update from main

.github/workflows/cancel.yml

@@ -0,0 +1,13 @@
+name: Cancel Workflows on Push
+on:
+  workflow_run:
+    workflows: ["Install and test"]
+    types:
+      - requested
+jobs:
+  cancel:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: styfle/cancel-workflow-action@0.9.1
+      with:
+        workflow_id: ${{ github.event.workflow.id }}

.github/workflows/test.yml

@@ -0,0 +1,182 @@
+name: Install and test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+      - id: file_changes
+        uses: trilom/file-changes-action@v1.2.4
+        with:
+          output: " "
+      - name: List changed files
+        run: echo '${{ steps.file_changes.outputs.files}}'
+      - uses: pre-commit/action@v3.0.0
+        with:
+          extra_args: --files ${{ steps.file_changes.outputs.files}}
+      - name: Check for missing init files
+        run: build_tools/fail_on_missing_init_files.sh
+        shell: bash
+
+  run-notebook-examples:
+    needs: code-quality
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .[all_extras,binder,dev,mlflow]
+      - name: Run example notebooks
+        run: build_tools/run_examples.sh
+        shell: bash
+
+  test-nosoftdeps:
+    needs: code-quality
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      - name: Install sktime and dependencies
+        run: |
+          python -m pip install .[dev]
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: make PYTESTOPTIONS="--cov --cov-report=xml --timeout=600" test_softdeps
+
+  test-nosoftdeps-full:
+    needs: test-nosoftdeps
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      - name: Install sktime and dependencies
+        run: |
+          python -m pip install .[dev]
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: make PYTESTOPTIONS="--cov --cov-report=xml --timeout=600" test_softdeps_full
+
+  test-mlflow:
+    needs: test-nosoftdeps
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      - name: Install sktime and dependencies
+        run: |
+          python -m pip install .[all_extras,dev,mlflow_tests] --no-cache-dir
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: make PYTESTOPTIONS="--cov --cov-report=xml --timeout=600" test_mlflow
+
+  test-windows:
+    needs: test-nosoftdeps
+    runs-on: windows-2019
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10']
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          channels: anaconda, conda-forge,
+
+      - run: conda --version
+      - run: which python
+
+      - name: Fix windows paths
+        if: ${{ runner.os == 'Windows' }}
+        run: echo "C:\Program Files (x86)\Windows Kits\10\bin\10.0.18362.0\x64" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+
+      - name: Install conda libpython
+        run: conda install -c anaconda libpython
+
+      - name: Install sktime and dependencies
+        run: python -m pip install .[all_extras,dev]
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: |
+          mkdir -p testdir/
+          cp .coveragerc testdir/
+          cp setup.cfg testdir/
+          python -m pytest
+
+      - name: Publish code coverage
+        uses: codecov/codecov-action@v3
+
+  test-unix:
+    needs: test-nosoftdeps
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10']
+        os: [ubuntu-20.04, macOS-11]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      - name: Install sktime and dependencies
+        run: |
+          python -m pip install .[all_extras,dev] --no-cache-dir
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: make test
+
+      - name: Publish code coverage
+        uses: codecov/codecov-action@v3

.github/workflows/update_contributors.yml

@@ -0,0 +1,33 @@
+name: Update Contributors
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - '.all-contributorsrc'
+
+jobs:
+  generate-markdown-and-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Node
+        uses: actions/setup-node@v3
+        with:
+          node-version: 18
+      - name: Set up tool
+        run: npm install -g all-contributors-cli@6.24.0
+      - name: Generate file
+        id: generate
+        run: npx all-contributors generate
+      - name: commit-and-push
+        id: candp
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_message: '[AUTOMATED] update CONTRIBUTORS.md'
+          file_pattern: 'CONTRIBUTORS.md'
+          commit_user_name: github-actions[bot]
+      - name: Echo Results
+        if: steps.candp.outputs.changes_detected == 'true'
+        run: echo "changes detected and committed."

.github/workflows/wheels.yml

@@ -0,0 +1,151 @@
+name: Build wheels and publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build_wheels:
+    name: Build wheels
+    runs-on: ubuntu-20.04
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Build wheel
+        run: |
+          python -m pip install build
+          python -m build --wheel --sdist --outdir wheelhouse
+
+      - name: Store wheels
+        uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: wheelhouse/*
+
+  test_unix_wheels:
+    needs: build_wheels
+    name: Test wheels on ${{ matrix.os }} with ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macOS-11]
+        python-version: ['3.7', '3.8', '3.9', '3.10']
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/download-artifact@v2
+        with:
+          name: wheels
+          path: wheelhouse
+
+      - name: Get wheel filename
+        run: echo "WHEELNAME=$(ls ./wheelhouse/sktime-*none-any.whl)" >> $GITHUB_ENV
+
+      - name: Install wheel and extras
+        run: python -m pip install "${{ env.WHEELNAME }}[all_extras,dev]"
+
+      - name: Run tests
+        run: make test
+
+  test_windows_wheels:
+    needs: build_wheels
+    name: Test wheels on ${{ matrix.os }} with ${{ matrix.python-version }}
+    runs-on: windows-2019
+    strategy:
+      matrix:
+        include:
+          # Window 64 bit
+          - os: windows-2019
+            python: 37
+            python-version: '3.7'
+            bitness: 64
+            platform_id: win_amd64
+          - os: windows-2019
+            python: 38
+            python-version: '3.8'
+            bitness: 64
+            platform_id: win_amd64
+          - os: windows-2019
+            python: 39
+            python-version: '3.9'
+            bitness: 64
+            platform_id: win_amd64
+          - os: windows-2019
+            python: 310
+            python-version: '3.10'
+            bitness: 64
+            platform_id: win_amd64
+          - os: windows-2019
+            python: 39
+            python-version: 3.9
+            bitness: 64
+            platform_id: win_amd64
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          channels: anaconda, conda-forge,
+
+      - run: conda --version
+      - run: which python
+
+      - uses: actions/download-artifact@v2
+        with:
+          name: wheels
+          path: wheelhouse
+
+      - name: Install conda libpython
+        run: conda install -c anaconda -n test -y libpython
+
+      - name: Display downloaded artifacts
+        run: ls -l wheelhouse
+
+      - name: Get wheel filename
+        run: echo "WHEELNAME=$(ls ./wheelhouse/sktime-*none-any.whl)" >> $env:GITHUB_ENV
+
+      - name: Activate conda env
+        run: conda activate test
+
+      - name: Install wheel and extras
+        run: python -m pip install "${env:WHEELNAME}[all_extras,dev]"
+
+      - name: Show conda packages
+        run: conda list -n test
+
+      - name: Run tests
+        run: |
+          mkdir -p testdir/
+          cp .coveragerc testdir/
+          cp setup.cfg testdir/
+          python -m pytest
+
+  upload_wheels:
+    name: Upload wheels to PyPI
+    runs-on: ubuntu-latest
+    needs: [build_wheels,test_unix_wheels,test_windows_wheels]
+
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: wheels
+          path: wheelhouse
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: ${{ secrets.PYPI_USERNAME }}
+          password: ${{ secrets.PYPI_PASSWORD }}
+          packages_dir: wheelhouse/

.pre-commit-config.yaml

@@ -59,11 +59,3 @@ repos:
     hooks:
       - id: pydocstyle
         args: ["--config=setup.cfg"]
-
-  # We use the Python version instead of the original version which seems to require Docker
-  # https://github.com/koalaman/shellcheck-precommit
-  - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: v0.8.0.4
-    hooks:
-      - id: shellcheck
-        name: shellcheck