Metadata-Version: 2.1
Name: cellpack
Version: 1.0.1
Summary: algorthim to pack molecular recipes
Home-page: https://github.com/mesoscope/cellpack
Author: Megan Riel-Mehan
Author-email: meganr@alleninstitute.org
License: MIT license
Description: # cellPack
        
        [![Build Status](https://github.com/mesoscope/cellpack/workflows/Build%20Main/badge.svg)](https://github.com/mesoscope/cellpack/actions)
        [![Documentation](https://github.com/mesoscope/cellpack/workflows/Documentation/badge.svg)](https://mesoscope.github.io/cellpack/)
        [![Code Coverage](https://codecov.io/gh/mesoscope/cellpack/branch/main/graph/badge.svg)](https://codecov.io/gh/mesoscope/cellpack)
        
        algorithm to pack molecular recipes
        
        
        ### Setup 
        1. create a virtual env: `conda create -n autopack`
        2. `activate autopack`
        3. `pip install -e .[dev]`
        
        ### Run analysis code
        By default analyze will run all packing methods on `cellpack/test-recipes/NM_Analysis_FigureB1.0.json
        Examples:
        * `analyze -o [PATH/TO/OUTPUT/FOLDER]` will create subfolders for each packing method at your output folder
        * To run just one packing method: `analyze -o [PATH/TO/OUTPUT/FOLDER] -p jitter`
        * To change the dimension of the packing: `analyze -r cellpack/test-recipes/NM_Analysis_FigureC1.json  -o /Users/meganriel-mehan/Dropbox/cellPack/NM_Analysis_C_1 -d 3`
        * Turn off plotly plot: `analyze -o [PATH/TO/OUTPUT/FOLDER] -ng` or `analyze -o [PATH/TO/OUTPUT/FOLDER] --no-grid-plot`
        
        ### Run conversion code 
        * To convert to simularium and view at https://staging.simularium.allencell.org/viewer
        `convert -r [FULL_PATH_TO_INPUT_RECIPE_FILE] -p [FULL_PATH_TO_PACKING_RESULT] -o [OUTPUT_PATH]`
        ## Installation
        
        **Stable Release:** `pip install cellpack`<br>
        **Development Head:** `pip install git+https://github.com/mesoscope/cellpack.git`
        
        ## Documentation
        
        For full package documentation please visit [mesoscope.github.io/cellpack](https://mesoscope.github.io/cellpack).
        
        ## Development
        
        See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.
        
        ### Contributing cheat sheet
        
        1. `pip install -e .[dev]`
        
            This will install your package in editable mode with all the required development
            dependencies (i.e. `tox`).
        
        2. `make build`
        
            This will run `tox` which will run all your tests in both Python 3.7
            and Python 3.8 as well as linting your code.
        
        3. `make clean`
        
            This will clean up various Python and build generated files so that you can ensure
            that you are working in a clean environment.
        
        4. `make docs`
        
            This will generate and launch a web browser to view the most up-to-date
            documentation for your Python package.
        
        #### Suggested Git Branch Strategy
        
        1. `main` is for the most up-to-date development, very rarely should you directly
           commit to this branch. GitHub Actions will run on every push and on a CRON to this
           branch but still recommended to commit to your development branches and make pull
           requests to main. If you push a tagged commit with bumpversion, this will also release to PyPI.
        2. Your day-to-day work should exist on branches separate from `main`. Even if it is
           just yourself working on the repository, make a PR from your working branch to `main`
           so that you can ensure your commits don't break the development head. GitHub Actions
           will run on every push to any branch or any pull request from any branch to any other
           branch.
        3. It is recommended to use "Squash and Merge" commits when committing PR's. It makes
           each set of changes to `main` atomic and as a side effect naturally encourages small
           well defined PR's.
        
        
        **MIT license**
        
        
Keywords: cellpack
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: setup
Provides-Extra: test
Provides-Extra: dev
Provides-Extra: all
