Merge branch 'master' into pr/1417

sktime · Sep 7, 2024 · 3c8e30b · 3c8e30b
2 parents 7720d07 + e2bf3fd
commit 3c8e30b
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diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -7,65 +7,20 @@ on:
     branches: [master]
 
 jobs:
-  linter-black:
-      name: Check code formatting with Black
-      runs-on: ubuntu-latest
-      steps:
-        - name: Checkout
-          uses: actions/checkout@v2
-        - name: Set up Python 3.8
-          uses: actions/setup-python@v2
-          with:
-            python-version: 3.8
-        - name: Install Black
-          run: pip install black[jupyter]
-        - name: Run Black
-          run: black --check .
-
-  imports-check-isort:
-    name: Check valid import formatting with isort
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - name: Install isort
-        run: pip install isort==5.6.4
-      - name: Run isort
-        run: isort --check-only --diff .
-
-  linter-flake8:
-    name: Check valid formatting with flake8
-    runs-on: ubuntu-latest
-    timeout-minutes: 10
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-
-      - name: Install dependencies
-        run: pip install flake8
-      - name: Run checks
-        run: flake8
-
-
   pre-commit-hooks:
     name: Check that pre-commit hooks pass
     runs-on: ubuntu-latest
-    timeout-minutes: 10
     steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - name: repository checkout step
+        uses: actions/checkout@v4
+      - name: python environment step
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
-      - name: Install dependencies
-        run: pip install pre-commit
-
-      - name: Run checks
-        run: pre-commit run --all-files
+          python-version: "3.11"
+      - name: install pre-commit
+        run: python3 -m pip install pre-commit
+      - id: changed-files
+        name: identify modified files
+        uses: tj-actions/changed-files@v44
+      - name: run pre-commit hooks on modified files
+        run: pre-commit run --color always --files ${{ steps.changed-files.outputs.all_changed_files }} --show-diff-on-failure
diff --git a/.github/workflows/pypi_release.yml b/.github/workflows/pypi_release.yml
@@ -19,7 +19,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install poetry
         shell: bash

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -9,19 +9,45 @@ on:
   pull_request:
     branches: [master]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  build:
+  run-notebook-tutorials:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[dev,all_extras,github-actions]"
+
+      - name: Show dependencies
+        run:  python -m pip list
+
+      - name: Run example notebooks
+        run: build_tools/run_examples.sh
+        shell: bash
+
+  pytest-nosoftdeps:
+    name: no-softdeps
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-latest, macOS-latest] # add windows-2019 when poetry allows installation with `-f` flag
-        python-version: ["3.8", "3.9", "3.10"]
+        os: [ubuntu-latest, macos-13, windows-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -30,58 +56,63 @@ jobs:
         run: |
           brew install libomp  # https://github.com/pytorch/pytorch/issues/20030
 
-      - name: Setup macOS
-        if: runner.os == 'windows'
-        run: |
-          brew install libomp  # https://github.com/pytorch/pytorch/issues/20030
-
       - name: Get full Python version
         id: full-python-version
         shell: bash
-        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+        run: echo version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))") >> $GITHUB_OUTPUT
 
-      - name: Install poetry
+      - name: Install dependencies
         shell: bash
         run: |
-          curl -sSL https://install.python-poetry.org | python3 -
+          pip install ".[dev,github-actions]"
 
-      - name: Set poetry path variable
-        run: echo "/Users/runner/.local/bin" >> $GITHUB_PATH
+      - name: Show dependencies
+        run: python -m pip list
 
-      - name: Configure poetry
+      - name: Run pytest
         shell: bash
-        run: poetry config virtualenvs.in-project true
+        run: python -m pytest tests
 
-      - name: Set up cache
-        uses: actions/cache@v2
-        id: cache
+  pytest:
+    name: Run pytest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-13, windows-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
         with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}
+          python-version: ${{ matrix.python-version }}
 
-      - name: Ensure cache is healthy
-        if: steps.cache.outputs.cache-hit == 'true'
-        shell: bash
-        run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv
+      - name: Setup macOS
+        if: runner.os == 'macOS'
+        run: |
+          brew install libomp  # https://github.com/pytorch/pytorch/issues/20030
 
-      - name: Upgrade pip
+      - name: Get full Python version
+        id: full-python-version
         shell: bash
-        run: poetry run python -m pip install pip -U
+        run: echo version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))") >> $GITHUB_OUTPUT
 
       - name: Install dependencies
         shell: bash
-        run: poetry install -E "github-actions graph mqf2"
+        run: |
+          pip install ".[dev,all_extras,github-actions]"
 
-      - name: Install pytorch geometric dependencies
-        shell: bash
-        run: poetry run pip install torch-scatter torch-sparse torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.12.1+cpu.html
+      - name: Show dependencies
+        run: python -m pip list
 
       - name: Run pytest
         shell: bash
-        run: poetry run pytest tests
+        run: python -m pytest tests
 
       - name: Statistics
-        if: success()
         run: |
           pip install coverage
           coverage report
@@ -99,43 +130,41 @@ jobs:
           fail_ci_if_error: false
 
   docs:
-    name: Test docs build
+    name: Docs build
     runs-on: ubuntu-latest
-
+    defaults:
+      run:
+        shell: bash
     steps:
       - name: Check out Git repository
         uses: actions/checkout@v2
 
       - name: Set up Python
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Cache pip
         uses: actions/cache@v2
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('docs/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          restore-keys: ${{ runner.os }}-pip-
 
       - name: Install dependencies
         run: |
-          sudo apt-get update && sudo apt-get install -y pandoc
-          python -m pip install --upgrade pip
+          sudo apt-get update --fix-missing
+          sudo apt-get install -y pandoc
           pip install -r docs/requirements.txt
-        shell: bash
 
       - name: Build sphinx documentation
-        run: |
-          cd docs
-          make clean
-          make html --debug --jobs 2 SPHINXOPTS="-W"
+        working-directory: docs/
+        run: make html --debug --jobs 2 SPHINXOPTS="-W"
 
       - name: Upload built docs
         uses: actions/upload-artifact@v2
         with:
           name: docs-results-${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.requires }}
           path: docs/build/html/
         # Use always() to always run this step to publish test results when there are test failures
-        if: success()
+        #if: success()
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,26 +2,26 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.6.0
     hooks:
-    - id: trailing-whitespace
-    - id: end-of-file-fixer
-    - id: check-yaml
-    - id: check-ast
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: "3.9.2"
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-ast
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.1.1
     hooks:
-    - id: flake8
+      - id: flake8
   - repo: https://github.com/pre-commit/mirrors-isort
     rev: v5.10.1
     hooks:
-    - id: isort
+      - id: isort
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 24.8.0
     hooks:
-    - id: black
+      - id: black
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.3.1
+    rev: 1.8.7
     hooks:
       - id: nbqa-black
       - id: nbqa-isort

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -9,7 +9,7 @@ version: 2
 # reference: https://docs.readthedocs.io/en/stable/config-file/v2.html#sphinx
 sphinx:
   configuration: docs/source/conf.py
-  fail_on_warning: true
+  # fail_on_warning: true
 
 # Build documentation with MkDocs
 #mkdocs:
@@ -21,6 +21,6 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
+  version: 3.11
   install:
     - requirements: docs/requirements.txt
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,16 @@
 # Release Notes
 
-## v0.10.4 UNRELEASED (xx/xx/xxxx)
+## v1.0.0 Update to pytorch 2.0 (10/04/2023)
+
+
+### Breaking Changes
+
+- Upgraded to pytorch 2.0 and lightning 2.0. This brings a couple of changes, such as configuration of trainers. See the [lightning upgrade guide](https://lightning.ai/docs/pytorch/latest/upgrade/migration_guide.html). For PyTorch Forecasting, this particularly means if you are developing own models, the class method `epoch_end` has been renamed to `on_epoch_end` and replacing `model.summarize()` with `ModelSummary(model, max_depth=-1)` and `Tuner(trainer)` is its own class, so `trainer.tuner` needs replacing. (#1280)
+- Changed the `predict()` interface returning named tuple - see tutorials.
+
+### Changes
+
+- The predict method is now using the lightning predict functionality and allows writing results to disk (#1280).
 
 ### Fixed
 
@@ -81,7 +91,7 @@
 
 ### Added
 
-- Added support for running `pytorch_lightning.trainer.test` (#759)
+- Added support for running `lightning.trainer.test` (#759)
 
 ### Fixed
 
@@ -402,7 +412,7 @@ This release has only one purpose: Allow usage of PyTorch Lightning 1.0 - all te
   - Using `LearningRateMonitor` instead of `LearningRateLogger`
   - Use `EarlyStopping` callback in trainer `callbacks` instead of `early_stopping` argument
   - Update metric system `update()` and `compute()` methods
-  - Use `trainer.tuner.lr_find()` instead of `trainer.lr_find()` in tutorials and examples
+  - Use `Tuner(trainer).lr_find()` instead of `trainer.lr_find()` in tutorials and examples
 - Update poetry to 1.1.0
 
 ---