diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 2db425a..d7970a9 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -5,9 +5,6 @@ concurrency: group: ${{ github.head_ref || github.run_id }} cancel-in-progress: true -env: - CONDA_EXE: mamba - on: push: branches: @@ -15,40 +12,48 @@ on: pull_request: branches: - '*' + merge_group: jobs: + run-type-checking: + + name: Run tests for type-checking + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v7 + with: + version: "0.9.9" + enable-cache: true + - name: Install just + uses: extractions/setup-just@v3 + - run: just typing + run-tests: name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }} runs-on: ${{ matrix.os }} - env: - CONDA_EXE: mamba strategy: fail-fast: false matrix: os: ['ubuntu-latest', 'macos-latest', 'windows-latest'] - python-version: ['3.7', '3.8', '3.9', '3.10', '3.11'] + python-version: ['3.10', '3.11', '3.12', '3.13', '3.14'] steps: - - uses: actions/checkout@v3 - - uses: conda-incubator/setup-miniconda@v2.2.0 + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v7 with: - auto-update-conda: false + version: "0.9.9" + enable-cache: true python-version: ${{ matrix.python-version }} - channels: conda-forge,nodefaults - miniforge-variant: Mambaforge - - - name: Install core dependencies. - shell: bash -l {0} - run: mamba install -c conda-forge tox-conda coverage - - - name: Run end-to-end tests. - shell: bash -l {0} - run: tox -e pytest -- tests -m end_to_end --cov=./ --cov-report=xml -n auto - - - name: Upload coverage reports of end-to-end tests. - if: runner.os == 'Linux' && matrix.python-version == '3.9' - shell: bash -l {0} - run: bash <(curl -s https://codecov.io/bash) -F end_to_end -c + - name: Install just + uses: extractions/setup-just@v3 + - name: Run end-to-end tests + run: just test + + - name: Upload coverage reports of tests. + if: runner.os == 'Linux' && matrix.python-version == '3.11' + uses: codecov/codecov-action@v5 diff --git a/.gitignore b/.gitignore index cc3765b..09d4326 100644 --- a/.gitignore +++ b/.gitignore @@ -39,7 +39,6 @@ pip-delete-this-directory.txt # Unit test / coverage reports htmlcov/ -.tox/ .nox/ .coverage .coverage.* @@ -135,7 +134,6 @@ coverage.* # Folders .idea .ipynb_checkpoints -.tox .vscode _build __pycache__ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 105f30f..d588d14 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -5,7 +5,7 @@ exclude: | repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 + rev: v6.0.0 hooks: - id: check-added-large-files args: ['--maxkb=25'] @@ -15,7 +15,6 @@ repos: - id: check-yaml exclude: | (?x)^( - {{cookiecutter.package_name}}/environment.yml| {{cookiecutter.package_name}}/.pre-commit-config.yaml )$ - id: debug-statements @@ -34,48 +33,39 @@ repos: - id: python-no-log-warn - id: python-use-type-annotations - id: text-unicode-replacement-char -- repo: https://github.com/asottile/reorder_python_imports - rev: v3.9.0 - hooks: - - id: reorder-python-imports - args: [--py37-plus, --add-import, 'from __future__ import annotations'] - repo: https://github.com/asottile/setup-cfg-fmt - rev: v2.2.0 + rev: v3.2.0 hooks: - id: setup-cfg-fmt exclude: | (?x)^( {{cookiecutter.package_name}}/setup.cfg )$ -- repo: https://github.com/psf/black - rev: 23.1.0 - hooks: - - id: black -- repo: https://github.com/charliermarsh/ruff-pre-commit - rev: v0.0.241 +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.15.2 hooks: - - id: ruff + - id: ruff + args: [--fix, hooks, tests] + pass_filenames: false + - id: ruff-format args: [hooks, tests] pass_filenames: false - repo: https://github.com/dosisod/refurb - rev: v1.10.0 + rev: v2.3.0 hooks: - id: refurb args: [--ignore, FURB126] exclude: ({{cookiecutter.package_name}}) - repo: https://github.com/econchick/interrogate - rev: 1.5.0 + rev: 1.7.0 hooks: - id: interrogate args: [-v, --fail-under=40] - repo: https://github.com/executablebooks/mdformat - rev: 0.7.16 + rev: 1.0.0 hooks: - id: mdformat - additional_dependencies: [ - mdformat-gfm, - mdformat-black, - ] + additional_dependencies: [mdformat-gfm] args: [--wrap, "88"] files: (README\.md) exclude: | @@ -83,27 +73,20 @@ repos: {{cookiecutter.package_name}}/README.md )$ - repo: https://github.com/executablebooks/mdformat - rev: 0.7.16 + rev: 1.0.0 hooks: - id: mdformat - additional_dependencies: [ - mdformat-myst, - mdformat-black, - ] + additional_dependencies: [mdformat-myst] args: [--wrap, "88"] files: (docs/.) - # Exclude files with admonitions. - # exclude: | - # (?x)^( - # path/to/file.py - # )$ - repo: https://github.com/codespell-project/codespell - rev: v2.2.2 + rev: v2.4.1 hooks: - id: codespell additional_dependencies: [tomli] + exclude: (^|/)uv\.lock$ - repo: https://github.com/pre-commit/mirrors-mypy - rev: 'v0.991' + rev: 'v1.19.1' hooks: - id: mypy args: [ @@ -115,4 +98,3 @@ repos: hooks: - id: check-hooks-apply - id: check-useless-excludes - # - id: identity # Prints all files passed to pre-commits. Debugging. diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 5e35e9f..e05f872 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,10 +1,18 @@ version: 2 build: - image: latest + os: ubuntu-24.04 + tools: + python: "3.11" + jobs: + create_environment: + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + - UV_NO_EDITABLE=1 UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv sync --group docs + install: + - "true" -python: - version: 3.8 - -conda: - environment: docs/rtd_environment.yml +sphinx: + configuration: docs/source/conf.py + fail_on_warning: false diff --git a/README.md b/README.md index 258bb0f..71c0794 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![image](https://img.shields.io/github/actions/workflow/status/pytask-dev/cookiecutter-pytask-plugin/main.yml?branch=main)](https://github.com/pytask-dev/cookiecutter-pytask-plugin/actions?query=branch%3Amain) [![image](https://codecov.io/gh/pytask-dev/cookiecutter-pytask-plugin/branch/main/graph/badge.svg)](https://codecov.io/gh/pytask-dev/cookiecutter-pytask-plugin) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/pytask-dev/cookiecutter-pytask-plugin/main.svg)](https://results.pre-commit.ci/latest/github/pytask-dev/cookiecutter-pytask-plugin/main) -[![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![code style: ruff](https://img.shields.io/badge/code%20style-ruff-261230.svg)](https://github.com/astral-sh/ruff) This repository contains a minimal cookiecutter template for a plugin for [pytask](https://github.com/pytask-dev/pytask) . @@ -16,8 +16,6 @@ First, install cookiecutter. ```console $ pip install cookiecutter - -$ conda install -c conda-forge cookiecutter ``` Then, set up the template for the new plugin with diff --git a/codecov.yml b/codecov.yml index 7fc9643..c1cf322 100644 --- a/codecov.yml +++ b/codecov.yml @@ -21,6 +21,3 @@ coverage: threshold: 1% flags: - end_to_end - -ignore: - - ".tox/**/*" diff --git a/cookiecutter.json b/cookiecutter.json index 1bdecca..f2c571f 100644 --- a/cookiecutter.json +++ b/cookiecutter.json @@ -6,7 +6,6 @@ "github_username": "{{ cookiecutter.author.lower().replace(' ', '') }}", "github_email": "{{ cookiecutter.email }}", "python_version": "3.10", - "add_tox": ["yes", "no"], "add_github_actions": ["yes", "no"], "add_readthedocs": ["yes", "no"], "add_codecov": ["yes", "no"], @@ -19,8 +18,6 @@ "Not open source" ], "make_initial_commit": ["no", "yes"], - "conda_environment_name": "{{ cookiecutter.package_name }}", - "create_conda_environment_at_finish": ["no", "yes"], "_copy_without_render": [ ".github/workflows/main.yml", ".github/workflows/publish-to-pypi.yml" ], diff --git a/docs/rtd_environment.yml b/docs/rtd_environment.yml deleted file mode 100644 index 14c44a3..0000000 --- a/docs/rtd_environment.yml +++ /dev/null @@ -1,23 +0,0 @@ -channels: - - conda-forge - - nodefaults - -dependencies: - - python >= 3.8 - - pip - - setuptools_scm - - toml - - # Documentation - - furo - - ipython - - nbsphinx - - sphinx - - sphinx-autoapi - - sphinx-click - - sphinx-copybutton - - sphinx-panels - - - pip: - - ../ - - sphinxext-opengraph diff --git a/docs/source/conf.py b/docs/source/conf.py index f8958ad..9f1d964 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -4,6 +4,7 @@ documentation: https://www.sphinx-doc.org/en/master/usage/configuration.html """ + # -- Project information ----------------------------------------------------- from __future__ import annotations diff --git a/environment.yml b/environment.yml deleted file mode 100644 index aba047d..0000000 --- a/environment.yml +++ /dev/null @@ -1,37 +0,0 @@ -name: cpp - -channels: - - conda-forge - - nodefaults - -dependencies: - - python >=3.7 - - pip - - setuptools_scm - - toml - - # Package dependencies - - cookiecutter >=2.1.0 - - pytask >=0.2 - - # Misc - - black - - mypy - - pre-commit - - pytest - # - pytest-cookies>=0.6.2 - - pytest-cov - - pytest-xdist - - tox-conda - - # Documentation - - furo - - nbsphinx - - sphinx - - sphinx-autoapi - - sphinx-click - - sphinx-copybutton - - sphinx-panels - - - pip: - - git+https://github.com/andriihomiak/pytest-cookies.git@fix/quotes_in_user_config diff --git a/hooks/post_gen_project.py b/hooks/post_gen_project.py index efe9511..0be3a6d 100644 --- a/hooks/post_gen_project.py +++ b/hooks/post_gen_project.py @@ -1,9 +1,9 @@ """This module contains hooks which are executed after the template is rendered.""" + from __future__ import annotations import shutil import subprocess -import warnings from contextlib import suppress from pathlib import Path @@ -28,10 +28,6 @@ def main() -> None: if "{{ cookiecutter.open_source_license }}" == "Not open source": remove_file(project_path, "LICENSE") - if "{{ cookiecutter.add_tox }}" == "no": - remove_directory(project_path, ".github", "workflows") - remove_file("tox.ini") - if "{{ cookiecutter.add_github_actions }}" == "no": remove_directory(project_path, ".github", "workflows") @@ -59,31 +55,6 @@ def main() -> None: capture_output=True, ) - if "{{ cookiecutter.create_conda_environment_at_finish }}" == "yes": - if shutil.which("mamba") is not None: - conda_exe = shutil.which("mamba") - else: - conda_exe = shutil.which("conda") - - if conda_exe: - subprocess.run( - ( - conda_exe, - "env", - "create", - "-f", - (project_path / "environment.yml").absolute().as_posix(), - "--force", - ), - check=True, - capture_output=True, - ) - else: - warnings.warn( - "conda environment could not be created since no conda or mamba " - "executable was found." - ) - if __name__ == "__main__": main() diff --git a/hooks/pre_gen_project.py b/hooks/pre_gen_project.py index d6ffcb8..970585d 100644 --- a/hooks/pre_gen_project.py +++ b/hooks/pre_gen_project.py @@ -1,12 +1,12 @@ """This module contains hooks which are executed before the template is rendered.""" + from __future__ import annotations import re MODULE_REGEX = r"^[_a-zA-Z][_a-zA-Z0-9]*$" -ENVIRON_REGEX = r"^[-_a-zA-Z0-9]*$" -PYTHONVERSION_REGEX = r"^(3\.(1[0-9]|[7-9])(\.[0-9]{1,2})?)$" -PYTHONVERSION_MIN = "3.7" +PYTHONVERSION_REGEX = r"^(3\.(1[0-9]|[2-9][0-9])(\.[0-9]{1,2})?)$" +PYTHONVERSION_MIN = "3.10" EXCEPTION_MSG_MODULE_NAME = """ ERROR: The project slug ({module_name}) is not a valid Python module name. @@ -15,13 +15,6 @@ The first character must not be a number. """ -EXCEPTION_MSG_ENVIRON_NAME = """ -ERROR: The project slug ({environment_name}) is not a valid conda environment name. - -Please do not use anything other than letters, numbers, underscores '_', -and minus signs '-'. -""" - EXCEPTION_MSG_PYTHONVERSION = """ ERROR: The python version must be >= {min_python_version}, got {python_version}. """ @@ -42,11 +35,6 @@ def main() -> None: if not re.match(MODULE_REGEX, module_name): raise ValueError(EXCEPTION_MSG_MODULE_NAME.format(module_name=module_name)) - environment_name = "{{ cookiecutter.conda_environment_name }}" - - if not re.match(ENVIRON_REGEX, environment_name): - raise ValueError(EXCEPTION_MSG_ENVIRON_NAME.format(environment_name)) - python_version = "{{ cookiecutter.python_version }}" if not re.match(PYTHONVERSION_REGEX, python_version): diff --git a/justfile b/justfile new file mode 100644 index 0000000..fa9fd17 --- /dev/null +++ b/justfile @@ -0,0 +1,23 @@ +# Install all dependencies +install: + uv sync --all-groups + +# Run end-to-end tests +# Keep parity with the previous CI behavior. +test: + uv run --group test pytest tests -m end_to_end --cov=./ --cov-report=xml -n auto + +# Run type checking +typing: + uv run --group typing mypy hooks/ tests/ + +# Run linting and formatting +lint: + uv run --group lint pre-commit run --all-files + +# Build docs +docs: + uv run --group docs sphinx-build -n -T -b html -d docs/build/doctrees docs/source docs/build/html + +# Run all checks +check: lint typing test diff --git a/pyproject.toml b/pyproject.toml index 7e9d1ad..833adfa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,70 @@ +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "cookiecutter_pytask_plugin" +version = "1.0.0" +description = "A minimal template for plugins for pytask." +requires-python = ">=3.10" +dependencies = ["cookiecutter"] +classifiers = [ + "Development Status :: 3 - Alpha", + "Intended Audience :: Science/Research", + "Operating System :: MacOS :: MacOS X", + "Operating System :: Microsoft :: Windows", + "Operating System :: POSIX", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3 :: Only", + "Topic :: Scientific/Engineering", +] + +[[project.authors]] +name = "Tobias Raabe" +email = "raabe@posteo.de" + +[project.readme] +file = "README.md" +content-type = "text/markdown" + +[project.license] +text = "MIT" + +[project.urls] +Changelog = "https://cookiecutter-pytask-plugin.readthedocs.io/en/latest/changes.html" +Documentation = "https://cookiecutter-pytask-plugin.readthedocs.io/en/latest" +Github = "https://github.com/pytask-dev/cookiecutter-pytask-plugin" +Tracker = "https://github.com/pytask-dev/cookiecutter-pytask-plugin/issues" + +[dependency-groups] +docs = [ + "furo", + "ipython", + "myst-parser", + "nbsphinx", + "sphinx", + "sphinx-autoapi", + "sphinx-click", + "sphinx-copybutton", + "sphinx-panels", + "sphinxext-opengraph", +] +test = [ + "cookiecutter", + "pytest", + "pytest-cookies", + "pytest-cov", + "pytest-xdist", +] +typing = ["mypy"] +lint = ["pre-commit"] + +[tool.hatch.build.targets.wheel] +only-include = ["cookiecutter.json", "hooks", "{{cookiecutter.package_name}}"] + +[tool.hatch.build.targets.sdist] +only-include = ["cookiecutter.json", "hooks", "{{cookiecutter.package_name}}"] + [tool.mypy] files = ["tests"] check_untyped_defs = true @@ -8,19 +75,18 @@ no_implicit_optional = true warn_redundant_casts = true warn_unused_ignores = true - [[tool.mypy.overrides]] module = "tests.*" disallow_untyped_defs = false ignore_errors = true - [tool.ruff] -target-version = "py37" -select = ["ALL"] fix = true +unsafe-fixes = true + +[tool.ruff.lint] +select = ["ALL"] extend-ignore = [ - # Numpy docstyle "D107", "D203", "D212", @@ -30,27 +96,37 @@ extend-ignore = [ "D415", "D416", "D417", - # Others. - "D404", # Do not start module docstring with "This". - "RET504", # unnecessary variable assignment before return. - "S101", # raise errors for asserts. - "B905", # strict parameter for zip that was implemented in py310. - "I", # ignore isort - "ANN101", # type annotating self - "ANN102", # type annotating cls - "FBT", # flake8-boolean-trap - "EM", # flake8-errmsg - "ANN401", # flake8-annotate typing.Any - "PD", # pandas-vet - "COM812", # trailing comma missing, but black takes care of that + "D404", + "RET504", + "S101", + "B905", + "FBT", + "EM", + "ANN401", + "PD", + "COM812", + "ISC001", ] - -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "hooks/post_gen_project.py" = ["PLR0133"] "hooks/*" = ["INP001"] "tests/*" = ["D", "ANN"] - -[tool.ruff.pydocstyle] +[tool.ruff.lint.pydocstyle] convention = "numpy" + +[tool.pytest.ini_options] +addopts = ["--doctest-modules"] +filterwarnings = [ + "ignore: the imp module is deprecated in favour of importlib", + "ignore: Using or importing the ABCs from 'collections' instead of from", + "ignore: The (parser|symbol) module is deprecated and will be removed in future", +] +markers = [ + "wip: Tests that are work-in-progress.", + "unit: Flag for unit tests which target mainly a single function.", + "integration: Flag for integration tests which may comprise of multiple unit tests.", + "end_to_end: Flag for tests that cover the whole program.", +] +norecursedirs = [".idea"] diff --git a/setup.cfg b/setup.cfg index 5616eeb..8c50cca 100644 --- a/setup.cfg +++ b/setup.cfg @@ -7,12 +7,11 @@ url = https://cookiecutter-pytask-plugin.readthedocs.io/en/latest author = Tobias Raabe author_email = raabe@posteo.de license = MIT -license_file = LICENSE +license_files = LICENSE platforms = unix, linux, osx, cygwin, win32 classifiers = Development Status :: 3 - Alpha Intended Audience :: Science/Research - License :: OSI Approved :: MIT License Operating System :: MacOS :: MacOS X Operating System :: Microsoft :: Windows Operating System :: POSIX @@ -26,5 +25,5 @@ project_urls = Tracker = https://github.com/pytask-dev/cookiecutter-pytask-plugin/issues [options] -python_requires = >=3.7 +python_requires = >=3.10 zip_safe = False diff --git a/tests/__init__.py b/tests/__init__.py index 83a9d18..71bd238 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -1,2 +1,3 @@ """This file is necessary to apply custom mypy configurations for the tests.""" + from __future__ import annotations diff --git a/tests/test_cookie.py b/tests/test_cookie.py index b4cbf4e..37df895 100644 --- a/tests/test_cookie.py +++ b/tests/test_cookie.py @@ -1,13 +1,11 @@ from __future__ import annotations -import os -import subprocess import sys import pytest -@pytest.mark.end_to_end() +@pytest.mark.end_to_end def test_bake_project(cookies): major, minor = sys.version_info[:2] python_version = f"{major}.{minor}" @@ -25,7 +23,7 @@ def test_bake_project(cookies): assert result.project_path.is_dir() -@pytest.mark.end_to_end() +@pytest.mark.end_to_end def test_remove_readthedocs(cookies): result = cookies.bake(extra_context={"add_readthedocs": "no"}) @@ -39,7 +37,7 @@ def test_remove_readthedocs(cookies): assert "readthedocs" not in readme -@pytest.mark.end_to_end() +@pytest.mark.end_to_end def test_remove_github_actions(cookies): result = cookies.bake(extra_context={"add_github_actions": "no"}) @@ -53,21 +51,7 @@ def test_remove_github_actions(cookies): assert "github/workflow/status" not in readme -@pytest.mark.end_to_end() -def test_remove_tox(cookies): - result = cookies.bake(extra_context={"add_tox": "no"}) - - ga_config = result.project_path.joinpath(".github", "workflows", "main.yml") - tox = result.project_path.joinpath("tox.ini") - - assert result.exit_code == 0 - assert result.exception is None - - assert not ga_config.exists() - assert not tox.exists() - - -@pytest.mark.end_to_end() +@pytest.mark.end_to_end def test_remove_license(cookies): result = cookies.bake(extra_context={"open_source_license": "Not open source"}) @@ -77,38 +61,3 @@ def test_remove_license(cookies): assert result.exception is None assert not license_.exists() - - -@pytest.mark.end_to_end() -@pytest.mark.skipif(os.environ.get("CI") is None, reason="Run only in CI.") -def test_check_conda_environment_creation_and_run_all_checks(cookies): - """Test that the conda environment is created and pre-commit passes.""" - result = cookies.bake( - extra_context={ - "conda_environment_name": "__test__", - "make_initial_commit": "yes", - "create_conda_environment_at_finish": "yes", - } - ) - - assert result.exit_code == 0 - assert result.exception is None - - if sys.platform != "win32": - # Switch branch before pre-commit because otherwise failure because on main - # branch. - subprocess.run( - ("git", "checkout", "-b", "test"), cwd=result.project_path, check=True - ) - - # Check linting, but not on the first try since formatters fix stuff. - subprocess.run( - ("conda", "run", "-n", "__test__", "pre-commit", "run", "--all-files"), - cwd=result.project_path, - check=False, - ) - subprocess.run( - ("conda", "run", "-n", "__test__", "pre-commit", "run", "--all-files"), - cwd=result.project_path, - check=True, - ) diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 29e35d4..0000000 --- a/tox.ini +++ /dev/null @@ -1,46 +0,0 @@ -[tox] -envlist = pytest, sphinx - -[testenv] -usedevelop = true -passenv = CI - -[testenv:pytest] -conda_channels = - conda-forge - nodefaults -conda_deps = - # pytest - pytest - pytest-cov - pytest-xdist - - # Package dependencies - cookiecutter -deps = - git+https://github.com/andriihomiak/pytest-cookies.git@fix/quotes_in_user_config - -commands = - pytest {posargs} - -[testenv:sphinx] -changedir = docs/source -conda_env = docs/rtd_environment.yml -commands = - sphinx-build -T -b html -d {envtmpdir}/doctrees . {envtmpdir}/html - - sphinx-build -T -b linkcheck -d {envtmpdir}/doctrees . {envtmpdir}/linkcheck - -[pytest] -addopts = --doctest-modules -filterwarnings = - ignore: the imp module is deprecated in favour of importlib - ignore: Using or importing the ABCs from 'collections' instead of from - ignore: The (parser|symbol) module is deprecated and will be removed in future -markers = - wip: Tests that are work-in-progress. - unit: Flag for unit tests which target mainly a single function. - integration: Flag for integration tests which may comprise of multiple unit tests. - end_to_end: Flag for tests that cover the whole program. 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b/{{cookiecutter.package_name}}/.github/workflows/main.yml @@ -5,9 +5,6 @@ concurrency: group: ${{ github.head_ref || github.run_id }} cancel-in-progress: true -env: - CONDA_EXE: mamba - on: push: branches: @@ -15,9 +12,25 @@ on: pull_request: branches: - '*' + merge_group: jobs: + run-type-checking: + + name: Run tests for type-checking + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v7 + with: + version: "0.9.9" + enable-cache: true + - name: Install just + uses: extractions/setup-just@v3 + - run: just typing + run-tests: name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }} @@ -27,37 +40,20 @@ jobs: fail-fast: false matrix: os: ['ubuntu-latest', 'macos-latest', 'windows-latest'] - python-version: ['3.7', '3.8', '3.9', '3.10', '3.11'] + python-version: ['3.10', '3.11', '3.12', '3.13', '3.14'] steps: - - uses: actions/checkout@v3 - - uses: conda-incubator/setup-miniconda@v2.2.0 + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v7 with: - auto-update-conda: false + version: "0.9.9" + enable-cache: true python-version: ${{ matrix.python-version }} - channels: conda-forge,nodefaults - miniforge-variant: Mambaforge - - - name: Install core dependencies. - shell: bash -l {0} - run: mamba install -c conda-forge tox-conda coverage - - # Unit, integration, and end-to-end tests. - - - name: Run unit tests and doctests. - shell: bash -l {0} - run: tox -e pytest -- -m "unit or (not integration and not end_to_end)" --cov=./ --cov-report=xml -n auto - - - name: Upload coverage report for unit tests and doctests. - if: runner.os == 'Linux' && matrix.python-version == '3.9' - shell: bash -l {0} - run: bash <(curl -s https://codecov.io/bash) -F unit -c - - - name: Run end-to-end tests. - shell: bash -l {0} - run: tox -e pytest -- -m end_to_end --cov=./ --cov-report=xml -n auto - - - name: Upload coverage reports of end-to-end tests. - if: runner.os == 'Linux' && matrix.python-version == '3.9' - shell: bash -l {0} - run: bash <(curl -s https://codecov.io/bash) -F end_to_end -c + - name: Install just + uses: extractions/setup-just@v3 + - name: Run tests and doctests + run: just test-cov + + - name: Upload coverage report + if: runner.os == 'Linux' && matrix.python-version == '3.11' + uses: codecov/codecov-action@v5 diff --git a/{{cookiecutter.package_name}}/.gitignore b/{{cookiecutter.package_name}}/.gitignore index 7e1ae82..a7935c6 100644 --- a/{{cookiecutter.package_name}}/.gitignore +++ b/{{cookiecutter.package_name}}/.gitignore @@ -5,7 +5,6 @@ coverage.* # Folders .idea .ipynb_checkpoints -.tox .vscode _build __pycache__ diff --git a/{{cookiecutter.package_name}}/.pre-commit-config.yaml b/{{cookiecutter.package_name}}/.pre-commit-config.yaml index e15e2c8..5ebe4dc 100644 --- a/{{cookiecutter.package_name}}/.pre-commit-config.yaml +++ b/{{cookiecutter.package_name}}/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 + rev: v6.0.0 hooks: - id: check-added-large-files args: ['--maxkb=100'] @@ -16,7 +16,7 @@ repos: args: [--branch, main] - id: trailing-whitespace - repo: https://github.com/pre-commit/pygrep-hooks - rev: v1.9.0 + rev: v1.10.0 hooks: - id: python-check-blanket-noqa - id: python-check-mock-methods @@ -24,73 +24,36 @@ repos: - id: python-no-log-warn - id: python-use-type-annotations - id: text-unicode-replacement-char -{% if cookiecutter.python_version not in ["3.10", "3.11", "3.12"] %}- repo: https://github.com/asottile/pyupgrade - rev: v3.3.1 - hooks: - - id: pyupgrade - args: [--py{{ cookiecutter.python_version | replace('.', '') }}-plus] -{% endif %} -- repo: https://github.com/asottile/reorder_python_imports - rev: v3.9.0 - hooks: - - id: reorder-python-imports - args: [--py37-plus, --add-import, 'from __future__ import annotations'] - repo: https://github.com/asottile/setup-cfg-fmt - rev: v2.2.0 + rev: v3.2.0 hooks: - id: setup-cfg-fmt -- repo: https://github.com/psf/black - rev: 23.1.0 - hooks: - - id: black -- repo: https://github.com/PyCQA/docformatter - rev: v1.5.1 - hooks: - - id: docformatter - args: [--in-place, --wrap-summaries, "88", --wrap-descriptions, "88", --blank] -{% if cookiecutter.python_version in ["3.10", "3.11", "3.12"] %}- repo: https://github.com/charliermarsh/ruff-pre-commit - rev: v0.0.241 +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.15.2 hooks: - - id: ruff + - id: ruff + args: [--fix] + - id: ruff-format - repo: https://github.com/dosisod/refurb - rev: v1.9.1 + rev: v2.3.0 hooks: - id: refurb args: [--ignore, FURB126] -{% endif %} - repo: https://github.com/econchick/interrogate - rev: 1.5.0 + rev: 1.7.0 hooks: - id: interrogate args: [-v, --fail-under=75] exclude: ^(tests/) - repo: https://github.com/executablebooks/mdformat - rev: 0.7.16 + rev: 1.0.0 hooks: - id: mdformat - additional_dependencies: [ - mdformat-gfm, - mdformat-black, - ] + additional_dependencies: [mdformat-gfm] args: [--wrap, "88"] files: (README\.md) -# - repo: https://github.com/executablebooks/mdformat -# rev: 0.7.16 -# hooks: -# - id: mdformat -# additional_dependencies: [ -# mdformat-myst, -# mdformat-black, -# ] -# args: [--wrap, "88"] -# files: (docs/.) -# # Exclude files with admonitions. -# exclude: | -# (?x)^( -# path/to/file.py -# )$ - repo: https://github.com/pre-commit/mirrors-mypy - rev: 'v0.991' + rev: 'v1.19.1' hooks: - id: mypy args: [ @@ -98,18 +61,11 @@ repos: --ignore-missing-imports, ] pass_filenames: false -- repo: https://github.com/codespell-project/codespell - rev: v2.2.2 - hooks: - - id: codespell -- repo: https://github.com/mgedmin/check-manifest - rev: "0.49" +- repo: https://github.com/codespell-project/codespell + rev: v2.4.1 hooks: - - id: check-manifest - args: [--no-build-isolation] - additional_dependencies: [setuptools-scm, toml] + - id: codespell - repo: meta hooks: - id: check-hooks-apply - id: check-useless-excludes - # - id: identity # Prints all files passed to pre-commits. Debugging. diff --git a/{{cookiecutter.package_name}}/README.md b/{{cookiecutter.package_name}}/README.md index a23cecf..ae2d651 100644 --- a/{{cookiecutter.package_name}}/README.md +++ b/{{cookiecutter.package_name}}/README.md @@ -16,21 +16,16 @@ cookiecutter.github_username }}/{{ cookiecutter.package_name }}) {% endif %} cookiecutter.github_username }}/{{ cookiecutter.package_name }}/main.svg)](https://results.pre-commit.ci/latest/github/{{ cookiecutter.github_username }}/{{ cookiecutter.package_name }}/main) -[![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![code style: ruff](https://img.shields.io/badge/code%20style-ruff-261230.svg)](https://github.com/astral-sh/ruff) ## Installation {{ cookiecutter.package_name }} is available on [PyPI](https://pypi.org/project/{{ -cookiecutter.package_name }}) and [Anaconda.org](https://anaconda.org/conda-forge/{{ cookiecutter.package_name }}). Install it with ```console $ pip install {{ cookiecutter.package_name }} - -# or - -$ conda install -c conda-forge {{ cookiecutter.package_name }} ``` ## Changes diff --git a/{{cookiecutter.package_name}}/codecov.yml b/{{cookiecutter.package_name}}/codecov.yml index 7838ed0..16152e1 100644 --- a/{{cookiecutter.package_name}}/codecov.yml +++ b/{{cookiecutter.package_name}}/codecov.yml @@ -20,5 +20,4 @@ coverage: - end_to_end ignore: - - ".tox/**/*" - "src/{{ cookiecutter.__package_name }}/_version.py" diff --git a/{{cookiecutter.package_name}}/environment.yml b/{{cookiecutter.package_name}}/environment.yml deleted file mode 100644 index fc996f1..0000000 --- a/{{cookiecutter.package_name}}/environment.yml +++ /dev/null @@ -1,23 +0,0 @@ -name: {{ cookiecutter.conda_environment_name }} - -channels: - - conda-forge - - nodefaults - -dependencies: - - python - - pip - - setuptools_scm - - toml - - # Package dependencies - - pytask >=0.2 - - pytask-parallel >=0.2 - - # Misc - - black - - jupyterlab - - pre-commit - - pytest-cov - - pytest-xdist - - tox-conda diff --git a/{{cookiecutter.package_name}}/justfile b/{{cookiecutter.package_name}}/justfile new file mode 100644 index 0000000..b84afe6 --- /dev/null +++ b/{{cookiecutter.package_name}}/justfile @@ -0,0 +1,22 @@ +# Install all dependencies +install: + uv sync --all-groups + +# Run tests +test: + uv run --group test --with-editable . pytest + +# Run tests with coverage +test-cov: + uv run --group test --with-editable . pytest --cov=./ --cov-report=xml + +# Run type checking +typing: + uv run --group typing --with-editable . mypy src/ tests/ + +# Run linting and formatting +lint: + uv run --group lint pre-commit run --all-files + +# Run all checks +check: lint typing test diff --git a/{{cookiecutter.package_name}}/pyproject.toml b/{{cookiecutter.package_name}}/pyproject.toml index 6ab45ce..de998cf 100644 --- a/{{cookiecutter.package_name}}/pyproject.toml +++ b/{{cookiecutter.package_name}}/pyproject.toml @@ -6,6 +6,28 @@ build-backend = "setuptools.build_meta" [tool.setuptools_scm] write_to = "src/{{ cookiecutter.__package_name }}/_version.py" +[dependency-groups] +docs = [ + "furo", + "ipython", + "myst-parser", + "nbsphinx", + "sphinx", + "sphinx-click", + "sphinx-copybutton", + "sphinx-design>=0.3", + "sphinx-toolbox", + "sphinxext-opengraph", +] +test = [ + "pytest", + "pytest-cov", + "pytest-xdist", + "pytask-parallel>=0.2", +] +typing = ["mypy"] +lint = ["pre-commit"] + [tool.mypy] files = ["src", "tests"] @@ -49,13 +71,11 @@ extend-ignore = [ "S101", # raise errors for asserts. "B905", # strict parameter for zip that was implemented in py310. "I", # ignore isort - "ANN101", # type annotating self - "ANN102", # type annotating cls "FBT", # flake8-boolean-trap "EM", # flake8-errmsg "ANN401", # flake8-annotate typing.Any "PD", # pandas-vet - "COM812", # trailing comma missing, but black takes care of that + "COM812", # trailing comma missing, but ruff format takes care of that ] @@ -65,3 +85,20 @@ extend-ignore = [ [tool.ruff.pydocstyle] convention = "numpy" + + +[tool.pytest.ini_options] +addopts = ["--doctest-modules"] +filterwarnings = [ + "ignore: the imp module is deprecated in favour of importlib", + "ignore: Using or importing the ABCs from 'collections' instead of", + "ignore: The (parser|symbol) module is deprecated and will be removed in future", +] +junit_family = "xunit2" +markers = [ + "wip: Tests that are work-in-progress.", + "unit: Flag for unit tests which target mainly a single function.", + "integration: Flag for integration tests which may comprise of multiple unit tests.", + "end_to_end: Flag for tests that cover the whole program.", +] +norecursedirs = [".idea"] diff --git a/{{cookiecutter.package_name}}/setup.cfg b/{{cookiecutter.package_name}}/setup.cfg index f76457a..6d97768 100644 --- a/{{cookiecutter.package_name}}/setup.cfg +++ b/{{cookiecutter.package_name}}/setup.cfg @@ -7,7 +7,7 @@ url = https://github.com/pytask-dev/{{ cookiecutter.package_name }} author = {{ cookiecutter.author }} author_email = {{ cookiecutter.email }} license = {{ cookiecutter.open_source_license }} -license_file = LICENSE +license_files = LICENSE platforms = any classifiers = Development Status :: 3 - Alpha @@ -15,10 +15,11 @@ classifiers = Operating System :: OS Independent Programming Language :: Python :: 3 Programming Language :: Python :: 3 :: Only - Programming Language :: Python :: 3.7 - Programming Language :: Python :: 3.8 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 + Programming Language :: Python :: 3.13 + Programming Language :: Python :: 3.14 project_urls = Changelog = https://github.com/pytask-dev/{{ cookiecutter.package_name }}/blob/main/CHANGES.rst Documentation = https://github.com/pytask-dev/{{ cookiecutter.package_name }} @@ -30,7 +31,7 @@ packages = find: install_requires = click pytask>=0.2 -python_requires = >=3.7 +python_requires = >=3.10 include_package_data = True package_dir = =src zip_safe = False diff --git a/{{cookiecutter.package_name}}/src/{{cookiecutter.__package_name}}/__init__.py b/{{cookiecutter.package_name}}/src/{{cookiecutter.__package_name}}/__init__.py index 5769aa6..483c821 100644 --- a/{{cookiecutter.package_name}}/src/{{cookiecutter.__package_name}}/__init__.py +++ b/{{cookiecutter.package_name}}/src/{{cookiecutter.__package_name}}/__init__.py @@ -1,4 +1,5 @@ """This module contains the main namespace of the package.""" + from __future__ import annotations try: diff --git a/{{cookiecutter.package_name}}/tox.ini b/{{cookiecutter.package_name}}/tox.ini deleted file mode 100644 index 9043784..0000000 --- a/{{cookiecutter.package_name}}/tox.ini +++ /dev/null @@ -1,42 +0,0 @@ -[tox] -envlist = pytest, sphinx - -[testenv] -usedevelop = true -passenv = CI - -[testenv:pytest] -conda_channels = - conda-forge - nodefaults -conda_deps = - pytask >=0.2 - pytask-parallel >=0.2 - pytest - pytest-cov - pytest-xdist -commands = - pytest {posargs} - -[testenv:sphinx] -changedir = docs/source -conda_env = docs/docs_environment.yml -commands = - sphinx-build -T -b html -d {envtmpdir}/doctrees . {envtmpdir}/html - - sphinx-build -T -b linkcheck -d {envtmpdir}/doctrees . {envtmpdir}/linkcheck - -[pytest] -addopts = --doctest-modules -filterwarnings = - ignore: the imp module is deprecated in favour of importlib - ignore: Using or importing the ABCs from 'collections' instead of - ignore: The (parser|symbol) module is deprecated and will be removed in future -junit_family = xunit2 -markers = - wip: Tests that are work-in-progress. - unit: Flag for unit tests which target mainly a single function. - integration: Flag for integration tests which may comprise of multiple unit tests. - end_to_end: Flag for tests that cover the whole program. -norecursedirs = - .idea - .tox