Merge pull request #746 from automl/development

Development
automl · Jul 27, 2021 · 3df3a74 · 3df3a74
2 parents 6058475 + 12b3a5b
commit 3df3a74
Show file tree

Hide file tree

Showing 81 changed files with 1,347 additions and 962 deletions.
diff --git a/.flake8 b/.flake8
@@ -0,0 +1,14 @@
+[flake8]
+max-line-length = 120
+ignore = W605,E402,W503
+show-source = True
+application-import-names = smac
+exclude =
+    venv
+    build
+    .git
+    __pycache__
+    doc
+    build
+    dist
+    examples/spear_qcp/*
diff --git a/.github/workflows/dist.yml b/.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=$(ls -t dist/smac-*.tar.gz | head -n 1)
+        twine_output=`twine check "$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/smac-*.tar.gz | head -n 1)
+        pip install $last_dist
+    - name: PEP 561 Compliance
+      run: |
+        pip install mypy
+        cd ..  # required to use the installed version of smac
+        if ! python -c "import smac"; then exit 1; fi
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -0,0 +1,44 @@
+name: Docs
+on: [pull_request, push]
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        pip install -e .[all]
+    - name: Make docs
+      run: |
+        cd doc
+        make buildapi
+        make html
+    - name: Pull latest gh-pages
+      if: (contains(github.ref, 'develop') || contains(github.ref, 'master')) && github.event_name == 'push'
+      run: |
+        cd ..
+        git clone https://github.com/automl/SMAC3.git --branch gh-pages --single-branch gh-pages
+    - name: Copy new doc into gh-pages
+      if: (contains(github.ref, 'develop') || contains(github.ref, 'master')) && github.event_name == 'push'
+      run: |
+        branch_name=${GITHUB_REF##*/}
+        cd ../gh-pages
+        rm -rf $branch_name
+        cp -r ../SMAC3/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 $branch_name/
+        git config --global user.name 'Github Actions'
+        git config --global user.email '[email protected]'
+        git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}
+        git commit -am "$last_commit"
+        git push
diff --git a/.github/workflows/pre-commit.yaml b/.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
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -0,0 +1,102 @@
+name: Tests
+
+on:
+  push:
+  pull_request:
+  schedule:
+    # Every Monday at 7AM UTC
+    - cron: '0 07 * * 1'
+
+jobs:
+  ubuntu:
+
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+        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
+      # A note on checkout: When checking out the repository that
+      # triggered a workflow, this defaults to the reference or SHA for that event.
+      # Otherwise, uses the default branch (master) is used.
+      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
+        $CONDA/envs/testenv/bin/pip3 install -e .[all]
+    - name: Install test dependencies
+      if: matrix.use-conda == false && matrix.use-dist == false
+      run: |
+        python -m pip install --upgrade pip
+        if [[ `python -c 'import platform; print(platform.python_version())' | cut -d '.' -f 2` -eq 6 ]]; then
+          # Numpy 1.20 dropped suppert for Python3.6
+          pip install "numpy<=1.19"
+        fi
+        sudo apt-get update
+        sudo apt-get remove swig
+        sudo apt-get install swig3.0
+        sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
+        pip install -e .[all]
+    - name: Dist Install test dependencies
+      if: matrix.use-conda == false && matrix.use-dist == true
+      run: |
+        python -m pip install --upgrade pip
+        sudo apt-get update
+        sudo apt-get remove swig
+        sudo apt-get install swig3.0
+        sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
+        # We need to install for the dependencies, like pytest
+        python setup.py sdist
+        last_dist=$(ls -t dist/smac-*.tar.gz | head -n 1)
+        pip install $last_dist[all]
+    - name: Store repository status
+      id: status-before
+      run: |
+        echo "::set-output name=BEFORE::$(git status --porcelain -b)"
+    - name: Conda Run tests
+      timeout-minutes: 45
+      if: matrix.use-conda == true
+      run: |
+        # Activate anaconda so default python is from conda
+        export PATH="$CONDA/envs/testenv/bin:$PATH"
+        if [ ${{ matrix.code-cov }} ]; then codecov='--cov=smac --cov-report=xml'; fi
+        $CONDA/envs/testenv/bin/python3 -m pytest --forked --durations=20 --timeout=300 --timeout-method=thread --fulltrace --full-trace -sv $codecov test
+    - name: Run tests
+      timeout-minutes: 45
+      if: matrix.use-conda == false
+      run: |
+        if [ ${{ matrix.code-cov }} ]; then codecov='--cov=smac --cov-report=xml'; fi
+        pytest --forked --durations=20 --timeout=300 --timeout-method=thread --fulltrace --full-trace -sv $codecov test
+    - name: Check for files left behind by test
+      if: ${{ always() }}
+      run: |
+        before="${{ steps.status-before.outputs.BEFORE }}"
+        after="$(git status --porcelain -b)"
+        if [[ "$before" != "$after" ]]; then
+            echo "git status from before: $before"
+            echo "git status from after: $after"
+            echo "Not all generated files have been deleted!"
+            exit 1
+        fi
+    - name: Upload coverage
+      if: matrix.code-cov && always()
+      uses: codecov/codecov-action@v1
+      with:
+        fail_ci_if_error: true
+        verbose: true
diff --git a/.github/workflows/terminal_examples.yml b/.github/workflows/terminal_examples.yml
@@ -0,0 +1,53 @@
+name: examples
+
+on: [push, pull_request]
+
+jobs:
+  ubuntu:
+
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        python-version: [3.8]
+      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
+      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
+        $CONDA/envs/testenv/bin/pip3 install -e .[all]
+    - name: Spear QCP SMAC
+      timeout-minutes: 20
+      run: |
+        # Activate anaconda so default python is from conda
+        export PATH="$CONDA/envs/testenv/bin:$PATH"
+        cd examples/spear_qcp
+        bash run_SMAC.sh
+    - name: Spear QCP ROAR
+      timeout-minutes: 20
+      run: |
+        # Activate anaconda so default python is from conda
+        export PATH="$CONDA/envs/testenv/bin:$PATH"
+        cd examples/spear_qcp
+        bash run_ROAR.sh
+    - name: Spear QCP Successive halving
+      timeout-minutes: 20
+      run: |
+        # Activate anaconda so default python is from conda
+        export PATH="$CONDA/envs/testenv/bin:$PATH"
+        cd examples/spear_qcp
+        python SMAC4AC_SH_spear_qcp.py
+    - name:  Branin from the command line
+      timeout-minutes: 20
+      run: |
+        # Activate anaconda so default python is from conda
+        export PATH="$CONDA/envs/testenv/bin:$PATH"
+        cd examples/branin
+        python ../../scripts/smac --scenario scenario.txt
diff --git a/.gitignore b/.gitignore
@@ -16,7 +16,6 @@ target_algo_runs.json
 
 # Other
 .tox
-.coverage
 .pypirc
 .ipynb_checkpoints/
 *.ipynb
@@ -33,3 +32,24 @@ doc/main_options.rst
 doc/scenario_options.rst
 doc/smac_options.rst
 doc/apidoc
+
+# Dask created work space
+dask-worker-space
+
+# Python distribution generated files
+.eggs
+
+# Unit test / coverage reports
+htmlcov/
+cover
+coverage
+htmlcov
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+prof/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,31 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.761
+    hooks:
+      - id: mypy
+        # We would like to have the following options set, 
+        # but for now we have to use the ones above to get started
+        # --ignore-missing-imports --strict"
+        # --disallow-any-unimported"
+        # --disallow-any-expr"
+        # --disallow-any-decorated"
+        # --disallow-any-explicit"
+        # --disallow-any-generics"
+        # Add the following once the scenario is removed from the main code or typed
+        # https://mypy.readthedocs.io/en/stable/command_line.html#configuring-warnings
+        # --warn-unused-ignores"
+        args: [--show-error-codes, --ignore-missing-imports, --disallow-untyped-decorators, --disallow-incomplete-defs, --disallow-untyped-defs, --follow-imports, skip]
+        name: mypy SMAC
+        files: smac/.*
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.3
+    hooks:
+      - id: flake8
+        name: flake8 SMAC
+        files: smac
+      - id: flake8
+        name: flake8 test
+        files: test
+      - id: flake8
+        name: flake8 examples
+        files: examples