Port to BestieTemplate

.JuliaFormatter.toml

@@ -0,0 +1,3 @@
+indent = 4
+# margin = 92
+normalize_line_endings = "unix"

.copier-answers.yml

@@ -0,0 +1,40 @@
+# Changes here will be overwritten by Copier
+AddAllcontributors: false
+AddCitationCFF: false
+AddCodeOfConduct: false
+AddContributionDocs: false
+AddCopierCI: false
+AddDocs: true
+AddDocsCI: true
+AddFormatterAndLinterConfigFiles: true
+AddGitHubPRTemplate: true
+AddGitHubTemplates: false
+AddLintCI: true
+AddLychee: true
+AddMacToCI: true
+AddPrecommit: true
+AddPrecommitUpdateCI: false
+AddTagBotCI: true
+AddTestCI: true
+AddWinToCI: true
+Authors: Gabriel Weymouth <gabriel.weymouth@gmail.com>
+CheckExplicitImports: false
+ConfigIndentation: 2
+GitHubActionVersionAutoUpdate: dependabot
+JuliaCompatAutoUpdate: dependabot
+JuliaIndentation: 4
+JuliaMinCIVersion: '1.11'
+JuliaMinVersion: '1.10'
+License: MIT
+LicenseCopyrightHolders: Gabriel Weymouth
+MarkdownIndentation: 2
+PackageName: WaterLily
+PackageOwner: WaterLily-jl
+PackageUUID: ed894a53-35f9-47f1-b17f-85db9237eebd
+RunJuliaNightlyOnCI: false
+StrategyConfirmIncluded: true
+StrategyLevel: 2
+StrategyReviewExcluded: true
+TestingStrategy: testitem_basic
+UseCirrusCI: false
+_src_path: /home/b-fg/.julia/packages/BestieTemplate/hXGfI

.editorconfig

@@ -0,0 +1,18 @@
+# https://editorconfig.org
+root = true
+
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+indent_style = space
+trim_trailing_whitespace = true
+
+[*.jl]
+indent_size = 4
+
+[*.md]
+indent_size = 2
+
+[*.{yml,toml,json}]
+indent_size = 2

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,25 @@
+<!--
+Thanks for making a pull request to WaterLily.jl.
+We have added this PR template to help you help us.
+See the comments below, fill the required fields, and check the items.
+-->
+
+## Related issues
+
+<!-- We normally work with (i) create issue; (ii) discussion if necessary; (iii) create PR. So, at least one of the following should be true:-->
+
+<!-- Option 1, this closes an existing issue. Fill the number below-->
+Closes #
+
+<!-- Option 2, this is a small fix that arguably won't need an issue. Uncomment below -->
+<!--
+There is no related issue.
+-->
+
+## Checklist
+
+<!-- mark true if NA -->
+<!-- leave PR as draft until all is checked -->
+- [ ] Tests are passing
+- [ ] Lint workflow is passing
+- [ ] Docs were updated and workflow is passing

.github/dependabot.yml

@@ -4,4 +4,12 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/" # Location of package manifests
     schedule:
-      interval: "monthly"
+      interval: "weekly"
+  - package-ecosystem: "julia"
+    directories:
+      - "/"
+      - "/docs"
+      - "/test"
+    schedule:
+      interval: "weekly"
+

.github/workflows/Docs.yml

@@ -0,0 +1,57 @@
+name: Docs
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "docs/**"
+      - "src/**"
+      - "*.toml"
+    tags: ["*"]
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "docs/**"
+      - "src/**"
+      - "*.toml"
+    types: [opened, synchronize, reopened]
+
+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:
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: "1"
+      - name: Use Julia cache
+        uses: julia-actions/cache@v5
+      - name: Instantiate environment with development version of the package
+        run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - name: Run doctest
+        run: |
+          julia --project=docs -e '
+            using Documenter: DocMeta, doctest
+            using WaterLily
+            DocMeta.setdocmeta!(WaterLily, :DocTestSetup, :(using WaterLily); recursive=true)
+            doctest(WaterLily)'
+      - name: Generate and deploy documentation
+        run: julia --project=docs docs/make.jl
+        env:
+          JULIA_PKG_SERVER: ""
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988

.github/workflows/Lint.yml

@@ -0,0 +1,62 @@
+name: Lint
+
+on:
+  push:
+    branches:
+      - main
+    tags: ["*"]
+  pull_request:
+
+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:
+
+  lint:
+    name: Linting
+    runs-on: ubuntu-latest
+    steps:
+      - name: Clone
+        uses: actions/checkout@v6
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: "1"
+      - name: Use Julia cache
+        uses: julia-actions/cache@v5
+      - name: Install Julia packages
+        run: julia -e 'using Pkg; pkg"add JuliaFormatter"'
+      - name: Hack for setup-python cache # https://github.com/actions/setup-python/issues/807
+        run: touch requirements.txt
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          cache: "pip"
+          python-version: "3.11"
+      - name: Hack for setup-python cache # https://github.com/actions/setup-python/issues/807
+        run: rm requirements.txt
+      - name: Cache pre-commit
+        uses: actions/cache@v5
+        with:
+          path: ~/.cache/pre-commit
+          key: ${{ runner.os }}-pre-commit-${{ hashFiles('**/.pre-commit-config.yaml') }}
+      - name: Install pre-commit
+        run: pip install pre-commit
+      - name: Run pre-commit
+        run: SKIP=no-commit-to-branch pre-commit run -a
+  link-checker:
+    name: Link checker
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Link Checker
+        id: lychee
+        uses: lycheeverse/lychee-action@v2
+        with:
+          fail: true
+          args: --config '.lychee.toml' .
+

.github/workflows/ReusableTest.yml

@@ -0,0 +1,63 @@
+name: Reusable test
+
+on:
+  workflow_call:
+    inputs:
+      version:
+        required: false
+        type: string
+        default: "1"
+      os:
+        required: false
+        type: string
+        default: ubuntu-latest
+      arch:
+        required: false
+        type: string
+        default: x64
+      allow_failure:
+        required: false
+        type: boolean
+        default: false
+      run_codecov:
+        required: false
+        type: boolean
+        default: false
+    secrets:
+      codecov_token:
+        required: true
+
+jobs:
+  test:
+    name: Julia ${{ inputs.version }} - ${{ inputs.os }} - ${{ inputs.arch }} - ${{ github.event_name }}
+    runs-on: ${{ inputs.os }}
+    continue-on-error: ${{ inputs.allow_failure }}
+
+    steps:
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ inputs.version }}
+          arch: ${{ inputs.arch }}
+      - name: Use Julia cache
+        uses: julia-actions/cache@v5
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: WaterLily tests
+        env:
+          JULIA_NUM_THREADS: ${{ matrix.nthreads }}
+        shell: bash
+        run: |
+          if [ "${{ matrix.nthreads }}" = "auto" ]
+          then
+            printf "[WaterLily]\nbackend = \"KernelAbstractions\"" > LocalPreferences.toml
+          else
+            printf "[WaterLily]\nbackend = \"SIMD\"" > LocalPreferences.toml
+          fi
+          julia --proj --color=yes -e "using Pkg; Pkg.instantiate(); Pkg.test(; coverage=true);"
+      - uses: julia-actions/julia-processcoverage@v1
+        if: ${{ inputs.run_codecov }}
+      - uses: codecov/codecov-action@v4
+        if: ${{ inputs.run_codecov }}
+        with:
+          file: lcov.info
+          token: ${{ secrets.codecov_token }}

.github/workflows/TagBot.yml

@@ -1,9 +1,29 @@
 name: TagBot
+
 on:
   issue_comment:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        type: number
+        default: 3
+
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
@@ -12,4 +32,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          ssh: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/Test.yml

@@ -0,0 +1,52 @@
+name: Test
+
+on:
+  pull_request:
+    paths:
+      - '.github/workflows/ci.yml'
+      - 'ext/**'
+      - 'src/**'
+      - 'test/**'
+      - 'Project.toml'
+  push:
+    branches:
+      - master
+    tags: '*'
+    paths:
+      - '.github/workflows/ci.yml'
+      - 'ext/**'
+      - 'src/**'
+      - 'test/**'
+      - 'Project.toml'
+  workflow_dispatch:
+
+jobs:
+  test:
+    uses: ./.github/workflows/ReusableTest.yml
+    with:
+      os: ${{ matrix.os }}
+      version: ${{ matrix.version }}
+      arch: ${{ matrix.arch }}
+      allow_failure: ${{ matrix.allow_failure }}
+      run_codecov: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' }}
+    secrets:
+      codecov_token: ${{ secrets.CODECOV_TOKEN }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.11'
+          - '1.12'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+        nthreads:
+          - '1'
+          - 'auto'
+        exclude:
+          - os: macOS-latest
+            arch: x86
+        allow_failure: [false]