an initial, coarse set of annotations that must be further refined.
+
 ## Installation
 
 You need to have Python 3.10 or newer installed on your system.
@@ -73,3 +77,4 @@ If you found a bug, please use the [issue tracker][].
 [coverage]: https://codecov.io/gh/quadbio/cell-annotator
 [documentation]: https://cell-annotator.readthedocs.io
 [pre-commit]: https://results.pre-commit.ci/latest/github/quadbio/cell-annotator/main
+[pypi]: https://pypi.org/project/cell-annotator/

docs/conf.py

@@ -20,7 +20,7 @@
 info = metadata("cell-annotator")
 project_name = info["Name"]
 author = info["Author"]
-copyright = f"{datetime.now():%Y}, {author}."
+copyright = f"{datetime.now():%Y}, QuaDBio Lab."
 version = info["Version"]
 urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
 repository_url = urls["Source"]