Fix doc warnings and make docs build strict

docs/make.jl

@@ -42,7 +42,7 @@ bibtex_plugin = CitationBibliography(
     ),
     sitename = "Ferrite.jl",
     doctest = false,
-    warnonly = true,
+    warnonly = is_ci ? false : [:cross_references], # Local build exception required for Literate's `@__NBVIEWER_ROOT_URL__`
     draft = liveserver,
     pages = Any[
         "Home" => "index.md",

docs/src/assets/references.bib

@@ -80,7 +80,7 @@ @article{SimMie:1992:act
 pages = {41-104},
 year = {1992},
 issn = {0045-7825},
-doi = {https://doi.org/10.1016/0045-7825(92)90170-O},
+doi = {10.1016/0045-7825(92)90170-O},
 url = {https://www.sciencedirect.com/science/article/pii/004578259290170O},
 author = {J.C. Simo and C. Miehe},
 }
@@ -117,7 +117,7 @@ @article{Mu:2014:IP
 pages = {432-440},
 year = {2014},
 issn = {0377-0427},
-doi = {https://doi.org/10.1016/j.cam.2013.06.003},
+doi = {10.1016/j.cam.2013.06.003},
 url = {https://www.sciencedirect.com/science/article/pii/S0377042713002999},
 author = {Lin Mu and Junping Wang and Yanqiu Wang and Xiu Ye},
 keywords = {Discontinuous Galerkin, Finite element, Interior penalty, Second-order elliptic equations, Hybrid mesh},

docs/src/devdocs/FEValues.md

@@ -39,7 +39,7 @@ Custom FEValues, `fe_v::AbstractValues`, should normally implement the [`reinit!
   * [`getnquadpoints`](@ref)
   * [`getnbasefunctions`](@ref)
 * [`spatial_coordinate`](@ref), requires
-  * [`geometric_value`](@ref)
+  * [`geometric_value`](@ref Ferrite.geometric_value)
   * `getngeobasefunctions`
   * [`getnquadpoints`](@ref)
 

docs/src/devdocs/dofhandler.md

@@ -3,9 +3,9 @@
 ## Type definitions
 
 Dof handlers are subtypes of `AbstractDofhandler{sdim}`, i.e. they are
-parametrized by the spatial dimension. Internally a helper struct [`InterpolationInfo`](@ref) is utilized to enforce type stability during
-dof distribution, because the interpolations are not available as concrete
-types.
+parametrized by the spatial dimension. Internally a helper struct
+[`InterpolationInfo`](@ref Ferrite.InterpolationInfo) is utilized to enforce type stability
+during dof distribution, because the interpolations are not available as concrete types.
 
 ```@docs
 Ferrite.InterpolationInfo
@@ -16,12 +16,13 @@ Ferrite.SurfaceOrientationInfo
 
 ## Internal API
 
-The main entry point for dof distribution is [`__close!`](@ref).
+The main entry point for dof distribution is [`__close!`](@ref Ferrite.__close!).
 
 ```@docs
 Ferrite.__close!
 Ferrite.get_grid
-Ferrite.find_field(dh::DofHandler, field_name::Symbol)
+Ferrite.find_field
+Ferrite._find_field
 Ferrite._close_subdofhandler!
 Ferrite._distribute_dofs_for_cell!
 Ferrite.permute_and_push!

docs/src/devdocs/interpolations.md

@@ -8,7 +8,6 @@ parametrized by the reference element and its characteristic order.
 ### Fallback methods applicable for all subtypes of `Interpolation`
 
 ```@docs
-Ferrite.getrefdim(::Interpolation)
 Ferrite.getrefshape(::Interpolation)
 Ferrite.getorder(::Interpolation)
 Ferrite.reference_shape_gradient(::Interpolation, ::Vec, ::Int)

docs/src/devdocs/reference_cells.md

@@ -30,3 +30,8 @@ which automatically defines
 ```@docs
 Ferrite.reference_facets(::Type{<:Ferrite.AbstractRefShape})
 ```
+
+### Applicable methods to `AbstractRefShape`s
+```@docs
+Ferrite.getrefdim(::Type{<:Ferrite.AbstractRefShape})
+```

docs/src/literate-gallery/topology_optimization.jl

@@ -541,7 +541,7 @@ end
 
 #md # ## References
 #md # ```@bibliography
-#md # Pages = ["gallery/topology_optimization.md"]
+#md # Pages = ["topology_optimization.md"]
 #md # Canonical = false
 #md # ```
 

docs/src/literate-tutorials/dg_heat_equation.jl

@@ -344,7 +344,7 @@ using Test                        #src
 
 #md # ## References
 #md # ```@bibliography
-#md # Pages = ["tutorials/dg_heat_equation.md"]
+#md # Pages = ["dg_heat_equation.md"]
 #md # Canonical = false
 #md # ```
 

docs/src/reference/grid.md

@@ -35,7 +35,7 @@ getcoordinates!
 geometric_interpolation(::Ferrite.AbstractCell)
 get_node_coordinate
 Ferrite.getspatialdim(::Ferrite.AbstractGrid)
-Ferrite.getrefdim
+Ferrite.getrefdim(::Ferrite.AbstractCell)
 ```
 
 ### Topology

docs/src/topics/assembly.md

@@ -24,8 +24,8 @@ into the sparse matrix `K` directly. Therefore we will instead use an
 matrix and the global force vector. It is also often convenient to create the
 sparse matrix just once, and reuse the allocated matrix. This is useful for
 e.g. iterative solvers or time dependent problems where the sparse matrix
-structure, or [Sparsity Pattern](@ref) will stay the same in every iteration/
-time step.
+structure, or [Sparsity Pattern](@ref "Sparsity pattern and sparse matrices")
+will stay the same in every iteration/time step.
 
 ## `Assembler`
 

docs/src/topics/boundary_conditions.md

@@ -9,7 +9,7 @@ conditions, and they need to be handled in different ways. Below we discuss how
 the most common ones, Dirichlet and Neumann boundary conditions, and how to do it `Ferrite`.
 
 While boundary conditions can be applied directly to nodes, vertices, edges, or faces,
-they are most commonly applied to [facets](@ref Reference shapes). Each facet is described
+they are most commonly applied to [facets](@ref "Reference shapes"). Each facet is described
 by a [`FacetIndex`](@ref).
 When adding boundary conditions to points instead, vertices are preferred over nodes.
 

docs/src/topics/reference_shapes.md

@@ -86,4 +86,4 @@ Ferrite.reference_facets(RefQuadrilateral)
     The functions `reference_vertices`, `reference_edges`, `reference_faces`, and `reference_facets`
     are not public and only shown here to explain the numbering concept.
     The specific ordering may also change, and is therefore only documented in the
-    [Developer documentation](../devdocs/reference_cells/).
+    [Developer documentation](@ref).

docs/src/topics/sparse_matrix.md

@@ -33,10 +33,10 @@ precision (`Float64`, 8 bytes) it would require 8 TB of memory. If instead the s
 99.9973% (which is the case when solving the heat equation on a three dimensional hypercube
 with linear Lagrange interpolation) this would be reduced to 216 MB.
 
-[1]: Structurally nonzero means that there is a possibility of a nonzero value even though
+[^1]: Structurally nonzero means that there is a possibility of a nonzero value even though
      the computed value might become zero in the end for various reasons.
 
-[2]: At least for most practical problems using low order interpolations.
+[^2]: At least for most practical problems using low order interpolations.
 
 
 !!! details "Sparsity pattern example"

ext/FerriteMetis.jl

@@ -21,7 +21,7 @@ end
 Fill-reducing permutation order from [Metis.jl](https://github.com/JuliaSparse/Metis.jl).
 
 Since computing the permutation involves constructing the structural couplings between all
-DoFs the field/component coupling can be provided; see [`create_sparsity_pattern`](@ref) for
+DoFs the field/component coupling can be provided; see [`allocate_matrix`](@ref) for
 details.
 """
 function DofOrder.Ext{Metis}(;

src/Dofs/DofHandler.jl

@@ -796,7 +796,7 @@ field was found and the 2nd entry is the index of the field within the `SubDofHa
     Always finds the 1st occurrence of a field within `DofHandler`.
 
 See also: [`find_field(sdh::SubDofHandler, field_name::Symbol)`](@ref),
-[`_find_field(sdh::SubDofHandler, field_name::Symbol)`](@ref).
+[`Ferrite._find_field(sdh::SubDofHandler, field_name::Symbol)`](@ref).
 """
 function find_field(dh::DofHandler, field_name::Symbol)
     for (sdh_idx, sdh) in pairs(dh.subdofhandlers)

src/Dofs/sparsity_pattern.jl

@@ -391,7 +391,7 @@ allocate_matrix(MatrixType, sp)
 ````
 
 Refer to [`allocate_matrix`](@ref allocate_matrix(::Type{<:Any}, ::SparsityPattern)) for
-supported matrix types, and to [`create_sparsity_pattern`](@ref) for details about supported
+supported matrix types, and to [`init_sparsity_pattern`](@ref) for details about supported
 arguments `args` and keyword arguments `kwargs`.
 
 !!! note

src/Ferrite.jl

@@ -58,6 +58,7 @@ struct RefPyramid       <: AbstractRefShape{3} end
 
 Get the dimension of the reference shape
 """
+getrefdim(::Type{<:AbstractRefShape}) # To get correct doc filtering
 getrefdim(::Type{<:AbstractRefShape{rdim}}) where rdim = rdim
 
 abstract type AbstractCell{refshape <: AbstractRefShape} end

src/Grid/coloring.jl

@@ -179,7 +179,7 @@ Two different algorithms are available, specified with the `alg` keyword argumen
  - `alg = ColoringAlgorithm.Greedy`: greedy algorithm that works well for structured quadrilateral grids such as
    e.g. quadrilateral grids from `generate_grid`.
 
-The resulting colors can be visualized using [`vtk_cell_data_colors`](@ref).
+The resulting colors can be visualized using [`Ferrite.write_cell_colors`](@ref).
 
 !!! note "Cell to color mapping"
     In a previous version of Ferrite this function returned a dictionary mapping

src/L2_projection.jl

@@ -234,7 +234,7 @@ Supported data types to project are `Number`s and `AbstractTensor`s.
 !!! note
     The order of the returned data correspond to the order of the `L2Projector`'s internal
     `DofHandler`. The data can be further analyzed with [`evaluate_at_points`](@ref) and
-    [`evaluate_at_grid_nodes`](@ref). Use [`write_projected`](@ref) to export the result.
+    [`evaluate_at_grid_nodes`](@ref). Use [`write_projection`](@ref) to export the result.
 
 """
 function project(proj::L2Projector, vars::Union{AbstractVector, AbstractDict})

src/assembler.jl

@@ -241,7 +241,7 @@ function _missing_sparsity_pattern_error(Krow::Int, Kcol::Int)
     throw(ErrorException(
         "You are trying to assemble values in to K[$(Krow), $(Kcol)], but K[$(Krow), " *
         "$(Kcol)] is missing in the sparsity pattern. Make sure you have called `K = " *
-        "create_sparsity_pattern(dh)` or `K = create_sparsity_pattern(dh, ch)` if you " *
+        "allocate_matrix(dh)` or `K = allocate_matrix(dh, ch)` if you " *
         "have affine constraints. This error might also happen if you are using " *
         "`::AssemblerSparsityPattern` in a threaded assembly loop (you need to create an " *
         "`assembler::AssemblerSparsityPattern` for each task)."

src/interpolations.jl

@@ -111,6 +111,7 @@ Base.copy(ip::Interpolation) = ip
 
 Return the dimension of the reference element for a given interpolation.
 """
+getrefdim(::Interpolation) # To make doc-filtering work
 @inline getrefdim(::Interpolation{RefShape}) where RefShape = getrefdim(RefShape)
 
 """