Documentation updates and fixes

docs/Project.toml

@@ -1,7 +1,8 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 NESSie = "f00e83c4-bd01-11e9-272c-ff1b96fb444d"
 
 [compat]
 Documenter = "1"
-julia = "1.6"
+julia = "1.10"

docs/make.jl

@@ -1,4 +1,4 @@
-using Documenter, NESSie
+using Documenter, GeometryBasics, NESSie
 
 const pages = [
     "Home" => "index.md",
@@ -25,7 +25,13 @@ const pages = [
 ]
 
 makedocs(
-    modules   = [NESSie, NESSie.BEM, NESSie.Format, NESSie.TestModel],
+    modules   = [
+        NESSie,
+        NESSie.BEM,
+        NESSie.Format,
+        NESSie.TestModel,
+        Base.get_extension(NESSie, :GeometryBasicsExt)
+    ],
     clean     = true,
     doctest   = true,
     linkcheck = true,

docs/src/intern/base.md

@@ -3,6 +3,10 @@
     CurrentModule = NESSie
 ```
 
+```@index
+Pages = ["base.md"]
+```
+
 ## [Constants](@id int-constants)
 ```@docs
     _etol

docs/src/intern/bem.md

@@ -3,6 +3,10 @@
     CurrentModule = NESSie.BEM
 ```
 
+```@index
+Pages = ["bem.md"]
+```
+
 ## Solvers
 ``` @docs
     _get_laplace_matrices

docs/src/intern/format.md

@@ -3,6 +3,10 @@
     CurrentModule = NESSie.Format
 ```
 
+```@index
+Pages = ["format.md"]
+```
+
 ## [Input formats](@id int-input)
 ```@docs
     readhmo_nodes

docs/src/intern/radon.md

@@ -3,6 +3,11 @@
     CurrentModule = NESSie.Radon
 ```
 
+```@index
+Pages = ["radon.md"]
+```
+
+
 ```@docs
     radoncoll
     radoncoll!

docs/src/intern/rjasanow.md

@@ -3,6 +3,10 @@
     CurrentModule = NESSie.Rjasanow
 ```
 
+```@index
+Pages = ["rjasanow.md"]
+```
+
 ```@docs
     ObservationPosition
     InPlane

docs/src/intern/testmodel.md

@@ -3,6 +3,10 @@
     CurrentModule = NESSie.TestModel
 ```
 
+```@index
+Pages = ["testmodel.md"]
+```
+
 ## [Utility functions](@id int-util-testmodel)
 ```@docs
     coefficients

docs/src/lib/constants.md

@@ -1,4 +1,11 @@
 # Constants
+```@meta
+    CurrentModule = NESSie
+```
+
+```@index
+Pages = ["constants.md"]
+```
 
 ## Global constants
 ```@docs

docs/src/lib/electrostatics.md

@@ -1,4 +1,11 @@
 # Electrostatics
+```@meta
+    CurrentModule = NESSie
+```
+
+```@index
+Pages = ["electrostatics.md"]
+```
 
 ## Potential types
 ```@docs
@@ -20,23 +27,23 @@
 ```@docs
     φmol
     ∂ₙφmol
-    NESSie.∇φmol
+    ∇φmol
 ```
 
 ### Interior potentials
 ```@docs
-    NESSie.BEM.φΩ
-    NESSie.TestModel.φΩ
+    BEM.φΩ
+    TestModel.φΩ
 ```
 
 
 ### Exterior potentials
 ```@docs
-    NESSie.BEM.φΣ
-    NESSie.TestModel.φΣ
+    BEM.φΣ
+    TestModel.φΣ
 ```
 
 ## Energies
 ```@docs
-    NESSie.BEM.rfenergy
+    BEM.rfenergy
 ```

docs/src/lib/models.md

@@ -1,4 +1,11 @@
 # Models
+```@meta
+    CurrentModule = NESSie
+```
+
+```@index
+Pages = ["models.md"]
+```
 
 ## Elements
 ```@docs

docs/src/lib/quadrature.md

@@ -1,4 +1,11 @@
 # Quadrature
+```@meta
+    CurrentModule = NESSie
+```
+
+```@index
+Pages = ["quadrature.md"]
+```
 
 ## Quadrature points
 ```@docs
@@ -20,12 +27,12 @@
 
 ## Laplace potential
 ```@docs
-    NESSie.Rjasanow.laplacecoll
-    NESSie.Rjasanow.laplacecoll!
+    Rjasanow.laplacecoll
+    Rjasanow.laplacecoll!
 ```
 
 ## Yukawa potential
 ```@docs
-    NESSie.Radon.regularyukawacoll
-    NESSie.Radon.regularyukawacoll!
+    Radon.regularyukawacoll
+    Radon.regularyukawacoll!
 ```

docs/src/lib/solvers.md

@@ -1,4 +1,11 @@
 # Solvers
+```@meta
+    CurrentModule = NESSie
+```
+
+```@index
+Pages = ["solvers.md"]
+```
 
 ## BEM solvers
 ```@meta

docs/src/lib/util.md

@@ -1,7 +1,12 @@
 # Utility functions
 
+```@index
+Pages = ["util.md"]
+```
+
 ```@docs
     meshunion
     obspoints_line
     obspoints_plane
+    GeometryBasics.mesh
 ```

ext/GeometryBasicsExt.jl

@@ -4,6 +4,16 @@ import GeometryBasics
 
 using NESSie
 
+"""
+    GeometryBasics.mesh(model::Model{T, Triangle{T}})
+
+Converts the given model into a GeometryBasics.jl-compatible mesh, e.g., for visualization
+through [Makie.jl](https://docs.makie.org/stable/reference/plots/mesh).
+
+# Return type
+[`GeometryBasics.Mesh`]
+(https://juliageometry.github.io/GeometryBasics.jl/stable/meshes/#GeometryBasics.Mesh-meshes)
+"""
 function GeometryBasics.mesh(model::Model{T, Triangle{T}}) where T
     ridx = NESSie._reverseindex(model.nodes)
 

src/Radon.jl

@@ -163,7 +163,7 @@ to use the shorthand signature `regularyukawacoll!` instead.
  * `yukawa` [Exponent](@ref int-constants) of the Yukawa operator's fundamental solution
 
 # Return type
-`Void`
+`Nothing`
 """
 function radoncoll!(
         dest    ::AbstractVector{T},
@@ -254,7 +254,7 @@ to use the shorthand signature `regularyukawacoll` instead.
  * `yukawa` [Exponent](@ref int-constants) of the Yukawa operator's fundamental solution
 
 # Return type
-`Void`
+`T`
 """
 function radoncoll(
         ξ       ::AbstractVector{T},
@@ -306,7 +306,7 @@ vector.
  * `yukawa` [Exponent](@ref int-constants) of the Yukawa operator's fundamental solution
 
 # Return type
-`Void`
+`Nothing`
 """
 @inline regularyukawacoll!(
             ::Type{SingleLayer},
@@ -368,7 +368,7 @@ triangle and observation point `ξ`.
  * `yukawa` [Exponent](@ref int-constants) of the Yukawa operator's fundamental solution
 
 # Return type
-`Void`
+`T`
 """
 @inline regularyukawacoll(
           ::Type{SingleLayer},

src/Rjasanow.jl

@@ -282,7 +282,7 @@ vector.
     The result is premultiplied by 4π.
 
 # Return type
-`Void`
+`Nothing`
 """
 function laplacecoll!(
         ptype   ::Type{P},
@@ -357,7 +357,7 @@ and observation point `ξ` [[Rja90]](@ref Bibliography).
     The result is premultiplied by 4π.
 
 # Return type
-`Void`
+`T`
 """
 function laplacecoll(
         ptype::Type{P},

src/base/constants.jl

@@ -103,10 +103,10 @@ end
     defaultopt(T::Type{Float64} = Float64)
     defaultopt(T::Type{Float32})
 
-Default system parameters
+Default system parameters for proteins in water.
 
 # Return type
-[`Option{T}`](@ref NESSie.Option)
+[`Option{T}`](@ref Option)
 
 # Default values
  * ``ε_Ω = 2``

src/base/quadrature.jl

@@ -68,7 +68,7 @@ Generator function for quadrature points:
  * *Tetrahedra*: 5 points per element [[Kea86]](@ref Bibliography)
 
 # Return type
-`QuadPts2D` or `QuadPts3D`
+[`QuadPts2D`](@ref) or [`QuadPts3D`](@ref)
 """ quadraturepoints
 for T in [:Float64, :Float32]
     varname = Symbol("triquadpts_", T)
@@ -121,7 +121,7 @@ Quadrature points on a specific surface triangle, including weights.
 # Special constructors
 ```julia
 TriangleQuad(elem::Triangle{T})
-````
+```
 Computes quadrature points and weights for the given triangle.
 """
 struct TriangleQuad{T} <: ElementQuad{T}

src/base/util.jl

@@ -11,7 +11,7 @@ and area. Returns the completely initialized Triangle as a copy.
     The given triangle remains unchanged!
 
 # Return type
-`Triangle`
+[`Triangle`](@ref)
 """
 function props(elem::Triangle)
     # reject degenerate triangles
@@ -47,7 +47,7 @@ Merges two volume models, e.g., the models of a protein and the solvent. Duplica
 and charges (if any) are retained as well as the system constants of the first model.
 
 # Return type
-`Model{T, Tetrahedron{T}}`
+[`Model{T, Tetrahedron{T}}`](@ref)
 
 !!! note
     This function assumes that there are no duplicates within either of the node lists!
@@ -176,7 +176,7 @@ is no such line, the stream handle will be set to EOF.
  * `skiptheline`    If true, said line will also be skipped
 
 # Return type
-`Void`
+`Nothing`
 """
 function _seek(fh::IOStream, prefix::String, skiptheline::Bool=true)
     m = -1

src/bem/implicit.jl

@@ -99,7 +99,8 @@ Constructs and returns implicit representations for the single- and double-layer
 potential matrices `V` and `K` for the given observation points and surface elements.
 
 # Return type
-`Tuple{InteractionMatrix{T}, InteractionMatrix{T}}`
+[`Tuple{InteractionMatrix{T}, InteractionMatrix{T}}`]
+(https://tkemmer.github.io/ImplicitArrays.jl/stable/#ImplicitArrays.InteractionMatrix)
 """
 @inline function _get_laplace_matrices(
     Ξ       ::Vector{Vector{T}},
@@ -123,7 +124,8 @@ Constructs and returns implicit representations for the single- and double-layer
 potential matrices `V^Y` and `K^Y` for the given observation points and surface elements.
 
 # Return type
-`Tuple{InteractionMatrix{T}, InteractionMatrix{T}}`
+[`Tuple{InteractionMatrix{T}, InteractionMatrix{T}}`]
+(https://tkemmer.github.io/ImplicitArrays.jl/stable/#ImplicitArrays.InteractionMatrix)
 """
 @inline function _get_yukawa_matrices(
     Ξ::Vector{Vector{T}},

src/bem/local.jl

@@ -33,7 +33,7 @@ end
 Computes the full local or nonlocal cauchy data on the surface of the given biomolecule.
 
 # Return type
-`LocalBEMResult{T, Triangle{T}}` or `NonlocalBEMResult{T, Triangle{T}}`
+[`LocalBEMResult{T, Triangle{T}}`](@ref) or [`NonlocalBEMResult{T, Triangle{T}}`](@ref)
 
 # Supported keyword arguments
  - `method::Symbol = :gmres`
@@ -70,7 +70,7 @@ Computes the full local or nonlocal cauchy data on the surface of the biomolecul
 *explicit* representation of the BEM system.
 
 # Return type
-`LocalBEMResult{T, Triangle{T}}` or `NonlocalBEMResult{T, Triangle{T}}`
+[`LocalBEMResult{T, Triangle{T}}`](@ref) or [`NonlocalBEMResult{T, Triangle{T}}`](@ref)
 """
 function _solve_explicit(
          ::Type{LocalES},
@@ -199,7 +199,7 @@ Computes the full local or nonlocal cauchy data on the surface of the biomolecul
 *implicit* representation of the BEM system.
 
 # Return type
-`LocalBEMResult{T, Triangle{T}}` or `NonlocalBEMResult{T, Triangle{T}}`
+[`LocalBEMResult{T, Triangle{T}}`](@ref) or [`NonlocalBEMResult{T, Triangle{T}}`](@ref)
 """
 function _solve_implicit(
          ::Type{LocalES},