add codespell action and correct spelling errors (#5011)

JuliaPlots · Nov 1, 2024 · 8119dac · 8119dac
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diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -3,6 +3,7 @@ name: benchmarks
 on:
   workflow_dispatch:
   pull_request:
+    branches: [master]
 
 concurrency: 
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}

diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,17 @@
+name: codespell
+
+on: [pull_request]
+
+concurrency: 
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: codespell-project/actions-codespell@v2
+      with:
+        ignore_words_list: nd,nax,linez,ist
+        only_warn: 0
diff --git a/GraphRecipes/src/graph_layouts.jl b/GraphRecipes/src/graph_layouts.jl
@@ -132,7 +132,7 @@ function shell_graph(
     kw...,
 )
     @assert dim == 2
-    positions = NetworkLayout.shell(adjmat; nlist = nlist)
+    positions = NetworkLayout.shell(adjmat; nlist)
 
     ([p[1] for p ∈ positions], [p[2] for p ∈ positions], nothing)
 end
@@ -234,16 +234,16 @@ function by_axis_local_stress_graph(
     for k ∈ 1:maxiter
         for p ∈ free_dims
             for i ∈ 1:n
-                numer, denom = 0.0, 0.0
+                num, den = 0.0, 0.0
                 for j ∈ 1:n
                     i == j && continue
-                    numer +=
+                    num +=
                         w[i, j] *
                         (X[p][j] + dist[i, j] * (X[p][i] - X[p][j]) / norm_ij(X, i, j))
-                    denom += w[i, j]
+                    den += w[i, j]
                 end
-                if denom != 0
-                    X[p][i] = numer / denom
+                if den != 0
+                    X[p][i] = num / den
                 end
             end
         end

diff --git a/NEWS.md b/NEWS.md
@@ -62,7 +62,7 @@ import GR # loads backend code
 - stephist logscale improvements
 
 ## 0.25.2
-- improvements to handle missings
+- improvements to handle `missing`s
 - pyplot: allow setting the color gradient for z values
 - document :colorbar_entry
 - limit number of automatic bins
@@ -162,7 +162,7 @@ import GR # loads backend code
 - implement guide position in gr, pyplot and pgfplots
 - inspectdr fixes
 - default appveyor
-- rudimentary missings support
+- rudimentary `missing`s support
 - deprecation fixes for PGFPlots
 
 ## 0.20.0
@@ -568,7 +568,7 @@ Many updates, min julia 1.0
 - GR:
 	- manually draw 2D axes... fixes several issues and missing features
 	- fontsize fix
-- PGFPlots: pass axis syle
+- PGFPlots: pass axis style
 
 #### 0.8.0
 

diff --git a/PlotsBase/ext/GRExt.jl b/PlotsBase/ext/GRExt.jl
@@ -2187,7 +2187,7 @@ function gr_z_normalized_log_scaled(scale, z, clims)
     any(x -> !isfinite(x), loglims) && throw(
         DomainError(
             loglims,
-            "Non-finite value in colorbar limits. Please provide explicits limits via `clims`.",
+            "Non-finite value in colorbar limits. Please provide explicit limits via `clims`.",
         ),
     )
     z_log, get_z_normalized.(z_log, loglims...)

diff --git a/PlotsBase/ext/GastonExt.jl b/PlotsBase/ext/GastonExt.jl
@@ -539,7 +539,7 @@ function gaston_parse_axes_attrs(
         # guide labels
         guide_font = guidefont(axis)
         if letter ≡ :y && dims == 2
-            # vertical by default (consistency witht other backends)
+            # vertical by default (consistency with other backends)
             guide_font = font(guide_font; rotation = guide_font.rotation + 90)
         end
         push!(

diff --git a/PlotsBase/src/Commons/attrs.jl b/PlotsBase/src/Commons/attrs.jl
@@ -957,13 +957,13 @@ end
 @attributes function process_font_attr!(plotattributes::AKW, fontname::Symbol, arg)
     T = typeof(arg)
     if fontname in (:legend_font,)
-        # TODO: this is neccessary while old and new font names coexist and should be standard after the transition
+        # TODO: this is necessary while old and new font names coexist and should be standard after the transition
         fontname = Symbol(fontname, :_)
     end
     if T <: PlotsBase.Font
         Symbol(fontname, :family) --> arg.family
 
-        # TODO: this is neccessary in the transition from old fontsize to new font_pointsize and should be removed when it is completed
+        # TODO: this is necessary in the transition from old fontsize to new font_pointsize and should be removed when it is completed
         if in(Symbol(fontname, :size), _all_attrs)
             Symbol(fontname, :size) --> arg.pointsize
         else

diff --git a/PlotsBase/src/arg_desc.jl b/PlotsBase/src/arg_desc.jl
@@ -101,9 +101,9 @@ const _arg_desc = KW(
     :foreground_color_title      => (ColorType, "Color of subplot title (`:match` matches :foreground_color_subplot`)."),
     :color_palette               => (Union{AVec{ColorType},Symbol}, "Iterable (cycle through) or color gradient (generate list from gradient) or `:auto` (generate a color list using `Colors.distiguishable_colors` and custom seed colors chosen to contrast with the background). The color palette is a color list from which series colors are automatically chosen."),
     :legend_position             => (Union{Bool,NTuple{2,Real},Symbol}, """
-                                    Show the legend ? Can also be a (x,y) tuple or Symbol (legend position) or angle (angle,inout) tuple. Bottom left corner of legend is placed at (x,y).
+                                    Show the legend ? Can also be a (x,y) tuple or Symbol (legend position) or angle (angle,in-out) tuple. Bottom left corner of legend is placed at (x,y).
                                     Choose from (`:none`, `:best`, `:inline`, `:inside`, `:legend`) or any valid combination of `:(outer ?)(top/bottom ?)(right/left ?)`, i.e.: `:top`, `:topright`, `:outerleft`, `:outerbottomright` ... (note: only some may be supported in each backend)."""),
-    :legend_column               => (Integer, "Number of columns in the legend. `-1` stands for maximum number of colums (horizontal legend)."),
+    :legend_column               => (Integer, "Number of columns in the legend. `-1` stands for maximum number of columns (horizontal legend)."),
     :legend_title_font           => (Font, "Font of the legend title."),
     :legend_font_family          => (Union{AStr,Symbol}, "Font family of legend entries."),
     :legend_font_pointsize       => (Integer, "Font pointsize of legend entries."),

diff --git a/PlotsBase/src/examples.jl b/PlotsBase/src/examples.jl
@@ -328,7 +328,7 @@ const _examples = PlotExample[
         "Custom Markers",
         """A `PlotsBase.Shape` is a light wrapper around vertices of a polygon.  For supported
         backends, pass arbitrary polygons as the marker shapes.  Note: The center is (0,0) and
-        the size is expected to be rougly the area of the unit circle.
+        the size is expected to be roughly the area of the unit circle.
         """,
         quote
             verts = [
@@ -1308,7 +1308,7 @@ _backend_skips = Dict(
         31,  # animations - needs github.com/mbaz/Gaston.jl/pull/178
         49,  # TODO: support polar
         60,  # :perspective projection unsupported
-        63,  # FXIME: twin axes misalignement
+        63,  # FXIME: twin axes misalignment
     ],
 )
 _backend_skips[:plotly] = _backend_skips[:plotlyjs]

diff --git a/PlotsBase/src/layouts.jl b/PlotsBase/src/layouts.jl
@@ -319,7 +319,7 @@ function build_layout(layout::GridLayout, n::Integer, plts::AVec{Plot})
             merge!(spmap, m)
             i += length(sps)
         elseif isa(l, Subplot) && empty
-            error("Subplot exists. Cannot re-use existing layout.  Please make a new one.")
+            error("Subplot exists. Cannot reuse existing layout.  Please make a new one.")
         end
         i ≥ n && break  # only add n subplots
     end

diff --git a/PlotsBase/src/plotly.jl b/PlotsBase/src/plotly.jl
@@ -381,7 +381,7 @@ function plotly_layout(plt::Plot)
 
     for sp ∈ plt.subplots
         spidx = multiple_subplots ? sp[:subplot_index] : ""
-        x_idx, y_idx = multiple_subplots ? plotly_link_indicies(plt, sp) : ("", "")
+        x_idx, y_idx = multiple_subplots ? plotly_link_indices(plt, sp) : ("", "")
 
         # add an annotation for the title
         if sp[:title] != ""
@@ -646,8 +646,8 @@ get_plotly_marker(k, def) = get(
     def,
 )
 
-# find indicies of axes to which the subplot links to
-function plotly_link_indicies(plt::Plot, sp::Subplot)
+# find indices of axes to which the subplot links to
+function plotly_link_indices(plt::Plot, sp::Subplot)
     if plt[:link] in (:x, :y, :both)
         x_idx = sp[:xaxis].sps[1][:subplot_index]
         y_idx = sp[:yaxis].sps[1][:subplot_index]
@@ -657,7 +657,7 @@ function plotly_link_indicies(plt::Plot, sp::Subplot)
     x_idx, y_idx
 end
 
-# the Shape contructor will automatically close the shape. since we need it closed,
+# the Shape constructor will automatically close the shape. since we need it closed,
 # we split by NaNs and then construct/destruct the shapes to get the closed coords
 function plotly_close_shapes(x, y)
     xs, ys = nansplit(x), nansplit(y)
@@ -735,7 +735,7 @@ function plotly_series(plt::Plot, series::Series)
         plotattributes_out[:zaxis] = "z$spidx"
         plotattributes_out[:scene] = "scene$spidx"
     else
-        x_idx, y_idx = length(plt.subplots) > 1 ? plotly_link_indicies(plt, sp) : ("", "")
+        x_idx, y_idx = length(plt.subplots) > 1 ? plotly_link_indices(plt, sp) : ("", "")
         plotattributes_out[:xaxis] = "x$(x_idx)"
         plotattributes_out[:yaxis] = "y$(y_idx)"
     end
@@ -940,7 +940,7 @@ function plotly_series_shapes(plt::Plot, series::Series, clims)
     # x, y = series[:x], series[:y]
 
     # these are the axes that the series should be mapped to
-    x_idx, y_idx = plotly_link_indicies(plt, series[:subplot])
+    x_idx, y_idx = plotly_link_indices(plt, series[:subplot])
     plotattributes_base = KW(
         :xaxis => "x$(x_idx)",
         :yaxis => "y$(y_idx)",

diff --git a/PlotsBase/src/recipes.jl b/PlotsBase/src/recipes.jl
@@ -1084,7 +1084,7 @@ end
 # Error Bars
 
 Commons.@attributes function error_style!(plotattributes::AKW)
-    # errorbar color should soley determined by markerstrokecolor
+    # errorbar color should solely determined by markerstrokecolor
     haskey(plotattributes, :marker_z) &&
         RecipesPipeline.reset_kw!(plotattributes, :marker_z)
     haskey(plotattributes, :line_z) && RecipesPipeline.reset_kw!(plotattributes, :line_z)

diff --git a/PlotsBase/src/shorthands.jl b/PlotsBase/src/shorthands.jl
@@ -520,7 +520,7 @@ for letter ∈ ("x", "y", "z")
             $($letter)error(x, y [, z]; $($letter)error = vals)
             $($letter)error!(x, y [, z]; $($letter)error = vals)
 
-        Create or add a series of $($letter)errorbars at the positions defined by `x`, `y` and `z` with the lenghts defined in `vals`.
+        Create or add a series of $($letter)errorbars at the positions defined by `x`, `y` and `z` with the lengths defined in `vals`.
 
         Markerstrokecolor will color the whole errorbars if not specified otherwise.
         """

diff --git a/PlotsBase/src/utils.jl b/PlotsBase/src/utils.jl
@@ -224,7 +224,7 @@ function heatmap_edges(
 )
     nx, ny = length(x), length(y)
     # ismidpoints = z_size == (ny, nx) # This fails some tests, but would actually be
-    # the correct check, since (4, 3) != (3, 4) and a missleading plot is produced.
+    # the correct check, since (4, 3) != (3, 4) and a misleading plot is produced.
     ismidpoints = prod(z_size) == (ny * nx)
     isedges = z_size == (ny - 1, nx - 1)
     (ismidpoints || isedges) ||
@@ -696,7 +696,7 @@ __straightline_data(xl, yl, x, y, exp_fact) =
         ___straightline_data(xl, yl, x, y, exp_fact)
     else
         k, r = divrem(n, 3)
-        @assert r == 0 "Misformed data. `straightline_data` either accepts vectors of length 2 or 3k. The provided series has length $n"
+        @assert r == 0 "Malformed data. `straightline_data` either accepts vectors of length 2 or 3k. The provided series has length $n"
         xdata, ydata = fill(NaN, n), fill(NaN, n)
         for i ∈ 1:k
             inds = (3i - 2):(3i - 1)
@@ -883,8 +883,8 @@ end
 # Function barrier because lims are type-unstable
 function _guess_best_legend_position(xl, yl, plt, weight = 100)
     scale = (maximum(xl) - minimum(xl), maximum(yl) - minimum(yl))
-    u = zeros(4) # faster than tuple
-    # Quadrants where the points will be tested
+    u = zeros(4)  # faster than tuple
+    # quadrants where the points will be tested
     quadrants = (
         ((0.00, 0.25), (0.00, 0.25)),   # bottomleft
         ((0.75, 1.00), (0.00, 0.25)),   # bottomright

diff --git a/PlotsBase/test/test_misc.jl b/PlotsBase/test/test_misc.jl
@@ -297,7 +297,7 @@ with(:gr) do
         p4 = [0.5, 0.5, 1.0]
         pts = [p0, p1, p2, p3, p4]
         x, y, z = broadcast(i -> getindex.(pts, i), (1, 2, 3))
-        # [x[i],y[i],z[i]] is the i-th vertix of the mesh
+        # [x[i],y[i],z[i]] is the i-th vertex of the mesh
         mesh3d(
             x,
             y,

diff --git a/PlotsBase/test/test_pgfplotsx.jl b/PlotsBase/test/test_pgfplotsx.jl
@@ -435,8 +435,8 @@ with(:pgfplotsx) do
     @testset "Latexify - LaTeXStrings" begin
         @test PlotsBase.pgfx_sanitize_string("A string, with 2 punctuation chars.") ==
               "A string, with 2 punctuation chars."
-        @test PlotsBase.pgfx_sanitize_string("Interpolação polinomial") ==
-              raw"Interpola$\textnormal{\c{c}}$$\tilde{a}$o polinomial"
+        @test PlotsBase.pgfx_sanitize_string("Interpolação polynomial") ==
+              raw"Interpola$\textnormal{\c{c}}$$\tilde{a}$o polynomial"
         @test PlotsBase.pgfx_sanitize_string("∫∞ ∂x") == raw"$\int$$\infty$ $\partial$x"
 
         # special LaTeX characters

diff --git a/RecipesPipeline/src/user_recipe.jl b/RecipesPipeline/src/user_recipe.jl
@@ -5,7 +5,7 @@
 
 Wrap input arguments in a `RecipeData' vector and recursively apply user recipes and type
 recipes on the first element. Prepend the returned `RecipeData` vector. If an element with
-empy `args` is returned pop it from the vector, finish up, and it to vector of `Dict`s with
+empty `args` is returned pop it from the vector, finish up, and it to vector of `Dict`s with
 processed series. When all arguments are processed return the series `Dict`.
 """
 function _process_userrecipes!(plt, plotattributes, args)

diff --git a/StatsPlots/README.md b/StatsPlots/README.md
@@ -337,11 +337,11 @@ The `group` syntax is also possible in combination with `groupedbar`:
 
 ```julia
 ctg = repeat(["Category 1", "Category 2"], inner = 5)
-nam = repeat("G" .* string.(1:5), outer = 2)
+name = repeat("G" .* string.(1:5), outer = 2)
 
-groupedbar(nam, rand(5, 2), group = ctg, xlabel = "Groups", ylabel = "Scores",
-        title = "Scores by group and category", bar_width = 0.67,
-        lw = 0, framestyle = :box)
+groupedbar(name, rand(5, 2), group = ctg, xlabel = "Groups", ylabel = "Scores",
+           title = "Scores by group and category", bar_width = 0.67,
+           lw = 0, framestyle = :box)
 ```
 
 ![](https://user-images.githubusercontent.com/6645258/32116755-b7018f02-bb2a-11e7-82c7-ca471ecaeecf.png)

diff --git a/StatsPlots/src/hist.jl b/StatsPlots/src/hist.jl
@@ -134,11 +134,11 @@ PlotsBase.wand_edges(x::AbstractVector, args...) = (binwidth = wand_bins(x, args
 (minimum(x) - binwidth):binwidth:(maximum(x) + binwidth))
 
 "Returns optimal histogram bin widths in accordance to Wand (1995)'s criterion'"
-function wand_bins(x, scalest = :minim, gridsize = 401, range_x = extrema(x), trun = true)
+function wand_bins(x, scalest = :minim, gridsize = 401, range_x = extrema(x), t_run = true)
     n = length(x)
     minx, maxx = range_x
     gpoints = range(minx, stop = maxx, length = gridsize)
-    gcounts = linbin(x, gpoints, trun = trun)
+    gcounts = linbin(x, gpoints; t_run)
 
     scalest = if scalest === :stdev
         sqrt(var(x))
@@ -156,7 +156,7 @@ function wand_bins(x, scalest = :minim, gridsize = 401, range_x = extrema(x), tr
     sb = (maxx - mean(x)) / scalest
 
     gpoints = range(sa, stop = sb, length = gridsize)
-    gcounts = linbin(sx, gpoints, trun = trun)
+    gcounts = linbin(sx, gpoints; t_run)
 
     hpi = begin
         alpha = ((2 / (11 * n))^(1 / 13)) * sqrt(2)
@@ -175,7 +175,7 @@ function wand_bins(x, scalest = :minim, gridsize = 401, range_x = extrema(x), tr
     scalest * hpi
 end
 
-function linbin(X, gpoints; trun = true)
+function linbin(X, gpoints; t_run = true)
     n, M = length(X), length(gpoints)
 
     a, b = gpoints[1], gpoints[M]
@@ -192,14 +192,9 @@ function linbin(X, gpoints; trun = true)
             gcnts[li + 1] += rem
         end
 
-        if !trun
-            if lt < 1
-                gcnts[1] += 1
-            end
-
-            if li >= M
-                gcnts[M] += 1
-            end
+        if !t_run
+            lt < 1 && (gcnts[1] += 1)
+            li ≥ M && (gcnts[M] += 1)
         end
     end
     gcnts

diff --git a/docs/make.jl b/docs/make.jl
@@ -436,7 +436,7 @@ function generate_graph_attr_markdown()
             "Font size for the node labels and the edge labels.",
             "Shape of the nodes, choose from `:hexagon`, `:circle`, `:ellipse`, `:rect` or `:rectangle`.",
             "The size of nodes in the plot coordinates. Note that if `names` is not empty, then nodes will be scaled to fit the labels inside them.",
-            "The color of the nodes. If `nodecolor` is an integer, then it will be taken from the current color pallette. Otherwise, the user can pass any color that would be recognised by the Plots `color` attribute.",
+            "The color of the nodes. If `nodecolor` is an integer, then it will be taken from the current color palette. Otherwise, the user can pass any color that would be recognised by the Plots `color` attribute.",
             "The coordinates of the nodes.",
             "The method that GraphRecipes uses to produce an optimal layout, choose from `:spectral`, `:sfdp`, `:circular`, `:shell`, `:stress`, `:spring`, `:tree`, `:buchheim`, `:arcdiagram` or `:chorddiagram`. See [NetworkLayout](https://github.com/JuliaGraphs/NetworkLayout.jl) for further details.",
             "A layout algorithm that can be passed in by the user.",

diff --git a/docs/src/GraphRecipes/introduction.md b/docs/src/GraphRecipes/introduction.md
@@ -12,7 +12,7 @@ GraphRecipes can be installed with the package manager:
 ```
 
 ## Usage
-The main user interface is through the fuction `graphplot`:
+The main user interface is through the function `graphplot`:
 ```@example graphintro
 using GraphRecipes, Plots
 

diff --git a/docs/src/RecipesBase/types.md b/docs/src/RecipesBase/types.md
@@ -335,7 +335,7 @@ seriespie(rand(4, 2), layout = 2)
 ## Remarks
 
 Plot recipes and series recipes are actually very similar.
-In fact, a pie recipe could be also implemented as a plot recipe by acessing the data through `plotattributes`.
+In fact, a pie recipe could be also implemented as a plot recipe by accessing the data through `plotattributes`.
 
 ```@example types
 @recipe function f(::Type{Val{:plotpie}}, plt::AbstractPlot)

diff --git a/docs/src/attributes.md b/docs/src/attributes.md
@@ -19,7 +19,7 @@ plotattr(:Subplot)
 plotattr(:Axis)
 ```
 
-Once you acquire the list of attributes, you can either use the aliases of a specific attribute or investigate a specific attribut to print that attribute's aliases and its description.
+Once you acquire the list of attributes, you can either use the aliases of a specific attribute or investigate a specific attribute to print that attribute's aliases and its description.
 
 ```@repl attr
 # Specific Attribute Example

diff --git a/docs/src/backends.md b/docs/src/backends.md
@@ -393,7 +393,7 @@ Pros:
 - Drag & drop &Delta;-markers (measure/display &Delta;x, &Delta;y & slope).
 - Designed with larger datasets in mind.
   - Responsive even with moderate (>200k points) datasets.
-  - Confirmed to handle 2GB datsets with reasonable speed on older desktop running Windows 7 (drag+pan of data area highly discouraged).
+  - Confirmed to handle 2GB datasets with reasonable speed on older desktop running Windows 7 (drag+pan of data area highly discouraged).
 
 Cons:
 
@@ -509,7 +509,7 @@ Primary author: Tim Holy
 
 ### [Qwt](https://github.com/tbreloff/Qwt.jl)
 
-My package which wraps PyQwt.  Similar to PyPlot, it uses PyCall to convert calls to python.  Though Qwt.jl was the "first draft" of Plots, the functionality is superceded by other backends, and it's not worth my time to maintain.
+My package which wraps PyQwt.  Similar to PyPlot, it uses PyCall to convert calls to python.  Though Qwt.jl was the "first draft" of Plots, the functionality is supersded by other backends, and it's not worth my time to maintain.
 
 Primary author: Thomas Breloff