Don't ship docs with Manifest (#3521)

* add docs/Manifest.toml

* don't ship docs w Manifest

* missing quote

* comment out init gpu

* update deps

* bring back all steps

* update doc build instructions

* reorder examples

* add doi

* reduce grid size for tests

64^3 seems bit much

* add SeawaterPolynomials

* add StructArrays

* add compat entries

* fix doctest

* add Rotations

* remove Plots from extras

.buildkite/pipeline.yml

@@ -592,6 +592,7 @@ steps:
       JULIA_DEBUG: "Documenter"
       TMPDIR: "$TARTARUS_HOME/tmp"
     commands:
+      - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'"
       - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes --project=docs/ docs/make.jl"
     agents:
       queue: Oceananigans

.gitignore

@@ -12,7 +12,8 @@ deps/deps.jl
 # Documenter.jl and MkDocs
 docs/build
 docs/site
-docs/src/generated
+docs/src/literated
+docs/Manifest.toml
 
 # Model output
 *.dat

Manifest.toml

@@ -20,9 +20,9 @@ version = "1.5.0"
 
 [[deps.Adapt]]
 deps = ["LinearAlgebra", "Requires"]
-git-tree-sha1 = "e2a9873379849ce2ac9f9fa34b0e37bde5d5fe0a"
+git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "4.0.2"
+version = "4.0.4"
 weakdeps = ["StaticArrays"]
 
     [deps.Adapt.extensions]
@@ -33,15 +33,16 @@ uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
 version = "1.1.1"
 
 [[deps.ArrayInterface]]
-deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "881e43f1aa014a6f75c8fc0847860e00a1500846"
+deps = ["Adapt", "LinearAlgebra", "SparseArrays", "SuiteSparse"]
+git-tree-sha1 = "44691067188f6bd1b2289552a23e4b7572f4528d"
 uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
-version = "7.8.0"
+version = "7.9.0"
 
     [deps.ArrayInterface.extensions]
     ArrayInterfaceBandedMatricesExt = "BandedMatrices"
     ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices"
     ArrayInterfaceCUDAExt = "CUDA"
+    ArrayInterfaceChainRulesExt = "ChainRules"
     ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore"
     ArrayInterfaceReverseDiffExt = "ReverseDiff"
     ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore"
@@ -51,6 +52,7 @@ version = "7.8.0"
     BandedMatrices = "aae01518-5342-5314-be14-df237901396f"
     BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0"
     CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
+    ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2"
     GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
     StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
@@ -164,9 +166,9 @@ version = "1.1.0+0"
 
 [[deps.ConstructionBase]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9"
+git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2"
 uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
-version = "1.5.4"
+version = "1.5.5"
 
     [deps.ConstructionBase.extensions]
     ConstructionBaseIntervalSetsExt = "IntervalSets"
@@ -272,9 +274,9 @@ version = "3.3.10+0"
 
 [[deps.FileIO]]
 deps = ["Pkg", "Requires", "UUIDs"]
-git-tree-sha1 = "c5c28c245101bd59154f649e19b038d15901b5dc"
+git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.16.2"
+version = "1.16.3"
 
 [[deps.FileWatching]]
 uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
@@ -427,9 +429,9 @@ version = "0.9.18"
 
 [[deps.LLVM]]
 deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"]
-git-tree-sha1 = "ddab4d40513bce53c8e3157825e245224f74fae7"
+git-tree-sha1 = "ab01dde107f21aa76144d0771dccc08f152ccac7"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "6.6.0"
+version = "6.6.2"
 weakdeps = ["BFloat16s"]
 
     [deps.LLVM.extensions]
@@ -731,9 +733,9 @@ version = "1.4.3"
 
 [[deps.PrecompileTools]]
 deps = ["Preferences"]
-git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f"
+git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f"
 uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
-version = "1.2.0"
+version = "1.2.1"
 
 [[deps.Preferences]]
 deps = ["TOML"]
@@ -1013,9 +1015,9 @@ uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 version = "0.5.23"
 
 [[deps.TranscodingStreams]]
-git-tree-sha1 = "3caa21522e7efac1ba21834a03734c57b4611c7e"
+git-tree-sha1 = "14389d51751169994b2e1317d5c72f7dc4f21045"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
-version = "0.10.4"
+version = "0.10.6"
 weakdeps = ["Random", "Test"]
 
     [deps.TranscodingStreams.extensions]
@@ -1057,9 +1059,9 @@ version = "2.12.5+0"
 
 [[deps.XZ_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "37195dcb94a5970397ad425b95a9a26d0befce3a"
+git-tree-sha1 = "31c421e5516a6248dfb22c194519e37effbf1f30"
 uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
-version = "5.6.0+0"
+version = "5.6.1+0"
 
 [[deps.Zlib_jll]]
 deps = ["Libdl"]

Project.toml

@@ -84,11 +84,12 @@ Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 MPIPreferences = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
 OpenMPI_jll = "fe0851c0-eecd-5654-98d4-656369965a5c"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 TimesDates = "bdfc003b-8df8-5c39-adcd-3a9087f5df4a"
 
 [targets]
-test = ["BenchmarkTools", "Coverage", "CUDA_Runtime_jll", "DataDeps", "Enzyme", "InteractiveUtils", "MPIPreferences", "OpenMPI_jll", "Plots", "Test", "TimerOutputs", "TimesDates", "SafeTestsets"]
+test = ["BenchmarkTools", "Coverage", "CUDA_Runtime_jll", "DataDeps", "Enzyme",
+        "InteractiveUtils", "MPIPreferences", "OpenMPI_jll", "Test", "TimerOutputs",
+        "TimesDates", "SafeTestsets"]