rebase

.JuliaFormatter.toml

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

.buildkite/0_webui.yml

@@ -0,0 +1,10 @@
+steps:
+  - label: ":pipeline:"
+    plugins:
+      - staticfloat/cryptic#v2:
+          signed_pipelines:
+            - pipeline: .buildkite/pipeline.yml
+              signature_file: .buildkite/pipeline.yml.signature
+    command: "true"
+    agents:
+      queue: "juliaecosystem"

.buildkite/cryptic_repo_keys/.gitignore

@@ -0,0 +1,7 @@
+
+# Ignore the unencrypted repo_key
+repo_key
+
+# Ignore any agent keys (public or private) we have stored
+agent_key*
+

.buildkite/pipeline.yml

@@ -0,0 +1,29 @@
+steps:
+  - label: "Build and Deploy Documentation"
+    env:
+      BUILDKITE_PLUGIN_CRYPTIC_BASE64_SIGNED_JOB_ID_SECRET: ${BUILDKITE_PLUGIN_CRYPTIC_BASE64_SIGNED_JOB_ID_SECRET?}
+    plugins:
+      - staticfloat/cryptic#v2:
+          variables:
+            - DOCUMENTER_KEY="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"
+      - staticfloat/ssh-agent:
+          keyvars:
+            - "DOCUMENTER_KEY"
+      - JuliaCI/julia#v1:
+          version: "1.10"
+      - staticfloat/sandbox#v2:
+          rootfs_url: "https://github.com/JuliaCI/rootfs-images/releases/download/v5.45/aws_uploader.x86_64.tar.gz"
+          rootfs_treehash: "8f1a718279b12f889395723b856fc868a8890dfa"
+          workspaces:
+            # Include `/cache` so that `julia` install can properly cache its Julia downloads
+            - "/cache:/cache"
+
+    command: |
+      julia --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      git config user.name buildkite
+      git config user.email [email protected]
+      julia --project=docs docs/make.jl
+    agents:
+      queue: "juliaecosystem"
+      arch: "x86_64"
+      sandbox_capable: true

.buildkite/pipeline.yml.signature

@@ -0,0 +1 @@
+Salted__��t\�������ryM?�*�K����C�)��S8���2$~,\3�H�LT��e��2s)^tR�ų��{�M-9$�b��gwK�

.github/workflows/Downstream.yml

@@ -14,19 +14,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        julia-version: [1,1.6]
+        julia-version: [1]
         os: [ubuntu-latest]
         package:
           - {user: SciML, repo: PDESystemLibrary.jl, group: MOL}
     steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.julia-version }}
           arch: x64
       - uses: julia-actions/julia-buildpkg@latest
       - name: Clone Downstream
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: ${{ matrix.package.user }}/${{ matrix.package.repo }}
           path: downstream
@@ -48,6 +48,8 @@ jobs:
             exit(0)  # Exit immediately, as a success
           end
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v5
         with:
-          file: lcov.info
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

.github/workflows/FormatCheck.yml

@@ -0,0 +1,13 @@
+name: "Format Check"
+
+on:
+  push:
+    branches:
+      - 'master'
+    tags: '*'
+  pull_request:
+
+jobs:
+  format-check:
+    name: "Format Check"
+    uses: "SciML/.github/.github/workflows/format-suggestions-on-pr.yml@v1"

.github/workflows/Invalidations.yml

@@ -1,4 +1,4 @@
-name: Invalidations
+name: "Invalidations"
 
 on:
   pull_request:
@@ -10,31 +10,8 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  evaluate:
-    # Only run on PRs to the default branch.
-    # In the PR trigger above branches can be specified only explicitly whereas this check should work for master, main, or any other default branch
-    if: github.base_ref == github.event.repository.default_branch
-    runs-on: ubuntu-latest
-    steps:
-    - uses: julia-actions/setup-julia@v1
-      with:
-        version: '1'
-    - uses: actions/checkout@v3
-    - uses: julia-actions/julia-buildpkg@v1
-    - uses: julia-actions/julia-invalidations@v1
-      id: invs_pr
-
-    - uses: actions/checkout@v3
-      with:
-        ref: ${{ github.event.repository.default_branch }}
-    - uses: julia-actions/julia-buildpkg@v1
-    - uses: julia-actions/julia-invalidations@v1
-      id: invs_default
-
-    - name: Report invalidation counts
-      run: |
-        echo "Invalidations on default branch: ${{ steps.invs_default.outputs.total }} (${{ steps.invs_default.outputs.deps }} via deps)" >> $GITHUB_STEP_SUMMARY
-        echo "This branch: ${{ steps.invs_pr.outputs.total }} (${{ steps.invs_pr.outputs.deps }} via deps)" >> $GITHUB_STEP_SUMMARY
-    - name: Check if the PR does increase number of invalidations
-      if: steps.invs_pr.outputs.total > steps.invs_default.outputs.total
-      run: exit 1
+  evaluate-invalidations:
+    name: "Evaluate Invalidations"
+    uses: "SciML/.github/.github/workflows/invalidations.yml@v1"
+    with:
+      julia-version: "1.10"

.github/workflows/TagBot.yml

@@ -4,6 +4,22 @@ on:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        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 +28,6 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
+          # Edit the following line to reflect the actual name of the GitHub Secret containing your private key
           ssh: ${{ secrets.DOCUMENTER_KEY }}
+          # ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}

.github/workflows/Tests.yml

@@ -0,0 +1,55 @@
+name: "Tests"
+
+on:
+  pull_request:
+    branches:
+      - master
+      - 'release-'
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref_name != github.event.repository.default_branch || github.ref != 'refs/tags/v*' }}
+
+jobs:
+  tests:
+    name: "Tests"
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - "1"
+          - "lts"
+          - "pre"
+        group:
+          - "Components"
+          - "Sol_Interface"
+          - "MOL_Interface1"
+          - "MOL_Interface2"
+          - "Diffusion"
+          - "Diffusion_NU"
+          - "Nonlinear_Diffusion"
+          - "Nonlinear_Diffusion_NU"
+          - "2D_Diffusion"
+          - "Convection"
+          - "Convection_WENO"
+          - "Higher_Order"
+          - "Stationary"
+          - "DAE"
+          - "Integrals"
+          - "Burgers"
+          - "Brusselator"
+          - "Mixed_Derivatives"
+          - "Wave_Eq_Staggered"
+          - "Complex"
+    uses: "SciML/.github/.github/workflows/tests.yml@v1"
+    with:
+      julia-version: "${{ matrix.version }}"
+      group: "${{ matrix.group }}"
+    secrets: "inherit"

.gitignore

@@ -16,3 +16,4 @@ dev/*
 # Build artifacts for creating documentation generated by the Documenter package
 docs/build/
 docs/site/
+.DS_Store

Project.toml

@@ -1,7 +1,7 @@
 name = "MethodOfLines"
 uuid = "94925ecb-adb7-4558-8ed8-f975c56a0bf4"
-authors = ["Alex Jones, <alex.lemony@gmail.com>"]
-version = "0.9.5"
+authors = ["Alex Jones, <alex.jones@juliahub.com>"]
+version = "0.11.7"
 
 [deps]
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
@@ -14,35 +14,42 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 PDEBase = "a7812802-0625-4b9e-961c-d332478797e5"
+PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
+RuntimeGeneratedFunctions = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 TermInterface = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c"
 
 [compat]
 Combinatorics = "1"
 DiffEqBase = "6"
-DomainSets = "0.5, 0.6"
+DomainSets = "0.7"
 IfElse = "0.1"
-Interpolations = "0.14"
+Interpolations = "0.14, 0.15"
 Latexify = "0.15, 0.16"
-ModelingToolkit = "8"
+ModelingToolkit = "9.17"
 OrdinaryDiffEq = "6"
-PDEBase = "0.1.4"
+PDEBase = "0.1.17"
+PrecompileTools = "1"
+RuntimeGeneratedFunctions = "0.5.9"
 SafeTestsets = "0.0.1"
-SciMLBase = "1.90, 1.91"
+SciMLBase = "2"
 StaticArrays = "1"
-SymbolicUtils = "1"
-Symbolics = "5"
-TermInterface = "0.2, 0.3"
-julia = "1.6"
+SymbolicIndexingInterface = "0.3.0"
+SymbolicUtils = "2, 3"
+Symbolics = "6"
+TermInterface = "0.4, 2"
+julia = "1.10"
 
 [extras]
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "NonlinearSolve", "SafeTestsets", "StableRNGs"]
+test = ["Test", "NonlinearSolve", "SafeTestsets", "StableRNGs", "Pkg"]