Attempts to make tests work better using the buildkite plugin

.buildkite/pipeline.yml

@@ -5,55 +5,57 @@ env:
   DATADEPS_ALWAYS_ACCEPT: true
 
 steps:
-  - label: ":building_construction: initialize environment"
+  - label: ":construction: setup julia"
     key: "init"
-    commands: 
-     - "wget -N -P $JULIA_PATH https://julialang-s3.julialang.org/bin/linux/x64/$JULIA_MINOR_VERSION/julia-$JULIA_VERSION-linux-x86_64.tar.gz"
-     - "tar xf $JULIA_PATH/julia-$JULIA_VERSION-linux-x86_64.tar.gz -C $JULIA_PATH"
-     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.instantiate(; verbose=true)'"
-     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.build()'"
-     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.precompile()'"
-     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.status()'"
+    plugins:
+      - JuliaCI/julia#v1:
+          version: "1.10"
+    command: "julia --color=yes --project -e 'using Pkg; Pkg.status()'"
     notify:
       - github_commit_status:
-          context: "Initialise environment"
+          context: "Setup test environment"
+
 
-  - label: ":speedboat: GPU unit tests"
-    commands: 
-     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.Registry.update(); Pkg.test()'"
+  - label: ":speedboat: GPU tests"
     depends_on: "init"
+    plugins:
+      - JuliaCI/julia#v1:
+          version: "1.10"
+      - JuliaCI/julia-test#v1:
+          update_registry: false
+          coverage: false
     notify:
       - github_commit_status:
           context: "GPU tests"
-
-  - label: ":rowboat: CPU unit tests"
-    env:
-     CUDA_VISIBLE_DEVICES: "-1"
-    commands: 
-     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.Registry.update(); Pkg.test()'"
+    if: !build.pull_request.draft
+
+  - label: ":rowboat: CPU tests"
     depends_on: "init"
+    env:
+      CUDA_VISIBLE_DEVICES: "-1"
+    plugins:
+      - JuliaCI/julia#v1:
+          version: "1.10"
+      - JuliaCI/julia-test#v1:
+          update_registry: false
+          coverage: true
     notify:
       - github_commit_status:
           context: "CPU tests"
-
+    if: !build.pull_request.draft
+
   - label: ":docusaurus: Documentation"
+    depends_on: "init"
     env:
       CUDA_VISIBLE_DEVICES: "-1"
       JULIA_DEBUG: "Documenter"
-      TMPDIR: "/var/lib/buildkite-agent/tmp"
-    commands:
-      - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia --color=yes --project=docs/ -e 'using Pkg; Pkg.Registry.update(); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'"
-      - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia --color=yes --project=docs/ docs/make.jl"
-    depends_on: "init"
+    plugins:
+      - JuliaCI/julia#v1:
+          version: "1.10"
+    command: 
+      - "julia --color=yes --project=docs/ -e 'using Pkg; Pkg.Registry.update(); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'"
+      - "julia --color=yes --project=docs/ docs/make.jl"
     notify:
       - github_commit_status:
           context: "Documentation"
-
-  - wait: ~
-    continue_on_failure: true
-
-  - label: ":skeleton-dance: clean up environment"
-    command: "rm -rf $JULIA_PATH"
-    notify:
-      - github_commit_status:
-          context: "Clean up"
+    if: !build.pull_request.draft

docs/make.jl

@@ -32,7 +32,8 @@ examples = [
 
 example_scripts = [ filename * ".jl" for (title, filename) in examples ]
 
-replace_silly_warning(content) = replace(content, r"┌ Warning:.*\s+└ @ JLD2 ~/\.julia/packages/JLD2/.*/reconstructing_datatypes\.jl.*\n" => "")
+replace_silly_warning(content) = replace(content, r"┌ Warning:.*\s+└ @ JLD2 ~/\.julia/packages/JLD2/.*/reconstructing_datatypes\.jl.*\n" => "",
+                                                  r"┌ Warning:.*\s+└ @ JLD2 ~/.*/packages/JLD2/.*/reconstructing_datatypes\.jl.*\n" => "")
 
 for example in example_scripts
     example_filepath = joinpath(EXAMPLES_DIR, example)

test/runtests.jl

@@ -1,17 +1,21 @@
 include("dependencies_for_runtests.jl")
 
-include("test_utils.jl")
-include("test_light.jl")
-include("test_slatissima.jl")
-include("test_LOBSTER.jl")
-include("test_NPZD.jl")
-include("test_gasexchange.jl")
-include("test_sediments.jl")
+group = get(ENV, "TEST_GROUP", :all) |> Symbol
 
-if architecture == CPU() 
-    include("test_boxmodel.jl") # box models (probably) don't work on GPU, and it wouldn't be faster anyway
-end
+if group == :all
+    include("test_utils.jl")
+    include("test_light.jl")
+    include("test_slatissima.jl")
+    include("test_LOBSTER.jl")
+    include("test_NPZD.jl")
+    include("test_gasexchange.jl")
+    include("test_sediments.jl")
+
+    if architecture == CPU() 
+        include("test_boxmodel.jl") # box models (probably) don't work on GPU, and it wouldn't be faster anyway
+    end
 
-architecture == CPU() && @testset "Doctests" begin
-    doctest(OceanBioME)
+    architecture == CPU() && @testset "Doctests" begin
+        doctest(OceanBioME)
+    end
 end