Geometry corrections, segmentization, type stability, benchmarks (Jul…

…iaGeo#69)

# Change log:
## New features
- Add a geometry correction framework with `fix` and one method, `ClosedRing()`, for it.  Others can be added in future.
- Add a `segmentize` method that corresponds to LibGEOS's density, that upsamples any geometry more complex than a line.
- Add a benchmark framework which runs quickly and well, and can plot on CI.
	- Implement proof of concept benchmarks for some functions (`simplify` and `segmentize`).
## Code changes
- Factor `reproject`'s implementation out to an extension on Proj
	- Provide a nice error hint if Proj isn't loaded and a user tries to use `reproject`.
- Since we're getting rid of Proj, also factor out the GeodesicSegments implementation for `segementize`.
- Various comment changes and documentation improvements.

Project.toml

@@ -4,28 +4,40 @@ authors = ["Anshul Singhvi <[email protected]> and contributors"]
 version = "0.0.1"
 
 [deps]
+CoordinateTransformations = "150eb455-5306-5404-9cee-2592286d6298"
+ExactPredicates = "429591f6-91af-11e9-00e2-59fbe8cec110"
 GeoInterface = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-Proj = "c94c279d-25a6-4763-9509-64d165bea63e"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
+[weakdeps]
+Proj = "c94c279d-25a6-4763-9509-64d165bea63e"
+
+[extensions]
+GeometryOpsProjExt = "Proj"
+
 [compat]
+CoordinateTransformations = "0.5, 0.6"
+ExactPredicates = "2"
 GeoInterface = "1.2"
 GeometryBasics = "0.4.7"
+LinearAlgebra = "1"
 Proj = "1"
 Statistics = "1"
 julia = "1.9"
 
 [extras]
 ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
+CoordinateTransformations = "150eb455-5306-5404-9cee-2592286d6298"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 GeoFormatTypes = "68eda718-8dee-11e9-39e7-89f7f65f511f"
 GeoJSON = "61d90e0f-e114-555e-ac52-39dfb47a3ef9"
+Proj = "c94c279d-25a6-4763-9509-64d165bea63e"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LibGEOS = "a90b1aa1-3769-5649-ba7e-abc5a9d163eb"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["ArchGDAL", "Distributions", "GeoFormatTypes", "GeoJSON", "JLD2", "LibGEOS", "Random", "Test"]
+test = ["ArchGDAL", "CoordinateTransformations", "Distributions", "GeoFormatTypes", "GeoJSON", "Proj", "JLD2", "LibGEOS", "Random", "Test"]

benchmarks/benchmark_plots.jl

@@ -0,0 +1,149 @@
+using Printf, Statistics
+using Makie, MakieThemes
+using BenchmarkTools, Chairmarks
+
+function compute_gridsize(numplts::Int, nr::Int, nc::Int)
+    # figure out how many rows/columns we need
+    if nr < 1
+        if nc < 1
+            nr = round(Int, sqrt(numplts))
+            nc = ceil(Int, numplts / nr)
+        else
+            nr = ceil(Int, numplts / nc)
+        end
+    else
+        nc = ceil(Int, numplts / nr)
+    end
+    nr, nc
+end
+
+function _prettytime(t::Real)
+    if t < 1e-6
+        value, units = t * 1e9, "ns"
+    elseif t < 1e-3
+        value, units = t * 1e6, "μs"
+    elseif t < 1
+        value, units = t * 1e3, "ms"
+    else
+        value, units = t * 1,   "s"
+    end
+    return string(@sprintf("%.1f", value), " ", units)
+end
+
+_prettytime(ts::AbstractArray{<: Real}) = _prettytime.(ts)
+
+
+function results_to_numbers(result::BenchmarkGroup, postprocess_times = Statistics.median, postprocess_numbers = identity)
+    # First, we extract the keys from the result.  
+    # It's assumed that there is only one key per result, and that it's a number.
+    numbers = identity.(collect(keys(result)))
+    @assert numbers isa AbstractVector{<: Number} """
+        Extra keys involved in the benchmark group!  
+        Provide a pure group with only numerical keys.
+        Got key types:
+        $(unique(typeof.(numbers)))
+        """
+    # We sort the numbers, and then we use them to get the results
+    sort!(numbers)
+    result_objects = getindex.((result,), numbers)
+    # Now, we get the times, and return their medians.
+    postprocessed_objects = postprocess_times.(result_objects)
+    return postprocess_numbers.(numbers), getproperty.(postprocessed_objects, :time)
+end
+
+# function plot_trials(results; title = )
+
+
+
+"""
+    plot_trials(result, title_str; theme = MakieThemes.bbc())::Figure
+This function takes `result::BenchmarkTools.BenchmarkGroup` and plots the trials.  It returns the figure.
+"""
+plot_trials(results; kwargs...) = begin
+    fig = Figure()
+    plot_trials(fig[1, 1], results; kwargs...)
+    fig
+end
+
+function plot_trials(
+        gp::Makie.GridPosition,
+        results;
+        theme = merge(deepcopy(Makie.CURRENT_DEFAULT_THEME), MakieThemes.bbc()),
+        legend_position = Makie.automatic, #(1, 1, TopRight()),
+        legend_orientation = :horizontal,
+        legend_halign = 1.0,
+        legend_valign = -0.25,
+    )
+
+    xs, ys, labels = [], [], []
+    for label in keys(results)
+        current_result = results[label]
+        if isempty(current_result)
+            @warn "ResultSet with key $label is empty, skipping."
+            continue
+        end
+        x, y = results_to_numbers(current_result)
+        push!(xs, x)
+        push!(ys, y)
+        push!(labels, label)
+    end
+
+    tag_attrs = capture_tag_attrs(results.tags)
+    tag_theme = merge(theme, tag_attrs)
+
+    lp = if legend_position isa Makie.Automatic 
+        gp.layout[gp.span.rows, gp.span.cols, TopRight()] 
+    elseif legend_position isa Tuple 
+        gp.layout[legend_position...] 
+    elseif legend_position isa Union{Makie.GridPosition, Makie.GridSubposition}
+        legend_position
+    else
+        error()
+    end
+
+    return Makie.with_theme(tag_theme) do
+        ax = Axis(
+            gp;
+            tag_attrs.Axis...,
+            xlabel = "Number of points", ylabel = "Time to calculate",
+            xscale = log10, yscale = log10, ytickformat = _prettytime,
+        ) 
+        plots = [scatterlines!(ax, x, y; label = label) for (x, y, label) in zip(xs, ys, labels)]
+        setproperty!.(getindex.(getproperty.(plots, :plots), 1), :alpha, 0.1)
+        leg = Legend(
+            lp, ax; 
+            tellwidth = legend_position isa Union{Tuple, Makie.Automatic} && (legend_position isa Makie.Automatic || length(legend_position) != 3) && legend_orientation == :vertical, 
+            tellheight = legend_position isa Union{Tuple, Makie.Automatic} && (legend_position isa Makie.Automatic || length(legend_position) != 3) && legend_orientation == :horizontal, 
+            halign = legend_halign, 
+            valign = legend_valign, 
+            orientation = legend_orientation
+        )
+        ax.xticksvisible[] = true
+        ax.xtickcolor[] = ax.xgridcolor[]
+        ax.xticklabelsvisible[] = true
+        ax.yticks[] = Makie.LogTicks(Makie.WilkinsonTicks(7; k_min = 4))
+        ax.ygridwidth[] = 0.75
+        return ax
+    end
+end
+
+const _tag_includelist = ["title", "subtitle"]
+
+function capture_tag_attrs(tags)
+    attr_dict = Attributes()
+    axis = attr_dict.Axis = Attributes()
+    for tag in tags
+        for possibility in sort(_tag_includelist; by = length)
+            if startswith(tag, possibility)
+                axis[Symbol(possibility)] = tag[(length(possibility) + 2):end]
+                break
+            end
+        end
+    end
+    return attr_dict
+end
+
+function decompose_benchmarksuite_to_2ndlevel(result)
+    # here, `result` is a BenchmarkGroup.
+
+end