Merge branch 'main' into iterate_and_show_aaf

.buildkite/pipeline.yml

@@ -16,10 +16,10 @@ steps:
     if: build.message !~ /\[skip tests\]/
     timeout_in_minutes: 60
 
-  - label: "🏄🏻‍♂️ Julia 1.8"
+  - label: "🏄🏻‍♂️ Julia 1.9"
     plugins:
       - JuliaCI/julia#v1:
-          version: 1.8
+          version: 1.9
       - JuliaCI/julia-test#v1: ~
     agents:
       queue: "juliagpu"

.github/workflows/CompatHelper.yml

@@ -1,4 +1,4 @@
-name: CompatHelper
+ame: CompatHelper
 
 on:
   schedule:

Project.toml

@@ -4,7 +4,7 @@ license = "MIT"
 authors = ["Navid C. Constantinou <navidcy@gmail.com>", "Gregory L. Wagner <wagner.greg@gmail.com>"]
 documentation = "https://fourierflows.github.io/PassiveTracerFlowsDocumentation/dev/"
 repository = "https://github.com/FourierFlows/PassiveTracerFlows.jl"
-version = "0.9.0"
+version = "0.9.1"
 
 [deps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
@@ -18,13 +18,16 @@ Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
-CUDA = "^1.3, ^2, ^3"
+CUDA = "1.3, 2, 3.7.1, 4, 5"
 DocStringExtensions = "0.8, 0.9"
-FourierFlows = "0.10.0"
-GeophysicalFlows = "0.15.0"
-JLD2 = "^0.1, ^0.2, ^0.3, ^0.4"
-Reexport = "^0.2, ^1"
-julia = "^1.6"
+FourierFlows = "0.10.5"
+GeophysicalFlows = "0.15.4"
+JLD2 = "0.1, 0.2, 0.3, 0.4"
+LinearAlgebra = "1.6"
+Random = "1.6"
+Reexport = "0.2, 1"
+Statistics = "1.6"
+julia = "1.6"
 
 [extras]
 Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"

README.md

@@ -52,7 +52,7 @@ See `examples/` for example scripts.
 
 The code is citable via [zenodo](https://zenodo.org). Please cite as:
 
-> Navid C. Constantinou, Josef I. Bisits, and Gregory L. Wagner (2022). FourierFlows/PassiveTracerFlows.jl: PassiveTracerFlows v0.9.0 (Version v0.9.0). Zenodo. [https://doi.org/10.5281/zenodo.2535983](https://doi.org/10.5281/zenodo.2535983)
+> Navid C. Constantinou, Josef I. Bisits, and Gregory L. Wagner (2022). FourierFlows/PassiveTracerFlows.jl: PassiveTracerFlows v0.9.1 (Version v0.9.1). Zenodo. [https://doi.org/10.5281/zenodo.2535983](https://doi.org/10.5281/zenodo.2535983)
 
 ## Contributing
 

appveyor.yml

@@ -1,7 +1,7 @@
 environment:
   matrix:
   - julia_version: 1.6
-  - julia_version: 1.8
+  - julia_version: 1.9
 
 platform:
   # - x86 # 32-bit

docs/Project.toml

@@ -6,4 +6,5 @@ Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [compat]
+Documenter = "1"
 Literate = "≥2.9.0"

docs/make.jl

@@ -42,7 +42,8 @@ format = Documenter.HTML(
 
 makedocs(
    modules = [PassiveTracerFlows],
-   doctest = false,
+   doctest = true,
+  warnonly = [:footnote, :cross_references, :missing_docs],
      clean = true,
  checkdocs = :all,
     format = format,
@@ -67,9 +68,30 @@ makedocs(
            ]
 )
 
+@info "Clean up temporary .jld2 and .nc output created by doctests or literated examples..."
+
+"""
+    recursive_find(directory, pattern)
+
+Return list of filepaths within `directory` that contains the `pattern::Regex`.
+"""
+recursive_find(directory, pattern) =
+  mapreduce(vcat, walkdir(directory)) do (root, dirs, files)
+    joinpath.(root, filter(contains(pattern), files))
+  end
+
+files = []
+for pattern in [r"\.jld2", r"\.nc"]
+  global files = vcat(files, recursive_find(@__DIR__, pattern))
+end
+
+for file in files
+  rm(file)
+end
+
 withenv("GITHUB_REPOSITORY" => "FourierFlows/PassiveTracerFlowsDocumentation") do
   deploydocs(       repo = "github.com/FourierFlows/PassiveTracerFlowsDocumentation.git",
-                versions = ["stable" => "v^", "v#.#.#", "dev" => "dev"],
+                versions = ["stable" => "v^", "dev" => "dev", "v#.#.#"],
             push_preview = false,
                forcepush = true,
                devbranch = "main"