Metadata-Version: 2.1
Name: cell_feature_data
Version: 1.0.2
Summary: A Python package for creating a dataset for the Cell Feature Explorer.
Author-email: Ruge Li <ruge.li@alleninstitute.org>
License: MIT License
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: 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**
