CI improvements (#63)

* add format and spellcheck CI * more CI * YAS Style * fix arch * wrap tests into testsets * typos * formatter tweak * bump Julia compat * drop macos from testing
MakieOrg · Nov 18, 2024 · 07a95ea · 07a95ea
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diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml
@@ -0,0 +1 @@
+style = "yas"
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -13,29 +13,29 @@ concurrency:
   cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         version:
           - '1'
+          - 'min'
         os:
           - ubuntu-latest
-        arch:
-          - x64
+        #   - macos-latest # segfaults at the end of testing due to Python things
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
       - uses: julia-actions/cache@v2
         with:
           cache-registries: "true"
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - name: Percy Upload
+        if: ${{ matrix.version }} == '1' && ${{ matrix.os }} == 'ubuntu-latest'
         run: 'npx @percy/cli upload ./test/test_images'
         env:
           PERCY_TOKEN: ${{ secrets.PERCY_TOKEN }}

diff --git a/.github/workflows/formatcheck.yml b/.github/workflows/formatcheck.yml
@@ -0,0 +1,49 @@
+---
+name: Style Guide
+on:
+  push:
+    branches:
+      - master
+      - main
+      - /^release-.*$/
+    tags: ["*"]
+    paths:
+      - "**/*.jl"
+      - ".github/workflows/FormatCheck.yml"
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    paths:
+      - "**/*.jl"
+      - ".github/workflows/FormatCheck.yml"
+jobs:
+  format-check:
+    name: Julia
+    # These permissions are needed to:
+    # - Delete old caches: https://github.com/julia-actions/cache#usage
+    # - Post formatting suggestions: https://github.com/reviewdog/action-suggester#required-permissions
+    permissions:
+      actions: write
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: "1"
+      - uses: julia-actions/cache@v2
+      - name: Install JuliaFormatter
+        shell: julia --project=@format --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.add(PackageSpec(; name="JuliaFormatter", version="1"))
+      - name: Check formatting
+        shell: julia --project=@format --color=yes {0}
+        run: |
+          using JuliaFormatter
+          format(".", YASStyle(); verbose=true) || exit(1)
+      # Add formatting suggestions to non-draft PRs even if when "Check formatting" fails
+      - uses: reviewdog/action-suggester@185c9c06d0a28fbe43b50aca4b32777b649e7cbd # v1.12.0
+        if: ${{ !cancelled() && github.event_name == 'pull_request' && github.event.pull_request.draft == false }}
+        with:
+          tool_name: JuliaFormatter
diff --git a/.github/workflows/spellcheck.yml b/.github/workflows/spellcheck.yml
@@ -0,0 +1,21 @@
+# adapted from https://github.com/JuliaDocs/Documenter.jl/blob/master/.github/workflows/SpellCheck.yml
+# see docs at https://github.com/crate-ci/typos
+name: Spell Check
+on: [pull_request]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v4
+      - name: Check spelling
+        uses: crate-ci/typos@b74202f74b4346efdbce7801d187ec57b266bac8 # v1.27.3
+        with:
+            config: _typos.toml
+            write_changes: true
+      - uses: reviewdog/action-suggester@v1
+        with:
+          tool_name: Typos
+          fail_on_error: true
diff --git a/Project.toml b/Project.toml
@@ -31,10 +31,11 @@ PrecompileTools = "1"
 ScatteredInterpolation = "0.3.6"
 Statistics = "1"
 Test = "1"
-julia = "1.6"
+julia = "1.10"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
+# See test/Project.toml!!
 [targets]
 test = ["Test"]
diff --git a/_typos.toml b/_typos.toml
@@ -0,0 +1,3 @@
+[default.extend-words]
+# don't current this name
+Shepard = "Shepard"
diff --git a/assets/write_template-positions-bin.jl b/assets/write_template-positions-bin.jl
@@ -1,13 +1,14 @@
 using PyMNE, PythonCall, TopoPlots
-channels = ["fp1", "f3", "c3", "p3", "o1", "f7", "t3", "t5", "fz", "cz", "pz", "fp2", "f4", "c4", "p4", "o2", "f8", "t4", "t6"]
+channels = ["fp1", "f3", "c3", "p3", "o1", "f7", "t3", "t5", "fz", "cz", "pz", "fp2", "f4",
+            "c4", "p4", "o2", "f8", "t4", "t6"]
 info = pycall(PyMNE.mne.create_info, PyObject, channels, 120.0; ch_types="eeg")
 info.set_montage("standard_1020"; match_case=false)
 layout = PyMNE.mne.find_layout(info)
-write(TopoPlots.assetpath("layout_10_20.bin"),  hcat(layout.pos[:, 1], layout.pos[:, 2]))
+write(TopoPlots.assetpath("layout_10_20.bin"), hcat(layout.pos[:, 1], layout.pos[:, 2]))
 
 #---
 
-using CSV,DataFrames
+using CSV, DataFrames
 
-loc2d = CSV.read(TopoPlots.assetpath("1005.tsv"),DataFrame) # taken from https://github.com/sappelhoff/eeg_positions/blob/main/data/Fpz-T8-Oz-T7/standard_1005_2D.tsv
-write(TopoPlots.assetpath("layout_10_05.bin"),hcat(loc2d.x,loc2d.y))
+loc2d = CSV.read(TopoPlots.assetpath("1005.tsv"), DataFrame) # taken from https://github.com/sappelhoff/eeg_positions/blob/main/data/Fpz-T8-Oz-T7/standard_1005_2D.tsv
+write(TopoPlots.assetpath("layout_10_05.bin"), hcat(loc2d.x, loc2d.y))
diff --git a/docs/make.jl b/docs/make.jl
@@ -6,25 +6,20 @@ using TopoPlots: CHANNEL_TO_POSITION_10_05, CHANNEL_TO_POSITION_10_20
 DocMeta.setdocmeta!(TopoPlots, :DocTestSetup, :(using TopoPlots); recursive=true)
 
 makedocs(;
-    modules=[TopoPlots],
-    authors="Benedikt Ehinger, Simon Danisch, Beacon Biosignals",
-    sitename="TopoPlots.jl",
-    checkdocs=:exports,
-    format=Documenter.HTML(;
-        prettyurls=get(ENV, "CI", "false") == "true",
-        canonical="https://MakieOrg.github.io/TopoPlots.jl",
-        assets=String[],
-    ),
-    pages=[
-        "Home" => "index.md",
-        "General TopoPlots" => "general.md",
-        "EEG" => "eeg.md",
-        "Function reference" => "functions.md",
-        "Interpolator reference images" => "interpolator_reference.md"
-    ],
-)
+         modules=[TopoPlots],
+         authors="Benedikt Ehinger, Simon Danisch, Beacon Biosignals",
+         sitename="TopoPlots.jl",
+         checkdocs=:exports,
+         format=Documenter.HTML(;
+                                prettyurls=get(ENV, "CI", "false") == "true",
+                                canonical="https://MakieOrg.github.io/TopoPlots.jl",
+                                assets=String[],),
+         pages=["Home" => "index.md",
+                "General TopoPlots" => "general.md",
+                "EEG" => "eeg.md",
+                "Function reference" => "functions.md",
+                "Interpolator reference images" => "interpolator_reference.md"],)
 
 deploydocs(;
-    repo="github.com/MakieOrg/TopoPlots.jl",
-    devbranch="master", push_preview=true
-)
+           repo="github.com/MakieOrg/TopoPlots.jl",
+           devbranch="master", push_preview=true)
diff --git a/docs/src/topo_series.jl b/docs/src/topo_series.jl
@@ -6,39 +6,35 @@ using InteractiveUtils
 
 # ╔═╡ 2fafb0da-f3a9-11ec-0ddf-6725344070fe
 begin
-using Pkg
-Pkg.activate("../../devEnv") # docs
-#Pkg.add("PyMNE")
-#Pkg.add(path="../../../TopoPlotsjl/")
-Pkg.develop(path="../../../TopoPlotsjl/")
-#Pkg.add("DataFrames")
-#Pkg.add("AlgebraOfGraphics")
-	#Pkg.add("StatsBase")
-	#Pkg.add("CategoricalArrays")
-
-	#Pkg.add("JLD2")
-	
-	#Pkg.add("CairoMakie")
+    using Pkg
+    Pkg.activate("../../devEnv") # docs
+    #Pkg.add("PyMNE")
+    #Pkg.add(path="../../../TopoPlotsjl/")
+    Pkg.develop(; path="../../../TopoPlotsjl/")
+    #Pkg.add("DataFrames")
+    #Pkg.add("AlgebraOfGraphics")
+    #Pkg.add("StatsBase")
+    #Pkg.add("CategoricalArrays")
+
+    #Pkg.add("JLD2")
+
+    #Pkg.add("CairoMakie")
 end
 
 # ╔═╡ c4a25915-c7f5-453a-a4f0-4b40ebedea4c
 using Revise
 
 # ╔═╡ 59b87673-02d2-4deb-90be-74d923d170eb
-	using TopoPlots
-
+using TopoPlots
 
 # ╔═╡ 452a245c-773a-4303-a970-f2592c3e879f
 begin
-	#using TopoPlots
-	#using ../../../Topoplotsjl
-	using CairoMakie
-	using DataFrames
-
-
+    #using TopoPlots
+    #using ../../../Topoplotsjl
+    using CairoMakie
+    using DataFrames
 end
 
-
 # ╔═╡ 77dc1ba9-9484-485b-a49d-9aa231ef4983
 using Statistics
 
@@ -56,54 +52,59 @@ revise(TopoPlots)
 
 # ╔═╡ f4b81740-d907-42ae-a0df-f46fb2f2cb15
 begin
+    data = Array{Float32}(undef, 64, 400, 3)
+    #read!(TopoPlots.assetpath("example-data.bin"), data)
+    read!(splitdir(pathof(TopoPlots))[1] * "/../assets/example-data.bin", data)
 
-data = Array{Float32}(undef, 64, 400, 3)
-#read!(TopoPlots.assetpath("example-data.bin"), data)
-	read!(splitdir(pathof(TopoPlots))[1]*"/../assets/example-data.bin",data)
-
-positions = Vector{Point2f}(undef, 64)
-	read!(splitdir(pathof(TopoPlots))[1]*"/../assets/layout64.bin",positions)
-#read!(TopoPlots.assetpath("layout64.bin"), positions)
-
-end;
+    positions = Vector{Point2f}(undef, 64)
+    read!(splitdir(pathof(TopoPlots))[1] * "/../assets/layout64.bin", positions)
+    #read!(TopoPlots.assetpath("layout64.bin"), positions)
 
+end;
 
 # ╔═╡ 42f7755b-80f4-4185-8d21-42e11730e0fc
 begin
-	using Random
-	pos = positions[1:10]
-eeg_topoplot(rand(MersenneTwister(1),length(pos)), string.(1:length(pos));positions=pos,pad_value=0.)
+    using Random
+    pos = positions[1:10]
+    eeg_topoplot(rand(MersenneTwister(1), length(pos)), string.(1:length(pos));
+                 positions=pos, pad_value=0.0)
 end
 
 # ╔═╡ aad784ee-6bb7-4f3c-8444-be050456ddea
-eeg_topoplot(data[:, 340, 1], string.(1:length(positions));positions=positions)
+eeg_topoplot(data[:, 340, 1], string.(1:length(positions)); positions=positions)
 
 # ╔═╡ 237e4f4a-cdf2-4bac-8096-de8050251745
-eeg_topoplot(data[:, 340, 1], string.(1:length(positions));positions=positions,pad_value=0.1)
+eeg_topoplot(data[:, 340, 1], string.(1:length(positions)); positions=positions,
+             pad_value=0.1)
 
 # ╔═╡ f522329b-3653-4059-9955-8cd05570e923
-topoplot(rand(MersenneTwister(1),length(pos)),pos)
+topoplot(rand(MersenneTwister(1), length(pos)), pos)
 
 # ╔═╡ a9d2a2e2-6c8c-4cfc-9fed-b5e082cb44af
 let
-mon = PyMNE.channels.make_standard_montage("standard_1020")
-
-posMat = (Matrix(hcat(pos...)).-0.5).*0.5
-	#pos = PyMNE.channels.make_eeg_layout(mon).pos
-PyMNE.viz.plot_topomap(rand(MersenneTwister(1),length(pos)),posMat',cmap="RdBu_r",extrapolate="box",border=-1)
+    mon = PyMNE.channels.make_standard_montage("standard_1020")
+
+    posMat = (Matrix(hcat(pos...)) .- 0.5) .* 0.5
+    #pos = PyMNE.channels.make_eeg_layout(mon).pos
+    PyMNE.viz.plot_topomap(rand(MersenneTwister(1), length(pos)), posMat'; cmap="RdBu_r",
+                           extrapolate="box", border=-1)
 end
 
 # ╔═╡ c358633f-8d18-4c5e-80f7-ab972e8860be
 Pkg.status("TopoPlots")
 
 # ╔═╡ c0a2ad2e-ccce-4e80-b52c-75f1428ed182
-e1eg_topoplot(data[:, 340, 1], string.(1:length(positions));positions=positions,interpolation = TopoPlots.NormalMixtureInterpolator() )
+e1eg_topoplot(data[:, 340, 1], string.(1:length(positions)); positions=positions,
+              interpolation=TopoPlots.NormalMixtureInterpolator())
 
 # ╔═╡ d7620a42-d54c-4244-a820-d15aecdae626
-@time TopoPlots.eeg_topoplot_series(data[:,:,1],40;topoplotCfg=(positions=positions,label_scatter=false))
+@time TopoPlots.eeg_topoplot_series(data[:, :, 1], 40;
+                                    topoplotCfg=(positions=positions, label_scatter=false))
 
 # ╔═╡ ec59c704-ae33-4a62-82ce-63acc6b17793
-f, ax, pl = TopoPlots.eeg_topoplot(1:length(TopoPlots.CHANNELS_10_20),TopoPlots.CHANNELS_10_20; interpolation=TopoPlots.NullInterpolator(),)
+f, ax, pl = TopoPlots.eeg_topoplot(1:length(TopoPlots.CHANNELS_10_20),
+                                   TopoPlots.CHANNELS_10_20;
+                                   interpolation=TopoPlots.NullInterpolator(),)
 
 # ╔═╡ f3d1f3cc-f7c9-4ef4-ba4f-3d32f2509cad
 let
@@ -124,36 +125,36 @@ let
     minx, miny = minimum(rect)
     maxx, maxy = maximum(rect)
     # recreate the coordinates of the data
-    x = range(minx, maxx, length=size(m, 1))
-    y = range(miny, maxy, length=size(m, 2))
+    x = range(minx, maxx; length=size(m, 1))
+    y = range(miny, maxy; length=size(m, 2))
     xys = Point2f.(x, y')
 
     # find the highest point
     _, i = findmax(x -> isnan(x) ? -Inf : x, m)
     xy = xys[i]
-	@show peak_xy
-	@show xy
+    @show peak_xy
+    @show xy
     #@test isapprox(xy, peak_xy; atol=0.02)
-	@show isapprox(xy, peak_xy; atol=0.02)
-	fig
+    @show isapprox(xy, peak_xy; atol=0.02)
+    fig
 end
 
 # ╔═╡ 872ac6a4-ddaa-4dfb-a40d-9d5ea55bdb3d
 let
-	f = Figure()
-	axis = Axis(f[1, 1], aspect = 1)
-	xlims!(low = -2, high = 2)
-	ylims!(low = -2, high = 2)
-	
-	data = [0, 0, 0]
-	pos1 = [Point2f(-1, -1), Point2f(-1.0, 0.0), Point2f(0, -1)]
-	pos2 = [Point2f(1, 1), Point2f(1.0, 0.0), Point2f(0, 1)]
-
-	pos1 = pos1 .- mean(pos1)
-	pos2 = pos2 .- mean(pos2)
-	eeg_topoplot!(axis, data, positions=pos1)
-	eeg_topoplot!(axis, data, positions=pos2)
-	f
+    f = Figure()
+    axis = Axis(f[1, 1]; aspect=1)
+    xlims!(; low=-2, high=2)
+    ylims!(; low=-2, high=2)
+
+    data = [0, 0, 0]
+    pos1 = [Point2f(-1, -1), Point2f(-1.0, 0.0), Point2f(0, -1)]
+    pos2 = [Point2f(1, 1), Point2f(1.0, 0.0), Point2f(0, 1)]
+
+    pos1 = pos1 .- mean(pos1)
+    pos2 = pos2 .- mean(pos2)
+    eeg_topoplot!(axis, data; positions=pos1)
+    eeg_topoplot!(axis, data; positions=pos2)
+    f
 end
 
 # ╔═╡ Cell order: