Metadata-Version: 2.2
Name: neura-library
Version: 0.4.0
Summary: Utility tools for system neuroscience research, including Open Source Wrapper or Parser
Author-email: Yu-Ting Wei <ytsimon2004@gmail.com>, Ta-Shun Su <antoniost29@gmail.com>
License: BSD 3-Clause License
        
        Copyright (c) 2023, YT.WEI
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its
           contributors may be used to endorse or promote products derived from
           this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Project-URL: Homepage, https://github.com/ytsimon2004/neuralib
Project-URL: Documentation, https://neuralib.readthedocs.io/en/latest/index.html
Project-URL: Repository, https://github.com/ytsimon2004/neuralib
Project-URL: Issues, https://github.com/ytsimon2004/neuralib/issues
Keywords: Neuroscience,visual neuroscience,cellular imaging,brain mapping,spatial navigation
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering
Classifier: Intended Audience :: Science/Research
Classifier: Typing :: Typed
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: attrs
Requires-Dist: colorama
Requires-Dist: colorlog
Requires-Dist: matplotlib
Requires-Dist: seaborn
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: scikit-image
Requires-Dist: pandas
Requires-Dist: polars
Requires-Dist: pyarrow
Requires-Dist: tifffile
Requires-Dist: opencv-python>=4.8.0.76
Requires-Dist: tqdm
Requires-Dist: requests
Requires-Dist: gdown
Requires-Dist: rich
Requires-Dist: typing_extensions
Provides-Extra: atlas
Requires-Dist: brainrender; extra == "atlas"
Requires-Dist: iblatlas; extra == "atlas"
Requires-Dist: anytree; extra == "atlas"
Requires-Dist: plotly; extra == "atlas"
Provides-Extra: scanner
Requires-Dist: xmltodict; extra == "scanner"
Requires-Dist: aicspylibczi; extra == "scanner"
Provides-Extra: imaging
Requires-Dist: scanimage-tiff-reader; extra == "imaging"
Requires-Dist: suite2p; extra == "imaging"
Requires-Dist: sbxreader; extra == "imaging"
Requires-Dist: ruamel.yaml; extra == "imaging"
Requires-Dist: numba; extra == "imaging"
Provides-Extra: segmentation
Requires-Dist: pyqt6; extra == "segmentation"
Requires-Dist: pyqtgraph; extra == "segmentation"
Requires-Dist: cellpose; extra == "segmentation"
Requires-Dist: stardist; extra == "segmentation"
Requires-Dist: csbdeep; extra == "segmentation"
Requires-Dist: roifile; extra == "segmentation"
Requires-Dist: napari; extra == "segmentation"
Requires-Dist: numpy<2.0; extra == "segmentation" and extra == "segmentation"
Provides-Extra: model
Requires-Dist: rastermap; extra == "model"
Provides-Extra: plot
Requires-Dist: matplotlib_venn; extra == "plot"
Provides-Extra: track
Requires-Dist: facemap; extra == "track"
Requires-Dist: numpy<2.0; extra == "track" and extra == "track"
Provides-Extra: gpu
Requires-Dist: torch; extra == "gpu"
Requires-Dist: tensorflow; extra == "gpu"
Requires-Dist: psutil; extra == "gpu"
Provides-Extra: imagelib
Requires-Dist: pdf2image; extra == "imagelib"
Requires-Dist: imageio; extra == "imagelib"
Provides-Extra: tools
Requires-Dist: slackclient; extra == "tools"
Requires-Dist: gspread; extra == "tools"
Provides-Extra: all
Requires-Dist: bokeh; extra == "all"
Requires-Dist: neura-library[atlas]; extra == "all"
Requires-Dist: neura-library[scanner]; extra == "all"
Requires-Dist: neura-library[imaging]; extra == "all"
Requires-Dist: neura-library[plot]; extra == "all"
Requires-Dist: neura-library[model]; extra == "all"
Requires-Dist: neura-library[profile]; extra == "all"
Requires-Dist: neura-library[imagelib]; extra == "all"
Requires-Dist: neura-library[tools]; extra == "all"
Provides-Extra: dev
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: ruff; extra == "dev"
Requires-Dist: neura-library[segmentation]; extra == "dev"
Requires-Dist: neura-library[track]; extra == "dev"
Requires-Dist: neura-library[gpu]; extra == "dev"
Requires-Dist: neura-library[all]; extra == "dev"
Provides-Extra: doc
Requires-Dist: sphinx; extra == "doc"
Requires-Dist: nbsphinx; extra == "doc"
Requires-Dist: sphinx-toolbox; extra == "doc"
Requires-Dist: sphinx-rtd-theme; extra == "doc"
Requires-Dist: neura-library[segmentation]; extra == "doc"
Requires-Dist: neura-library[track]; extra == "doc"
Requires-Dist: neura-library[gpu]; extra == "doc"
Requires-Dist: neura-library[all]; extra == "doc"

# neuralib

![PyPI - Python Version](https://img.shields.io/pypi/pyversions/neura-library)
[![PyPI version](https://badge.fury.io/py/neura-library.svg)](https://badge.fury.io/py/neura-library)
[![Downloads](https://static.pepy.tech/badge/neura-library)](https://pepy.tech/project/neura-library)

[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
[![Document Status](https://readthedocs.org/projects/neuralib/badge/?version=latest)](https://neuralib.readthedocs.io/en/latest/index.html)

## Utility tools for rodent system neuroscience research, including Open Source Wrapper or Parser

## See the [Documentation ](https://neuralib.readthedocs.io/en/latest/index.html) and [Examples](https://github.com/ytsimon2004/neuralib/tree/main/doc/source/notebooks)

## Checkout [Release notes](https://github.com/ytsimon2004/neuralib/releases)

# Installation

## conda environment

- Create and activate a new conda environment (Python >=3.10, but >=3.12 not yet tested), then install:

```shell
conda create -n neuralib python=3.10
conda activate neuralib
pip install neura-library
```

- If you wish to install **all dependencies**, run:

```shell
pip install neura-library[all]
```

- If you wish to install the **minimal required dependencies** according to usage purpose:

Choices in []: atlas, scanner, imaging, segmentation, model, track, gpu, profile, imagelib, tools, full
Example of using the atlas module:

```shell
pip install neura-library[atlas]
```

- If installing in developer mode (Install pre-commit and linter check by ruff)

```shell
pip install neura-library[dev]
pre-commit install
ruff check .
```

## uv virtual environment

- Install uv, run in Unix or git bash (Windows):

```shell
curl -LsSf https://astral.sh/uv/install.sh | sh
```

- Follow uv project structure [doc](https://docs.astral.sh/uv/guides/projects/#creating-a-new-project):

```shell
uv init
```

- Make sure python version (>=3.10, but >=3.12 not yet tested), both in `pyproject.py` and `.python-version`

```shell
uv python install 3.10
```

- If you wish to install **all dependencies**, run:

```shell
uv add neura-library[all]
```

- If you wish to install the **minimal required dependencies** according to usage purpose:

Choices in []: atlas, scanner, imaging, segmentation, model, track, gpu, profile, imagelib, tools, full
Example of using the atlas module:

```shell
uv add neura-library[atlas]
```

- If installing in developer mode (Install pre-commit and linter check by ruff)

```shell
uv add neura-library[dev]
pre-commit install
ruff check .
```
