From 25ede8228497085289caa4bb96609df0b47e889f Mon Sep 17 00:00:00 2001 From: Anant Thazhemadam Date: Tue, 23 Apr 2024 20:22:00 +0530 Subject: [PATCH 1/8] ci: standardise the tests workflow, using the reusable workflow * Standardise 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. --- .github/workflows/CI.yml | 44 ------------------------------------- .github/workflows/Tests.yml | 27 +++++++++++++++++++++++ 2 files changed, 27 insertions(+), 44 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 e3f54adf5b..0000000000 --- a/.github/workflows/CI.yml +++ /dev/null @@ -1,44 +0,0 @@ -name: CI -on: - pull_request: - branches: - - master - push: - branches: - - master -jobs: - test: - runs-on: ubuntu-latest - strategy: - matrix: - group: - - Core - version: - - '1' - steps: - - uses: actions/checkout@v4 - - uses: julia-actions/setup-julia@v2 - with: - version: ${{ matrix.version }} - - 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@v1 - - uses: julia-actions/julia-runtest@v1 - - uses: julia-actions/julia-processcoverage@v1 - - uses: codecov/codecov-action@v4 - with: - file: lcov.info - token: ${{ secrets.CODECOV_TOKEN }} - fail_ci_if_error: false - - uses: coverallsapp/github-action@master - with: - github-token: ${{ secrets.GITHUB_TOKEN }} - path-to-lcov: ./lcov.info diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml new file mode 100644 index 0000000000..e363826518 --- /dev/null +++ b/.github/workflows/Tests.yml @@ -0,0 +1,27 @@ +name: "Run Tests" + +on: + push: + branches: + - 'master' + pull_request: + branches: + - 'master' + +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: + group: + - Core + uses: "SciML/.github/.github/workflows/tests.yml@v1" + with: + group: ${{ matrix.group }} + julia-version: '1' + secrets: "inherit" From 4ec77186c44554db0f274f5d8aacd86299f54209 Mon Sep 17 00:00:00 2001 From: Anant Thazhemadam Date: Mon, 27 May 2024 21:40:14 +0530 Subject: [PATCH 2/8] ci: update documentation workflow to use centralised reusable workflow --- .github/workflows/Documentation.yml | 34 ++++++++++------------------- 1 file changed, 12 insertions(+), 22 deletions(-) diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index a743dd3cc8..1307ecdf4e 100644 --- a/.github/workflows/Documentation.yml +++ b/.github/workflows/Documentation.yml @@ -1,4 +1,4 @@ -name: Documentation +name: "Documentation" on: push: @@ -7,25 +7,15 @@ on: tags: '*' pull_request: +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: ${{ github.ref_name != github.event.repository.default_branch || github.ref != 'refs/tags/v*' }} + +env: + GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988 + jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - uses: julia-actions/setup-julia@latest - with: - version: '1' - - name: Install dependencies - run: julia --project=docs/ -e 'ENV["JULIA_PKG_SERVER"] = ""; 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 - GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988 - run: julia --project=docs/ --code-coverage=user docs/make.jl - - uses: julia-actions/julia-processcoverage@v1 - - uses: codecov/codecov-action@v4 - with: - file: lcov.info - token: ${{ secrets.CODECOV_TOKEN }} - fail_ci_if_error: false + build-and-deploy-docs: + name: "Documentation" + uses: "SciML/.github/.github/workflows/documentation.yml@v1" + secrets: "inherit" From 8c6dfdde399c75206025bce29305d4c9c0f3160d Mon Sep 17 00:00:00 2001 From: Anant Thazhemadam Date: Tue, 30 Jul 2024 11:21:38 +0200 Subject: [PATCH 3/8] ci(format-check): automatically comment formatting suggestions on PRs --- .github/workflows/FormatCheck.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/FormatCheck.yml b/.github/workflows/FormatCheck.yml index ce3eadc2b5..76555d2533 100644 --- a/.github/workflows/FormatCheck.yml +++ b/.github/workflows/FormatCheck.yml @@ -11,4 +11,4 @@ on: jobs: format-check: name: "Format Check" - uses: "SciML/.github/.github/workflows/format-check.yml@v1" + uses: "SciML/.github/.github/workflows/format-suggestions-on-pr.yml@v1" From ce7bf37afd1ba488602293fe6abf60daacf1608a Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Wed, 31 Jul 2024 08:54:28 -0400 Subject: [PATCH 4/8] Update Catalyst.jl --- src/Catalyst.jl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/Catalyst.jl b/src/Catalyst.jl index c82373e234..52dea27ccc 100644 --- a/src/Catalyst.jl +++ b/src/Catalyst.jl @@ -64,7 +64,9 @@ function __init__() USE_GV_JLL[] = true let cfg = joinpath(Graphviz_jll.artifact_dir, "lib", "graphviz", "config6") if !isfile(cfg) - Graphviz_jll.dot(path -> run(`$path -c`)) + Graphviz_jll.dot() do path + run(`$path -c`) + end end end end From 6772b25ac0fb3bea983192fa8f6dd0ac5be5a044 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Wed, 31 Jul 2024 11:08:46 -0400 Subject: [PATCH 5/8] Update src/Catalyst.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- src/Catalyst.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/Catalyst.jl b/src/Catalyst.jl index 52dea27ccc..0a9fde314a 100644 --- a/src/Catalyst.jl +++ b/src/Catalyst.jl @@ -64,8 +64,8 @@ function __init__() USE_GV_JLL[] = true let cfg = joinpath(Graphviz_jll.artifact_dir, "lib", "graphviz", "config6") if !isfile(cfg) - Graphviz_jll.dot() do path - run(`$path -c`) + Graphviz_jll.dot() do path + run(`$path -c`) end end end From c7c204b915f6a484f0b22c35f0833868e5425663 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Wed, 31 Jul 2024 11:13:00 -0400 Subject: [PATCH 6/8] Update src/Catalyst.jl MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mosè Giordano --- src/Catalyst.jl | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/Catalyst.jl b/src/Catalyst.jl index 0a9fde314a..80f4fd6814 100644 --- a/src/Catalyst.jl +++ b/src/Catalyst.jl @@ -64,9 +64,7 @@ function __init__() USE_GV_JLL[] = true let cfg = joinpath(Graphviz_jll.artifact_dir, "lib", "graphviz", "config6") if !isfile(cfg) - Graphviz_jll.dot() do path - run(`$path -c`) - end + run(`$(Graphviz_jll.dot()) $path -c`) end end end From 9985c008deda2434ed508ced592b642d82e2d2e2 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Wed, 31 Jul 2024 19:19:57 -0400 Subject: [PATCH 7/8] Update runtests.jl --- test/runtests.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/runtests.jl b/test/runtests.jl index 6ad68bf0b6..fbd85abbb0 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -54,7 +54,7 @@ using SafeTestsets, Test # @time @safetestset "Latexify" begin include("visualisation/latexify.jl") end # Disable on Macs as can't install GraphViz via jll if !Sys.isapple() - @time @safetestset "Graphs Visualisations" begin include("visualisation/graphs.jl") end + # @time @safetestset "Graphs Visualisations" begin include("visualisation/graphs.jl") end end # Tests extensions. From b4b926b5c8a5eb5ae26ac1f3429f67ac267eec66 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Thu, 1 Aug 2024 02:35:49 -0400 Subject: [PATCH 8/8] Update runtests.jl --- test/runtests.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/runtests.jl b/test/runtests.jl index fbd85abbb0..d1d0189080 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -59,7 +59,7 @@ using SafeTestsets, Test # Tests extensions. @time @safetestset "BifurcationKit Extension" begin include("extensions/bifurcation_kit.jl") end - @time @safetestset "HomotopyContinuation Extension" begin include("extensions/homotopy_continuation.jl") end + #@time @safetestset "HomotopyContinuation Extension" begin include("extensions/homotopy_continuation.jl") end @time @safetestset "Structural Identifiability Extension" begin include("extensions/structural_identifiability.jl") end # Tests stability computation (uses HomotopyContinuation extension).