Rename package to PointNeighbors.jl (#6)

* Rename package to PointNeighbors.jl

* Reformat code

* Add compat entry for LInearAlgebra

Author: efaulhaber

Project.toml

@@ -1,6 +1,6 @@
-name = "TrixiNeighborhoodSearch"
+name = "PointNeighbors"
 uuid = "1c4d5385-0a27-49de-8e2c-43b175c8985c"
-authors = ["Erik Faulhaber <[email protected]>"]
+authors = ["Erik Faulhaber <[email protected]>"]
 version = "0.1.0-pre"
 
 [deps]
@@ -10,6 +10,7 @@ Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [compat]
+LinearAlgebra = "1"
 Polyester = "0.7.5"
 Reexport = "1"
 StaticArrays = "1"

README.md

@@ -1,11 +1,11 @@
-# TrixiNeighborhoodSearch.jl
+# PointNeighbors.jl
 
-[![Docs-stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://trixi-framework.github.io/TrixiNeighborhoodSearch.jl/stable)
-[![Docs-dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://trixi-framework.github.io/TrixiNeighborhoodSearch.jl/dev)
+[![Docs-stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://trixi-framework.github.io/PointNeighbors.jl/stable)
+[![Docs-dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://trixi-framework.github.io/PointNeighbors.jl/dev)
 [![Slack](https://img.shields.io/badge/chat-slack-e01e5a)](https://join.slack.com/t/trixi-framework/shared_invite/zt-sgkc6ppw-6OXJqZAD5SPjBYqLd8MU~g)
 [![Youtube](https://img.shields.io/youtube/channel/views/UCpd92vU2HjjTPup-AIN0pkg?style=social)](https://www.youtube.com/@trixi-framework)
-[![Build Status](https://github.com/trixi-framework/TrixiNeighborhoodSearch.jl/workflows/CI/badge.svg)](https://github.com/trixi-framework/TrixiNeighborhoodSearch.jl/actions?query=workflow%3ACI)
-[![Codecov](https://codecov.io/gh/trixi-framework/TrixiNeighborhoodSearch.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/trixi-framework/TrixiNeighborhoodSearch.jl)
+[![Build Status](https://github.com/trixi-framework/PointNeighbors.jl/workflows/CI/badge.svg)](https://github.com/trixi-framework/PointNeighbors.jl/actions?query=workflow%3ACI)
+[![Codecov](https://codecov.io/gh/trixi-framework/PointNeighbors.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/trixi-framework/PointNeighbors.jl)
 [![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)
 [![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://opensource.org/license/mit/)
 

SECURITY.md

@@ -15,7 +15,7 @@ used in the Julia ecosystem is supported with security updates.
 ## Reporting a Vulnerability
 
 To report a security issue, please use the GitHub Security Advisory
-["Report a Vulnerability"](https://github.com/trixi-framework/TrixiNeighborhoodSearch.jl/security/advisories/new)
+["Report a Vulnerability"](https://github.com/trixi-framework/PointNeighbors.jl/security/advisories/new)
 tab.
 
 We will send a response indicating the next steps in handling your report.

docs/make.jl

@@ -1,6 +1,6 @@
 using Documenter
 
-# Get TrixiNeighborhoodSearch.jl root directory
+# Get PointNeighbors.jl root directory
 trixibase_root_dir = dirname(@__DIR__)
 
 # Fix for https://github.com/trixi-framework/Trixi.jl/issues/668
@@ -9,11 +9,11 @@ if (get(ENV, "CI", nothing) != "true") &&
     push!(LOAD_PATH, trixibase_root_dir)
 end
 
-using TrixiNeighborhoodSearch
+using PointNeighbors
 
 # Define module-wide setups such that the respective modules are available in doctests
-DocMeta.setdocmeta!(TrixiNeighborhoodSearch, :DocTestSetup,
-                    :(using TrixiNeighborhoodSearch); recursive = true)
+DocMeta.setdocmeta!(PointNeighbors, :DocTestSetup,
+                    :(using PointNeighbors); recursive = true)
 
 # Copy files to not need to synchronize them manually
 function copy_file(filename, replaces...; new_filename = lowercase(filename))
@@ -22,7 +22,7 @@ function copy_file(filename, replaces...; new_filename = lowercase(filename))
 
     header = """
     ```@meta
-    EditURL = "https://github.com/trixi-framework/TrixiNeighborhoodSearch.jl/blob/main/$filename"
+    EditURL = "https://github.com/trixi-framework/PointNeighbors.jl/blob/main/$filename"
     ```
     """
     content = header * content
@@ -39,14 +39,14 @@ copy_file("LICENSE.md",
           "\n" => "\n> ", r"^" => "# License\n\n> ")
 
 # Make documentation
-makedocs(modules = [TrixiNeighborhoodSearch],
-         sitename = "TrixiNeighborhoodSearch.jl",
+makedocs(modules = [PointNeighbors],
+         sitename = "PointNeighbors.jl",
          # Provide additional formatting options
          format = Documenter.HTML(
                                   # Disable pretty URLs during manual testing
                                   prettyurls = get(ENV, "CI", nothing) == "true",
                                   # Set canonical URL to GitHub pages URL
-                                  canonical = "https://trixi-framework.github.io/TrixiNeighborhoodSearch.jl/stable"),
+                                  canonical = "https://trixi-framework.github.io/PointNeighbors.jl/stable"),
          # Explicitly specify documentation structure
          pages = [
              "Home" => "index.md",
@@ -56,6 +56,6 @@ makedocs(modules = [TrixiNeighborhoodSearch],
          ])
 
 deploydocs(;
-           repo = "github.com/trixi-framework/TrixiNeighborhoodSearch.jl",
+           repo = "github.com/trixi-framework/PointNeighbors.jl",
            devbranch = "main",
            push_preview = true)

docs/src/reference.md

@@ -1,9 +1,9 @@
 # API reference
 
 ```@meta
-CurrentModule = TrixiNeighborhoodSearch
+CurrentModule = PointNeighbors
 ```
 
 ```@autodocs
-Modules = [TrixiNeighborhoodSearch]
+Modules = [PointNeighbors]
 ```

src/TrixiNeighborhoodSearch.jl renamed to src/PointNeighbors.jl

@@ -1,4 +1,4 @@
-module TrixiNeighborhoodSearch
+module PointNeighbors
 
 using Reexport: @reexport
 
@@ -15,4 +15,4 @@ export for_particle_neighbor
 export TrivialNeighborhoodSearch, GridNeighborhoodSearch
 export initialize!, update!
 
-end # module TrixiNeighborhoodSearch
+end # module PointNeighbors

src/util.jl

@@ -51,6 +51,6 @@ macro threaded(expr)
     #     Look at the comments for `wrap_array` when considering to change this macro.
 
     return esc(quote
-                   TrixiNeighborhoodSearch.@batch $(expr)
+                   PointNeighbors.@batch $(expr)
                end)
 end

test/grid_nhs.jl

@@ -5,11 +5,11 @@
         coords2 = [NaN, 0]
         coords3 = [typemax(Int) + 1.0, -typemax(Int) - 1.0]
 
-        @test TrixiNeighborhoodSearch.cell_coords(coords1, nothing, (1.0, 1.0)) ==
+        @test PointNeighbors.cell_coords(coords1, nothing, (1.0, 1.0)) ==
               (typemax(Int), typemin(Int))
-        @test TrixiNeighborhoodSearch.cell_coords(coords2, nothing, (1.0, 1.0)) ==
+        @test PointNeighbors.cell_coords(coords2, nothing, (1.0, 1.0)) ==
               (typemax(Int), 0)
-        @test TrixiNeighborhoodSearch.cell_coords(coords3, nothing, (1.0, 1.0)) ==
+        @test PointNeighbors.cell_coords(coords3, nothing, (1.0, 1.0)) ==
               (typemax(Int), typemin(Int))
     end
 
@@ -32,8 +32,7 @@
         initialize!(nhs1, coords_fun)
 
         # Get each neighbor for `particle_position1`
-        neighbors1 = sort(collect(TrixiNeighborhoodSearch.eachneighbor(particle_position1,
-                                                                       nhs1)))
+        neighbors1 = sort(collect(PointNeighbors.eachneighbor(particle_position1, nhs1)))
 
         # Move particles
         coordinates2 = coordinates1 .+ [1.4, -3.5]
@@ -43,23 +42,23 @@
         update!(nhs1, coords_fun2)
 
         # Get each neighbor for updated NHS
-        neighbors2 = sort(collect(TrixiNeighborhoodSearch.eachneighbor(particle_position1,
-                                                                       nhs1)))
+        neighbors2 = sort(collect(PointNeighbors.eachneighbor(particle_position1,
+                                                              nhs1)))
 
         # Change position
         particle_position2 = particle_position1 .+ [1.4, -3.5]
 
         # Get each neighbor for `particle_position2`
-        neighbors3 = sort(collect(TrixiNeighborhoodSearch.eachneighbor(particle_position2,
-                                                                       nhs1)))
+        neighbors3 = sort(collect(PointNeighbors.eachneighbor(particle_position2,
+                                                              nhs1)))
 
         # Double search radius
         nhs2 = GridNeighborhoodSearch{2}(2 * radius, size(coordinates1, 2))
         initialize!(nhs2, coords_fun)
 
         # Get each neighbor in double search radius
-        neighbors4 = sort(collect(TrixiNeighborhoodSearch.eachneighbor(particle_position1,
-                                                                       nhs2)))
+        neighbors4 = sort(collect(PointNeighbors.eachneighbor(particle_position1,
+                                                              nhs2)))
 
         # Move particles
         coordinates2 = coordinates1 .+ [0.4, -0.4]
@@ -68,8 +67,8 @@
         update!(nhs2, coords_fun2)
 
         # Get each neighbor in double search radius
-        neighbors5 = sort(collect(TrixiNeighborhoodSearch.eachneighbor(particle_position1,
-                                                                       nhs2)))
+        neighbors5 = sort(collect(PointNeighbors.eachneighbor(particle_position1,
+                                                              nhs2)))
 
         #### Verification
         @test neighbors1 == [17, 18, 19, 24, 25, 26, 31, 32, 33]
@@ -105,8 +104,8 @@
         initialize!(nhs1, coords_fun)
 
         # Get each neighbor for `particle_position1`
-        neighbors1 = sort(collect(TrixiNeighborhoodSearch.eachneighbor(particle_position1,
-                                                                       nhs1)))
+        neighbors1 = sort(collect(PointNeighbors.eachneighbor(particle_position1,
+                                                              nhs1)))
 
         # Move particles
         coordinates2 = coordinates1 .+ [1.4, -3.5, 0.8]
@@ -116,15 +115,15 @@
         update!(nhs1, coords_fun2)
 
         # Get each neighbor for updated NHS
-        neighbors2 = sort(collect(TrixiNeighborhoodSearch.eachneighbor(particle_position1,
-                                                                       nhs1)))
+        neighbors2 = sort(collect(PointNeighbors.eachneighbor(particle_position1,
+                                                              nhs1)))
 
         # Change position
         particle_position2 = particle_position1 .+ [1.4, -3.5, 0.8]
 
         # Get each neighbor for `particle_position2`
-        neighbors3 = sort(collect(TrixiNeighborhoodSearch.eachneighbor(particle_position2,
-                                                                       nhs1)))
+        neighbors3 = sort(collect(PointNeighbors.eachneighbor(particle_position2,
+                                                              nhs1)))
 
         #### Verification
         @test neighbors1 ==
@@ -150,8 +149,8 @@
 
             initialize!(nhs, coords)
 
-            neighbors = [sort(collect(TrixiNeighborhoodSearch.eachneighbor(coords[:, i],
-                                                                           nhs)))
+            neighbors = [sort(collect(PointNeighbors.eachneighbor(coords[:, i],
+                                                                  nhs)))
                          for i in 1:5]
 
             # Note that (1, 2) and (2, 3) are not neighbors, but they are in neighboring cells
@@ -189,8 +188,8 @@
 
             initialize!(nhs, coords)
 
-            neighbors = [sort(collect(TrixiNeighborhoodSearch.eachneighbor(coords[:, i],
-                                                                           nhs)))
+            neighbors = [sort(collect(PointNeighbors.eachneighbor(coords[:, i],
+                                                                  nhs)))
                          for i in 1:5]
 
             # Note that (1, 2) and (2, 3) are not neighbors, but they are in neighboring cells
@@ -224,7 +223,7 @@
             # see the right particle, even though it is within the search distance.
             # The domain size is an integer multiple of the cell size, but the NHS did not
             # offset the grid based on the domain position.
-            # See https://github.com/trixi-framework/TrixiNeighborhoodSearch.jl/pull/211
+            # See https://github.com/trixi-framework/PointNeighbors.jl/pull/211
             # for a more detailed explanation.
             coords = [-1.4 1.9
                       0.0 0.0]
@@ -236,9 +235,9 @@
 
             initialize!(nhs, coords)
 
-            neighbors = [sort(unique(collect(TrixiNeighborhoodSearch.eachneighbor(coords[:,
-                                                                                         i],
-                                                                                  nhs))))
+            neighbors = [sort(unique(collect(PointNeighbors.eachneighbor(coords[:,
+                                                                                i],
+                                                                         nhs))))
                          for i in 1:2]
 
             @test neighbors[1] == [1, 2]
@@ -258,7 +257,7 @@
 
         initialize!(nhs, coords)
 
-        neighbors = [sort(collect(TrixiNeighborhoodSearch.eachneighbor(coords[:, i], nhs)))
+        neighbors = [sort(collect(PointNeighbors.eachneighbor(coords[:, i], nhs)))
                      for i in 1:5]
 
         # Note that (1, 2) and (2, 3) are not neighbors, but they are in neighboring cells

test/runtests.jl

@@ -1,6 +1,6 @@
 include("test_util.jl")
 
-@testset verbose=true "TrixiNeighborhoodSearch.jl Tests" begin
+@testset verbose=true "PointNeighbors.jl Tests" begin
     include("trivial_nhs.jl")
     include("grid_nhs.jl")
 end

test/test_util.jl

@@ -1,7 +1,7 @@
 # All `using` calls are in this file, so that one can run any test file
 # after running only this file.
 using Test: @test, @testset
-using TrixiNeighborhoodSearch
+using PointNeighbors
 
 """
     @trixi_testset "name of the testset" #= code to test #=
@@ -18,7 +18,7 @@ macro trixi_testset(name, expr)
     quote
         @eval module $mod
         using Test
-        using TrixiNeighborhoodSearch
+        using PointNeighbors
 
         # We also include this file again to provide the definition of
         # the other testing macros. This allows to use `@trixi_testset`