[MRG] Cleanup minimal build and add separate build for pep8 (#210)

* cleanup requiorement minimal

* add pep8 build

* cleanup sklearn

* skip test if no sklearn

* debug build yaml

* comment error out in test (test sklearn)

* maybe small stuff for better robustness : copy the sub-array

* bump verison minimal build

* update version strict requireent

* update version strict requirement last change

Author: rflamary

.github/requirements_strict.txt

@@ -1,7 +1,4 @@
-numpy==1.16.*
-scipy==1.0.*
-cython==0.23.*
-matplotlib
-cvxopt
-scikit-learn
+numpy
+scipy>=1.3
+cython
 pytest

.github/workflows/build_tests.yml

@@ -30,14 +30,7 @@ jobs:
       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
+        pip install pytest "pytest-cov<2.6" codecov
     - name: Install POT
       run: |
         pip install -e .
@@ -48,14 +41,37 @@ jobs:
       run: |
         codecov
 
+  pep8:
+    runs-on: ubuntu-latest
+    strategy:
+       max-parallel: 4
+       matrix:
+         python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - 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]
+        python-version: [3.8]
 
     steps:
     - uses: actions/checkout@v1
@@ -68,7 +84,6 @@ jobs:
         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 .
@@ -95,7 +110,6 @@ jobs:
          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 .
@@ -122,7 +136,6 @@ jobs:
         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 .

.gitignore

@@ -40,6 +40,9 @@ var/
 *.manifest
 *.spec
 
+# env
+pythonenv3.8/
+
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt

Makefile

@@ -45,10 +45,10 @@ pep8 :
 	flake8 examples/ ot/ test/
 
 test : FORCE pep8
-	$(PYTHON) -m pytest -v test/ --doctest-modules --ignore ot/gpu/  --cov=ot --cov-report html:cov_html
+	$(PYTHON) -m pytest -v test/ --doctest-modules --ignore ot/gpu/  
 
 pytest : FORCE 
-	$(PYTHON) -m pytest -v test/ --doctest-modules --ignore ot/gpu/  --cov=ot
+	$(PYTHON) -m pytest -v test/ --doctest-modules --ignore ot/gpu/  
 
 release :
 	twine upload dist/*

ot/lp/__init__.py

@@ -426,7 +426,7 @@ def f(b):
     nb = b.shape[1]
 
     if processes > 1:
-        res = parmap(f, [b[:, i] for i in range(nb)], processes)
+        res = parmap(f, [b[:, i].copy() for i in range(nb)], processes)
     else:
         res = list(map(f, [b[:, i].copy() for i in range(nb)]))
 

test/test_da.py

@@ -6,11 +6,18 @@
 
 import numpy as np
 from numpy.testing import assert_allclose, assert_equal
+import pytest
 
 import ot
 from ot.datasets import make_data_classif
 from ot.utils import unif
 
+try:  # test if cudamat installed
+    import sklearn  # noqa: F401
+    nosklearn = False
+except ImportError:
+    nosklearn = True
+
 
 def test_sinkhorn_lpl1_transport_class():
     """test_sinkhorn_transport
@@ -691,6 +698,7 @@ def test_jcpot_barycenter():
     np.testing.assert_allclose(prop, [1 - pt, pt], rtol=1e-3, atol=1e-3)
 
 
+@pytest.mark.skipif(nosklearn, reason="No sklearn available")
 def test_emd_laplace_class():
     """test_emd_laplace_transport
     """