Metadata-Version: 2.4
Name: annsel
Version: 0.1.0
Summary: A Narwhals powered DataFrame-style selection, filtering and indexing operations on AnnData Objects.
Project-URL: Documentation, https://annsel.readthedocs.io/
Project-URL: Homepage, https://github.com/srivarra/annsel
Project-URL: Source, https://github.com/srivarra/annsel
Author: Sricharan Reddy Varra
Maintainer-email: Sricharan Reddy Varra <srivarra@stanford.edu>
License: MIT License
        
        Copyright (c) 2024, Sricharan Reddy Varra
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
License-File: LICENSE
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Description-Content-Type: text/markdown

# annsel

<div align="center">

|               |                                                                                                                                                                                                              |
| :-----------: | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
|  **Status**   | [![Build][badge-build]][link-build] [![Tests][badge-test]][link-test] [![Documentation][badge-docs]][link-docs] [![codecov][badge-codecov]][link-codecov] [![pre-commit][badge-pre-commit]][link-pre-commit] |
|   **Meta**    |         [![Hatch project][badge-hatch]][link-hatch] [![Ruff][badge-ruff]][link-ruff] [![uv][badge-uv]][link-uv] [![License][badge-license]][link-license] [![gitmoji][badge-gitmoji]][link-gitmoji]          |
|  **Package**  |                                                                 [![PyPI][badge-pypi]][link-pypi] [![PyPI][badge-python-versions]][link-pypi]                                                                 |
| **Ecosystem** |                                                                                  [![scverse][badge-scverse]][link-scverse]                                                                                   |
|               |                                                                                                                                                                                                              |

</div>

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[badge-docs]: https://img.shields.io/readthedocs/annsel?logo=readthedocs
[badge-codecov]: https://codecov.io/gh/srivarra/annsel/graph/badge.svg?token=ST0ST1BTWU
[badge-ruff]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
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[badge-license]: https://img.shields.io/badge/License-MIT-yellow.svg
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[badge-gitmoji]: https://img.shields.io/badge/gitmoji-😜😍-FFDD67.svg

Annsel is a user-friendly library that brings familiar dataframe-style operations to [`AnnData`](https://anndata.readthedocs.io/en/latest/) objects.

It's built on the [narwhals][link-narwhals] compatibility layer for dataframes.

Take a look at the GitHub Projects board for features and future plans: [Annsel Features][link-gh-project]

<!-- done -->

## Getting started

Please refer to the [documentation][link-docs], in particular, the [API documentation][link-api].

## Installation

You need to have Python 3.10 or newer installed on your system. If you don't have
Python installed, we recommend installing [uv][link-uv].
There are several ways to install `annsel`:

1. Install the most recent release:

    With `uv`:

    ```zsh
    uv add annsel
    ```

    With `pip`:

    ```zsh
    pip install annsel
    ```

2. Install the latest development version:

    With `uv`:

    ```zsh
    uv add git+https://github.com/srivarra/annsel
    ```

    With `pip`:

    ```zsh
    pip install git+https://github.com/srivarra/annsel.git@main
    ```

## Examples

```python
import annsel as an

adata=an.datasets.leukemic_bone_marrow_dataset()
```

### Filter

```python
adata.an.filter(
    obs=(
        an.col(["Cell_label"]).is_in(["Classical Monocytes", "CD8+CD103+ tissue resident memory T cells"]),
        an.col(["sex"]) == "male",
    ),
    var=an.col(["vst.mean"]) >= 3,
)
```

### Select

```python
adata.an.select(
    obs=an.col(["Cell_label"]),
    var=an.col(["vst.mean", "vst.std"]),
)
```

### Group By

```python
adata.an.group_by(
    obs=an.col(["Cell_label"]),
    var=an.col(["feature_type"]),
    return_group_names=True,
)
```

## Release notes

See the [changelog][changelog].

## Contact

For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse] or the [discussions][link-disucssions] tab.
If you found a bug, please use the [issue tracker][issue-tracker].

## Citation

> Varra, S. R. annsel [Computer software]. <https://github.com/srivarra/annsel>

<!-- done3 -->

[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/srivarra/annsel/issues
[changelog]: https://annsel.readthedocs.io/en/latest/changelog.html
[link-docs]: https://annsel.readthedocs.io
[link-api]: https://annsel.readthedocs.io/en/latest/api/index.html
[link-pypi]: https://pypi.org/project/annsel
[link-codecov]: https://codecov.io/gh/srivarra/annsel
[link-test]: https://github.com/srivarra/annsel/actions/workflows/test.yml
[link-build]: https://github.com/srivarra/annsel/actions/workflows/build.yaml
[link-ruff]: https://github.com/astral-sh/ruff
[link-uv]: https://github.com/astral-sh/uv
[link-license]: https://opensource.org/licenses/MIT
[link-hatch]: https://github.com/pypa/hatch
[link-narwhals]: https://github.com/narwhals-dev/narwhals
[link-disucssions]: https://github.com/srivarra/annsel/discussions
[link-pre-commit]: https://results.pre-commit.ci/latest/github/srivarra/annsel/main
[link-gitmoji]: https://gitmoji.dev/
[link-gh-project]: https://github.com/users/srivarra/projects/9
[link-scverse]: https://scverse.org/packages/#ecosystem
