Merge pull request #5 from s-ccs/docum

Docum

Adding basic scripts for docs and tests

.github/workflows/CI.yml

@@ -0,0 +1,64 @@
+name: CI
+on:
+  push:
+      branches:
+      - main
+  pull_request:
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - run: |
+          julia --project=docs -e '
+            using Documenter: DocMeta, doctest
+            using ERPExplorer
+            DocMeta.setdocmeta!(ERPExplorer, :DocTestSetup, :(using ERPExplorer); recursive=true)
+            doctest(ERPExplorer)'
+      - run: julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/CompatHelper.yml

@@ -0,0 +1,16 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/format.yml

@@ -0,0 +1,8 @@
+name: Format suggestions
+on:
+  pull_request:
+jobs:
+  code-style:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: julia-actions/[email protected]

Project.toml

@@ -17,8 +17,12 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TopoPlots = "2bdbdf9c-dbd8-403f-947b-1a4e0dd41a7a"
 Unfold = "181c99d8-e21b-4ff3-b70b-c233eddec679"
 UnfoldMakie = "69a5ce3b-64fb-4f22-ae69-36dd4416af2a"
 UnfoldSim = "ed8ae6d2-84d3-44c6-ab46-0baf21700804"
 WGLMakie = "276b4fcb-3e11-5398-bf8b-a0c2d153d008"
+
+[compat]
+Test = "1.11.0"

docs/Project.toml

@@ -0,0 +1,10 @@
+[deps]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+DataFramesMeta = "1313f7d8-7da2-5740-9ea0-a2ca25f37964"
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+ERPExplorer = "a0936657-5da6-42c1-a2f2-44cfa89f194c"
+Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+Unfold = "181c99d8-e21b-4ff3-b70b-c233eddec679"

docs/index.md

@@ -0,0 +1,4 @@
+# ERPExplorer Highlights
+
+# ERPExplorer.jl allows interactive exploration of regression-ERPs.
+# You can switch on and off formula terms, term values, row and column faceting, line colours and style, marker style.

docs/make.jl

@@ -0,0 +1,48 @@
+using ERPExplorer
+using Documenter
+using DocStringExtensions
+
+# preload once
+
+using CairoMakie
+const Makie = CairoMakie # - for references
+using Unfold
+using DataFrames
+using DataFramesMeta
+using Literate
+using Glob
+
+GENERATED = joinpath(@__DIR__, "src", "generated")
+SOURCE = joinpath(@__DIR__, "literate")
+for subfolder ∈ ["intro"] #["how_to", "intro", "tutorials", "explanations"]
+    local SOURCE_FILES = Glob.glob(subfolder * "/*.jl", SOURCE)
+    foreach(fn -> Literate.markdown(fn, GENERATED * "/" * subfolder), SOURCE_FILES)
+end
+
+DocMeta.setdocmeta!(ERPExplorer, :DocTestSetup, :(using ERPExplorer); recursive = true)
+
+makedocs(;
+    modules = [ERPExplorer],
+    authors = "Vladimir Mikheev, Simon Danisch, Benedikt Ehinger",
+    repo = Documenter.Remotes.GitHub("s-ccs", "ERPExplorer.jl"),
+    sitename = "ERPExplorer.jl",
+    warnonly = :cross_references,
+    format = Documenter.HTML(;
+        prettyurls = get(ENV, "CI", "false") == "true",
+        canonical = "https://s-css.github.io/ERPExplorer.jl",
+        assets = String[],
+    ),
+    pages = [
+        "ERPExplorer highlights" => "index.md",
+        #"Plotting" => "generated/intro/toposeries.md",
+        #"Diagnostics" => "generated/intro/gnostics.md",
+        "API / DocStrings" => "api.md",
+    ],
+)
+
+deploydocs(;
+    repo = "github.com/s-ccs/ERPExplorer.jl",
+    devbranch = "main",
+    versions = "v#.#",
+    push_preview = true,
+)

docs/run_liveserver.jl

@@ -0,0 +1,7 @@
+using LiveServer
+servedocs(
+    skip_dir = joinpath("src", "generated"),
+    literate_dir = joinpath("literate"),
+    literate = joinpath("literate"),
+    foldername = ".",
+)

docs/src/api.md

@@ -0,0 +1,6 @@
+```@autodocs
+Modules = [ERPExplorer]
+Order   = [:function]
+```
+
+Internally, we use a `PlotConfig` struct to keep track of common plotting options, so that all functions have a similar API.

docs/src/index.md

@@ -0,0 +1,4 @@
+# ERPExplorer Highlights
+
+# ERPExplorer.jl allows interactive exploration of regression-ERPs.
+# You can switch on and off formula terms, term values, row and column faceting, line colours and style, marker style.

src/formula_extractor.jl

@@ -1,4 +1,6 @@
 const BSplineTerm = Base.get_extension(Unfold, :UnfoldBSplineKitExt).BSplineTerm
+
+
 get_sym(t::InterceptTerm) = ""
 get_sym(t::AbstractTerm) = t.sym
 get_sym(t::BSplineTerm) = t.term.sym

test/basic.jl

@@ -0,0 +1,9 @@
+dataS, evts, pos2d = gen_data()
+formulaS = @formula(0 ~ 1 + luminance + fruit + animal)
+times = range(0, length = size(dataS, 2), step = 1 ./ 100)
+model = Unfold.fit(UnfoldModel, formulaS, evts, dataS, times)
+_, positions = TopoPlots.example_data()
+
+@testset "basic test" begin
+    explore(model; positions = positions)
+end

test/runtests.jl

@@ -0,0 +1 @@
+include("setup.jl")

test/setup.jl

@@ -0,0 +1,5 @@
+using ERPExplorer
+using Test
+
+path = dirname(Base.current_project())
+include(path * "/docs/gen_data.jl")