Transition from Travis CI to github workflow (#1004)

* Transition from travis

* Fix examples

* Give rerun failures a try

* Try pytest directly

* Trying to make cov work

* removed wrong long

* Try serial runs as before

* No Rerun

* Incorporated PR comments

* Fix conda and dist failures

* Fix flake

* Output check

.flake8

@@ -0,0 +1,7 @@
+[flake8]
+max-line-length = 100
+show-source = True
+application-import-names = autosklearn
+exclude =
+    venv
+    build

.github/workflows/dist.yml

@@ -0,0 +1,31 @@
+name: dist-check
+
+on: [push, pull_request]
+
+jobs:
+  dist:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Build dist
+      run: |
+        python setup.py sdist
+    - name: Twine check
+      run: |
+        pip install twine
+        last_dist=$(ls -t dist/auto-sklearn-*.tar.gz | head -n 1)
+        twine_output=`twine check "$last_dist"`
+        if [[ "$twine_output" != "Checking $last_dist: PASSED" ]]; then echo $twine_output && exit 1;fi
+    - name: Install dist
+      run: |
+        last_dist=$(ls -t dist/auto-sklearn-*.tar.gz | head -n 1)
+        pip install $last_dist
+    - name: PEP 561 Compliance
+      run: |
+        pip install mypy
+        cd ..  # required to use the installed version of autosklearn
+        if ! python -c "import autosklearn"; then exit 1; fi

.github/workflows/docs.yml

@@ -0,0 +1,43 @@
+name: Docs
+on: [pull_request, push]
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        pip install -e .[docs,examples,examples_unix]
+    - name: Make docs
+      run: |
+        cd doc
+        make html
+    - name: Pull latest gh-pages
+      if: (contains(github.ref, 'develop') || contains(github.ref, 'master')) && github.event_name == 'push'
+      run: |
+        cd ..
+        git clone https://github.com/automl/auto-sklearn.git --branch gh-pages --single-branch gh-pages
+    - name: Copy new doc into gh-pages
+      if: (contains(github.ref, 'develop') || contains(github.ref, 'master')) && github.event_name == 'push'
+      run: |
+        branch_name=${GITHUB_REF##*/}
+        cd ../gh-pages
+        rm -rf $branch_name
+        cp -r ../autosklearn/doc/build/html $branch_name
+    - name: Push to gh-pages
+      if: (contains(github.ref, 'develop') || contains(github.ref, 'master')) && github.event_name == 'push'
+      run: |
+        last_commit=$(git log --pretty=format:"%an: %s")
+        cd ../gh-pages
+        branch_name=${GITHUB_REF##*/}
+        git add $branch_name/
+        git config --global user.name 'Github Actions'
+        git config --global user.email 'not@mail.com'
+        git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}
+        git commit -am "$last_commit"
+        git push

.github/workflows/pre-commit.yaml

@@ -0,0 +1,20 @@
+name: pre-commit
+
+on: [push, pull_request]
+
+jobs:
+  run-all-files:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python 3.7
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+    - name: Install pre-commit
+      run: |
+        pip install pre-commit
+        pre-commit install
+    - name: Run pre-commit
+      run: |
+        pre-commit run --all-files

.github/workflows/pytest.yml

@@ -0,0 +1,83 @@
+name: Tests
+
+on: [push, pull_request]
+
+jobs:
+  ubuntu:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+        use-conda: [true, false]
+        use-dist: [false]
+        include:
+          - python-version: 3.8
+            code-cov: true
+          - python-version: 3.7
+            use-conda: false
+            use-dist: true
+      fail-fast:  false
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Conda Install test dependencies 
+      if: matrix.use-conda == true
+      run: |
+        # Miniconda is available in $CONDA env var
+        $CONDA/bin/conda create -n testenv --yes pip wheel gxx_linux-64 gcc_linux-64 swig python=${{ matrix.python-version }}
+        $CONDA/envs/testenv/bin/python3 -m pip install --upgrade pip
+        $CONDA/envs/testenv/bin/pip3 install -e .[test]
+    - name: Install test dependencies 
+      if: matrix.use-conda == false && matrix.use-dist == false
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[test]
+        sudo apt-get update
+        sudo apt-get remove swig
+        sudo apt-get install swig3.0
+        sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
+    - name: Dist Install test dependencies 
+      if: matrix.use-conda == false && matrix.use-dist == true
+      run: |
+        python -m pip install --upgrade pip
+        sudo apt-get update
+        sudo apt-get remove swig
+        sudo apt-get install swig3.0
+        sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
+        # We need to install for the dependencies, like pytest
+        pip install -e .[test]
+        # Then we remove autosklearn and install from DIST
+        pip uninstall --yes auto-sklearn
+        python setup.py sdist
+        last_dist=$(ls -t dist/auto-sklearn-*.tar.gz | head -n 1)
+        pip install $last_dist
+    - name: Conda Run tests
+      if: matrix.use-conda == true
+      run: |
+        export OPENBLAS_NUM_THREADS=1
+        export OMP_NUM_THREADS=1
+        export MKL_NUM_THREADS=1
+        # We activate conda as metalearning uses python directly, so we need
+        # to change the default python
+        export PATH="$CONDA/envs/testenv/bin:$PATH"
+        if [ ${{ matrix.code-cov }} ]; then codecov='--cov=autosklearn --cov-report=xml'; fi
+        $CONDA/envs/testenv/bin/python3 -m pytest --durations=20 -sv $codecov test
+    - name: Run tests
+      if: matrix.use-conda == false
+      run: |
+        export OPENBLAS_NUM_THREADS=1
+        export OMP_NUM_THREADS=1
+        export MKL_NUM_THREADS=1
+        if [ ${{ matrix.code-cov }} ]; then codecov='--cov=autosklearn --cov-report=xml'; fi
+        pytest --durations=20 -sv $codecov test
+    - name: Upload coverage
+      if: matrix.code-cov && always()
+      uses: codecov/codecov-action@v1
+      with:
+        fail_ci_if_error: true
+        verbose: true

.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.761
+    hooks:
+      - id: mypy
+        name: mypy auto-sklearn-ensembles
+        files: autosklearn/ensembles
+      - id: mypy
+        name: mypy auto-sklearn-metrics
+        files: autosklearn/metrics
+      - id: mypy
+        name: mypy auto-sklearn-data
+        files: autosklearn/data
+      - id: mypy
+        name: mypy auto-sklearn-util
+        files: autosklearn/util
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.3
+    hooks:
+      - id: flake8
+        name: flake8 auto-sklearn
+        files: autosklearn/*
+      - id: flake8
+        name: flake8 file-order-data
+        files: autosklearn/data
+        additional_dependencies:
+          - flake8-import-order
+      - id: flake8
+        name: flake8 file-order-ensemble
+        files: autosklearn/ensembles
+        additional_dependencies:
+          - flake8-import-order
+      - id: flake8
+        name: flake8 file-order-metrics
+        files: autosklearn/metrics
+        additional_dependencies:
+          - flake8-import-order
+      - id: flake8
+        name: flake8 file-order-util
+        files:  autosklearn/util
+        additional_dependencies:
+          - flake8-import-order
+      - id: flake8
+        name: flake8 autosklearn-test
+        files: test/*