Merge pull request #9 from jpthiele/codespell

Add and apply codespell config

CHANGELOG.md

@@ -15,7 +15,7 @@
 
 ## October 28, 2024
 
-Moved repositiory from https://github.com/chmerdon/ExtendableFEMBase.jl to https://github.com/WIAS-PDELib/ExtendableFEMBase.jl.
+Moved repository from https://github.com/chmerdon/ExtendableFEMBase.jl to https://github.com/WIAS-PDELib/ExtendableFEMBase.jl.
 [WIAS-PDELib](https://github.com/WIAS-PDELib/) is a github organization created to collectively manage the Julia packages developed under
 the lead of the [WIAS Numerical Mathematics and Scientific Computing](https://wias-berlin.de/research/rgs/fg3)  research group.
 According to the [github docs on repository transfer](https://docs.github.com/en/repositories/creating-and-managing-repositories/transferring-a-repository#whats-transferred-with-a-repository),

docs/src/examples_intro.md

@@ -14,7 +14,7 @@ The examples have been designed with the following issues in mind:
 
 ## Running the examples
 
-In order to run `ExampleXXX`, peform the following steps:
+In order to run `ExampleXXX`, perform the following steps:
 
 - Download the example file (e.g. via the source code link at the top)
 - Make sure all used packages are installed in your Julia environment

docs/src/fems.md

@@ -41,7 +41,7 @@ AbstractFiniteElement
 
 #### Remarks
 - each type depends on one/two or three parameters, the first one is always the number of components (ncomponents) that determines if the
-  finite element is scalar- or veector-valued; some elements additionaly require the parameter edim <: Int if they are structurally different in different space dimensions; arbitrary order elements require a third parameter that determines the order
+  finite element is scalar- or veector-valued; some elements additionally require the parameter edim <: Int if they are structurally different in different space dimensions; arbitrary order elements require a third parameter that determines the order
 - each finite elements mainly comes with a set of basis functions in reference coordinates for each applicable AbstractElementGeometry and degrees of freedom maps for each mesh entity
 - broken finite elements are possible via the broken switch in the [FESpace](@ref) constructor
 - the type steers how the basis functions are transformed from local to global coordinates and how FunctionOperators are evaluated
@@ -54,7 +54,7 @@ AbstractFiniteElement
 
 ## List of implemented Finite Elements
 
-The following table lists all curently implemented finite elements and on which geometries they are available (in brackets a dofmap pattern for CellDofs is shown and the number of local degrees of freedom for a vector-valued realisation). Click on the FEType to find out more details.
+The following table lists all currently implemented finite elements and on which geometries they are available (in brackets a dofmap pattern for CellDofs is shown and the number of local degrees of freedom for a vector-valued realisation). Click on the FEType to find out more details.
 
 | FEType | Triangle2D | Parallelogram2D | Tetrahedron3D | Parallelepiped3D |
 | :----------------: | :----------------: |  :----------------: |  :----------------: |  :----------------: | 
@@ -93,7 +93,7 @@ Note: the dofmap pattern describes the connection of the local degrees of freedo
 
 ### P0 finite element
 
-Piecewise constant finite element that has one degree of freedom on each cell of the grid. (It is masked as a H1-conforming finite element, because it uses the same operator evaulations.)
+Piecewise constant finite element that has one degree of freedom on each cell of the grid. (It is masked as a H1-conforming finite element, because it uses the same operator evaluations.)
 
 The interpolation of a given function into this space preserves the cell integrals.
 
@@ -205,7 +205,7 @@ H1P3
 
 ### Pk finite element (experimental)
 
-The Pk finite element method generically generates polynomials of abitrary order k on simplices (Edge1D, Triangle2D so far).
+The Pk finite element method generically generates polynomials of arbitrary order k on simplices (Edge1D, Triangle2D so far).
 
 The interpolation of a given function into this space performs point evaluations at the nodes and preserves cell and face integrals in 2D (moment order depends on the order and the element dimension).
 

docs/src/interpolations.md

@@ -17,7 +17,7 @@ The qpinfo argument communicates vast information of the current quadrature poin
 | qpinfo.region      | Integer            | region number of item |
 | qpinfo.xref        | Vector{Real}       | reference coordinates within item of qpinfo.x |
 | qpinfo.volume      | Real               | volume of item |
-| qpinfo.params      | Vector{Any}        | parameters that can be transfered via keyword arguments |
+| qpinfo.params      | Vector{Any}        | parameters that can be transferred via keyword arguments |
 
 
 ## Standard Interpolations

docs/src/notebooks_intro.md

@@ -2,6 +2,6 @@
 
 This sections contains [Pluto.jl](https://github.com/fonsp/Pluto.jl) notebooks.
 
-Plese note, that in the html version, interactive elements like sliders are disabled.
+Please note, that in the html version, interactive elements like sliders are disabled.
 Navigation via the table of contents does work, though.
 

examples/Example200_LowLevelPoisson.jl

@@ -203,7 +203,7 @@ function runtests(; order = 2, kwargs...) #hide
 	## first assembly causes allocations when filling sparse matrix
 	loop_allocations = assemble!(A.entries, b.entries, FES, f, μ)
 	@info "allocations in 1st assembly: $loop_allocations"
-	## second assebly in same matrix should have allocation-free inner loop
+	## second assembly in same matrix should have allocation-free inner loop
 	loop_allocations = assemble!(A.entries, b.entries, FES, f, μ)
 	@info "allocations in 2nd assembly: $loop_allocations"
 	@test loop_allocations == 0

pluto-examples/LowLevelNavierStokes.jl

@@ -292,7 +292,7 @@ function solve_stokes_lowlevel(FES, μ, f!)
 	Alin = deepcopy(A) # = keep linear part of system matrix
 	blin = deepcopy(b) # = keep linear part of right-hand side
 
-	println("Pepare boundary conditions...")
+	println("Prepare boundary conditions...")
 	@time begin
 		u_init = FEVector(FES)
 		interpolate!(u_init[1], u!; time = teval)

src/dofmaps.jl

@@ -189,7 +189,7 @@ EffAT4AssemblyType(::Type{ON_EDGES}, ::Type{<:ON_EDGES}) = ON_CELLS
 """
 	$(TYPEDEF)
 
-Abstrat type for all dof types
+Abstract type for all dof types
 """
 abstract type DofType end
 

src/fedefs/h1_pk.jl

@@ -99,7 +99,7 @@ function ExtendableGrids.interpolate!(Target, FE::FESpace{Tv, Ti, H1Pk{ncomponen
 	end
 end
 
-## standard interpolation on cells = perserve cell moments up to order-3
+## standard interpolation on cells = preserve cell moments up to order-3
 function ExtendableGrids.interpolate!(Target, FE::FESpace{Tv, Ti, H1Pk{ncomponents, edim, order}, APT}, ::Type{ON_CELLS}, exact_function!; items = [], kwargs...) where {ncomponents, edim, order, Tv, Ti, APT}
 	if edim == 2
 		# delegate cell faces to face interpolation
@@ -116,7 +116,7 @@ function ExtendableGrids.interpolate!(Target, FE::FESpace{Tv, Ti, H1Pk{ncomponen
 		#     subitems = slice(FE.dofgrid[CellEdges], items)
 		#     interpolate!(Target, FE, ON_EDGES, exact_function!; items = subitems, time = time)
 
-		#     # fixe face means
+		#     # fix face means
 
 		#     # fix cell bubble value by preserving integral mean
 		#     ensure_cell_moments!(Target, FE, exact_function!; facedofs = 1, edgedofs = 2, items = items, time = time)
@@ -194,7 +194,7 @@ function get_basis(::Type{<:AssemblyType}, FEType::Type{H1Pk{ncomponents, edim,
 	end
 	if order > 3 # use recursion to fill the interior dofs (+multiplication with cell bubble)
 		interior_basis = get_basis(ON_CELLS, H1Pk{1, edim, order - 3}, Triangle2D)
-		# todo: scaling factors for interior dofs (but may be ommited)
+		# todo: scaling factors for interior dofs (but may be omitted)
 	end
 	function closure(refbasis, xref)
 		fill!(refbasis, 0)
@@ -217,7 +217,7 @@ function get_basis(::Type{<:AssemblyType}, FEType::Type{H1Pk{ncomponents, edim,
 		# edge basis functions
 		if order > 1
 			for k ∈ 1:order-1
-				# on each face find basis funktion that is 1 at s = k//order
+				# on each face find basis function that is 1 at s = k//order
 
 				# first face (nodes [1,2])
 				refbasis[3+k, 1] = refbasis[end] * xref[1] / factors_face[k]

src/fedefs/h1v_p1teb.jl

@@ -5,7 +5,7 @@ abstract type H1P1TEB{edim} <: AbstractH1FiniteElementWithCoefficients where {ed
 ````
 
 vector-valued (ncomponents = edim) element that uses P1 functions + tangential-weighted edge bubbles
-as suggested by [Diening, L., Storn, J. & Tscherpel, T., "Fortin operator for the Taylor–Hood element", Numer. Math. 150, 671–689 (2022)]
+as suggested by [Diening, L., Storn, J. & Tscherpel, T., "Fortin operator for the Taylor–Hood element", Num. Math. 150, 671–689 (2022)]
 
 (is inf-sup stable for Stokes if paired with continuous P1 pressure space, less degrees of freedom than MINI)
 

src/fedefs/hdiv_rtk_enrich.jl

@@ -99,7 +99,7 @@ function get_basis(::Type{ON_CELLS}, ::Type{HDIVRTkENRICH{3, order, false}}, EG:
 		refbasis[3, 3] = 2 * xref[1] * xref[3]
 
 		if order == 1
-			# nothing to add (but enrichment need additional RT0 handled by seperate FESpace/FEVectorBlock)
+			# nothing to add (but enrichment need additional RT0 handled by separate FESpace/FEVectorBlock)
 		elseif order == 2
 			for k ∈ 1:3
 				refbasis[4, k] = (6 * (1 - xref[1] - xref[2] - xref[3]) - 1) * refbasis[3, k] + (6 * xref[1] - 1) * (-refbasis[1, k] - refbasis[2, k] - refbasis[3, k]) # (1,2)

src/interpolations.jl

@@ -108,7 +108,7 @@ function ensure_moments!(target::AbstractArray{T, 1}, FE::FESpace{Tv, Ti, FEType
 	xItemDofs::DofMapTypes{Ti} = Dofmap4AssemblyType(FE, AT)
 	EGs = xgrid[GridComponentUniqueGeometries4AssemblyType(AT)]
 
-	bestapprox::Bool = false # if true interior dofs are set acoording to a constrained bestapproximation, otherwise to preserve the moments up to order, might become a kwarg later
+	bestapprox::Bool = false # if true interior dofs are set according to a constrained bestapproximation, otherwise to preserve the moments up to order, might become a kwarg later
 
 	@assert length(EGs) == 1 "ensure_moments! currently only works with grids with a single element geometry"
 	EG = EGs[1]
@@ -292,7 +292,7 @@ function ExtendableGrids.interpolate!(target::FEVectorBlock,
 ````
 
 Interpolates the given source into the finite elements space assigned to the target FEVectorBlock with the specified AssemblyType
-(usualy ON_CELLS). 
+(usually ON_CELLS). 
 
 The source functions should adhere to the interface
 ```julia
@@ -301,7 +301,7 @@ The source functions should adhere to the interface
 The qpinfo argument communicates vast information of the current quadrature/evaluation point.
 
 The bonus_quadorder argument can be used to steer the quadrature order of integrals that needs to be computed
-for the interpolation (the default quadrature order corressponds to the polynomial order of the finite element).
+for the interpolation (the default quadrature order corresponds to the polynomial order of the finite element).
 """
 function ExtendableGrids.interpolate!(
 	target::FEVectorBlock{T, Tv, Ti},
@@ -312,7 +312,7 @@ function ExtendableGrids.interpolate!(
 
 	FEType = eltype(target.FES)
 	if target.FES.broken == true
-		## interpolate continously
+		## interpolate continuously
 		FESc = FESpace{FEType}(target.FES.dofgrid)
 		Targetc = FEVector{T}(FESc)
 		interpolate!(Targetc[1], FESc, AT, source; items = items, kwargs...)
@@ -358,7 +358,7 @@ The source functions should adhere to the interface
 The qpinfo argument communicates vast information of the current quadrature/evaluation point.
 
 The bonus_quadorder argument can be used to steer the quadrature order of integrals that needs to be computed
-for the interpolation (the default quadrature order corressponds to the polynomial order of the finite element).
+for the interpolation (the default quadrature order corresponds to the polynomial order of the finite element).
 """
 function ExtendableGrids.interpolate!(target::FEVectorBlock, source; kwargs...)
 	interpolate!(target, ON_CELLS, source; kwargs...)

src/lazy_interpolate.jl

@@ -24,7 +24,7 @@ search. To activate this put 'use_cellparents' = true). By some given kernel fun
 the operator evaluation (=input) can be further postprocessed. The qpinfo argument
 allows to access information at the current quadrature point.
 
-Note: discontinuous quantities at vertices of the target grid will be evaluted in the first found cell of the
+Note: discontinuous quantities at vertices of the target grid will be evaluated in the first found cell of the
 source grid. No averaging is performed. With eps the tolerances of the cell search via ExtendableGrids.CellFinder can be steered.
 """
 function lazy_interpolate!(

src/point_evaluator.jl

@@ -140,7 +140,7 @@ function initialize!(O::PointEvaluator{T, UT}, sol; time = 0, kwargs...) where {
 			# update basis evaluations at xref
 			relocate_xref!(BE_args[id], xref)
 
-			# update operator eveluation on item
+			# update operator evaluation on item
 			update_basis!(BE_args[id], item)
 		end
 

src/quadrature.jl

@@ -596,7 +596,7 @@ function get_generic_quadrature_Stroud(order::Int)
 	r = F.values
 	a = 2 * F.vectors[1, :] .^ 2
 
-	# compute 1D Gauss-Jacobi Points for Intervall [-1,1] and weights
+	# compute 1D Gauss-Jacobi Points for Interval [-1,1] and weights
 	delta = -1 ./ (4 .* (1:ngpts) .^ 2 .- ones(ngpts, 1))
 	gamma = sqrt.((2:ngpts) .* (1:ngpts-1)) ./ (2 .* (2:ngpts) .- ones(ngpts - 1, 1))
 	F = eigen(diagm(0 => delta[:], 1 => gamma[:], -1 => gamma[:]))

src/reconstructionoperators.jl

@@ -44,7 +44,7 @@ function FEEvaluator(
 	xgrid = FE.xgrid
 	FE2 = FESpace{FETypeReconst}(xgrid)
 
-	## collect dimension informations
+	## collect dimension information
 	ncomponents::Int = get_ncomponents(FEType)
 	ncomponents2::Int = get_ncomponents(FETypeReconst)
 	if AT <: Union{ON_BFACES, <:ON_FACES}

src/segment_integrator.jl

@@ -17,7 +17,7 @@ segment_geometry(::SegmentIntegrator{Tv, UT, KFT, EG}) where {Tv, UT, KFT, EG} =
 default_segint_kwargs() = Dict{Symbol, Tuple{Any, String}}(
 	:name => ("SegmentIntegrator", "name for operator used in printouts"),
 	:resultdim => (0, "dimension of result field (default = length of arguments)"),
-	:matrix_mode => (false, "integrator integrates basis functions of FEspace seperately to assembly a matrix that maps solution to segment integrations (requires that kernel is linear)"),
+	:matrix_mode => (false, "integrator integrates basis functions of FEspace separately to assembly a matrix that maps solution to segment integrations (requires that kernel is linear)"),
 	:entry_tolerance => (0, "threshold to add entry to sparse matrix (only in matrix_mode)"),
 	:params => (nothing, "array of parameters that should be made available in qpinfo argument of kernel function"),
 	:factor => (1, "factor that should be multiplied during assembly"),
@@ -44,7 +44,7 @@ function SegmentIntegrator(
 	kwargs...)
 ````
 
-Generates an SegmentIntegrator that can intgrate over segments
+Generates an SegmentIntegrator that can integrate over segments
 of the specified geometry EG.
 To do so, it evaluates, at each quadrature point, the specified operator evaluations,
 postprocesses them with the kernel function (if provided)
@@ -105,7 +105,7 @@ function initialize!(O::SegmentIntegrator{T, UT}, sol; time = 0, kwargs...) wher
 	xgrid = FES_args[1].xgrid
 	itemregions = xgrid[CellRegions]
 
-	## prepare quadrature formuale
+	## prepare quadrature formulae
 	SG = segment_geometry(O)
 	EG = xgrid[UniqueCellGeometries][1]
 	dimfill = dim_element(EG) - dim_element(SG)