Update CI (#18)

* Update CI.yml

* Update Docs.yml

* Update JuliaNightly.yml

* Simplify docs and remove Manifest file

* Update sinkhorn2 doctest

* Actually fix doctest

* Use example from POT documentation

* Actually use example

* Update lib.jl

* Update lib.jl

* Revert example

Author: devmotion

.github/workflows/CI.yml

@@ -6,6 +6,12 @@ on:
       - main
   pull_request:
 
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ (matrix.python && 'system Python') || 'conda' }}
@@ -38,9 +44,6 @@ jobs:
           python-version: '3.x'
           architecture: ${{ matrix.arch }}
         if: matrix.python
-      # Limitation of pip: https://pythonot.github.io/index.html#pip-installation
-      - run: python -m pip install cython numpy
-        if: matrix.python
       - run: python -m pip install pot
         if: matrix.python
       - uses: julia-actions/setup-julia@v1
@@ -67,7 +70,7 @@ jobs:
           PYTHON: ${{ matrix.python }}
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.coverage
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v2
         if: matrix.coverage
         with:
           file: lcov.info

.github/workflows/Docs.yml

@@ -7,6 +7,12 @@ on:
     tags: '*'
   pull_request:
 
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   docs:
     name: Documentation
@@ -16,14 +22,7 @@ jobs:
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1'
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()'
-        env:
-          PYTHON: ''
-      - run: julia --project=docs docs/make.jl
+      - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/JuliaNightly.yml

@@ -9,6 +9,12 @@ on:
       - main
   pull_request:
 
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ (matrix.python && 'system Python') || 'conda' }}
@@ -35,9 +41,6 @@ jobs:
           python-version: '3.x'
           architecture: ${{ matrix.arch }}
         if: matrix.python
-      # Limitation of pip: https://pythonot.github.io/index.html#pip-installation
-      - run: python -m pip install cython numpy
-        if: matrix.python
       - run: python -m pip install pot
         if: matrix.python
       - uses: julia-actions/setup-julia@v1

.gitignore

@@ -1,6 +1,5 @@
 *.jl.*.cov
 *.jl.cov
 *.jl.mem
-/Manifest.toml
-/test/Manifest.toml
+Manifest.toml
 /docs/build/

docs/Manifest.toml

@@ -222,9 +222,8 @@ julia> ν = [0.0, 1.0];
 
 julia> C = [0.0 1.0; 2.0 0.0; 0.5 1.5];
 
-julia> round.(sinkhorn2(μ, ν, C, 0.01); sigdigits=6)
-1-element Vector{Float64}:
- 0.95
+julia> round(sinkhorn2(μ, ν, C, 0.01); sigdigits=6)
+0.95
 ```
 
 It is possible to provide multiple target marginals as columns of a matrix.
@@ -258,17 +257,17 @@ in the Python Optimal Transport package. Keyword arguments are listed in the doc
 # Examples
 
 ```jldoctest
-julia> xsource = [1];
+julia> xsource = [1.0];
 
-julia> xtarget = [2, 3];
+julia> xtarget = [2.0, 3.0];
 
 julia> ε = 0.01;
 
 julia> empirical_sinkhorn_divergence(xsource, xtarget, ε) ≈
-       sinkhorn2([1], [0.5, 0.5], [1 4], ε) -
+       sinkhorn2([1], [0.5, 0.5], [1.0 4.0], ε) -
        (
            sinkhorn2([1], [1], zeros(1, 1), ε) +
-           sinkhorn2([0.5, 0.5], [0.5, 0.5], [0 1; 1 0], ε)
+           sinkhorn2([0.5, 0.5], [0.5, 0.5], Float64[0 1; 1 0], ε)
        ) / 2
 true
 ```