Merge master

.JuliaFormatter.toml

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

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
+    ignore:
+      - dependency-name: "crate-ci/typos"
+        update-types: ["version-update:semver-patch", "version-update:semver-minor"]

.github/workflows/Documentation.yml

@@ -1,28 +1,20 @@
-name: Documentation
+name: "Documentation"
 
 on:
   push:
     branches:
       - master
     tags: '*'
   pull_request:
+  schedule:
+    - cron: '48 8 * * 5'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref_name != github.event.repository.default_branch || github.ref != 'refs/tags/v*' }}
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: '1.6'
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-        run: julia --project=docs/ --code-coverage=user docs/make.jl
-      - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
-        with:
-          file: lcov.info
+  build-and-deploy-docs:
+    name: "Documentation"
+    uses: "SciML/.github/.github/workflows/documentation.yml@v1"
+    secrets: "inherit"

.github/workflows/Downgrade.yml

@@ -0,0 +1,41 @@
+name: Downgrade
+on:
+  pull_request:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+  schedule:
+    - cron: '48 8 * * 5'
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    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: julia-actions/julia-downgrade-compat@v1
+        with:
+          skip: Pkg,TOML
+      - uses: julia-actions/cache@v2
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1

.github/workflows/FormatCheck.yml

@@ -1,42 +1,13 @@
-name: format-check
+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@v1
-      - 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'
+  format-check:
+    name: "Format Check"
+    uses: "SciML/.github/.github/workflows/format-check.yml@v1"

.github/workflows/Invalidations.yml

@@ -1,4 +1,4 @@
-name: Invalidations
+name: "Invalidations"
 
 on:
   pull_request:
@@ -10,31 +10,6 @@ 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"

.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@v4
+      - name: Check spelling
+        uses: crate-ci/[email protected] 

.github/workflows/ci.yml

@@ -1,33 +1,46 @@
 name: CI
-on: [push, pull_request]
+on:
+  pull_request:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+  schedule:
+    - cron: '48 8 * * 5'
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         group:
           - Core
         version:
           - '1'
-          - '1.6'
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
+      - uses: julia-actions/cache@v2
         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@v1
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

.gitignore

@@ -2,3 +2,4 @@
 *.jl.*.cov
 *.jl.mem
 Manifest.toml
+docs/build

.typos.toml

@@ -0,0 +1,5 @@
+[default.extend-words]
+ba = "ba"
+caf = "caf"
+ths = "ths"
+allo = "allo"

Project.toml

@@ -1,7 +1,7 @@
 name = "CellMLToolkit"
 uuid = "03cb29e0-1ef4-4721-aa24-cf58a006576f"
 authors = ["Shahriar Iravanian <[email protected]>"]
-version = "2.9.2"
+version = "2.11.0"
 
 [deps]
 EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
@@ -14,18 +14,25 @@ SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
+Aqua = "0.8"
 EzXML = "1.1"
-MathML = "0.1.9"
-Memoize = "0.4"
+MathML = "0.1.14"
+Memoize = "0.4.2"
 ModelingToolkit = "9"
+OrdinaryDiffEq = "6"
+Random = "1.10"
+SafeTestsets = "0.1"
 Setfield = "0.8, 1"
-SymbolicUtils = "2"
-julia = "1.6"
+SymbolicUtils = "1.2, 2"
+Test = "1.10"
+julia = "1.10"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "ModelingToolkit", "OrdinaryDiffEq"]
+test = ["Aqua", "Test", "ModelingToolkit", "OrdinaryDiffEq", "SafeTestsets"]