tinybike / augur.jl

Simulations, statistics and plots for Augur consensus.

Augur Simulator

Monte Carlo simulations, statistics and plotting tools for the Augur event consensus algorithm.

Installation

julia> Pkg.add("Augur")

Usage

Run simulations with default settings using all available cores:

$ julia -p `nproc` test/controller.jl

Simulation results are automatically saved to test/data. If sim.SAVE_RAW_DATA = true, in addition to the output data, full time traces will be saved to test/data/raw. (Caution: this option both slows down the simulations and requires considerable storage space to store the results.)

Augur.jl includes plotters written for PyPlot and Gadfly. To generate plots, just specify pyplot or gadfly when you run the simulations:

$ julia -p `nproc` test/controller.jl pyplot

Plots are saved to test/plots.

Tests

Unit tests are included with Augur.jl, and can be run from the test/runtests.jl script:

$ julia test/runtests.jl

augur.jl's Issues

Info about upcoming removal of packages in the General registry

As described in https://discourse.julialang.org/t/ann-plans-for-removing-packages-that-do-not-yet-support-1-0-from-the-general-registry/ we are planning on removing packages that do not support 1.0 from the General registry. This package has been detected to not support 1.0 and is thus slated to be removed. The removal of packages from the registry will happen approximately a month after this issue is open.

To transition to the new Pkg system using Project.toml, see https://github.com/JuliaRegistries/Registrator.jl#transitioning-from-require-to-projecttoml.
To then tag a new version of the package, see https://github.com/JuliaRegistries/Registrator.jl#via-the-github-app.

If you believe this package has erroneously been detected as not supporting 1.0 or have any other questions, don't hesitate to discuss it here or in the thread linked at the top of this post.

Changed meaning of .-= in Julia 0.5

Your code uses x .-= y, so you should know that in Julia 0.5 this has changed meaning to be equivalent to broadcast!(identity, x, x .- y), so that it mutates the x array (see JuliaLang/julia#17510 … in Julia 0.6 the whole operation will occur in-place without temporaries). So .- should only be used if the left-hand side is a mutable array, and you don't mind mutating it.

At first glance, this looks like it is okay for you, because you use it in cases where it looks like you want to work in-place anyway? But if it were a problem you could always change it to -=.