algorthim to pack molecular recipes
Project description
cellPack
algorithm to pack molecular recipes
Features
- Store values and retain the prior value in memory
- ... some other functionality
Quick Start
from cellpack import Example
a = Example()
a.get_value() # 10
in terminal:
Setup
- create a virtual env:
conda create -n autopack
activate autopack
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
oranalyze -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
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
-
pip install -e .[dev]
This will install your package in editable mode with all the required development dependencies (i.e.
tox
). -
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. -
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.
-
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
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.- 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 tomain
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. - 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
Project details
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