Doc ci build

.circleci/artifact_path

@@ -0,0 +1 @@
+0/docs/build/html/index.html

.circleci/config.yml

@@ -0,0 +1,137 @@
+# Tagging a commit with [circle front] will build the front page and perform test-doc.
+# Tagging a commit with [circle full] will build everything.
+version: 2
+jobs:
+    build_docs:
+      docker:
+        - image: circleci/python:3.7-stretch
+      steps:
+        - checkout
+        - run:
+            name: Set BASH_ENV
+            command: |
+              echo "set -e" >> $BASH_ENV
+              echo "export DISPLAY=:99" >> $BASH_ENV
+              echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV
+              echo "BASH_ENV:"
+              cat $BASH_ENV
+
+        - run:
+            name: Merge with upstream
+            command: |
+              echo $(git log -1 --pretty=%B) | tee gitlog.txt
+              echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
+              if [[ $(cat merge.txt) != "" ]]; then
+                echo "Merging $(cat merge.txt)";
+                git remote add upstream git://github.com/PythonOT/POT.git;
+                git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge";
+                git fetch upstream master;
+              fi
+
+        # Load our data
+        - restore_cache:
+            keys:
+              - data-cache-0
+              - pip-cache
+
+        - run:
+            name: Spin up Xvfb
+            command: |
+              /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
+
+        # https://github.com/ContinuumIO/anaconda-issues/issues/9190#issuecomment-386508136
+        # https://github.com/golemfactory/golem/issues/1019
+        - run:
+            name: Fix libgcc_s.so.1 pthread_cancel bug
+            command: |
+              sudo apt-get install qt5-default
+
+        - run:
+            name: Get Python running
+            command: |
+              python -m pip install --user --upgrade --progress-bar off pip
+              python -m pip install --user --upgrade --progress-bar off -r requirements.txt
+              python -m pip install --user --upgrade --progress-bar off -r docs/requirements.txt
+              python -m pip install --user --upgrade --progress-bar off ipython "https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master" memory_profiler
+              python -m pip install --user -e .
+
+        - save_cache:
+            key: pip-cache
+            paths:
+              - ~/.cache/pip
+
+        # Look at what we have and fail early if there is some library conflict
+        - run:
+            name: Check installation
+            command: |
+               which python
+               python -c "import ot"
+
+        # Build docs
+        - run:
+            name: make html
+            command: |
+              cd docs;
+              make html;
+
+        # Save the outputs
+        - store_artifacts:
+            path: docs/build/html/
+            destination: dev
+        - persist_to_workspace:
+            root: docs/build
+            paths:
+              - html
+
+    deploy:
+      docker:
+        - image: circleci/python:3.6-jessie
+      steps:
+        - attach_workspace:
+            at: /tmp/build
+        - run:
+            name: Fetch docs
+            command: |
+              set -e
+              mkdir -p ~/.ssh
+              echo -e "Host *\nStrictHostKeyChecking no" > ~/.ssh/config
+              chmod og= ~/.ssh/config
+              if [ ! -d ~/PythonOT.github.io ]; then
+                git clone git@github.com:/PythonOT/PythonOT.github.io.git ~/PythonOT.github.io --depth=1
+              fi
+        - run:
+            name: Deploy docs
+            command: |
+              set -e;
+              if [ "${CIRCLE_BRANCH}" == "master" ]; then
+                git config --global user.email "circle@PythonOT.com";
+                git config --global user.name "Circle CI";
+                cd ~/PythonOT.github.io;
+                git checkout master
+                git remote -v
+                git fetch origin
+                git reset --hard origin/master
+                git clean -xdf
+                echo "Deploying dev docs for ${CIRCLE_BRANCH}.";
+                cp -a /tmp/build/html/* .;
+                touch .nojekyll;
+                git add -A;
+                git commit -m "CircleCI update of dev docs (${CIRCLE_BUILD_NUM}).";
+                git push origin master;
+              else
+                echo "No deployment (build: ${CIRCLE_BRANCH}).";
+              fi
+
+workflows:
+  version: 2
+
+  default:
+    jobs:
+      - build_docs
+      - deploy:
+          requires:
+            - build_docs
+          filters:
+            branches:
+              only:
+                - master

.github/workflows/main.yml

@@ -0,0 +1,12 @@
+on: [status]
+jobs:
+  circleci_artifacts_redirector_job:
+    runs-on: ubuntu-latest
+    name: Run CircleCI artifacts redirector
+    steps:
+      - name: GitHub Action step
+        uses: larsoner/circleci-artifacts-redirector-action@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          artifact-path: 0/dev/index.html
+          circleci-jobs: build_docs

.github/workflows/pythonpackage.yml

@@ -1,6 +1,14 @@
 name: Test Package
 
-on: [push]
+on:
+  push:
+    branches:
+      - '**'
+  create:
+    branches:
+      - 'master'
+    tags:
+      - '**'
 
 jobs:
   build:
@@ -9,7 +17,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [2.7, 3.5, 3.6, 3.7]
+        python-version: [3.5, 3.6, 3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v1
@@ -21,10 +29,20 @@ 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: |
-        pip install flake8
         # 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 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics        
+    - name: Install POT
+      run: |
+        pip install -e .
+    - name: Run tests
+      run: |
+        python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot
+    - name: Upload codecov
+      run: |
+        codecov

.travis.yml

@@ -34,7 +34,7 @@ before_install:
 install:
   - pip install -r requirements.txt
   - pip install -U "numpy>=1.14" scipy  # for numpy array formatting in doctests
-  - pip install flake8 pytest "pytest-cov<2.6"
+  - pip install flake8 pytest "pytest-cov<2.6" codecov
   - pip install -U "sklearn"
   - pip install .
 # command to run tests + check syntax style
@@ -45,3 +45,6 @@ script:
   - flake8 examples/ ot/ test/
   - python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot
   # - py.test ot test
+after_script:
+  # Need to run from source dir to execute "git" commands
+  - codecov;

README.md

@@ -3,6 +3,7 @@
 [![PyPI version](https://badge.fury.io/py/POT.svg)](https://badge.fury.io/py/POT)
 [![Anaconda Cloud](https://anaconda.org/conda-forge/pot/badges/version.svg)](https://anaconda.org/conda-forge/pot)
 [![Build Status](https://travis-ci.org/PythonOT/POT.svg?branch=master)](https://travis-ci.org/PythonOT/POT)
+[![Codecov Status](https://codecov.io/gh/PythonOT/POT/branch/master/graph/badge.svg)](https://codecov.io/gh/PythonOT/POT)
 [![Documentation Status](https://readthedocs.org/projects/pot/badge/?version=latest)](http://pot.readthedocs.io/en/latest/?badge=latest)
 [![Downloads](https://pepy.tech/badge/pot)](https://pepy.tech/project/pot)
 [![Anaconda downloads](https://anaconda.org/conda-forge/pot/badges/downloads.svg)](https://anaconda.org/conda-forge/pot)

codecov.yml

@@ -0,0 +1,14 @@
+coverage:
+  precision: 2
+  round: down
+  range: "70...100"
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 0.01
+    patch: false
+    changes: false
+comment:
+  layout: "header, diff, sunburst, uncovered"
+  behavior: default

docs/requirements.txt

@@ -0,0 +1,5 @@
+sphinx_gallery
+sphinx_rtd_theme
+numpydoc
+memory_profiler
+pillow