Update CI and dependencies + format code consistently (#8)

.JuliaFormatter.toml

@@ -0,0 +1 @@
+style="blue"

.github/workflows/ci.yml → .github/workflows/CI.yml

@@ -3,7 +3,7 @@ name: CI
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
 
 jobs:
@@ -60,25 +60,3 @@ jobs:
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: lcov.info
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1'
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()'
-      - run: |
-          julia --project=docs -e '
-            using Documenter: doctest
-            using StochasticOptimalTransport
-            doctest(StochasticOptimalTransport)'
-      - run: julia --project=docs docs/make.jl
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/CompatHelper.yml

@@ -7,10 +7,19 @@ jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "2"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main(; subdirs=["", "test", "docs"])
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/Docs.yml

@@ -0,0 +1,27 @@
+name: Docs
+
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+
+jobs:
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - run: julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/DocsPreviewCleanup.yml

@@ -0,0 +1,26 @@
+name: DocsPreviewCleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "documenter@juliadocs.github.io"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

.github/workflows/Format.yml

@@ -0,0 +1,20 @@
+name: Format
+
+on:
+  pull_request:
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: 1
+      - run: |
+          julia  -e 'using Pkg; Pkg.add("JuliaFormatter")'
+          julia  -e 'using JuliaFormatter; format("."; verbose=true)'
+      - uses: reviewdog/action-suggester@v1
+        with:
+          tool_name: JuliaFormatter
+          fail_on_error: true

Project.toml

@@ -1,14 +1,14 @@
 name = "StochasticOptimalTransport"
 uuid = "d0107fbf-5e6e-4997-ac8d-099d2392f4a6"
 authors = ["David Widmann <david.widmann@it.uu.se>"]
-version = "0.1.0"
+version = "0.1.1"
 
 [deps]
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 
 [compat]
-StatsFuns = "0.9"
+LogExpFunctions = "0.2"
 julia = "1.3"

README.md

@@ -4,9 +4,10 @@ Julia implementation of stochastic optimization algorithms for large-scale optim
 
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://devmotion.github.io/StochasticOptimalTransport.jl/stable)
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://devmotion.github.io/StochasticOptimalTransport.jl/dev)
-[![Build Status](https://github.com/devmotion/StochasticOptimalTransport.jl/workflows/CI/badge.svg?branch=master)](https://github.com/devmotion/StochasticOptimalTransport.jl/actions?query=workflow%3ACI%20branch%3Amaster)
-[![Coverage](https://codecov.io/gh/devmotion/StochasticOptimalTransport.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/devmotion/StochasticOptimalTransport.jl)
-[![Coverage](https://coveralls.io/repos/github/devmotion/StochasticOptimalTransport.jl/badge.svg?branch=master)](https://coveralls.io/github/devmotion/StochasticOptimalTransport.jl?branch=master)
+[![Build Status](https://github.com/devmotion/StochasticOptimalTransport.jl/workflows/CI/badge.svg?branch=main)](https://github.com/devmotion/StochasticOptimalTransport.jl/actions?query=workflow%3ACI%20branch%3Amain)
+[![Coverage](https://codecov.io/gh/devmotion/StochasticOptimalTransport.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/devmotion/StochasticOptimalTransport.jl)
+[![Coverage](https://coveralls.io/repos/github/devmotion/StochasticOptimalTransport.jl/badge.svg?branch=main)](https://coveralls.io/github/devmotion/StochasticOptimalTransport.jl?branch=main)
+[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
 
 # Bibliography
 

docs/Manifest.toml

@@ -1,27 +1,33 @@
 # This file is machine-generated - editing it directly is not advised
 
+[[ArgTools]]
+uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
+
+[[Artifacts]]
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[Dates]]
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
-[[Distributed]]
-deps = ["Random", "Serialization", "Sockets"]
-uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
-
 [[DocStringExtensions]]
 deps = ["LibGit2", "Markdown", "Pkg", "Test"]
-git-tree-sha1 = "50ddf44c53698f5e784bbebb3f4b21c5807401b1"
+git-tree-sha1 = "9d4f64f79012636741cf01133158a54b24924c32"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-version = "0.8.3"
+version = "0.8.4"
 
 [[Documenter]]
 deps = ["Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
-git-tree-sha1 = "c01a7e8bcf7a6693444a52a0c5ac8b4e9528600e"
+git-tree-sha1 = "3ebb967819b284dc1e3c0422229b58a40a255649"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "0.26.0"
+version = "0.26.3"
+
+[[Downloads]]
+deps = ["ArgTools", "LibCURL", "NetworkOptions"]
+uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 
 [[IOCapture]]
 deps = ["Logging"]
@@ -39,39 +45,71 @@ git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.21.1"
 
+[[LibCURL]]
+deps = ["LibCURL_jll", "MozillaCACerts_jll"]
+uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
+
+[[LibCURL_jll]]
+deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
+uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
+
 [[LibGit2]]
-deps = ["Printf"]
+deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 
+[[LibSSH2_jll]]
+deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
+uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
+
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
+[[LinearAlgebra]]
+deps = ["Libdl"]
+uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[LogExpFunctions]]
+deps = ["DocStringExtensions", "LinearAlgebra"]
+git-tree-sha1 = "ed26854d7c2c867d143f0e07c198fc9e8b721d10"
+uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
+version = "0.2.3"
+
 [[Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[Markdown]]
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
+[[MbedTLS_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
+[[MozillaCACerts_jll]]
+uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
+
+[[NetworkOptions]]
+uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
+
 [[Parsers]]
 deps = ["Dates"]
-git-tree-sha1 = "6370b5b3cf2ce5a3d2b6f7ab2dc10f374e4d7d2b"
+git-tree-sha1 = "c8abc88faa3f7a3950832ac5d6e690881590d6dc"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "1.0.14"
+version = "1.1.0"
 
 [[Pkg]]
-deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[Printf]]
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [[REPL]]
-deps = ["InteractiveUtils", "Markdown", "Sockets"]
+deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 
 [[Random]]
@@ -87,13 +125,30 @@ uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 [[Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
+[[SparseArrays]]
+deps = ["LinearAlgebra", "Random"]
+uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[[Statistics]]
+deps = ["LinearAlgebra", "SparseArrays"]
+uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
 [[StochasticOptimalTransport]]
+deps = ["LinearAlgebra", "LogExpFunctions", "Random", "Statistics"]
 path = ".."
 uuid = "d0107fbf-5e6e-4997-ac8d-099d2392f4a6"
-version = "0.1.0"
+version = "0.1.1"
+
+[[TOML]]
+deps = ["Dates"]
+uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+
+[[Tar]]
+deps = ["ArgTools", "SHA"]
+uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
 
 [[Test]]
-deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[UUIDs]]
@@ -102,3 +157,15 @@ uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[Zlib_jll]]
+deps = ["Libdl"]
+uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+
+[[nghttp2_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
+
+[[p7zip_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"

docs/Project.toml

@@ -1,3 +1,8 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 StochasticOptimalTransport = "d0107fbf-5e6e-4997-ac8d-099d2392f4a6"
+
+[compat]
+Documenter = "0.26"
+StochasticOptimalTransport = "0.1"
+julia = "1.3"