Merge pull request #118 from ArnoStrouwen/ci

ChrisRackauckas · web-flow · commit 15b06d910056 · 2024-04-07T09:01:41.000-04:00
CI
diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml
@@ -1,2 +1,3 @@
 style = "sciml"
-format_markdown = true
+format_markdown = true
+format_docstrings = true
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -5,3 +5,6 @@ updates:
     directory: "/" # Location of package manifests
     schedule:
       interval: "weekly"
+    ignore:
+      - dependency-name: "crate-ci/typos"
+        update-types: ["version-update:semver-patch", "version-update:semver-minor"]
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -10,33 +10,36 @@ on:
       - master
     paths-ignore:
       - 'docs/**'
+  schedule:
+    - cron: '25 15 * * 4'
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    env:
+      GROUP: ${{ matrix.group }}
     strategy:
+      fail-fast: false
       matrix:
         group:
           - Core
         version:
           - '1'
-          - '1.6'
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-      - uses: actions/cache@v4
-        env:
-          cache-name: cache-artifacts
+      - uses: julia-actions/cache@v1
         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 }}-
+          token: ${{ secrets.GITHUB_TOKEN }}
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+        with:
+          depwarn: error
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v4
         with:
diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
@@ -7,7 +7,8 @@ on:
       - 'release-'
     tags: '*'
   pull_request:
-
+  schedule:
+    - cron: '25 15 * * 4'
 jobs:
   build:
     runs-on: ubuntu-latest
diff --git a/.github/workflows/Downgrade.yml b/.github/workflows/Downgrade.yml
@@ -0,0 +1,43 @@
+name: Downgrade
+on:
+  pull_request:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+  schedule:
+    - cron: '25 15 * * 4'
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    env:
+      GROUP: ${{ matrix.group }}    
+    strategy:
+      fail-fast: false
+      matrix:
+        group:
+          - Core
+        version:
+          - '1'
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+      - uses: cjdoris/julia-downgrade-compat-action@v1
+        with:
+          skip: Pkg,TOML
+      - uses: julia-actions/cache@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
diff --git a/.github/workflows/SpellCheck.yml b/.github/workflows/SpellCheck.yml
@@ -0,0 +1,13 @@
+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@v3
+      - name: Check spelling
+        uses: crate-ci/typos@v1.16.23 
diff --git a/.typos.toml b/.typos.toml
@@ -0,0 +1 @@
+[default.extend-words]
diff --git a/Project.toml b/Project.toml
@@ -14,19 +14,25 @@ Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 
 [compat]
-DataStructures = "0.17, 0.18"
-DiffEqBase = "6.5"
-DocStringExtensions = "0.8, 0.9"
-Latexify = "0.14, 0.15, 0.16"
-ModelingToolkit = "7, 8, 9"
-Reexport = "0.2, 1.0"
-SciMLBase = "1.3, 2"
-julia = "1.6"
+Aqua = "0.8"
+DataStructures = "0.18.13"
+DiffEqBase = "6.144"
+DocStringExtensions = "0.9"
+InteractiveUtils = "1.10"
+Latexify = "0.16"
+LinearAlgebra = "1.10"
+ModelingToolkit = "8.74, 9"
+Reexport = "1"
+SciMLBase = "2.15"
+SpecialFunctions = "2"
+Test = "1.10"
+julia = "1.10"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["InteractiveUtils", "SpecialFunctions", "Test"]
+test = ["Aqua", "InteractiveUtils", "SpecialFunctions", "Test"]
diff --git a/docs/make.jl b/docs/make.jl
@@ -6,12 +6,12 @@ cp("./docs/Project.toml", "./docs/src/assets/Project.toml", force = true)
 include("pages.jl")
 
 makedocs(sitename = "ParameterizedFunctions.jl",
-         authors = "Chris Rackauckas",
-         modules = [ParameterizedFunctions],
-         clean = true, doctest = false, linkcheck = true,
-         format = Documenter.HTML(assets = ["assets/favicon.ico"],
-                                  canonical = "https://docs.sciml.ai/ParameterizedFunctions/stable/"),
-         pages = pages)
+    authors = "Chris Rackauckas",
+    modules = [ParameterizedFunctions],
+    clean = true, doctest = false, linkcheck = true,
+    format = Documenter.HTML(assets = ["assets/favicon.ico"],
+        canonical = "https://docs.sciml.ai/ParameterizedFunctions/stable/"),
+    pages = pages)
 
 deploydocs(repo = "github.com/SciML/ParameterizedFunctions.jl.git";
-           push_preview = true)
+    push_preview = true)
diff --git a/docs/pages.jl b/docs/pages.jl
@@ -2,5 +2,5 @@
 
 pages = [
     "Home" => "index.md",
-    "ode_def.md",
+    "ode_def.md"
 ]
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -49,16 +49,16 @@ Latexify directly works on the generated expression. Example:
 using ParameterizedFunctions, Latexify
 
 lotka_volterra = @ode_def begin
-    dx = a*x -b*x*y
-    dy = -c*y + d*x*y
+    dx = a * x - b * x * y
+    dy = -c * y + d * x * y
 end a b c d
 
 latexify(lotka_volterra.sys)
 ```
 
 Generates:
 
-```julia
+```
 L"\begin{align}
 \frac{\mathrm{d} x\left( t \right)}{\mathrm{d}t} =& a x\left( t \right) - b x\left( t \right) y\left( t \right) \\
 \frac{\mathrm{d} y\left( t \right)}{\mathrm{d}t} =&  - c y\left( t \right) + d x\left( t \right) y\left( t \right)
diff --git a/src/macros.jl b/src/macros.jl
@@ -34,13 +34,13 @@ symbolic tools.
 """
 macro ode_def(name, ex, params...)
     opts = Dict{Symbol, Bool}(:build_tgrad => true,
-                              :build_jac => true,
-                              :build_expjac => false,
-                              :build_invjac => false,
-                              :build_invW => false,
-                              :build_hes => false,
-                              :build_invhes => false,
-                              :build_dpfuncs => true)
+        :build_jac => true,
+        :build_expjac => false,
+        :build_invjac => false,
+        :build_invW => false,
+        :build_hes => false,
+        :build_invhes => false,
+        :build_dpfuncs => true)
     name isa Expr ? ode_def_opts(gensym(), opts, __module__, name, ex, params...) :
     ode_def_opts(name, opts, __module__, ex, params...)
 end
@@ -57,13 +57,13 @@ See the `@ode_def` docstring for more details.
 """
 macro ode_def_bare(name, ex, params...)
     opts = Dict{Symbol, Bool}(:build_tgrad => false,
-                              :build_jac => false,
-                              :build_expjac => false,
-                              :build_invjac => false,
-                              :build_invW => false,
-                              :build_hes => false,
-                              :build_invhes => false,
-                              :build_dpfuncs => false)
+        :build_jac => false,
+        :build_expjac => false,
+        :build_invjac => false,
+        :build_invW => false,
+        :build_hes => false,
+        :build_invhes => false,
+        :build_dpfuncs => false)
     name isa Expr ? ode_def_opts(gensym(), opts, __module__, name, ex, params...) :
     ode_def_opts(name, opts, __module__, ex, params...)
 end
@@ -80,13 +80,13 @@ See the `@ode_def` docstring for more details.
 """
 macro ode_def_all(name, ex, params...)
     opts = Dict{Symbol, Bool}(:build_tgrad => true,
-                              :build_jac => true,
-                              :build_expjac => false,
-                              :build_invjac => false,
-                              :build_invW => true,
-                              :build_hes => false,
-                              :build_invhes => false,
-                              :build_dpfuncs => true)
+        :build_jac => true,
+        :build_expjac => false,
+        :build_invjac => false,
+        :build_invW => true,
+        :build_hes => false,
+        :build_invhes => false,
+        :build_dpfuncs => true)
     name isa Expr ? ode_def_opts(gensym(), opts, __module__, name, ex, params...) :
     ode_def_opts(name, opts, __module__, ex, params...)
 end
diff --git a/src/ode_def_opts.jl b/src/ode_def_opts.jl
@@ -7,7 +7,7 @@ findreplace(ex, dict) = ex
 """
 ```julia
 ode_def_opts(name::Symbol, opts::Dict{Symbol, Bool}, curmod, ex::Expr, params...;
-             depvar = :t)
+    depvar = :t)
 ```
 
 The core internal. Users should only interact with this through the `@ode_def_*` macros.
@@ -30,18 +30,18 @@ Example:
 
 ```julia
 opts = Dict{Symbol, Bool}(:build_tgrad => true,
-                          :build_jac => true,
-                          :build_expjac => false,
-                          :build_invjac => true,
-                          :build_invW => true,
-                          :build_invW_t => true,
-                          :build_hes => false,
-                          :build_invhes => false,
-                          :build_dpfuncs => true)
+    :build_jac => true,
+    :build_expjac => false,
+    :build_invjac => true,
+    :build_invW => true,
+    :build_invW_t => true,
+    :build_hes => false,
+    :build_invhes => false,
+    :build_dpfuncs => true)
 ```
 """
 function ode_def_opts(name::Symbol, opts::Dict{Symbol, Bool}, curmod, ex::Expr, params...;
-                      depvar = :t)
+        depvar = :t)
     # depvar is the dependent variable. Defaults to t
     # M is the mass matrix in RosW, must be a constant!
 
@@ -191,8 +191,8 @@ function ode_def_opts(name::Symbol, opts::Dict{Symbol, Bool}, curmod, ex::Expr,
         $full_wex
 
         $name($fname, ParameterizedFunctions.LinearAlgebra.I, nothing, $tname, $jname,
-              nothing, nothing,
-              nothing, nothing, $Wname, $W_tname, nothing, $syms, $(Meta.quot(depvar)),
-              nothing, $sys)
+            nothing, nothing,
+            nothing, nothing, $Wname, $W_tname, nothing, $syms, $(Meta.quot(depvar)),
+            nothing, $sys)
     end |> esc
 end
diff --git a/test/qa.jl b/test/qa.jl
@@ -0,0 +1,12 @@
+using ParameterizedFunctions, Aqua
+@testset "Aqua" begin
+    Aqua.find_persistent_tasks_deps(ParameterizedFunctions)
+    Aqua.test_ambiguities(ParameterizedFunctions, recursive = false)
+    Aqua.test_deps_compat(ParameterizedFunctions)
+    Aqua.test_piracies(ParameterizedFunctions,
+        treat_as_own = [ParameterizedFunctions.SciMLBase.AbstractParameterizedFunction])
+    Aqua.test_project_extras(ParameterizedFunctions)
+    Aqua.test_stale_deps(ParameterizedFunctions)
+    Aqua.test_unbound_args(ParameterizedFunctions)
+    Aqua.test_undefined_exports(ParameterizedFunctions, broken = true)
+end
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -3,6 +3,8 @@ using Test, InteractiveUtils, Latexify
 
 using SpecialFunctions
 
+include("./qa.jl")
+
 ### ODE Macros
 
 println("Build some examples")

Original file line number	Diff line number	Diff line change
`@@ -2,5 +2,5 @@`
`2`	`2`
`3`	`3`	`pages = [`
`4`	`4`	`"Home" => "index.md",`
`5`		`- "ode_def.md",`
	`5`	`+ "ode_def.md"`
`6`	`6`	`]`