rename package

gszep · gszep · commit 192e311c5b33 · 2021-06-11T11:26:15.000+01:00
diff --git a/Project.toml b/Project.toml
@@ -1,5 +1,5 @@
-name = "BifurcationFit"
-uuid = "47d09c00-5f3c-4df8-b294-580a3cc966fd"
+name = "BifurcationInference"
+uuid = "7fe238d6-d31e-4646-aa16-9d8429fd6da8"
 authors = ["gszep <gregory.szep@gmail.com>"]
 version = "0.1.0"
 
diff --git a/README.md b/README.md
@@ -1,15 +1,15 @@
-# BifurcationFit.jl : Inference with Bifurcation Diagrams
+# BifurcationInference.jl : Inference with Bifurcation Diagrams
 
 This library implements the method described in **Szep, G. Dalchau, N. and Csikasz-Nagy, A. 2021. [Parameter Inference with Bifurcation Diagrams](https://arxiv.org/abs/2106.04243)** using parameter continuation library [`BifurcationKit.jl`](https://github.com/rveltz/BifurcationKit.jl) and auto-differentiation [`ForwardDiff.jl`](https://github.com/JuliaDiff/ForwardDiff.jl). This implementation enables continuation methods can be used as layers in machine learning proceedures, and inference can be run end-to-end directly on the geometry of state space.
 
-[![Build Status](https://travis-ci.com/gszep/BifurcationFit.jl.svg?branch=master)](https://travis-ci.com/gszep/BifurcationFit.jl)
-[![Coverage](https://codecov.io/gh/gszep/BifurcationFit.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/gszep/BifurcationFit.jl)
+[![Build Status](https://travis-ci.com/gszep/BifurcationInference.jl.svg?branch=master)](https://travis-ci.com/gszep/BifurcationInference.jl)
+[![Coverage](https://codecov.io/gh/gszep/BifurcationInference.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/gszep/BifurcationInference.jl)
 [![arXiv](https://img.shields.io/badge/arXiv-2106.04243-b31b1b.svg)](https://arxiv.org/abs/2106.04243)
 
 ## Basic Usage
 The model definition requires a distpatched method on `F(z::BorderedArray,θ::AbstractVector)` where `BorderedArray` is a type that contains the state vector `u` and control condition `p` used by the library [`BifurcationKit.jl`](https://github.com/rveltz/BifurcationKit.jl). `θ` is a vector of parameters to be optimised.
 ```julia
-using BifurcationFit, StaticArrays
+using BifurcationInference, StaticArrays
 
 F(z::BorderedArray,θ::AbstractVector) = F(z.u,(θ=θ,p=z.p))
 function F(u::AbstractVector,parameters::NamedTuple)
diff --git a/docs/article.tex b/docs/article.tex
@@ -35,7 +35,7 @@ \section{Introduction}
 \begin{itemize}
     \item An end-to-end differentiable method for locating bifurcations in parameter space and then matching their dependency on a control condition to user-specified locations
     \item Implementation of the method as a Julia package\\
-\href{https://github.com/gszep/BifurcationFit.jl}{\texttt{github.com/gszep/BifurcationFit.jl}}
+\href{https://github.com/gszep/BifurcationInference.jl}{\texttt{github.com/gszep/BifurcationInference.jl}}
     \item Leveraging the cost landscape for a novel way of organising differential equation models in terms of geometric and topological equivalence
 \end{itemize}
 
diff --git a/docs/checklist.tex b/docs/checklist.tex
@@ -23,7 +23,7 @@
 \item If you ran experiments...
 \begin{enumerate}
   \item Did you include the code, data, and instructions needed to reproduce the main experimental results (either in the supplemental material or as a URL)?
-    \answerYes{Figures can be reproduced using unit tests in the GitHub repository for \texttt{BifurcationFit.jl}}
+    \answerYes{Figures can be reproduced using unit tests in the GitHub repository for \texttt{BifurcationInference.jl}}
   \item Did you specify all the training details (e.g., data splits, hyperparameters, how they were chosen)?
     \answerYes{In Section \ref{section:results} we details of optimisations with \texttt{Flux.jl}}
 	\item Did you report error bars (e.g., with respect to the random seed after running experiments multiple times)?
diff --git a/docs/refs.bib b/docs/refs.bib
@@ -2276,13 +2276,13 @@ @article{Chickarmane2005BifurcationTool
     doi = {10.1093/bioinformatics/bti603}
 }
 
-@misc{Szep2021BifurcationFit.jlDiagrams,
-    title = {{BifurcationFit.jl : Parameter Inference with Bifurcation Diagrams}},
+@misc{Szep2021BifurcationInference.jlDiagrams,
+    title = {{BifurcationInference.jl : Parameter Inference with Bifurcation Diagrams}},
     year = {2021},
     booktitle = {GitHub Repository},
     author = {Szep, Gregory},
     publisher = {GitHub},
-    url = {https://github.com/gszep/BifurcationFit.jl}
+    url = {https://github.com/gszep/BifurcationInference.jl}
 }
 
 @techreport{Veltz2020BifurcationKit.jl,
diff --git a/src/BifurcationInference.jl b/src/BifurcationInference.jl
@@ -1,4 +1,4 @@
-module BifurcationFit
+module BifurcationInference
 
 	using BifurcationKit: ContIterable, newton, ContinuationPar, NewtonPar, DeflationOperator
 	using BifurcationKit: BorderedArray, AbstractLinearSolver, AbstractEigenSolver, BorderingBLS
diff --git a/test/figures.jl b/test/figures.jl
@@ -1,4 +1,4 @@
-using BifurcationFit
+using BifurcationInference
 using ForwardDiff
 
 using LaTeXStrings,Plots
@@ -110,7 +110,7 @@ savefig("docs/figures/scaling.pdf")
 ####################################################################################################
 ####################################################################################################
 ################################################################################ two-state-optima
-using BifurcationFit,Plots,StaticArrays
+using BifurcationInference,Plots,StaticArrays
 using Clustering,JLD
 using StatsBase: median
 
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,5 +1,5 @@
 using FiniteDiff: finite_difference_gradient
-using BifurcationFit, Test
+using BifurcationInference, Test
 
 error_tolerance = 0.05
 @testset "Gradients" begin

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-module BifurcationFit`
	`1`	`+module BifurcationInference`
`2`	`2`
`3`	`3`	`using BifurcationKit: ContIterable, newton, ContinuationPar, NewtonPar, DeflationOperator`
`4`	`4`	`using BifurcationKit: BorderedArray, AbstractLinearSolver, AbstractEigenSolver, BorderingBLS`