Merge 74ec9df into 0fb8a98

.travis.yml

@@ -5,26 +5,26 @@ os:
   - linux
 
 julia:
-  - 0.7
   - 1.0
   - nightly
 
 matrix:
   allow_failures:
-    - julia: 1.0
     - julia: nightly
 
-before_script:
- - julia -e 'using Pkg; Pkg.add("FourierFlows");'
-
-# script:
-#   - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-#   - julia -e 'using Pkg; Pkg.test("FourierFlows", coverage=true)'
-
 after_success:
-  - julia -e 'using Pkg; Pkg.add("Documenter")'
-  - julia -e 'using Pkg; Pkg.add("Documenter"); Pkg.dir("PassiveTracerFlows"); include(joinpath("docs", "make.jl"))'
-  - julia -e 'using Pkg; Pkg.add("Coverage"); Pkg.dir("PassiveTracerFlows"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
+  - julia --project -e 'using Pkg; Pkg.add("Coverage"); Pkg.dir("GeophysicalFlows"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
+
+jobs:
+  include:
+    - stage: "Documentation"
+      julia: 1.0
+      os: linux
+      script:
+        - julia --project=docs/ -e 'using Pkg; Pkg.instantiate();
+                                    Pkg.develop(PackageSpec(path=pwd()))'
+        - julia --project=docs/ docs/make.jl
+      after_success: skip
 
 notifications:
   email: true

Manifest.toml

@@ -13,23 +13,17 @@ version = "0.3.0"
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
-[[BinDeps]]
-deps = ["Compat", "Libdl", "SHA", "URIParser"]
-git-tree-sha1 = "12093ca6cdd0ee547c39b1870e0c9c3f154d9ca9"
-uuid = "9e28174c-4ba2-5203-b857-d8d62c4213ee"
-version = "0.8.10"
-
 [[BinaryProvider]]
 deps = ["Libdl", "Pkg", "SHA", "Test"]
-git-tree-sha1 = "48c147e63431adbcee69bc40b04c3f0fec0a4982"
+git-tree-sha1 = "055eb2690182ebc31087859c3dd8598371d3ef9e"
 uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
-version = "0.5.0"
+version = "0.5.3"
 
 [[CodecZlib]]
-deps = ["BinaryProvider", "Libdl", "Pkg", "Test", "TranscodingStreams"]
-git-tree-sha1 = "83cb3d65c37ea1364c2d5bf7bcea41843ba645dc"
+deps = ["BinaryProvider", "Libdl", "Test", "TranscodingStreams"]
+git-tree-sha1 = "e3df104c84dfc108f0ca203fd7f5bbdc98641ae9"
 uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
-version = "0.5.0"
+version = "0.5.1"
 
 [[ColorTypes]]
 deps = ["FixedPointNumbers", "Random", "Test"]
@@ -38,34 +32,28 @@ uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
 version = "0.7.5"
 
 [[Colors]]
-deps = ["ColorTypes", "FixedPointNumbers", "InteractiveUtils", "Pkg", "Printf", "Reexport", "Test"]
-git-tree-sha1 = "8c89e0a9a583954eae3efcf6a531e51c02b38cee"
+deps = ["ColorTypes", "FixedPointNumbers", "InteractiveUtils", "Printf", "Reexport", "Test"]
+git-tree-sha1 = "9f0a0210450acb91c730b730a994f8eef1d3d543"
 uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
-version = "0.9.4"
+version = "0.9.5"
 
 [[Compat]]
 deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "ae262fa91da6a74e8937add6b613f58cd56cdad4"
+git-tree-sha1 = "ec61a16eed883ad0cfa002d7489b3ce6d039bb9a"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "1.1.0"
-
-[[ComputationalResources]]
-deps = ["Pkg", "Test"]
-git-tree-sha1 = "89e7e7ed20af73d9f78877d2b8d1194e7b6ff13d"
-uuid = "ed09eef8-17a6-5b46-8889-db040fac31e3"
-version = "0.3.0"
+version = "1.4.0"
 
 [[Conda]]
 deps = ["Compat", "JSON", "VersionParsing"]
-git-tree-sha1 = "a47f9a2c7b80095e6a935536795635522fe27f5d"
+git-tree-sha1 = "fb86fe40cb5b35990e368709bfdc1b46dbb99dac"
 uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d"
-version = "1.0.1"
+version = "1.1.1"
 
 [[DataStructures]]
-deps = ["InteractiveUtils", "OrderedCollections", "REPL", "Random", "Serialization", "Test"]
-git-tree-sha1 = "70c9a5215aa61d216f2f6ef209a8e190c3c17b40"
+deps = ["InteractiveUtils", "OrderedCollections", "Random", "Serialization", "Test"]
+git-tree-sha1 = "8fc6e166e24fda04b2b648d4260cdad241788c54"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.13.0"
+version = "0.14.0"
 
 [[Dates]]
 deps = ["Printf"]
@@ -80,38 +68,38 @@ deps = ["LinearAlgebra", "Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[FFTW]]
-deps = ["AbstractFFTs", "BinaryProvider", "Compat", "Conda", "Libdl", "LinearAlgebra", "Pkg", "Reexport", "Test"]
+deps = ["AbstractFFTs", "BinaryProvider", "Compat", "Conda", "Libdl", "LinearAlgebra", "Reexport", "Test"]
 git-tree-sha1 = "29cda58afbf62f35b1a094882ad6c745a47b2eaa"
 uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 version = "0.2.4"
 
 [[FileIO]]
 deps = ["Pkg", "Random", "Test"]
-git-tree-sha1 = "b80161b7e679a1241f9441ebfa60b62d4239cf99"
+git-tree-sha1 = "1a114d08094e7267ba8d4d684f930d5a722184de"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.0.1"
+version = "1.0.4"
 
 [[FixedPointNumbers]]
-deps = ["Pkg", "Test"]
+deps = ["Test"]
 git-tree-sha1 = "b8045033701c3b10bf2324d7203404be7aef88ba"
 uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
 version = "0.5.3"
 
 [[FourierFlows]]
-deps = ["ComputationalResources", "FFTW", "Interpolations", "JLD2", "LinearAlgebra", "Pkg", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics", "Test"]
-git-tree-sha1 = "da54d0bdc32940f7730ad34c29d2280f79ef16f3"
+deps = ["FFTW", "Interpolations", "JLD2", "LinearAlgebra", "Random", "Reexport", "Statistics"]
+git-tree-sha1 = "1addb960281c1cbd44156975ebb8e21a99f79232"
 uuid = "2aec4490-903f-5c70-9b11-9bed06a700e1"
-version = "0.2.1"
+version = "0.3.0"
 
 [[InteractiveUtils]]
 deps = ["LinearAlgebra", "Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
 [[Interpolations]]
 deps = ["AxisAlgorithms", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "Test", "WoodburyMatrices"]
-git-tree-sha1 = "8e7c47f73de4b0fea1059ddae77f971f52075ddc"
+git-tree-sha1 = "1ec5b78dbfb5ae2b3d7a4987a9287fed4cc31ded"
 uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
-version = "0.9.1"
+version = "0.11.1"
 
 [[JLD2]]
 deps = ["CodecZlib", "DataStructures", "FileIO", "LinearAlgebra", "Mmap", "Printf", "Random", "Test"]
@@ -120,16 +108,16 @@ uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 version = "0.1.2"
 
 [[JSON]]
-deps = ["Dates", "Distributed", "Mmap", "Pkg", "Sockets", "Test", "Unicode"]
-git-tree-sha1 = "fec8e4d433072731466d37ed0061b3ba7f70eeb9"
+deps = ["Dates", "Distributed", "Mmap", "Sockets", "Test", "Unicode"]
+git-tree-sha1 = "1f7a25b53ec67f5e9422f1f551ee216503f4a0fa"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-version = "0.19.0"
+version = "0.20.0"
 
 [[LaTeXStrings]]
 deps = ["Compat"]
 git-tree-sha1 = "7ab9b8788cfab2bdde22adf9004bda7ad9954b6c"
 uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
-version = "1.0.2"
+version = "1.0.3"
 
 [[LibGit2]]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
@@ -159,15 +147,15 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
 [[OffsetArrays]]
 deps = ["DelimitedFiles", "Test"]
-git-tree-sha1 = "f8cd140824f74f2948ff8660bc2292e16d29c1b7"
+git-tree-sha1 = "7d1442cb06fbfbc4fea936c3c56b38daffd22d3b"
 uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
-version = "0.8.1"
+version = "0.9.1"
 
 [[OrderedCollections]]
-deps = ["Pkg", "Random", "Serialization", "Test"]
-git-tree-sha1 = "41da1edba028376b58520ca01d9a41e29f855d55"
+deps = ["Random", "Serialization", "Test"]
+git-tree-sha1 = "85619a3f3e17bb4761fe1b1fd47f0e979f964d5b"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.0.1"
+version = "1.0.2"
 
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
@@ -179,9 +167,9 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [[PyCall]]
 deps = ["Compat", "Conda", "MacroTools", "Statistics", "VersionParsing"]
-git-tree-sha1 = "f56428481fd0caf01cc8ecd2a0892fdaf8fddd50"
+git-tree-sha1 = "ce4681263f41d98b3faf6107b28284bf8b866f5f"
 uuid = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
-version = "1.18.4"
+version = "1.18.5"
 
 [[PyPlot]]
 deps = ["Colors", "Compat", "LaTeXStrings", "PyCall", "VersionParsing"]
@@ -209,12 +197,6 @@ git-tree-sha1 = "7b1d07f411bc8ddb7977ec7f377b97b158514fe0"
 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
 version = "0.2.0"
 
-[[Requires]]
-deps = ["Test"]
-git-tree-sha1 = "f6fbf4ba64d295e146e49e021207993b6b48c7d1"
-uuid = "ae029012-a4dd-5104-9daa-d747884805df"
-version = "0.5.2"
-
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
@@ -232,17 +214,11 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 deps = ["LinearAlgebra", "Random"]
 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
-[[SpecialFunctions]]
-deps = ["BinDeps", "BinaryProvider", "Libdl", "Test"]
-git-tree-sha1 = "c35c9c76008babf4d658060fc64aeb369a41e7bd"
-uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "0.7.1"
-
 [[StaticArrays]]
 deps = ["InteractiveUtils", "LinearAlgebra", "Random", "Statistics", "Test"]
-git-tree-sha1 = "d432c79bef174a830304f8601427a4357dfdbfb7"
+git-tree-sha1 = "1eb114d6e23a817cd3e99abc3226190876d7c898"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "0.8.3"
+version = "0.10.2"
 
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -253,17 +229,11 @@ deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[TranscodingStreams]]
-deps = ["DelimitedFiles", "Pkg", "Random", "Test"]
+deps = ["Pkg", "Random", "Test"]
 git-tree-sha1 = "a34a2d588e2d2825602bf14a24216d5c8b0921ec"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.8.1"
 
-[[URIParser]]
-deps = ["Test", "Unicode"]
-git-tree-sha1 = "6ddf8244220dfda2f17539fa8c9de20d6c575b69"
-uuid = "30578b45-9adc-5946-b283-645ec420af67"
-version = "0.4.0"
-
 [[UUIDs]]
 deps = ["Random"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
@@ -275,7 +245,7 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 deps = ["Compat"]
 git-tree-sha1 = "c9d5aa108588b978bd859554660c8a5c4f2f7669"
 uuid = "81def892-9a0e-5fdd-b105-ffc91e053289"
-version = "1.1.2"
+version = "1.1.3"
 
 [[WoodburyMatrices]]
 deps = ["LinearAlgebra", "Random", "SparseArrays", "Test"]

Project.toml

@@ -12,6 +12,6 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

README.md

@@ -1,10 +1,35 @@
-# PassiveTracerFlows
-
-<table>
-    <tr align="center">
-        <td><b>Documentation</b></td> <td>Travis</td> <td>Appveyor</td>
-    </tr>
-    <tr align="center">
-        <td><a href="https://fourierflows.github.io/PassiveTracerFlows.jl/latest/"><img src="https://img.shields.io/badge/docs-latest-blue.svg"></a><!--</br><a href="https://fourierflows.github.io/PassiveTracerFlows.jl/stable/"><img src="https://img.shields.io/badge/docs-stable-blue.svg"></a>--></td> <td><a href="https://travis-ci.org/FourierFlows/PassiveTracerFlows.jl"><img src="https://travis-ci.org/FourierFlows/PassiveTracerFlows.jl.svg?branch=master" title="Build Status"></a><td><a href="https://ci.appveyor.com/project/navidcy/passivetracerflows-jl"><img src="https://ci.appveyor.com/api/projects/status/yb5ywk9bof6u3nyg?svg=true" title="Build Status"></a></td> 
-    </tr>
- </table>
+# PassiveTracerFlows.jl
+
+ <p align="left">
+     <a href="https://travis-ci.org/FourierFlows/PassiveTracerFlows.jl">
+          <img src="https://travis-ci.org/FourierFlows/PassiveTracerFlows.jl.svg?branch=master" title="Build Status">
+     </a>
+     <a href="https://ci.appveyor.com/project/navidcy/passivetracerflows-jl">
+          <img src="https://ci.appveyor.com/api/projects/status/yb5ywk9bof6u3nyg?svg=true" title="Build Status">
+     </a>
+     <a href="https://GeophysicalFlows.github.io/PassiveTracerFlows.jl/stable/">
+         <img src="https://img.shields.io/badge/docs-stable-blue.svg">
+     </a>
+     <a href="https://fourierflows.github.io/PassiveTracerFlows.jl/latest/">
+         <img src="https://img.shields.io/badge/docs-latest-blue.svg">
+     </a>
+     <a href='https://coveralls.io/github/FourierFlows/PassiveTracerFlows.jl?branch=master'><img src='https://coveralls.io/repos/github/FourierFlows/PassiveTracerFlows.jl/badge.svg?branch=master' alt='Coverage Status' /></a>
+ </p>
+
+ This package leverages the [FourierFlows.jl]() framework to provide modules for solving passive tracer advection-diffusion problems on periodic domains using Fourier-based pseudospectral methods.
+
+ ## Installation
+
+ To install, do
+ ```julia
+ ] add PassiveTracerFlows
+ ```
+
+ See `examples/` for example scripts.
+
+ ## Modules
+
+ * `TracerAdvDiff`: advection-diffusion of a passive tracer in 2D domain.
+
+
+ [FourierFlows.jl]: https://github.com/FourierFlows/FourierFlows.jl

REQUIRE

@@ -0,0 +1,7 @@
+julia 1.0
+
+FFTW
+FourierFlows 0.3.0
+JLD2
+PyPlot
+Reexport

appveyor.yml

@@ -1,6 +1,5 @@
 environment:
   matrix:
-  - julia_version: 0.7
   - julia_version: 1
   - julia_version: nightly
 
@@ -17,7 +16,6 @@ matrix:
 branches:
   only:
     - master
-    - TowardsJulia1.0
     - /release-.*/
 
 notifications:

docs/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+Documenter = "~0.20"

docs/make.jl

@@ -21,8 +21,6 @@ makedocs(
 deploydocs(
        repo = "github.com/FourierFlows/PassiveTracerFlows.jl.git",
      target = "build",
-      julia = "0.7",
-     osname = "linux",
-       deps = nothing,
-       make = nothing
- )
+      deps = nothing,
+      make = nothing
+)