From c78ec37dd225bd4cea86191fc356ba3bcbd19a3c Mon Sep 17 00:00:00 2001
From: Anant Thazhemadam <47104651+thazhemadam@users.noreply.github.com>
Date: Wed, 24 Apr 2024 02:08:01 +0530
Subject: [PATCH] ci: standardise workflows using SciML's reusable workflows
 (#289)

* ci: update invalidations workflow to use centralised reusable workflow

* ci: update format check workflow to use centralised reusable workflow

* ci: standardize the tests workflow, using the reusable workflow

* Standardize the tests workflow, using the reusab SciML tests workflow.
* Rename the tests workflow to `Tests.yml`, instead of `CI.yml`, since
it's more semantically correct and CI encompasses all the workflows that
are run.

* ci(Tests): remove the `exclude` block for the test matrix

Since we don't test with Julia 1.6 anyways, remove the exclude block.
Note: this was initially left in while the workflow was standardised to
maintain status quo (with the previous version of the workflow).

* Fix deprecations

* Fix more deprecations

---------

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>
---
 .github/workflows/CI.yml            | 82 -----------------------------
 .github/workflows/FormatCheck.yml   | 36 ++-----------
 .github/workflows/Invalidations.yml | 37 ++-----------
 .github/workflows/Tests.yml         | 39 ++++++++++++++
 test/interface/parameters.jl        |  4 +-
 test/interface/unconstrained.jl     | 10 ++--
 6 files changed, 53 insertions(+), 155 deletions(-)
 delete mode 100644 .github/workflows/CI.yml
 create mode 100644 .github/workflows/Tests.yml

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
deleted file mode 100644
index daf389b..0000000
--- a/.github/workflows/CI.yml
+++ /dev/null
@@ -1,82 +0,0 @@
-name: CI
-
-on:
-  push:
-    branches:
-      - master
-  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:
-  test:
-    continue-on-error: ${{ matrix.version == 'nightly' }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        version:
-          - '1'
-        os:
-          - ubuntu-latest
-        arch:
-          - x64
-          - x86
-        group:
-          - Interface
-          - Integrators
-          - Regression
-        exclude: # test 32bit only with Julia 1 but not LTS
-          - version: '1.6'
-            arch: x86
-    steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v2
-        with:
-          version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
-      - uses: actions/cache@v4
-        env:
-          cache-name: cache-artifacts
-        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 }}-
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-runtest@latest
-        with:
-          coverage: ${{ matrix.version == '1' && matrix.arch == 'x64' }}
-        env:
-          GROUP: ${{ matrix.group }}
-      - uses: julia-actions/julia-processcoverage@v1
-        if: matrix.version == '1' && matrix.arch == 'x64'
-      - uses: codecov/codecov-action@v4
-        if: matrix.version == '1' && matrix.arch == 'x64'
-        with:
-          file: lcov.info
-          token: ${{ secrets.CODECOV_TOKEN }} # required
-          fail_ci_if_error: true
-      - uses: coverallsapp/github-action@master
-        if: matrix.version == '1' && matrix.arch == 'x64'
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: lcov.info
-          flag-name: group-${{ matrix.group }} # unique name for coverage report of each group
-          parallel: true
-  # combine coveralls coverage reports
-  finish:
-    needs: test
-    runs-on: ubuntu-latest
-    steps:
-    - name: Coveralls Finished
-      uses: coverallsapp/github-action@master
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        parallel-finished: true
diff --git a/.github/workflows/FormatCheck.yml b/.github/workflows/FormatCheck.yml
index 0da7ebb..ce3eadc 100644
--- a/.github/workflows/FormatCheck.yml
+++ b/.github/workflows/FormatCheck.yml
@@ -1,4 +1,4 @@
-name: format-check
+name: "Format Check"
 
 on:
   push:
@@ -9,34 +9,6 @@ on:
   pull_request:
 
 jobs:
-  build:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        julia-version: [1]
-        julia-arch: [x64]
-        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'
+  format-check:
+    name: "Format Check"
+    uses: "SciML/.github/.github/workflows/format-check.yml@v1"
diff --git a/.github/workflows/Invalidations.yml b/.github/workflows/Invalidations.yml
index 66c86a3..45fcabd 100644
--- a/.github/workflows/Invalidations.yml
+++ b/.github/workflows/Invalidations.yml
@@ -3,38 +3,7 @@ name: Invalidations
 on:
   pull_request:
 
-concurrency:
-  # Skip intermediate builds: always.
-  # Cancel intermediate builds: always.
-  group: ${{ github.workflow }}-${{ github.ref }}
-  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@v2
-      with:
-        version: '1'
-    - uses: actions/checkout@v4
-    - uses: julia-actions/julia-buildpkg@v1
-    - uses: julia-actions/julia-invalidations@v1
-      id: invs_pr
-
-    - uses: actions/checkout@v4
-      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"
diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
new file mode 100644
index 0000000..b8744e0
--- /dev/null
+++ b/.github/workflows/Tests.yml
@@ -0,0 +1,39 @@
+name: "Run Tests"
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+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'
+        arch:
+          - x64
+          - x86
+        group:
+          - Interface
+          - Integrators
+          - Regression
+        include:
+          - coverage: false
+          - version: '1'
+            arch: x64
+            coverage: true
+    uses: "SciML/.github/.github/workflows/tests.yml@v1"
+    with:
+      group: ${{ matrix.group }}
+      julia-version: '1'
+      julia-arch: ${{ matrix.arch }}
+      coverage: ${{ matrix.coverage }}
+    secrets: "inherit"
diff --git a/test/interface/parameters.jl b/test/interface/parameters.jl
index 68fee38..e23b7e6 100644
--- a/test/interface/parameters.jl
+++ b/test/interface/parameters.jl
@@ -24,12 +24,12 @@ h(p, t; idxs = nothing) = 0.1
     sol1 = solve(prob, MethodOfSteps(Tsit5()))
     @test length(sol1) == 21
     @test first(sol1(12))≈0.884 atol=1e-4
-    @test first(sol1[end])≈1 atol=1e-5
+    @test first(sol1.u[end])≈1 atol=1e-5
 
     # solve problem with updated parameter
     prob.p[1] = 1.4
     sol2 = solve(prob, MethodOfSteps(Tsit5()))
     @test length(sol2) == 47
     @test first(sol2(12))≈1.125 atol=5e-4
-    @test first(sol2[end])≈0.994 atol=2e-5
+    @test first(sol2.u[end])≈0.994 atol=2e-5
 end
diff --git a/test/interface/unconstrained.jl b/test/interface/unconstrained.jl
index ad10f04..0e3dca3 100644
--- a/test/interface/unconstrained.jl
+++ b/test/interface/unconstrained.jl
@@ -46,9 +46,9 @@ using Test
             sol4 = solve(prob, alg4; abstol = 1e-12, reltol = 1e-12)
 
             # relaxed tests to prevent floating point issues
-            @test abs(sol1[end] - sol2[end]) < 2.5e-8
-            @test abs(sol1[end] - sol3[end]) < 3.7e-8
-            @test abs(sol1[end] - sol4[end]) < 9.0e-11 # 9.0e-13
+            @test abs(sol1.u[end] - sol2.u[end]) < 2.5e-8
+            @test abs(sol1.u[end] - sol3.u[end]) < 3.7e-8
+            @test abs(sol1.u[end] - sol4.u[end]) < 9.0e-11 # 9.0e-13
         end
     end
 
@@ -82,8 +82,8 @@ using Test
             sol4 = solve(prob, alg4; abstol = 1e-12, reltol = 1e-12)
 
             # relaxed tests to prevent floating point issues
-            @test abs(sol1[end] - sol3[end]) < 1.2e-13 # 1.2e-15
-            @test abs(sol1[end] - sol4[end]) < 3.1e-13 # 3.1e-15
+            @test abs(sol1.u[end] - sol3.u[end]) < 1.2e-13 # 1.2e-15
+            @test abs(sol1.u[end] - sol4.u[end]) < 3.1e-13 # 3.1e-15
         end
     end
 end