Merge branch 'dfsg/latest' into debian/sid

3 files changed, 161 insertions, 52 deletions

diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
index 41b08b3..ee5a435 100644
--- a/.github/workflows/build_tests.yml
+++ b/.github/workflows/build_tests.yml
@@ -1,10 +1,13 @@
-name: build
+name: Tests
 
 on:
-  push:
-
+  workflow_dispatch:
   pull_request:
-
+    branches:
+      - 'master'    
+  push:
+    branches:
+      - 'master'  
   create:
     branches:
       - 'master'
@@ -15,10 +18,11 @@ jobs:
   linux:
 
     runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'no ci')"
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.5, 3.6, 3.7, 3.8]
+        python-version: [ "3.6", "3.7", "3.8", "3.9"]
 
     steps:
     - uses: actions/checkout@v1
@@ -26,63 +30,70 @@ jobs:
       uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install POT
+      run: |
+        pip install -e .
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
-        pip install flake8 pytest "pytest-cov<2.6" codecov
-        pip install -U "sklearn"
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics
-    - name: Install POT
-      run: |
-        pip install -e .
+        pip install pytest "pytest-cov<2.6" codecov
     - name: Run tests
       run: |
-        python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot
+        python -m pytest --durations=20 -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot --color=yes
     - name: Upload codecov
       run: |
         codecov
 
+  pep8:
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'no pep8')"
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics
 
   linux-minimal-deps:
 
     runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 4
-      matrix:
-        python-version: [3.6]
-
+    if: "!contains(github.event.head_commit.message, 'no ci')"
     steps:
     - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python 
       uses: actions/setup-python@v1
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: 3.9
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r .github/requirements_strict.txt
         pip install pytest
-        pip install -U "sklearn"
     - name: Install POT
       run: |
         pip install -e .
     - name: Run tests
       run: |
-        python -m pytest -v test/ ot/ --ignore ot/gpu/
+        python -m pytest --durations=20 -v test/ ot/ --ignore ot/gpu/ --color=yes
 
 
   macos:
-     runs-on: macOS-latest
+     runs-on: macos-latest
+     if: "!contains(github.event.head_commit.message, 'no ci')"
      strategy:
        max-parallel: 4
        matrix:
-         python-version: [3.7]
+         python-version: ["3.7", "3.8", "3.9"]
 
      steps:
      - uses: actions/checkout@v1
@@ -90,26 +101,26 @@ jobs:
        uses: actions/setup-python@v1
        with:
          python-version: ${{ matrix.python-version }}
+     - name: Install POT
+       run: |
+         pip install -e .
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -r requirements.txt
          pip install pytest "pytest-cov<2.6"
-         pip install -U "sklearn"
-     - name: Install POT
-       run: |
-         pip install -e .
      - name: Run tests
        run: |
-         python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot
+         python -m pytest --durations=20  -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot --color=yes
 
 
   windows:
-    runs-on: windows-2019
+    runs-on: windows-latest
+    if: "!contains(github.event.head_commit.message, 'no ci')"
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.7]
+        python-version: ["3.7", "3.8", "3.9"]
 
     steps:
     - uses: actions/checkout@v1
@@ -117,15 +128,15 @@ jobs:
       uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install POT
+      run: |
+        python -m pip install -e .
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install pytest "pytest-cov<2.6"
-        pip install -U "sklearn"
-    - name: Install POT
-      run: |
-        pip install -e .
+        python -m pip install -r .github/requirements_test_windows.txt
+        python -m pip install torch==1.8.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install pytest "pytest-cov<2.6"
     - name: Run tests
       run: |
-        python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot
+        python -m pytest --durations=20  -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot --color=yes
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 662a604..a935a5e 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -1,19 +1,21 @@
-name: Build dist and wheels
+name: Build wheels
 
 on:
+  workflow_dispatch:
   release:
+  pull_request:
   push:
     branches:
-      - "master"
+      - "*"
 
 jobs:
   build_wheels:
     name: ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
+    if: "contains(github.event.head_commit.message, 'build wheels')"
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        # macos-latest, windows-latest
 
     steps:
     - uses: actions/checkout@v1
@@ -30,17 +32,58 @@ jobs:
 
     - name: Install cibuildwheel
       run: |
-        python -m pip install cibuildwheel==1.3.0
+        python -m pip install cibuildwheel==2.2.2
 
-    - name: Install Visual C++ for Python 2.7
-      if: startsWith(matrix.os, 'windows')
+    - name: Build wheels
+      env:
+        CIBW_SKIP: "pp*-win* pp*-macosx* cp2* pp*" # remove pypy on mac and win (wrong version)
+        CIBW_BEFORE_BUILD: "pip install numpy cython"
+      run: |
+        python -m cibuildwheel --output-dir wheelhouse
+
+    - uses: actions/upload-artifact@v1
+      with:
+        name: wheels
+        path: ./wheelhouse
+
+
+  build_all_wheels:
+    name: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    if: "contains(github.event.head_commit.message, 'build all wheels')"
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install -U "cython"
+
+    - name: Install cibuildwheel
       run: |
-        choco install vcpython27 -f -y
+        python -m pip install cibuildwheel==2.2.2
 
-    - name: Build wheel
+    - name: Set up QEMU
+      if: runner.os == 'Linux'
+      uses: docker/setup-qemu-action@v1
+      with:
+        platforms: all
+
+    - name: Build wheels
       env:
-        CIBW_SKIP: "pp*-win* pp*-macosx* cp2* pp*" # remove pypy on mac and win (wrong version)
+        CIBW_SKIP: "pp*-win* pp*-macosx* cp2* pp* cp*musl*" # remove pypy on mac and win (wrong version)
         CIBW_BEFORE_BUILD: "pip install numpy cython"
+        CIBW_ARCHS_LINUX: auto aarch64 # force aarch64 with QEMU
+        CIBW_ARCHS_MACOS: x86_64 universal2 arm64
       run: |
         python -m cibuildwheel --output-dir wheelhouse
 
@@ -48,3 +91,4 @@ jobs:
       with:
         name: wheels
         path: ./wheelhouse
+
diff --git a/.github/workflows/build_wheels_weekly.yml b/.github/workflows/build_wheels_weekly.yml
new file mode 100644
index 0000000..2964844
--- /dev/null
+++ b/.github/workflows/build_wheels_weekly.yml
@@ -0,0 +1,54 @@
+name: Build all wheels
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '30 0 * * 1'
+  push:
+    branches:
+      - "master"
+      
+jobs:
+  build_wheels:
+    name: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install -U "cython"
+
+    - name: Install cibuildwheel
+      run: |
+        python -m pip install cibuildwheel==2.2.2
+
+    - name: Set up QEMU
+      if: runner.os == 'Linux'
+      uses: docker/setup-qemu-action@v1
+      with:
+        platforms: all
+
+    - name: Build wheels
+      env:
+        CIBW_SKIP: "pp*-win* pp*-macosx* cp2* pp* cp*musl*" # remove pypy on mac and win (wrong version)
+        CIBW_BEFORE_BUILD: "pip install numpy cython"
+        CIBW_ARCHS_LINUX: auto aarch64 # force aarch64 with QEMU
+        CIBW_ARCHS_MACOS: x86_64 universal2 arm64
+      run: |
+        python -m cibuildwheel --output-dir wheelhouse
+
+    - uses: actions/upload-artifact@v1
+      with:
+        name: wheels
+        path: ./wheelhouse