Use PythonOT (#64)

Author: devmotion

.github/workflows/CI.yml

@@ -23,27 +23,13 @@ jobs:
           - macOS-latest 
         arch:
           - x64
-          - x86
-        exclude:
-          - os: ubuntu-latest
-            arch: x86
-          - os: macOS-latest
-            arch: x86
         include:
           - version: '1'
             os: ubuntu-latest
             arch: x64
             coverage: true
     steps:
       - uses: actions/checkout@v2
-      - name: Install python
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.x'
-          architecture: ${{ matrix.arch }}
-      # Limitation of pip: https://pythonot.github.io/index.html#pip-installation
-      - run: python -m pip install cython numpy
-      - run: python -m pip install pot
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
@@ -59,11 +45,11 @@ jobs:
             ${{ runner.os }}-test-
             ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@latest
-        env:
-          PYTHON: python
       - uses: julia-actions/julia-runtest@latest
+        with:
+          coverage: ${{ matrix.coverage || false }}
         env:
-          PYTHON: python
+          PYTHON: '' # Use Conda.jl also on Linux
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.coverage
       - uses: codecov/codecov-action@v1

.github/workflows/Documentation.yml

@@ -12,24 +12,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Install python
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.x'
-      # Limitation of pip: https://pythonot.github.io/index.html#pip-installation
-      - run: python -m pip install cython numpy
-      - run: python -m pip install pot
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1'
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-        env:
-          PYTHON: python
-      - name: Build and deploy
+      - name: Install dependencies, build and deploy
+        run: |
+          using Pkg: Pkg
+          Pkg.develop(Pkg.PackageSpec(path=pwd()))
+          Pkg.instantiate()
+          include(joinpath(pwd(), "docs", "make.jl"))
         env:
-          PYTHON: python
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+          PYTHON: '' # Use Conda.jl also on Linux
           GKSwstype: nul # avoid (irrelevant) error messages from GR
-        run: julia --project=docs/ docs/make.jl
+        shell: julia --color=yes --project=docs/ {0}

Project.toml

@@ -1,28 +1,26 @@
 name = "OptimalTransport"
 uuid = "7e02d93a-ae51-4f58-b602-d97af76e3b33"
 authors = ["zsteve <[email protected]>"]
-version = "0.2.4"
+version = "0.3.0"
 
 [deps]
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [compat]
 Distances = "0.9.0, 0.10"
 IterativeSolvers = "0.8.4, 0.9"
 MathOptInterface = "0.9"
-Requires = "1.1"
 julia = "1"
 
 [extras]
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
+PythonOT = "3c485715-4278-42b2-9b5f-8f00e43c12ef"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Tulip = "6dd1b50a-3aae-11e9-10b5-ef983d2400fa"
 
 [targets]
-test = ["Tulip", "PyCall", "Random", "Test"]
+test = ["Tulip", "PythonOT", "Random", "Test"]

README.md

@@ -39,6 +39,11 @@ Contributors include:
 - Davi Barreira (FGV)
 - Stephen Zhang (UBC)
 
+## Related packages
+
+- [PythonOT.jl](https://github.com/JuliaOptimalTransport/PythonOT.jl): Julia interface for the [Python Optimal Transport (POT) package](https://pythonot.github.io/).
+- [StochasticOptimalTransport.jl](https://github.com/JuliaOptimalTransport/StochasticOptimalTransport.jl): Julia implementation of stochastic optimization algorithms for large-scale optimal transport.
+
 ## References
 
 - Peyré, G. and Cuturi, M., 2019. Computational optimal transport. Foundations and Trends® in Machine Learning, 11(5-6), pp.355-607.

docs/Manifest.toml

@@ -17,9 +17,9 @@ version = "0.7.0"
 
 [[Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "c3598e525718abcc440f69cc6d5f60dda0a1b61e"
+git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2"
 uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
-version = "1.0.6+5"
+version = "1.0.8+0"
 
 [[CodecBzip2]]
 deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"]
@@ -33,12 +33,6 @@ git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da"
 uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
 version = "0.7.0"
 
-[[Conda]]
-deps = ["JSON", "VersionParsing"]
-git-tree-sha1 = "299304989a5e6473d985212c28928899c74e9421"
-uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d"
-version = "1.5.2"
-
 [[Dates]]
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -66,10 +60,10 @@ deps = ["ArgTools", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 
 [[HTTP]]
-deps = ["Base64", "Dates", "IniFile", "MbedTLS", "Sockets"]
-git-tree-sha1 = "c7ec02c4c6a039a98a15f955462cd7aea5df4508"
+deps = ["Base64", "Dates", "IniFile", "MbedTLS", "NetworkOptions", "Sockets", "URIs"]
+git-tree-sha1 = "b855bf8247d6e946c75bb30f593bfe7fe591058d"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "0.8.19"
+version = "0.9.8"
 
 [[IOCapture]]
 deps = ["Logging"]
@@ -89,9 +83,9 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
 [[IterativeSolvers]]
 deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"]
-git-tree-sha1 = "6f5ef3206d9dc6510a8b8e2334b96454a2ade590"
+git-tree-sha1 = "1a8c6237e78b714e901e406c096fc8a65528af7d"
 uuid = "42fd0dbc-a981-5370-80f2-aaf504508153"
-version = "0.9.0"
+version = "0.9.1"
 
 [[JLLWrappers]]
 deps = ["Preferences"]
@@ -143,12 +137,6 @@ version = "2.8.0"
 [[Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
-[[MacroTools]]
-deps = ["Markdown", "Random"]
-git-tree-sha1 = "6a8a2a625ab0dea913aba95c11370589e0239ff0"
-uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
-version = "0.5.6"
-
 [[Markdown]]
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
@@ -185,10 +173,10 @@ version = "0.2.19"
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 
 [[OptimalTransport]]
-deps = ["Distances", "IterativeSolvers", "LinearAlgebra", "MathOptInterface", "Requires", "SparseArrays"]
+deps = ["Distances", "IterativeSolvers", "LinearAlgebra", "MathOptInterface", "SparseArrays"]
 path = ".."
 uuid = "7e02d93a-ae51-4f58-b602-d97af76e3b33"
-version = "0.2.1"
+version = "0.3.0"
 
 [[OrderedCollections]]
 git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c"
@@ -215,12 +203,6 @@ version = "1.2.2"
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
-[[PyCall]]
-deps = ["Conda", "Dates", "Libdl", "LinearAlgebra", "MacroTools", "Serialization", "VersionParsing"]
-git-tree-sha1 = "169bb8ea6b1b143c5cf57df6d34d022a7b60c6db"
-uuid = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
-version = "1.92.3"
-
 [[REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
@@ -234,12 +216,6 @@ git-tree-sha1 = "b3fb709f3c97bfc6e948be68beeecb55a0b340ae"
 uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 version = "1.1.1"
 
-[[Requires]]
-deps = ["UUIDs"]
-git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621"
-uuid = "ae029012-a4dd-5104-9daa-d747884805df"
-version = "1.1.3"
-
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
@@ -280,18 +256,18 @@ git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.9.5"
 
+[[URIs]]
+git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355"
+uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
+version = "1.3.0"
+
 [[UUIDs]]
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
-[[VersionParsing]]
-git-tree-sha1 = "80229be1f670524750d905f8fc8148e5a8c4537f"
-uuid = "81def892-9a0e-5fdd-b105-ffc91e053289"
-version = "1.2.0"
-
 [[ZipFile]]
 deps = ["Libdl", "Printf", "Zlib_jll"]
 git-tree-sha1 = "c3a5637e27e914a7a445b8d0ad063d701931e9f7"

docs/Project.toml

@@ -2,11 +2,9 @@
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 OptimalTransport = "7e02d93a-ae51-4f58-b602-d97af76e3b33"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 
 [compat]
 Documenter = "0.26"
 Literate = "2.8"
-OptimalTransport = "0.2"
-PyCall = "1"
+OptimalTransport = "0.3"
 julia = "1"

docs/make.jl

@@ -55,10 +55,9 @@ for name in EXAMPLES
 end
 
 using Documenter
-using PyCall
 
 makedocs(;
-    modules=[OptimalTransport, POT],
+    modules=[OptimalTransport],
     repo="https://github.com/JuliaOptimalTransport/OptimalTransport.jl/blob/{commit}{path}#L{line}",
     sitename="OptimalTransport.jl",
     format=Documenter.HTML(;
@@ -68,7 +67,6 @@ makedocs(;
     ),
     pages=[
         "Home" => "index.md",
-        "POT" => "pot.md",
         "Examples" => [joinpath("examples", "$(name).md") for name in EXAMPLES],
     ],
     strict=true,