From 6e8f9b8680faefa9170ef7f185871e04fff82f46 Mon Sep 17 00:00:00 2001 From: Marius Lange Date: Wed, 29 Jan 2025 16:07:53 +0100 Subject: [PATCH 1/3] Update the Readme --- README.md | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c6e91fb..944349a 100644 --- a/README.md +++ b/README.md @@ -3,12 +3,14 @@ [![Tests][badge-tests]][tests] [![Coverage][badge-coverage]][coverage] [![Documentation][badge-docs]][documentation] +[![Pre-commit.ci][badge-pre-commit]][pre-commit] [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 -A tool to annotate cell types based on marker genes using OpenAI models. Inspired by [Hou et al., Nature Methods 2024](https://www.nature.com/articles/s41592-024-02235-4) and [https://github.com/VPetukhov/GPTCellAnnotator](https://github.com/VPetukhov/GPTCellAnnotator). +A tool to annotate cell types based on marker genes using OpenAI models. ## Key features @@ -16,6 +18,7 @@ A tool to annotate cell types based on marker genes using OpenAI models. Inspire - Generate consistent annotations across samples of your study. - Optionally infuse prior knowledge by providing information about your biological system. - Retrieve reliable results thanks to [OpenAI structured outputs](https://platform.openai.com/docs/guides/structured-outputs) +- Use 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)) ## Installation @@ -30,10 +33,14 @@ pip install git+https://github.com/quadbio/cell-annotator.git@main ## Getting started -After installation, head over to OpenAI to generate your API key: https://help.openai.com/en/articles/4936850-where-do-i-find-my-openai-api-key +After installation, head over to OpenAI to generate your [API key](https://help.openai.com/en/articles/4936850-where-do-i-find-my-openai-api-key) Keep this key private and don't share it with anyone. `CellAnnotator` will try to read the key as an environmental variable - either expose it to the environment yourself, or store it as an `.env` file anywhere within the repository where you conduct your analysis and plan to run `CellAnnotator`. The package will then use [dotenv](https://pypi.org/project/python-dotenv/) to export the key from the `env` file as an environmental variable. +## Credits + +This tool was inspired by [Hou et al., Nature Methods 2024](https://www.nature.com/articles/s41592-024-02235-4) and [https://github.com/VPetukhov/GPTCellAnnotator](https://github.com/VPetukhov/GPTCellAnnotator). + ## Contact If you found a bug, please use the [issue tracker][]. From 381a0c387de3118345b67b1d8e1ba6e37c5846a4 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 29 Jan 2025 15:11:31 +0000 Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- CHANGELOG.md | 2 +- README.md | 10 +++++----- docs/contributing.md | 18 +++++++++--------- 3 files changed, 15 insertions(+), 15 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e7b7808..c185628 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,4 +12,4 @@ and this project adheres to [Semantic Versioning][]. ### Added -- Basic tool, preprocessing and plotting functions +- Basic tool, preprocessing and plotting functions diff --git a/README.md b/README.md index 944349a..33d842a 100644 --- a/README.md +++ b/README.md @@ -14,11 +14,11 @@ A tool to annotate cell types based on marker genes using OpenAI models. ## Key features -- Automatically annotate cells including type, state and confidence fields. -- Generate consistent annotations across samples of your study. -- Optionally infuse prior knowledge by providing information about your biological system. -- Retrieve reliable results thanks to [OpenAI structured outputs](https://platform.openai.com/docs/guides/structured-outputs) -- Use 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)) +- Automatically annotate cells including type, state and confidence fields. +- Generate consistent annotations across samples of your study. +- Optionally infuse prior knowledge by providing information about your biological system. +- Retrieve reliable results thanks to [OpenAI structured outputs](https://platform.openai.com/docs/guides/structured-outputs) +- Use 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)) ## Installation diff --git a/docs/contributing.md b/docs/contributing.md index 83f9b62..ce9f153 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -155,11 +155,11 @@ This will automatically create a git tag and trigger a Github workflow that crea Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features: -- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text -- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension). -- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks)) -- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types -- Citations (like {cite:p}`virshup2023scverse`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/) +- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text +- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension). +- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks)) +- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types +- Citations (like {cite:p}`virshup2023scverse`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/) See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own. @@ -183,10 +183,10 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu #### Hints -- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. - Only if you do so can sphinx automatically create a link to the external documentation. -- If building the documentation fails because of a missing link that is outside your control, - you can add an entry to the `nitpick_ignore` list in `docs/conf.py` +- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. + Only if you do so can sphinx automatically create a link to the external documentation. +- If building the documentation fails because of a missing link that is outside your control, + you can add an entry to the `nitpick_ignore` list in `docs/conf.py` (docs-building)= From 3822aeca876b0481375f56c722b9678b3514b469 Mon Sep 17 00:00:00 2001 From: Marius Lange Date: Wed, 29 Jan 2025 16:14:47 +0100 Subject: [PATCH 3/3] Add pre-commit.ci badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 944349a..cc99a32 100644 --- a/README.md +++ b/README.md @@ -50,3 +50,4 @@ If you found a bug, please use the [issue tracker][]. [tests]: https://github.com/quadbio/cell-annotator/actions/workflows/test.yaml [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