MEDYAN.jl

Documentation for MEDYAN.

MEDYAN.jl WIP

Warning, the API is very unstable, and this package is not released yet.

Welcome to Papoian Lab’s Mechanochemical Dynamics of Active Networks Julia package.

This is based on the C++ medyan command line tool also developed by the Papoian Lab.

Copyright 2022, Papoian lab at the University of Maryland.

This code is distributed under the license found in this directory, license.txt.

Installation

1. Clone the repository

git clone https://github.com/medyan-dev/MEDYAN.jl.git
cd MEDYAN.jl

2. Install Julia

On Linux and macOS you can install the known working version of julia using:

curl -fsSLO https://github.com/nhz2/install-julia-linux/releases/download/v0.4.0/install-julia.sh
chmod +x install-julia.sh
mv install-julia.sh ~/.local/bin/
install-julia.sh manifest .

Run this from the repo root so it reads the version out of Manifest-v1.*.toml.

You can also download and install Julia binaries from https://julialang.org/downloads/manual-downloads/

3. Set up the workspace

This repository is a Julia workspace Instantiate the whole workspace at once from the repo root:

julia --project -e 'using Pkg; Pkg.instantiate(workspace=true)'

Usage

To use MEDYAN.jl from your own Julia environment, dev the MEDYAN sub package:

using Pkg; pkg"dev <path to repo>/MEDYAN"

Where <path to repo> should be replaced with a local or absolute path to the repo.

• Tutorials
• Reference

Authors

Active developers:

Name	Email
Nathan Zimmerberg	nzimmerb@umd.edu
Mengxin Gu	mxgu1234@umd.edu
Patrick Kelly	ptfk1677@umd.edu

All developers including developers of C++ medyan:

Garegin Papoian (gpapoian@umd.edu), Konstantin Popov, James Komianos, Aravind Chandrasekaran, Qin Ni, Carlos Floyd, Haoran Ni, Nathan Zimmerberg, Joshua Lucker, Mengxin Gu, Patrick Kelly

All general correspondence about the code and its applications should be directed to Garegin Papoian. All developer and more specific code, installation, and usage correspondence should be directed to Active developers via email or the issue tracker.

Running tests

In shell:

julia --project -e 'using Pkg; Pkg.instantiate(workspace=true)'
julia --project=MEDYAN/test MEDYAN/test/runtests.jl

You can also include individual test files to run just those tests.

Sub Packages

There are a number of sub packages found in the root directory.

For example “MEDYAN2Vtk”, can be tested using the following shell commands:

julia --project -e 'using Pkg; Pkg.instantiate(workspace=true)'
julia --project=MEDYAN2Vtk/test MEDYAN2Vtk/test/runtests.jl

To use “MEDYAN2Vtk” package in a new environment in Julia run:

using Pkg; pkg"dev <path to repo>/MEDYAN2Vtk"

If the sub package depends on other sub packages or depends on MEDYAN, you may have to dev multiple paths.

Running notebooks

To run interactively in a Pluto Notebook, run the following shell commands:

julia --project -e 'using Pkg; Pkg.instantiate(workspace=true)'
julia --project=notebooks -e 'import Pluto; Pluto.run()'

To generate static html files, run the following shell commands:

julia --project -e 'using Pkg; Pkg.instantiate(workspace=true)'
julia --project=notebooks notebooks/runnotebooks.jl

Editing Documentation

Previewing docs requires Linux.

Run the following to set up the environment and create a preview. Any changes to files in docs should auto update.

julia --project -e 'using Pkg; Pkg.instantiate(workspace=true)'
./docs/make.jl

or

julia --project -e 'using Pkg; Pkg.instantiate(workspace=true)'
julia --project=docs docs/make.jl

Run the following to refresh the docstrings for the site.

julia --project -e 'using Pkg; Pkg.instantiate(workspace=true)'
julia --project=docs docs/make-docstrings.jl

How to Cite

If you use MEDYAN.jl in your research, please cite the relevant papers. See CITATION.bib for BibTeX entries.