Merge pull request #20 from JuliaTurkuDataScience/rename

Replace MiaTools with MicrobiomeAnalysis globally
JuliaTurkuDataScience · Mar 20, 2022 · f4a33da · f4a33da
2 parents e908ace + c5acc48
commit f4a33da
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diff --git a/Project.toml b/Project.toml
@@ -1,4 +1,4 @@
-name = "MiaTools"
+name = "MicrobiomeAnalysis"
 uuid = "09137a06-29c6-4e66-9476-ab7e4b8c7492"
 authors = ["Giulio Benedetti <giuliobene2000@gmail.com> and contributors"]
 version = "0.1.0"

diff --git a/README.md b/README.md
@@ -1,8 +1,8 @@
-# MiaTools.jl
+# MicrobiomeAnalysis.jl
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliaturkudatascience.github.io/MiaTools.jl/stable/readme/)
-[![CI](https://github.com/JuliaTurkuDataScience/MiaTools.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/JuliaTurkuDataScience/MiaTools.jl/actions/workflows/CI.yml)
-[![codecov](https://codecov.io/gh/JuliaTurkuDataScience/MiaTools.jl/branch/main/graph/badge.svg?token=VHEH1ZQLPA)](https://codecov.io/gh/JuliaTurkuDataScience/MiaTools.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliaturkudatascience.github.io/MicrobiomeAnalysis.jl/stable/readme/)
+[![CI](https://github.com/JuliaTurkuDataScience/MicrobiomeAnalysis.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/JuliaTurkuDataScience/MicrobiomeAnalysis.jl/actions/workflows/CI.yml)
+[![codecov](https://codecov.io/gh/JuliaTurkuDataScience/MicrobiomeAnalysis.jl/branch/main/graph/badge.svg?token=VHEH1ZQLPA)](https://codecov.io/gh/JuliaTurkuDataScience/MicrobiomeAnalysis.jl)
 
 This package aims to integrate the R-based [SummarizedExperiment](https://github.com/LTLA/SummarizedExperiments.jl) objects with common methods for microbiome analysis, and intends to reflect the [mia project](https://github.com/microbiome/mia/) in the Julia ecosystem.
 
@@ -13,15 +13,15 @@ Microbial community dynamics and time series are simulated through [FdeSolver.jl
 To avail of its functionality, clone this repository on your local machine with:
 
 ```bash
-git clone https://github.com/JuliaTurkuDataScience/MiaTools.jl.git
-cd MiaTools.jl
+git clone https://github.com/JuliaTurkuDataScience/MicrobiomeAnalysis.jl.git
+cd MicrobiomeAnalysis.jl
 ```
 
 and run the following in Julia:
 
 ```julia
 ]activate .
-[esc]using MiaTools
+[esc]using MicrobiomeAnalysis
 ```
 
 Now you should be able to access and use all exported functions, for instance:
@@ -33,4 +33,4 @@ shannon
 
 ## Documentation
 
-Available functions are described in the [Manual page](https://juliaturkudatascience.github.io/MiaTools.jl/stable/) and used for a basic microbiome workflow in the [Examples page](https://juliaturkudatascience.github.io/MiaTools.jl/stable/examples/).
+Available functions are described in the [Manual page](https://juliaturkudatascience.github.io/MicrobiomeAnalysis.jl/stable/) and used for a basic microbiome workflow in the [Examples page](https://juliaturkudatascience.github.io/MicrobiomeAnalysis.jl/stable/examples/).
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,9 +1,9 @@
 push!(LOAD_PATH,"../src/")
-using MiaTools, Documenter
+using MicrobiomeAnalysis, Documenter
 ENV["GKSwstype"] = "100"
 
 generated_path = joinpath(@__DIR__, "src")
-base_url = "https://github.com/JuliaTurkuDataScience/MiaTools.jl/blob/main/"
+base_url = "https://github.com/JuliaTurkuDataScience/MicrobiomeAnalysis.jl/blob/main/"
 isdir(generated_path) || mkdir(generated_path)
 
 open(joinpath(generated_path, "readme.md"), "w") do io
@@ -24,12 +24,12 @@ end
 
 makedocs(format = Documenter.HTML(),
          authors = "Giulio Benedetti, Leo Lahti",
-         sitename = "MiaTools.jl",
-         modules = [MiaTools],
+         sitename = "MicrobiomeAnalysis.jl",
+         modules = [MicrobiomeAnalysis],
          pages=[
              "Home" => "readme.md",
              "Manual" => "index.md",
              "Examples" => "examples.md"
                ])
 
-deploydocs(repo="github.com/JuliaTurkuDataScience/MiaTools.jl", push_preview=true)
+deploydocs(repo="github.com/JuliaTurkuDataScience/MicrobiomeAnalysis.jl", push_preview=true)
diff --git a/docs/src/examples.md b/docs/src/examples.md
@@ -2,7 +2,7 @@
 
 ## Dependencies
 
-MiaTools.jl enables the analysis of microbial but also more generic data cantained by SummarizedExperiment objects, therefore its usage is closely related and applicable to the utilities from a few other packages:
+MicrobiomeAnalysis.jl enables the analysis of microbial but also more generic data cantained by SummarizedExperiment objects, therefore its usage is closely related and applicable to the utilities from a few other packages:
 
 - SummarizedExperiments.jl
 - Microbiome.jl
@@ -12,7 +12,7 @@ MiaTools.jl enables the analysis of microbial but also more generic data cantain
 - DataStructures.jl
 
 ```@setup mia
-using MiaTools, SummarizedExperiments
+using MicrobiomeAnalysis, SummarizedExperiments
 using DataFrames, DataStructures
 using Plots, MultivariateStats
 ```

diff --git a/examples/MAEexample.jl b/examples/MAEexample.jl
@@ -1,4 +1,4 @@
-using MiaTools
+using MicrobiomeAnalysis
 using MultiAssayExperiments, SummarizedExperiments
 using DataFrames, DataStructures
 using Plots, MultivariateStats

diff --git a/examples/SEexample.jl b/examples/SEexample.jl
@@ -1,6 +1,6 @@
 ##### DEPENDENCIES #####
 
-using MiaTools
+using MicrobiomeAnalysis
 using SummarizedExperiments
 using DataFrames, DataStructures
 using Plots, MultivariateStats

diff --git a/src/MiaTools.jl b/src/MiaTools.jl
@@ -1,4 +1,4 @@
-module MiaTools
+module MicrobiomeAnalysis
 
 import SummarizedExperiments: SummarizedExperiment, assay, rowdata, coldata
 import Distances: pairwise, BrayCurtis, HellingerDist, Jaccard

diff --git a/src/alpha.jl b/src/alpha.jl
@@ -7,7 +7,7 @@ Evaluates the shannon diversity index for each sample and returns it as a vector
 - `se::SummarizedExperiment`: the experiment object of interest.
 - `assay_name::String`: the name of the assay to base the evaluation on.
 """
-function MiaTools.shannon(se::SummarizedExperiment, assay_name::String)
+function MicrobiomeAnalysis.shannon(se::SummarizedExperiment, assay_name::String)
 
     # create empty vector with length = n° samples
     shannon_vector = zeros(size(assay(se, assay_name))[2])
@@ -57,7 +57,7 @@ Evaluates the ginisimpson diversity index for each sample and returns it as a ve
 - `se::SummarizedExperiment`: the experiment object of interest.
 - `assay_name::String`: the name of the assay to base the evaluation on.
 """
-function MiaTools.ginisimpson(se::SummarizedExperiment, assay_name::String)
+function MicrobiomeAnalysis.ginisimpson(se::SummarizedExperiment, assay_name::String)
 
     ginisimpson_vector = zeros(size(assay(se, assay_name))[2])
 

diff --git a/test/test_alpha.jl b/test/test_alpha.jl
@@ -1,17 +1,17 @@
-using MiaTools
+using MicrobiomeAnalysis
 using SummarizedExperiments, Microbiome
 using Test
 
-@testset "MiaTools.jl" begin
+@testset "MicrobiomeAnalysis.jl" begin
 
     se = exampleobject(40, 20)
 
-    shannon_output = MiaTools.shannon(se, "foo")
-    MiaTools.shannon!(se, "foo")
+    shannon_output = MicrobiomeAnalysis.shannon(se, "foo")
+    MicrobiomeAnalysis.shannon!(se, "foo")
     @test shannon_output == coldata(se).shannon
 
-    ginisimpson_output = MiaTools.ginisimpson(se, "bar")
-    MiaTools.ginisimpson!(se, "bar")
+    ginisimpson_output = MicrobiomeAnalysis.ginisimpson(se, "bar")
+    MicrobiomeAnalysis.ginisimpson!(se, "bar")
     @test ginisimpson_output == coldata(se).ginisimpson
 
     @test Microbiome.shannon(assay(se, "foo")[:, 1]) == coldata(se).shannon[1]

diff --git a/test/test_beta.jl b/test/test_beta.jl
@@ -1,8 +1,8 @@
-using MiaTools
+using MicrobiomeAnalysis
 using SummarizedExperiments, Microbiome
 using Test
 
-@testset "MiaTools.jl" begin
+@testset "MicrobiomeAnalysis.jl" begin
 
     se = exampleobject(40, 20)
 
@@ -12,23 +12,23 @@ using Test
     comm = CommunityProfile(mat, taxa, samps)
 
     microjack = Microbiome.jaccard(comm)
-    miajack = MiaTools.jaccard(se, "bar")
+    miajack = MicrobiomeAnalysis.jaccard(se, "bar")
 
     @test microjack == miajack
 
     microbray = Microbiome.braycurtis(comm)
-    miabray = MiaTools.braycurtis(se, "bar")
+    miabray = MicrobiomeAnalysis.braycurtis(se, "bar")
 
     @test microbray == miabray
 
     microhell = Microbiome.hellinger(comm)
-    miahell = MiaTools.hellinger(se, "bar")
+    miahell = MicrobiomeAnalysis.hellinger(se, "bar")
 
     @test microhell == miahell
 
 end
 
-# MiaTools.jl: Error During Test at /Users/giuliobene3000/Desktop/Projects/JuliaProjects/MiaTools.jl/test/test_beta.jl:5
+# MicrobiomeAnalysis.jl: Error During Test at /Users/giuliobene3000/Desktop/Projects/JuliaProjects/MicrobiomeAnalysis.jl/test/test_beta.jl:5
 #   Got exception outside of a @test
 #   MethodError: no method matching pairwise(::Distances.BrayCurtis, ::Array{Float32, 3}, ::Array{Float32, 3}; dims=2)
 #   Closest candidates are:

diff --git a/test/test_lv.jl b/test/test_lv.jl
@@ -1,8 +1,8 @@
-using MiaTools
+using MicrobiomeAnalysis
 using SummarizedExperiments, FdeSolver
 using Test
 
-@testset "MiaTools.jl" begin
+@testset "MicrobiomeAnalysis.jl" begin
 
     t, Xapp = LVmodel()
 

diff --git a/test/test_plot.jl b/test/test_plot.jl
@@ -1,8 +1,8 @@
-using MiaTools
+using MicrobiomeAnalysis
 using SummarizedExperiments
 using Test
 
-@testset "MiaTools.jl" begin
+@testset "MicrobiomeAnalysis.jl" begin
 
     se = exampleobject(40, 20)