Merge Master to clustering for new changes in GAMA Backend

.coveragerc

@@ -2,7 +2,6 @@
 ignore_errors = True
 omit =
     tests/*
-    gama/dashboard/*
 exclude_lines =
     pragma: no cover
     def __repr__

.github/actions/pytest/action.yaml

@@ -0,0 +1,67 @@
+name: "Pytest"
+description: "Run a test suite"
+
+inputs:
+  path:
+    description: "Path to test suite"
+    required: true
+  python-version:
+    description: "Python version to use"
+    default: "3.10"
+    required: true
+  use-cache:
+    description: "If set, use cached dependencies."
+    default: true
+    required: true
+  os:
+    description: "OS for runs-on. Only required when cache is set."
+    default: "ubuntu-latest"
+    required: false
+  pip-args:
+    description: "Additional pip args"
+    default: ""
+    required: false
+  pytest-args:
+    description: "Additional ptest args"
+    default: ""
+    required: false
+
+runs:
+  using: "composite"
+  steps:
+    - name: Set up Python ${{ inputs.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Get pip cache dir
+      id: get-cache-location
+      if: inputs.use-cache == 'true'
+      shell: bash
+      run: |
+        echo "::set-output name=dir::$(pip cache dir)"
+
+    - uses: actions/cache@v3
+      id: cache
+      if: inputs.use-cache == 'true'
+      with:
+        path: ${{ steps.get-cache-location.outputs.dir }}
+        key: ${{ inputs.os }}-pip-${{ inputs.python-version }}-${{ hashFiles('**/pyproject.toml') }}
+
+    - name: Install dependencies
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install ${{ inputs.pip-args }} ".[test]"
+
+    - name: Test with pytest
+      shell: bash
+      run: |
+        echo pytest ${{ inputs.path }}  --cov ${{ inputs.pytest-args }} 
+        pytest ${{ inputs.path }}  --cov ${{ inputs.pytest-args }}
+
+    - uses: codecov/codecov-action@v3
+      with:
+        flags: unit-tests
+        fail_ci_if_error: true
+        verbose: true

.github/workflows/build-docs.yaml

@@ -0,0 +1,49 @@
+name: Docs
+
+on:
+  push:
+    branches:
+      - master
+      - main
+      - "[0-9][0-9].[0-9]+.x"
+
+  pull_request:
+    branches:
+      - master
+      - main
+      - "[0-9][0-9].[0-9]+.x"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[doc]"
+
+      - name: Clone GH-Pages
+        if: ${{ github.event_name != 'pull_request' }}
+        uses: actions/checkout@v3
+        with:
+          ref: "gh-pages"
+          path: docs/build/
+
+      - name: Build Docs
+        run: |
+          sphinx-build docs/source docs/build/${{ github.ref_name }}
+
+      - name: Push GH-Pages
+        if: ${{ github.event_name != 'pull_request' }}
+        run: |
+          cd docs/build
+          git config user.name github-actions
+          git config user.email [email protected]
+          git add ${{ github.ref_name }}
+          git commit -m "Autodeploy docs"
+          git push

.github/workflows/changelog.yaml

@@ -0,0 +1,41 @@
+name: Changelog
+
+on:
+  pull_request:
+    branches:
+      - master
+      - main
+
+jobs:
+  check-and-comment:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Check Releases.rst Updated
+        run: |
+          git fetch origin master:master
+          updated_files=$(git diff master -- docs/source/releases.rst)
+          if [[ -z $updated_files ]]
+          then
+            exit 1
+          fi
+
+      - name: Thank you comment
+        uses: thollander/actions-comment-pull-request@v1
+        with:
+          comment_includes: "changelog"
+          message: |
+            Thank you for the pull request! :pray:
+            If CI reports any errors please address them.
+            If you believe the errors are unrelated to your PR, please state why.
+            This will make it easier for the maintainers to assess your PR :)
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Comment PR
+        if: ${{ failure() }}
+        uses: thollander/actions-comment-pull-request@v1
+        with:
+          comment_includes: "changelog" # To avoid creating additional comments
+          message: |
+            Please include the change for this PR in the changelog (`docs/source/releases.rst`).
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/precommit.yaml

@@ -0,0 +1,15 @@
+name: pre-commit
+
+on:
+  workflow_dispatch:
+  push:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - uses: pre-commit/[email protected]

.github/workflows/publish.yaml

@@ -0,0 +1,126 @@
+name: Publish
+
+on:
+  workflow_dispatch:
+    inputs:
+      year:
+        required: true
+        type: number
+      macro:
+        required: true
+        type: number
+      micro:
+        required: true
+        type: number
+      suffix:
+        required: false
+        type: string
+      i-know-what-i-am-doing:
+        required: true
+        type: boolean
+        default: false
+      test-pypi:
+        required: true
+        type: boolean
+        default: true
+
+jobs:
+  warn:
+    if: ${{ ! inputs.i-know-what-i-am-doing }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: "i-know-what-i-am-doing not set"
+        run: |
+          exit 1
+
+  build:
+    if: ${{ inputs.i-know-what-i-am-doing }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Match version with input
+        run: |
+          GAMA_VERSION=$(grep -Po "\d+\.\d+\.\d+((\.dev\d*)|(\.post\d*))?" "gama/__version__.py")
+          NEW_VERSION=${{ inputs.year }}.${{ inputs.macro }}.${{ inputs.micro }}${{ inputs.suffix }}
+          echo $GAMA_VERSION $NEW_VERSION
+          exit $([ $GAMA_VERSION == $NEW_VERSION ])
+      - name: Match version with tag
+        run: |
+          GAMA_VERSION=$(grep -Po "\d+\.\d+\.\d+((\.dev\d*)|(\.post\d*))?" "gama/__version__.py")
+          NEW_VERSION=${{ github.ref  }}
+          echo refs/tags/v$GAMA_VERSION $NEW_VERSION
+          exit $([ refs/tags/v$GAMA_VERSION == $NEW_VERSION ])
+      - name: Install build & publish dependencies
+        run: |
+          python -m pip install build
+      - name: Build Wheel
+        run: |
+          python -m build
+      - name: Upload Dist
+        uses: actions/upload-artifact@v3
+        with:
+          name: dist-folder
+          path: dist
+          retention-days: 1
+          if-no-files-found: error
+
+  test-install:
+    needs: build
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Download dist
+        uses: actions/[email protected]
+        with:
+          name: dist-folder
+          path: dist
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Wheel
+        shell: bash
+        run: |
+          python -m pip install dist/*.whl
+      - name: Run example
+        run: |
+          curl https://raw.githubusercontent.com/openml-labs/gama/master/examples/classification_example.py > example.py
+          # First reduce runtime for 3 minutes to 1 minute, does not work for Windows but fails silently.
+          sed -i.bak "s/180/60/" example.py
+          sed -i.bak "s/3/1/" example.py
+          python example.py
+
+  publish:
+    needs: test-install
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download dist
+        uses: actions/[email protected]
+        with:
+          name: dist-folder
+          path: dist
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install Twine
+        run: |
+          python -m pip install twine
+      - name: Upload to test server
+        if: ${{ inputs.test-pypi }}
+        run: |
+          python -m twine upload --repository testpypi -u __token__ -p ${{ secrets.TEST_PYPI }} dist/*
+      - name: Upload to real server
+        if: ${{ ! inputs.test-pypi }}
+        run: |
+          python -m twine upload -u __token__ -p ${{ secrets.PYPI }} dist/*

.github/workflows/pytest.yaml

@@ -0,0 +1,41 @@
+name: pytest
+on:
+  workflow_dispatch:
+  pull_request:
+
+jobs:
+  unit:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Invoke Unit Tests
+        uses: ./.github/actions/pytest
+        with:
+          path: tests/unit
+          os: ${{ matrix.os }}
+          python-version: ${{ matrix.python-version }}
+
+  system:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Invoke System Tests
+        uses: ./.github/actions/pytest
+        with:
+          path: tests/system
+          os: ${{ matrix.os }}
+          python-version: ${{ matrix.python-version }}

.github/workflows/test-with-pre.yaml

@@ -0,0 +1,26 @@
+name: Test --pre
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "00 0 * * 1"
+
+jobs:
+  unit:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Invoke Unit Tests
+        uses: ./.github/actions/pytest
+        with:
+          path: tests/unit
+          python-version: ${{ matrix.python-version }}
+          use-cache: false
+          pip-args: "--pre"
+          pytest-args: "-W error -W ignore::sklearn.exceptions.ConvergenceWarning"