Add pre-commit and setup from sktime

.github/workflows/tests.yaml

@@ -1,7 +1,25 @@
 name: tests
 on: [push, pull_request]
 jobs:
-  all-pytests:
+  code-quality:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+      - id: file_changes
+        uses: trilom/[email protected]
+        with:
+          output: " "
+      - name: List changed files
+        run: echo '${{ steps.file_changes.outputs.files}}'
+      - uses: pre-commit/[email protected]
+        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
+
+  pytests:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -14,12 +32,5 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install .[all_extras]
           python -m pip install pytest
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          #flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          #flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Test with pytest
         run: |
-          python -m pytest

.pre-commit-config.yaml

@@ -0,0 +1,80 @@
+# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+        args: ["--maxkb=1000"]
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+        exclude: "^docs/source/examples/"
+      - id: fix-encoding-pragma
+        args:
+          - --remove
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.10.1
+    hooks:
+      - id: pyupgrade
+        args:
+          - --py38-plus
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort
+
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+        language_version: python3
+        # args: [--line-length 79]
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+        exclude: docs/conf.py
+        additional_dependencies: [flake8-bugbear, flake8-print]
+
+  - repo: https://github.com/mgedmin/check-manifest
+    rev: "0.49"
+    hooks:
+      - id: check-manifest
+        stages: [manual]
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
+    hooks:
+      - id: nbqa-black
+        args: [--nbqa-mutate, --nbqa-dont-skip-bad-cells]
+        additional_dependencies: [black==22.3.0]
+      - id: nbqa-isort
+        args: [--nbqa-mutate, --nbqa-dont-skip-bad-cells]
+        additional_dependencies: [isort==5.6.4]
+      - id: nbqa-flake8
+        args: [--nbqa-dont-skip-bad-cells, "--extend-ignore=E402,E203"]
+        additional_dependencies: [flake8==3.8.3]
+
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: 6.3.0
+    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: v0.9.0.5
+    hooks:
+      - id: shellcheck
+        name: shellcheck

build_tools/fail_on_missing_init_files.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
+
+# Script to search for missing init FILES.
+set -euxo pipefail
+
+FILES=$( find ./skchange -type d '!' -exec test -e "{}/__init__.py" ";" -not -path "**/__pycache__" -not -path "**/datasets/data*" -not -path "**/contrib/*" -print )
+
+if [[ -n "$FILES" ]]
+then
+    echo "Missing __init__.py files detected in the following modules:"
+    echo "$FILES"
+    exit 1
+fi

pyproject.toml

@@ -60,6 +60,7 @@ all_extras = [
 # dev - the developer dependency set, install via "pip install skchange[dev]"
 dev = [
     "black>=23.1.0",
+    "pre-commit",
     "pytest>=7.2.1",
     "ipykernel>=6.23.0",
     "nbformat>=5.7.3",
@@ -73,14 +74,5 @@ requires = ["setuptools>61"]
 [tool.setuptools.packages.find]
 exclude = ["tests", "tests.*"]
 
-[tool.isort]
-profile = "black"
-src_paths = ["skchange/*"]
-multi_line_output = 3
-known_first_party = ["skchange"]
-
 [tool.black]
 line-length = 88
-
-[tool.pydocstyle]
-convention = "numpy"

setup.cfg

@@ -1,3 +1,31 @@
+[aliases]
+test = pytest
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+
+[tool:pytest]
+# ignore certain folders and pytest warnings
+addopts =
+    --ignore build_tools
+    --ignore interactive
+    --ignore docs
+    # --doctest-modules
+    # --durations 20
+    # --timeout 600
+    # --cov sktime
+    # --cov-report xml
+    # --cov-report html
+    # --showlocals
+    # --matrixdesign True
+    # --only_changed_modules True
+    # -n auto
+filterwarnings =
+    ignore::UserWarning
+    ignore:numpy.dtype size changed
+    ignore:numpy.ufunc size changed
+
 [flake8]
 # Default flake8 3.5 ignored flags
 ignore = E121, E123, E126, E226, E24, E704, W503, W504
@@ -9,4 +37,26 @@ extend-ignore =
 
 [metadata]
 description_file = README.md
-long_description_content_type = text/markdown
+long_description_content_type = text/markdown
+
+[check-manifest]
+ignore =
+    # .binder/**
+    # .all-contributorsrc
+    # .coveragerc
+    # examples/**
+    build_tools/**
+    # __check_build/**
+    # docs/**
+    # Makefile
+    # CODEOWNERS
+    # CONTRIBUTING.md
+    # *.yaml
+    # *.yml
+
+[isort]
+profile = black
+
+[pydocstyle]
+convention = numpy
+match = (?!test_).*\.py