Adding basic CI (#6)

* added dummy tests * add ci.yml * add Michael and Hendrik * add CompatHelper * add Documenter * add some docs to test the docs * add TagBot * add preview cleanup * add badges --------- Co-authored-by: Michael Schlottke-Lakemper <[email protected]> Co-authored-by: Benedict Geihe <[email protected]> Co-authored-by: Benedict <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]>
trixi-framework · Jul 16, 2024 · 1659683 · 1659683
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diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
@@ -0,0 +1,23 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: "Add CompatHelper"
+        run: |
+          import Pkg
+          Pkg.add("CompatHelper")
+        shell: julia --color=yes {0}
+
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main(; subdirs=["", "docs", "test"])
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
diff --git a/.github/workflows/DocPreviewCleanup.yml b/.github/workflows/DocPreviewCleanup.yml
@@ -0,0 +1,33 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+# Ensure that only one "Doc Preview Cleanup" workflow is force pushing at a time
+concurrency:
+  group: doc-preview-cleanup
+  cancel-in-progress: false
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+          if [ -d "${preview_dir}" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "${preview_dir}"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+          fi
+        env:
+          preview_dir: previews/PR${{ github.event.number }}
diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml
@@ -0,0 +1,50 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - 'main'
+    tags: '*'
+    paths-ignore:
+      - '.zenodo.json'
+      - '.github/workflows/ci.yml'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
+  pull_request:
+    paths-ignore:
+      - '.zenodo.json'
+      - '.github/workflows/ci.yml'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
+  workflow_dispatch:
+
+# Cancel redundant CI tests automatically
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-documentation:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+          show-versioninfo: true
+      - uses: julia-actions/cache@v2
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+          GKSwstype: 100 # To make GitHub Action work, disable showing a plot window with the GR backend of the Plots package
+      - name: Run doctests
+        run: |
+          julia --project=docs --color=yes -e '
+            using Documenter: DocMeta, doctest
+            using TrixiAtmo
+            DocMeta.setdocmeta!(TrixiAtmo, :DocTestSetup, :(using TrixiAtmo); recursive=true)
+            doctest(TrixiAtmo)'
diff --git a/.github/workflows/TagBot.yml b/.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 }}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,62 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags: ['*']
+    paths-ignore:
+      - 'LICENSE.md'
+      - 'README.md'
+      - '.zenodo.json'
+      - 'docs/**'
+  pull_request:
+    paths-ignore:
+      - 'LICENSE.md'
+      - 'README.md'
+      - '.zenodo.json'
+      - 'docs/**'
+  workflow_dispatch:
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.10'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+          show-versioninfo: true
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: Run tests
+        uses: julia-actions/julia-runtest@v1
+        with:
+          coverage: true
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v4
+        with:
+          files: lcov.info
+      - uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: ./lcov.info
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "TrixiAtmo"
 uuid = "c9ed1054-d170-44a9-8ee2-d5566f5d1389"
-authors = ["Benedict Geihe <[email protected]>"]
-version = "0.1.0"
+authors = ["Benedict Geihe <[email protected]>", "Tristan Montoya <[email protected]>", "Hendrik Ranocha <[email protected]>", "Michael Schlottke-Lakemper <[email protected]>"]
+version = "0.1.0-DEV"
 
 [deps]
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

diff --git a/README.md b/README.md
@@ -1,5 +1,18 @@
 # TrixiAtmo.jl
 
+<!--
+[![Docs-stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://trixi-framework.github.io/TrixiAtmo.jl/stable)
+-->
+[![Docs-dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://trixi-framework.github.io/TrixiAtmo.jl/dev)
+[![Slack](https://img.shields.io/badge/chat-slack-e01e5a)](https://join.slack.com/t/trixi-framework/shared_invite/zt-sgkc6ppw-6OXJqZAD5SPjBYqLd8MU~g)
+[![Build Status](https://github.com/trixi-framework/TrixiAtmo.jl/workflows/CI/badge.svg)](https://github.com/trixi-framework/TrixiAtmo.jl/actions?query=workflow%3ACI)
+[![Codecov](https://codecov.io/gh/trixi-framework/TrixiAtmo.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/trixi-framework/TrixiAtmo.jl)
+[![Coveralls](https://coveralls.io/repos/github/trixi-framework/TrixiAtmo.jl/badge.svg?branch=main)](https://coveralls.io/github/trixi-framework/TrixiAtmo.jl?branch=main)
+[![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://opensource.org/licenses/MIT)
+<!--
+[![DOI](https://zenodo.org/badge/DOI/TODO.svg)](https://doi.org/TODO)
+-->
+
 **Note: This repository is still in its alpha stage and anything might change at
 any time and without warning, including the deletion of this repository
 itself.**
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -0,0 +1,8 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
+TrixiAtmo = "c9ed1054-d170-44a9-8ee2-d5566f5d1389"
+
+[compat]
+Documenter = "1.3"
+DocumenterInterLinks = "0.3.1"
diff --git a/docs/make.jl b/docs/make.jl
@@ -0,0 +1,29 @@
+using TrixiAtmo
+using Documenter
+using DocumenterInterLinks
+
+# Provide external links to the Trixi.jl docs (project root and inventory file)
+links = InterLinks("Trixi" => ("https://trixi-framework.github.io/Trixi.jl/stable/",
+                               "https://trixi-framework.github.io/Trixi.jl/stable/objects.inv"))
+
+DocMeta.setdocmeta!(TrixiAtmo, :DocTestSetup, :(using TrixiAtmo);
+                    recursive = true)
+
+makedocs(;
+         modules = [TrixiAtmo],
+         authors = "Benedict Geihe <[email protected]>, Tristan Montoya <[email protected], Hendrik Ranocha <[email protected]>, Michael Schlottke-Lakemper <[email protected]>",
+         repo = Remotes.GitHub("trixi-framework",
+                               "TrixiAtmo.jl/blob/{commit}{path}#{line}"),
+         sitename = "TrixiAtmo.jl",
+         format = Documenter.HTML(;
+                                  prettyurls = get(ENV, "CI", "false") == "true",
+                                  canonical = "https://trixi-framework.github.io/TrixiAtmo.jl",
+                                  edit_link = "main",
+                                  assets = String[],),
+         pages = ["Home" => "index.md"],
+         plugins = [links],)
+
+deploydocs(;
+           repo = "github.com/trixi-framework/TrixiAtmo.jl",
+           devbranch = "main",
+           push_preview = true)
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -0,0 +1,14 @@
+```@meta
+CurrentModule = TrixiAtmo
+```
+
+# TrixiAtmo
+
+Documentation for [TrixiAtmo](https://github.com/trixi-framework/TrixiAtmo.jl).
+
+```@index
+```
+
+```@autodocs
+Modules = [TrixiAtmo]
+```
diff --git a/src/TrixiAtmo.jl b/src/TrixiAtmo.jl
@@ -1,3 +1,11 @@
+"""
+    🌍 TrixiAtmo 🌍
+
+**TrixiAtmo.jl** is a simulation package for atmospheric models based on
+[Trixi.jl](https://github.com/trixi-framework/Trixi.jl)
+
+See also: [trixi-framework/TrixiAtmo.jl](https://github.com/trixi-framework/TrixiAtmo.jl)
+"""
 module TrixiAtmo
 
 using Trixi
@@ -8,6 +16,10 @@ using StaticArrays: SVector
 using Static: True, False
 using LinearAlgebra: norm
 
+foo() = true
+bar() = false
+baz() = Trixi.examples_dir()
+
 include("equations/equations.jl")
 
 end # module TrixiAtmo
diff --git a/test/Project.toml b/test/Project.toml
@@ -0,0 +1,5 @@
+[deps]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[compat]
+Test = "1"
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -0,0 +1,24 @@
+using TrixiAtmo
+using Test
+
+# We run tests in parallel with CI jobs setting the `TRIXI_TEST` environment
+# variable to determine the subset of tests to execute.
+# By default, we just run the threaded tests since they are relatively cheap
+# and test a good amount of different functionality.
+const TRIXI_TEST = get(ENV, "TRIXI_TEST", "all")
+const TRIXI_MPI_NPROCS = clamp(Sys.CPU_THREADS, 2, 3)
+const TRIXI_NTHREADS = clamp(Sys.CPU_THREADS, 2, 3)
+
+@time @testset "TrixiAtmo.jl tests" begin
+    @time if TRIXI_TEST == "all"
+        @test TrixiAtmo.foo() == true
+        @test TrixiAtmo.bar() == false
+        @test TrixiAtmo.baz() isa String
+    end
+
+    @time if TRIXI_TEST == "all" || TRIXI_TEST == "upstream"
+        @testset "baz()" begin
+            @test TrixiAtmo.baz() isa String
+        end
+    end
+end