Merge #1234

1234: Switch CI to use Github Actions, run tests in parallel and fast fail when possible r=jakebolewski a=jakebolewski * Run subset on every push in parallel * Kill jobs that fail quickly * Kill stale jobs quickly upon new commits to a branch * Run all OS unit tests only on bors try / bors merge * Remove Azure Devops Pipelines # Description A clear and concise description of the code with usage. Co-authored-by: jakebolewski <[email protected]>
CliMA · Jun 13, 2020 · cef6389 · cef6389
2 parents 4a07b42 + c69ff9f
commit cef6389
Show file tree

Hide file tree

Showing 17 changed files with 158 additions and 154 deletions.
diff --git a/.github/workflows/Coverage.yaml b/.github/workflows/Coverage.yaml
@@ -8,18 +8,15 @@ on:
 
 jobs:
   coverage:
-    runs-on: ubuntu-16.04
-    strategy:
-      matrix:
-        julia-version: ['1.4']
-        project: ['ClimateMachine.jl']
+    runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/[email protected]
-    - name: "Set up Julia"
-      uses: julia-actions/setup-julia@v1
+    - uses: actions/[email protected]
+
+    - name: Set up Julia
+      uses: julia-actions/[email protected]
       with:
-        version: ${{ matrix.julia-version }}
+        version: 1.4
 
     - name: Test with coverage
       env:
@@ -35,8 +32,9 @@ jobs:
                                   using Coverage;
                                   LCOV.writefile("coverage-lcov.info", Codecov.process_folder())'
       if: success()
+
     - name: Submit coverage
-      uses: codecov/[email protected].2
+      uses: codecov/[email protected].7
       with:
         token: ${{secrets.CODECOV_TOKEN}}
       if: success()

diff --git a/.github/workflows/Documenter.yaml b/.github/workflows/Documenter.yaml
@@ -12,9 +12,14 @@ on:
 jobs:
   docs-build:
     runs-on: ubuntu-latest
+    timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/[email protected]
+      - uses: julia-actions/[email protected]
         with:
           version: 1.4
       - name: Install dependencies

diff --git a/.github/workflows/JuliaFormatter.yml b/.github/workflows/JuliaFormatter.yml
@@ -12,12 +12,17 @@ on:
 jobs:
   format:
     runs-on: ubuntu-latest
+    timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v2
+    - name: Cancel Previous Runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }}
+    - uses: actions/[email protected]
       with:
         fetch-depth: 0
     - run: git fetch origin
-    - uses: julia-actions/setup-julia@latest
+    - uses: julia-actions/setup-julia@v1.1.6
       with:
         version: 1.4
     - name: Apply JuliaFormatter

diff --git a/.github/workflows/Linux-UnitTests.yml b/.github/workflows/Linux-UnitTests.yml
@@ -0,0 +1,42 @@
+name: Unit Tests
+
+on:
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    strategy:
+      fail-fast: true
+      matrix:
+          test-modules: ["Arrays,Atmos,Common,Diagnostics,Driver,InputOutput,Utilities",
+                         "Numerics/DGMethods",
+                         "Numerics/Mesh",
+                         "Numerics/ODESolvers",
+                         "Numerics/SystemSolvers",
+                         "Ocean"]
+
+    steps:
+    - name: Cancel Previous Runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }}
+
+    - name: Checkout
+      uses: actions/[email protected]
+
+    - name: Set up Julia
+      uses: julia-actions/[email protected]
+      with:
+        version: 1.4
+
+    - name: Install Project Packages
+      run: |
+        julia --project=@. -e 'using Pkg; Pkg.instantiate(); Pkg.build()'
+
+    - name: Run Unit Tests
+      env:
+        TEST_MODULES: ${{ matrix.test-modules }}
+      run: |
+        julia --project=@. -e 'using Pkg; Pkg.test(test_args=map(String, split(ENV["TEST_MODULES"], ",")))'
diff --git a/.github/workflows/OS-UnitTests.yml b/.github/workflows/OS-UnitTests.yml
@@ -0,0 +1,43 @@
+name: OS Unit Tests
+
+on:
+  push:
+    branches:
+      - staging
+      - trying
+
+jobs:
+  test-os:
+    timeout-minutes: 120
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - name: Cancel Previous Runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }}
+
+    - name: Checkout
+      uses: actions/[email protected]
+
+    - name: Set up Julia
+      uses: julia-actions/[email protected]
+      with:
+        version: 1.4
+
+    - name: Install Project Packages
+      run: |
+        julia --project=@. -e 'using Pkg; Pkg.instantiate(); Pkg.build()'
+
+    - name: Build System Image
+      run: |
+        julia --project=@. .dev/systemimage/climate_machine_image.jl ClimateMachine.so true
+
+    - name: Run Unit Tests
+      run: |
+        julia --project=@. -J ClimateMachine.so -e 'using Pkg; Pkg.test()'
diff --git a/README.md b/README.md
@@ -15,9 +15,6 @@ The Climate Machine is a new Earth system model that leverages recent advances i
 [docs-latest-img]: https://img.shields.io/badge/docs-latest-blue.svg
 [docs-latest-url]: https://CliMA.github.io/ClimateMachine.jl/latest/
 
-[azure-img]: https://dev.azure.com/climate-machine/ClimateMachine.jl/_apis/build/status/azure-ci?branchName=master
-[azure-url]: https://dev.azure.com/climate-machine/ClimateMachine.jl/_build
-
 [codecov-img]: https://codecov.io/gh/CliMA/ClimateMachine.jl/branch/master/graph/badge.svg
 [codecov-url]: https://codecov.io/gh/CliMA/ClimateMachine.jl
 

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
diff --git a/bors.toml b/bors.toml
@@ -1,5 +1,7 @@
 status = [
-  "azure-ci",
+  "test-os (ubuntu-latest)",
+  "test-os (windows-latest)",
+  "test-os (macos-latest)",
   "ci/slurmci",
   "docs-build",
   "format"

diff --git a/docs/src/Contributing.md b/docs/src/Contributing.md
@@ -92,10 +92,22 @@ integration (CI) system.
 
 A `ClimateMachine` developer will look at your PR and provide feedback!
 
-We use [`bors`](https://bors.tech/) to manage the `ClimateMachine` repo.
+Currently a number of checks are run per commit for a given PR:
+
+- `JuliaFormatter` checks if the PR is formatted with `.dev/climaformat.jl`
+- `Documentation` rebuilds the documentation for the PR and checks if the docs are consistent and generate valid output.
+- `Unit Tests` run subsets of the unit tests defined in `tests/`, `Pkg.test()`.  The tests are run in parallel to ensure that they finish in a reasonable time.  The tests only run the latest commit for a PR, branch and will kill any stale jobs on push.  These tests are only run on linux (Ubuntu LTS).
+
+We use [`bors`](https://bors.tech/) to manage merging PR's in the the `ClimateMachine` repo.
 If you're a collaborator and have the necessary permissions, you can type
 `bors try` in a comment on a PR to have some additional tests run on that
-PR, or `bors r+` to try and merge the code.
+PR, or `bors r+` to try and merge the code.  Bors ensures that all tests
+for a given PR always pass before merging into `master`.
+
+Bors aggregates and checks the following test outputs:
+- `Documentation` checks that the documentation correctly builds for the merged PR.
+- `OS Unit Tests` checks that ClimateMachine.jl package unit tests can pass on every OS supported (linux, macOS, windows).
+- `slurmci` runs more extensive testing on both CPU and GPU hardware using Caltech HPC cluster resources.
 
 ## Contributing Documentation
 

diff --git a/slurmci-test.toml b/slurmci-test.toml
@@ -2,11 +2,13 @@
 #
 
 cpu = [
+  { file = "test/Numerics/DGMethods/advection_diffusion/advection_diffusion_model_1dimex_bgmres.jl", slurmargs = ["--ntasks=1"], args = [] },
   { file = "test/Numerics/DGMethods/advection_diffusion/pseudo1D_advection_diffusion.jl", slurmargs = ["--ntasks=3"], args = [] },
   { file = "test/Numerics/DGMethods/advection_diffusion/pseudo1D_advection_diffusion_1dimex.jl", slurmargs = ["--ntasks=3"], args = [] },
   { file = "test/Numerics/DGMethods/advection_diffusion/pseudo1D_advection_diffusion_mrigark_implicit.jl", slurmargs = ["--ntasks=3"], args = [] },
   { file = "test/Numerics/DGMethods/advection_diffusion/pseudo1D_heat_eqn.jl", slurmargs = ["--ntasks=3"], args = [] },
   { file = "test/Numerics/DGMethods/advection_diffusion/periodic_3D_hyperdiffusion.jl", slurmargs = ["--ntasks=3"], args = [] },
+  { file = "test/Numerics/DGMethods/compressible_Navier_Stokes/ref_state.jl", slurmargs = ["--ntasks=1"], args = [] },
   { file = "test/Numerics/Mesh/mpi_connect_1d.jl", slurmargs = ["--ntasks=5"], args = [] },
   { file = "test/Numerics/Mesh/mpi_connect_sphere.jl", slurmargs = ["--ntasks=5"], args = [] },
   { file = "test/Numerics/Mesh/mpi_getpartition.jl", slurmargs = ["--ntasks=5"], args = [] },

diff --git a/test/Atmos/runtests.jl b/test/Atmos/runtests.jl
@@ -3,9 +3,11 @@ using Test, Pkg
 @testset "Atmos" begin
     all_tests = isempty(ARGS) || "all" in ARGS ? true : false
     for submodule in ["Parameterizations", "TemperatureProfiles"]
-        if all_tests || "$submodule" in ARGS || "Atmos" in ARGS
+        if all_tests ||
+           "$submodule" in ARGS ||
+           "Atmos/$submodule" in ARGS ||
+           "Atmos" in ARGS
             include_test(submodule)
         end
     end
-
 end
diff --git a/test/Common/runtests.jl b/test/Common/runtests.jl
@@ -3,7 +3,10 @@ using Test, Pkg
 @testset "Common" begin
     all_tests = isempty(ARGS) || "all" in ARGS ? true : false
     for submodule in ["Thermodynamics", "SurfaceFluxes"]
-        if all_tests || "$submodule" in ARGS || "Common" in ARGS
+        if all_tests ||
+           "$submodule" in ARGS ||
+           "Common/$submodule" in ARGS ||
+           "Common" in ARGS
             include_test(submodule)
         end
     end

diff --git a/test/InputOutput/runtests.jl b/test/InputOutput/runtests.jl
@@ -3,7 +3,10 @@ using Test, Pkg
 @testset "InputOutput" begin
     all_tests = isempty(ARGS) || "all" in ARGS ? true : false
     for submodule in ["Writers"]
-        if all_tests || "$submodule" in ARGS || "InputOutput" in ARGS
+        if all_tests ||
+           "$submodule" in ARGS ||
+           "InputOutput/$submodule" in ARGS ||
+           "InputOutput" in ARGS
             include_test(submodule)
         end
     end

diff --git a/test/Numerics/DGMethods/runtests.jl b/test/Numerics/DGMethods/runtests.jl
@@ -2,21 +2,9 @@ using MPI, Test
 include(joinpath("..", "..", "testhelpers.jl"))
 
 @testset "DGMethods" begin
-    runmpi(joinpath(@__DIR__, "vars_test.jl"))
+    runmpi(joinpath(@__DIR__, "courant.jl"), ntasks = 2)
+    runmpi(joinpath(@__DIR__, "horizontal_integral_test.jl"))
     runmpi(joinpath(@__DIR__, "integral_test.jl"))
     runmpi(joinpath(@__DIR__, "integral_test_sphere.jl"))
-    runmpi(joinpath(@__DIR__, "Euler/isentropicvortex.jl"))
-    runmpi(joinpath(@__DIR__, "Euler/isentropicvortex_imex.jl"))
-    runmpi(joinpath(@__DIR__, "Euler/isentropicvortex_multirate.jl"))
-    runmpi(joinpath(
-        @__DIR__,
-        "advection_diffusion/pseudo1D_advection_diffusion.jl",
-    ))
-    runmpi(joinpath(
-        @__DIR__,
-        "advection_diffusion/advection_diffusion_model_1dimex_bgmres.jl",
-    ))
-    runmpi(joinpath(@__DIR__, "compressible_Navier_Stokes/ref_state.jl"))
-    runmpi(joinpath(@__DIR__, "horizontal_integral_test.jl"))
-    runmpi(joinpath(@__DIR__, "courant.jl"), ntasks = 2)
+    runmpi(joinpath(@__DIR__, "vars_test.jl"))
 end