Merge pull request #317 from ArnoStrouwen/docs1

Documenter 1.0 upgrade.

Author: ChrisRackauckas

.JuliaFormatter.toml

@@ -0,0 +1,2 @@
+style = "sciml"
+format_markdown = true

.github/workflows/CI.yml

@@ -3,9 +3,13 @@ on:
   pull_request:
     branches:
       - master
+    paths-ignore:
+      - 'docs/**'
   push:
     branches:
       - master
+    paths-ignore:
+      - 'docs/**'
 jobs:
   test:
     runs-on: ubuntu-latest

.github/workflows/FormatCheck.yml

@@ -0,0 +1,42 @@
+name: format-check
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'release-'
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v4
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

docs/Project.toml

@@ -10,9 +10,8 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 
 [compat]
 DifferentialEquations = "7.6"
-Documenter = "0.27"
+Documenter = "1"
 DomainSets = "0.5, 0.6"
-MethodOfLines = "0.8, 0.9"
 ModelingToolkit = "8"
 NonlinearSolve = "1"
 OrdinaryDiffEq = "6"

docs/make.jl

@@ -10,19 +10,10 @@ include("pages.jl")
 
 makedocs(sitename = "MethodOfLines.jl",
          authors = "Chris Rackauckas, Alex Jones et al.",
-         clean = true,
-         doctest = false,
-         strict = [
-             :doctest,
-             :linkcheck,
-             :parse_error,
-             :example_block,
-             # Other available options are
-             # :autodocs_block, :cross_references, :docs_block, :eval_block, :example_block, :footnote, :meta_block, :missing_docs, :setup_block,
-         ],
+         clean = true, doctest = false, linkcheck = true,
          modules = [MethodOfLines],
-         format = Documenter.HTML(analytics = "UA-90474609-3",
-                                  assets = ["assets/favicon.ico"],
+         warnonly = [:docs_block, :missing_docs, :cross_references],
+         format = Documenter.HTML(assets = ["assets/favicon.ico"],
                                   canonical = "https://docs.sciml.ai/MethodOfLines/stable/"),
          pages = pages)
 

docs/pages.jl

@@ -9,7 +9,7 @@ pages = [
         "tutorials/icbc_sampled.md",
         "tutorials/PIDE.md",
     ],
-    "Performance Tips" => "performance.md"
+    "Performance Tips" => "performance.md",
     "MOLFiniteDifference" => "MOLFiniteDifference.md",
     "Solution Interface - PDESolutions" => "solutions.md",
     "Grid and Solution Retrieval - Deprecated" => "get_grid.md",

docs/src/howitworks.md

@@ -6,7 +6,7 @@ See [here](https://github.com/SciML/MethodOfLines.jl/blob/master/src/MOL_discret
 
 Given your discretization and `PDESystem`, we take each independent variable defined on the space to be discretized and create a corresponding range. We then take each dependent variable and create an array of symbolic variables to represent it in its discretized form. This is stored in a [`DiscreteSpace`](https://github.com/SciML/MethodOfLines.jl/blob/master/src/discretization/discretize_vars.jl) object, a useful abstraction.
 
-We recognize boundary conditions, i.e. whether they are on the upper or lower ends of the domain, or periodic [here](https://github.com/SciML/MethodOfLines.jl/blob/master/src/system_parsing/bcs/parse_boundaries.jl), and use this information to construct the interior of the domain for each equation [here](https://github.com/SciML/MethodOfLines.jl/blob/master/src/system_parsing/interiormap.jl). Each PDE is matched to each dependent variable in this step by which variable is of highest order in each PDE, with precedence given to time derivatives. This dictates which boundary conditions reduce the size of the interior for which PDE. This is done to ensure that there will be the same number of equations as discrete variable states, so that the system of equations is balanced.
+We recognize boundary conditions, i.e. whether they are on the upper or lower ends of the domain, or periodic [here](https://github.com/SciML/PDEBase.jl/blob/master/src/parse_boundaries.jl), and use this information to construct the interior of the domain for each equation [here](https://github.com/SciML/MethodOfLines.jl/blob/master/src/system_parsing/interior_map.jl). Each PDE is matched to each dependent variable in this step by which variable is of highest order in each PDE, with precedence given to time derivatives. This dictates which boundary conditions reduce the size of the interior for which PDE. This is done to ensure that there will be the same number of equations as discrete variable states, so that the system of equations is balanced.
 
 Next, the boundary conditions are discretized, creating an equation for each point on the boundary in terms of the discretized variables, replacing any space derivatives in the direction of the boundary with their upwind finite difference expressions. [This](https://github.com/SciML/MethodOfLines.jl/blob/master/src/discretization/generate_bc_eqs.jl) is the place to look to see how this happens.
 

docs/src/index.md

@@ -109,26 +109,19 @@ Pkg.status(;mode = PKGMODE_MANIFEST) # hide
 ```@raw html
 </details>
 ```
-```@raw html
-You can also download the 
-<a href="
-```
 ```@eval
 using TOML
-version = TOML.parse(read("../../Project.toml",String))["version"]
-name = TOML.parse(read("../../Project.toml",String))["name"]
-link = "https://github.com/SciML/"*name*".jl/tree/gh-pages/v"*version*"/assets/Manifest.toml"
-```
-```@raw html
-">manifest</a> file and the
-<a href="
-```
-```@eval
-using TOML
-version = TOML.parse(read("../../Project.toml",String))["version"]
-name = TOML.parse(read("../../Project.toml",String))["name"]
-link = "https://github.com/SciML/"*name*".jl/tree/gh-pages/v"*version*"/assets/Project.toml"
-```
-```@raw html
-">project</a> file.
+using Markdown
+version = TOML.parse(read("../../Project.toml", String))["version"]
+name = TOML.parse(read("../../Project.toml", String))["name"]
+link_manifest = "https://github.com/SciML/" * name * ".jl/tree/gh-pages/v" * version *
+                "/assets/Manifest.toml"
+link_project = "https://github.com/SciML/" * name * ".jl/tree/gh-pages/v" * version *
+               "/assets/Project.toml"
+Markdown.parse("""You can also download the
+[manifest]($link_manifest)
+file and the
+[project]($link_project)
+file.
+""")
 ```

docs/src/performance.md

@@ -7,4 +7,4 @@ To overcome this limitation, and scale MOL to realistic physics simulations, Jul
 Whenever this package and MethodOfLines are loaded together, MOL will also load `MethodOfLinesJuliaSimCompilerExt.jl`, an extension that takes advantage of this backend to speed up your compilation and solves automatically, with the same interface you are used to. 
 
 !!! note
-    JuliaSimCompiler is part of JuliaSim and thus requires a valid JuliaSim license to use. JuliaSim is a proprietary software developed by JuliaHub Inc. Using the packages through the registry requires a valid JuliaSim license. It is free to use for non-commercial academic teaching and research purposes. For commercial users, license fees apply. Please refer to the [End User License Agreement](https://juliahub.com/company/eula/?_gl=1*120lqg6*_ga*MTAxODQ4OTE3Mi4xNjk0MDA4MDM5*_ga_8FC7JQQLXX*MTY5NDAwODAzOC4xLjEuMTY5NDAwODgxMC4wLjAuMA..) for details. Please contact [sales@juliahub.com](sales@juliahub.com) for purchasing information.
+    JuliaSimCompiler is part of JuliaSim and thus requires a valid JuliaSim license to use. JuliaSim is a proprietary software developed by JuliaHub Inc. Using the packages through the registry requires a valid JuliaSim license. It is free to use for non-commercial academic teaching and research purposes. For commercial users, license fees apply. Please refer to the [End User License Agreement](https://juliahub.com/company/eula/?_gl=1*120lqg6*_ga*MTAxODQ4OTE3Mi4xNjk0MDA4MDM5*_ga_8FC7JQQLXX*MTY5NDAwODAzOC4xLjEuMTY5NDAwODgxMC4wLjAuMA..) for details. Please contact [sales@juliahub.com](https://juliahub.com/products/pricing/) for purchasing information.