(0.9.1) Move testing and docs to buildkite (+ minor GPU bug fix)

.buildkite/pipeline.yml

@@ -0,0 +1,59 @@
+env:
+  JULIA_VERSION: "1.9.4"
+  JULIA_MINOR_VERSION: "1.9"
+  JULIA_PATH: /var/lib/buildkite-agent/julia
+  DATADEPS_ALWAYS_ACCEPT: true
+
+steps:
+  - label: ":building_construction: initialize environment"
+    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-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.status()'"
+    notify:
+      - github_commit_status:
+          context: "Initialise enviroment"
+
+  - label: ":speedboat: GPU unit tests"
+    commands: 
+     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.test()'"
+    depends_on: "init"
+    notify:
+      - github_commit_status:
+          context: "GPU tests"
+
+  - label: ":rowboat: CPU unit tests"
+    env:
+     CUDA_VISIBLE_DEVICES: "-1"
+    commands: 
+     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.test()'"
+    depends_on: "init"
+    notify:
+      - github_commit_status:
+          context: "CPU tests"
+
+  - label: ":docusaurus: Documentation"
+    env:
+      CUDA_VISIBLE_DEVICES: "-1"
+      JULIA_DEBUG: "Documenter"
+      TMPDIR: "/var/lib/buildkite-agent/tmp"
+    commands:
+      - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'"
+      - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia --color=yes --project=docs/ docs/make.jl"
+    depends_on: "init"
+    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"

Project.toml

@@ -1,7 +1,7 @@
 name = "OceanBioME"
 uuid = "a49af516-9db8-4be4-be45-1dad61c5a376"
 authors = ["Jago Strong-Wright <[email protected]> and contributors"]
-version = "0.9.0"
+version = "0.9.1"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

README.md

@@ -1,14 +1,13 @@
 ![](OceanBioME_headerbar.jpg?raw=true)
-[![Documentation](https://img.shields.io/badge/documentation-stable%20release-blue?style=flat-square)](https://oceanbiome.github.io/OceanBioME.jl/stable/)
-[![Documentation](https://img.shields.io/badge/documentation-dev%20release-orange?style=flat-square)](https://oceanbiome.github.io/OceanBioME.jl/dev/)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.05669/status.svg)](https://doi.org/10.21105/joss.05669)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10038575.svg)](https://doi.org/10.5281/zenodo.10038575)
 [![MIT license](https://img.shields.io/badge/License-MIT-blue.svg?style=flat-square)](https://mit-license.org)
 [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
 
-[![Testing](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/tests.yml/badge.svg)](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/tests.yml)
+[![Documentation](https://img.shields.io/badge/documentation-stable%20release-blue?style=flat-square)](https://oceanbiome.github.io/OceanBioME.jl/stable/)
+[![Documentation](https://img.shields.io/badge/documentation-dev%20release-orange?style=flat-square)](https://oceanbiome.github.io/OceanBioME.jl/dev/)
+[![Testing build status](https://badge.buildkite.com/3d79ccbf2cba42de1d4e54a2f31cc6f99d377198bf63334d0d.svg)](https://buildkite.com/oceanbiome-dot-jl/gpu-tests)
 [![codecov](https://codecov.io/gh/OceanBioME/OceanBioME.jl/branch/main/graph/badge.svg?token=3DIW4R7N3R)](https://codecov.io/gh/OceanBioME/OceanBioME.jl)
-[![Documentation](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/documentation.yml/badge.svg)](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/documentation.yml)
 # *Ocean* *Bio*geochemical *M*odelling *E*nvironment
 
 ## Description

src/Light/2band.jl

@@ -1,11 +1,9 @@
 @kernel function update_TwoBandPhotosyntheticallyActiveRadiation!(PAR, grid, P, surface_PAR, t, PAR_model) 
     i, j = @index(Global, NTuple)
 
-    LX, LY, _ = location(P)
-
     k, k′ = domain_boundary_indices(RightBoundary(), grid.Nz)
 
-    X = z_boundary_node(i, j, k′, grid, LX(), LY())
+    X = z_boundary_node(i, j, k′, grid, Center(), Center())
 
     PAR⁰ = surface_PAR(X..., t)