change name to PCCAPlus.jl

c.f. #5

.github/workflows/CI.yml

@@ -62,6 +62,6 @@ jobs:
       - run: |
           julia --project=docs -e '
             using Documenter: DocMeta, doctest
-            using PCCA
-            DocMeta.setdocmeta!(PCCA, :DocTestSetup, :(using PCCA); recursive=true)
-            doctest(PCCA)'
+            using PCCAPlus
+            DocMeta.setdocmeta!(PCCAPlus, :DocTestSetup, :(using PCCAPlus); recursive=true)
+            doctest(PCCAPlus)'

CITATION.bib

@@ -1,7 +1,7 @@
-@misc{PCCA.jl,
+@misc{PCCAPlus.jl,
 	author  = {Alexander Sikorski},
-	title   = {PCCA.jl},
-	url     = {https://github.com/axsk/PCCA.jl},
+	title   = {PCCAPlus.jl},
+	url     = {https://github.com/axsk/PCCAPlus.jl},
 	version = {v0.1.0},
 	year    = {2021},
 	month   = {11}

Project.toml

@@ -1,4 +1,4 @@
-name = "PCCA"
+name = "PCCAPlus"
 uuid = "f48fc343-7e38-490c-be15-e66d68689cd5"
 authors = ["Alexander Sikorski"]
 version = "0.2.0"

README.md

@@ -1,17 +1,17 @@
-# PCCA
+# PCCAPlus
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://axsk.github.io/PCCA.jl/stable)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://axsk.github.io/PCCA.jl/dev)
-[![Build Status](https://github.com/axsk/PCCA.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/axsk/PCCA.jl/actions/workflows/CI.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/axsk/PCCA.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/axsk/PCCA.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://axsk.github.io/PCCAPlus.jl/stable)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://axsk.github.io/PCCAPlus.jl/dev)
+[![Build Status](https://github.com/axsk/PCCAPlus.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/axsk/PCCAPlus.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/axsk/PCCAPlus.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/axsk/PCCAPlus.jl)
 
 A [KISS](https://en.wikipedia.org/wiki/KISS_principle) style implementation of PCCA+ (Robust Perron Cluster Analysis) [1,2] with support for non-reversible systems [3].
 For a similar python implementation see also the [cmdtools](https://github.com/zib-cmd/cmdtools/) package.
 
 ## Basic usage
 
 ```julia
-using PCCA
+using PCCAPlus
 
 P=rand(10,10)
 P = P ./ sum(P, dims=2) # row stochastic matrix

docs/Manifest.toml

@@ -57,7 +57,7 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 [[NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 
-[[PCCA]]
+[[PCCAPlus]]
 path = ".."
 uuid = "f48fc343-7e38-490c-be15-e66d68689cd5"
 version = "0.1.0"

docs/Project.toml

@@ -1,3 +1,3 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-PCCA = "f48fc343-7e38-490c-be15-e66d68689cd5"
+PCCAPlus = "f48fc343-7e38-490c-be15-e66d68689cd5"

docs/make.jl

@@ -1,16 +1,16 @@
-using PCCA
+using PCCAPlus
 using Documenter
 
-DocMeta.setdocmeta!(PCCA, :DocTestSetup, :(using PCCA); recursive=true)
+DocMeta.setdocmeta!(PCCAPlus, :DocTestSetup, :(using PCCAPlus); recursive=true)
 
 makedocs(;
-    modules=[PCCA],
+    modules=[PCCAPlus],
     authors="Alexander Sikorski",
-    repo="https://github.com/axsk/PCCA.jl/blob/{commit}{path}#{line}",
-    sitename="PCCA.jl",
+    repo="https://github.com/axsk/PCCAPlus.jl/blob/{commit}{path}#{line}",
+    sitename="PCCAPlus.jl",
     format=Documenter.HTML(;
         prettyurls=get(ENV, "CI", "false") == "true",
-        canonical="https://axsk.github.io/PCCA.jl",
+        canonical="https://axsk.github.io/PCCAPlus.jl",
         assets=String[],
     ),
     pages=[
@@ -19,6 +19,6 @@ makedocs(;
 )
 
 deploydocs(;
-    repo="github.com/axsk/PCCA.jl",
+    repo="github.com/axsk/PCCAPlus.jl",
     devbranch="main",
 )

docs/src/index.md

@@ -1,14 +1,14 @@
 ```@meta
-CurrentModule = PCCA
+CurrentModule = PCCAPlus
 ```
 
-# PCCA
+# PCCAPlus
 
-Documentation for [PCCA](https://github.com/axsk/PCCA.jl).
+Documentation for [PCCAPlus](https://github.com/axsk/PCCAPlus.jl).
 
 ```@index
 ```
 
 ```@autodocs
-Modules = [PCCA]
+Modules = [PCCAPlus]
 ```

ext/ArnoldiExt.jl

@@ -1,9 +1,9 @@
 module ArnoldiExt
 
-import PCCA
+import PCCAPlus
 import ArnoldiMethod
 
-function PCCA.schurvecs(T, n, israte, ::PCCA.ArnoldiSolver)
+function PCCAPlus.schurvecs(T, n, israte, ::PCCAPlus.ArnoldiSolver)
     which = israte ? ArnoldiMethod.LR() : ArnoldiMethod.LM()
     Q = ArnoldiMethod.partialschur(T; nev=n, which)[1].Q
     Q[:, 1:n]

ext/KrylovExt.jl

@@ -1,11 +1,11 @@
 module KrylovExt
-import PCCA
+import PCCAPlus
 import KrylovKit
 
 
 
 
-function PCCA.schurvecs(T, n, israte, ::PCCA.KrylovSolver)
+function PCCAPlus.schurvecs(T, n, israte, ::PCCAPlus.KrylovSolver)
     which = israte ? :LR : :LM
     R, Qs, = KrylovKit.schursolve(T, rand(size(T, 1)), n, which, KrylovKit.Arnoldi())
     Q = reduce(hcat, Qs)

src/PCCA.jl → src/PCCAPlus.jl

@@ -1,4 +1,4 @@
-module PCCA
+module PCCAPlus
 
 include("pccap.jl")
 include("schur.jl")

test/runtests.jl

@@ -1,10 +1,10 @@
-using PCCA
+using PCCAPlus
 using Test
 
 using ArnoldiMethod
 using KrylovKit
 
-@testset "PCCA.jl" begin
+@testset "PCCAPlus.jl" begin
     # Write your tests here.
     x = rand(10, 10)
     x = x ./ sum(x, dims=2)
@@ -20,10 +20,10 @@ using KrylovKit
 
     @testset "Reversible = $rev" for rev in [true, false]
         P = [randomstochasticmatrix(3 + mod(i, 12), rev) for i in 1:10]
-        @testset "Method $method" for method in [PCCA.BaseSolver, PCCA.ArnoldiSolver, PCCA.KrylovSolver]
+        @testset "Method $method" for method in [PCCAPlus.BaseSolver, PCCAPlus.ArnoldiSolver, PCCAPlus.KrylovSolver]
             for P in P, n in 2:size(P, 1)-1
                 χ = pcca(P, n, solver=method(), optimize=true)
-                a = PCCA.crispassignments(χ)
+                a = PCCAPlus.crispassignments(χ)
 
                 #@show χ
                 @test all(sum(χ, dims=2) .≈ 1)