Merge #196 #197 #198

196: Extend aqua tests r=charleskawczynski a=charleskawczynski This PR extends (and fixes) the aqua tests 197: Remove unincluded files r=charleskawczynski a=charleskawczynski This PR removes files that are not included anywhere 198: Upgrade to julia 1.9 r=charleskawczynski a=charleskawczynski This PR upgrades to julia 1.9 Co-authored-by: Charles Kawczynski <kawczynski.charles@gmail.com>
CliMA · Sep 8, 2023 · c4f76f4 · c4f76f4
4 parents 9d0fee8 + a980608 + c1bfc40 + 4bea47f
commit c4f76f4
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diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml
@@ -1,5 +1,5 @@
 env:
-  JULIA_VERSION: "1.8.3"
+  JULIA_VERSION: "1.9.2"
   CUDA_VERSION: "11.2"
   OPENMPI_VERSION: "4.1.1"
   OPENBLAS_NUM_THREADS: 1

diff --git a/.dev/Manifest.toml b/.dev/Manifest.toml
@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.8.5"
+julia_version = "1.9.3"
 manifest_format = "2.0"
 project_hash = "b280bcf3b481823c97fa1a62c1b5e65114b8fa18"
 
@@ -27,15 +27,17 @@ uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6"
 version = "0.8.12"
 
 [[deps.Compat]]
-deps = ["Dates", "LinearAlgebra", "UUIDs"]
-git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957"
+deps = ["UUIDs"]
+git-tree-sha1 = "e460f044ca8b99be31d35fe54fc33a5c33dd8ed7"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.6.1"
+version = "4.9.0"
 
-[[deps.CompilerSupportLibraries_jll]]
-deps = ["Artifacts", "Libdl"]
-uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.0.1+0"
+    [deps.Compat.extensions]
+    CompatLinearAlgebraExt = "LinearAlgebra"
+
+    [deps.Compat.weakdeps]
+    Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[deps.Crayons]]
 git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
@@ -44,9 +46,9 @@ version = "4.1.1"
 
 [[deps.DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0"
+git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.18.13"
+version = "0.18.15"
 
 [[deps.Dates]]
 deps = ["Printf"]
@@ -77,9 +79,9 @@ version = "0.21.4"
 
 [[deps.JuliaFormatter]]
 deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"]
-git-tree-sha1 = "60567b51bd9e1e19ae2fd8a54dcd6bc5994727f0"
+git-tree-sha1 = "680fb31c8b8e2cf482f48e55d8fa01ccc4469e04"
 uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-version = "1.0.34"
+version = "1.0.35"
 
 [[deps.LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
@@ -103,10 +105,6 @@ version = "1.10.2+0"
 [[deps.Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
-[[deps.LinearAlgebra]]
-deps = ["Libdl", "libblastrampoline_jll"]
-uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-
 [[deps.Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
@@ -117,45 +115,40 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 [[deps.MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
-version = "2.28.0+0"
+version = "2.28.2+0"
 
 [[deps.Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
 [[deps.MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
-version = "2022.2.1"
+version = "2022.10.11"
 
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 version = "1.2.0"
 
-[[deps.OpenBLAS_jll]]
-deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
-uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
-version = "0.3.20+0"
-
 [[deps.OrderedCollections]]
-git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282"
+git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.6.0"
+version = "1.6.2"
 
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
-git-tree-sha1 = "5a6ab2f64388fd1175effdf73fe5933ef1e0bac0"
+git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.7.0"
+version = "2.7.2"
 
 [[deps.Pkg]]
-deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
+deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-version = "1.8.0"
+version = "1.9.2"
 
 [[deps.PrecompileTools]]
 deps = ["Preferences"]
-git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81"
+git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f"
 uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
-version = "1.1.2"
+version = "1.2.0"
 
 [[deps.Preferences]]
 deps = ["TOML"]
@@ -188,22 +181,22 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 [[deps.TOML]]
 deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
-version = "1.0.0"
+version = "1.0.3"
 
 [[deps.Tar]]
 deps = ["ArgTools", "SHA"]
 uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
-version = "1.10.1"
+version = "1.10.0"
 
 [[deps.Tokenize]]
 git-tree-sha1 = "90538bf898832b6ebd900fa40f223e695970e3a5"
 uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624"
 version = "0.5.25"
 
 [[deps.URIs]]
-git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a"
+git-tree-sha1 = "b7a5e99f24892b6824a954199a45e9ffcc1c70f0"
 uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
-version = "1.4.2"
+version = "1.5.0"
 
 [[deps.UUIDs]]
 deps = ["Random", "SHA"]
@@ -215,12 +208,7 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 [[deps.Zlib_jll]]
 deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
-version = "1.2.12+3"
-
-[[deps.libblastrampoline_jll]]
-deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
-uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-version = "5.1.1+0"
+version = "1.2.13+0"
 
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]

diff --git a/.github/workflows/CodeCov.yml b/.github/workflows/CodeCov.yml
@@ -19,7 +19,7 @@ jobs:
     - name: Set up Julia
       uses: julia-actions/setup-julia@latest
       with:
-        version: 1.8
+        version: 1.9
 
     - name: Test with coverage
       env:

diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
@@ -16,7 +16,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
         with:
-          version: 1.8
+          version: 1.9
       - name: Install dependencies
         run: julia --project=docs -e 'using Pkg; Pkg.instantiate(;verbose=true)'
       - name: Build and deploy

diff --git a/.github/workflows/UnitTests.yml b/.github/workflows/UnitTests.yml
@@ -14,7 +14,7 @@ jobs:
     timeout-minutes: 120
     strategy:
       matrix:
-        julia-version: [1.8]
+        julia-version: [1.9]
         os: [ubuntu-latest, windows-latest, macos-latest]
 
     runs-on: ${{ matrix.os }}

diff --git a/.github/workflows/julia_formatter.yml b/.github/workflows/julia_formatter.yml
@@ -31,7 +31,7 @@ jobs:
     - uses: julia-actions/setup-julia@latest
       if: steps.filter.outputs.julia_file_change == 'true'
       with:
-        version: '1.8'
+        version: '1.9'
 
     - name: Apply JuliaFormatter
       if: steps.filter.outputs.julia_file_change == 'true'

diff --git a/bors.toml b/bors.toml
@@ -1,7 +1,7 @@
 status = [
-  "test-os (1.8, ubuntu-latest)",
-  "test-os (1.8, windows-latest)",
-  "test-os (1.8, macos-latest)",
+  "test-os (1.9, ubuntu-latest)",
+  "test-os (1.9, windows-latest)",
+  "test-os (1.9, macos-latest)",
   "buildkite/climatimesteppers-ci",
   "format",
   "docbuild"