cellPack

algorithm to pack molecular recipes

Prerequisite

1. Install Conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html

Setup

1. create a virtual env: conda create -n autopack python=3.9
2. conda activate autopack
3. pip install -e .[dev]

Run pack code

1. example pack recipe : pack -r cellpack/test-recipes/NM_Analysis_FigureB1.0.json -c packing-configs/run.json

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
Development Head: pip install git+https://github.com/mesoscope/cellpack.git

Documentation

For full package documentation please visit mesoscope.github.io/cellpack.

Development

See 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