Metadata-Version: 2.1
Name: cell_feature_data
Version: 1.0.4
Summary: A Python package for creating a dataset for the Cell Feature Explorer.
Author-email: Ruge Li <ruge.li@alleninstitute.org>
License: MIT License
        
        Copyright (c) 2024, Allen Institute
        
        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.
Classifier: Development Status :: 4 - Beta
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: click>=8.1.7
Requires-Dist: mypy-extensions>=1.0.0
Requires-Dist: numpy>=1.26.3
Requires-Dist: packaging>=23.2
Requires-Dist: pandas>=2.1.4
Requires-Dist: pathspec>=0.12.1
Requires-Dist: platformdirs>=4.1.0
Requires-Dist: prompt-toolkit>=3.0.36
Requires-Dist: python-dateutil>=2.8.2
Requires-Dist: pytz>=2023.3.post1
Requires-Dist: questionary>=2.0.1
Requires-Dist: six>=1.16.0
Requires-Dist: tzdata>=2023.4
Requires-Dist: wcwidth>=0.2.13
Requires-Dist: black>=22.3.0
Requires-Dist: check-manifest>=0.48
Provides-Extra: all
Requires-Dist: flake8>=4.0.1; extra == "all"
Requires-Dist: flake8-debugger>=3.2.1; extra == "all"
Requires-Dist: flake8-typing-imports>=1.9.0; extra == "all"
Requires-Dist: flake8-pyproject>=0.4.0; extra == "all"
Requires-Dist: coverage>=5.1; extra == "all"
Requires-Dist: pytest>=7.1.2; extra == "all"
Requires-Dist: pytest-cov>=4.0.0; extra == "all"
Requires-Dist: pytest-raises>=0.11; extra == "all"
Provides-Extra: lint
Requires-Dist: flake8>=4.0.1; extra == "lint"
Requires-Dist: flake8-debugger>=3.2.1; extra == "lint"
Requires-Dist: flake8-typing-imports>=1.9.0; extra == "lint"
Requires-Dist: flake8-pyproject>=0.4.0; extra == "lint"
Provides-Extra: test
Requires-Dist: coverage>=5.1; extra == "test"
Requires-Dist: pytest>=7.1.2; extra == "test"
Requires-Dist: pytest-cov>=4.0.0; extra == "test"
Requires-Dist: pytest-raises>=0.11; extra == "test"

# Cell Feature Data

[![Dataset validation](https://github.com/allen-cell-animated/cell-feature-data/actions/workflows/validate.yml/badge.svg?branch=main)](https://github.com/allen-cell-animated/cell-feature-data/actions/workflows/validate.yml)


**Python Package for Creating and Validating Cell Feature Datasets for [Cell Feature Explore](https://cfe.allencell.org/)**

---

## Documentation

For full documentation, please see the [full documentation on Github](https://github.com/allen-cell-animated/cell-feature-data).

---

## Install and Setup

```pip install cell-feature-data```

## To create a new dataset using the package:
1. Create a virtual environment if not already created: `python3 -m venv [ENV-PATH]`
2. Activate the virtual environment: 
   - On macOS/Linux: `source [ENV-PATH]/bin/activate`
   - On Windows: `[ENV-PATH]\Scripts\activate`
3. Install the dependencies: `pip install cell-feature-data`. 
4. Run `create-dataset` to start the dataset creation process. This will: 
   - Request the path of the file you want to process. Formats supported: `.csv`, with more formats to be added as development progresses
   - Ask for an output path to save your dataset. If not specified, a new dataset folder is created in `data`, named after the input file
   - Process the input file and generate the necessary json files for the dataset
   - Prompt for additional information about the dataset and update the json files accordingly
5. Deactivate the virtual environment when finished: `deactivate`

#### For more on what these files should look like, look at [Full spec documentation](https://allen-cell-animated.github.io/cell-feature-data/HandoffSpecification.html)

**MIT license**
