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name: tests | ||
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on: | ||
push: | ||
branches: | ||
- '*' | ||
tags: | ||
- '*' | ||
pull_request: | ||
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jobs: | ||
linting: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: neuroinformatics-unit/actions/lint@v2 | ||
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manifest: | ||
name: Check Manifest | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: neuroinformatics-unit/actions/check_manifest@v2 | ||
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test: | ||
needs: [linting, manifest] | ||
name: ${{ matrix.os }} py${{ matrix.python-version }} | ||
runs-on: ${{ matrix.os }} | ||
strategy: | ||
matrix: | ||
# Run all supported Python versions on linux | ||
python-version: ["3.9", "3.10", "3.11"] | ||
os: [ubuntu-latest] | ||
# Include one windows and macos run | ||
include: | ||
- os: macos-latest | ||
python-version: "3.10" | ||
- os: windows-latest | ||
python-version: "3.10" | ||
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steps: | ||
# Run tests | ||
- uses: neuroinformatics-unit/actions/test@v2 | ||
with: | ||
python-version: ${{ matrix.python-version }} | ||
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build_sdist_wheels: | ||
name: Build source distribution | ||
needs: [test] | ||
if: github.event_name == 'push' && github.ref_type == 'tag' | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: neuroinformatics-unit/actions/build_sdist_wheels@v2 | ||
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upload_all: | ||
name: Publish build distributions | ||
needs: [build_sdist_wheels] | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: neuroinformatics-unit/actions/upload_pypi@v2 | ||
with: | ||
secret-pypi-key: ${{ secrets.TWINE_API_KEY }} |
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# Byte-compiled / optimized / DLL files | ||
__pycache__/ | ||
*.py[cod] | ||
*$py.class | ||
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# C extensions | ||
*.so | ||
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# Distribution / packaging | ||
.Python | ||
env/ | ||
build/ | ||
develop-eggs/ | ||
dist/ | ||
downloads/ | ||
eggs/ | ||
.eggs/ | ||
lib/ | ||
lib64/ | ||
parts/ | ||
sdist/ | ||
var/ | ||
*.egg-info/ | ||
.installed.cfg | ||
*.egg | ||
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# PyInstaller | ||
# Usually these files are written by a python script from a template | ||
# before PyInstaller builds the exe, so as to inject date/other infos into it. | ||
*.manifest | ||
*.spec | ||
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# Installer logs | ||
pip-log.txt | ||
pip-delete-this-directory.txt | ||
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# Unit test / coverage reports | ||
htmlcov/ | ||
.tox/ | ||
.coverage | ||
.coverage.* | ||
.cache | ||
nosetests.xml | ||
coverage.xml | ||
*,cover | ||
.hypothesis/ | ||
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# Translations | ||
*.mo | ||
*.pot | ||
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# Django stuff: | ||
*.log | ||
local_settings.py | ||
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# Flask instance folder | ||
instance/ | ||
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# Sphinx documentation | ||
docs/_build/ | ||
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# MkDocs documentation | ||
/site/ | ||
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# PyBuilder | ||
target/ | ||
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# Pycharm and VSCode | ||
.idea/ | ||
venv/ | ||
.vscode/ | ||
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# IPython Notebook | ||
.ipynb_checkpoints | ||
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# pyenv | ||
.python-version | ||
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# OS | ||
.DS_Store | ||
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# written by setuptools_scm | ||
**/_version.py |
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# Configuring https://pre-commit.ci/ | ||
ci: | ||
autoupdate_schedule: monthly | ||
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repos: | ||
- repo: https://github.com/pre-commit/pre-commit-hooks | ||
rev: v5.0.0 | ||
hooks: | ||
- id: check-docstring-first | ||
- id: check-executables-have-shebangs | ||
- id: check-merge-conflict | ||
- id: check-toml | ||
- id: end-of-file-fixer | ||
- id: mixed-line-ending | ||
args: [--fix=lf] | ||
- id: requirements-txt-fixer | ||
- id: trailing-whitespace | ||
- repo: https://github.com/astral-sh/ruff-pre-commit | ||
rev: v0.7.2 | ||
hooks: | ||
- id: ruff | ||
args: [ --config=pyproject.toml ] | ||
- id: ruff-format | ||
args: [ --config=pyproject.toml ] | ||
- repo: https://github.com/pre-commit/mirrors-mypy | ||
rev: v1.13.0 | ||
hooks: | ||
- id: mypy | ||
additional_dependencies: | ||
- types-setuptools | ||
- repo: https://github.com/mgedmin/check-manifest | ||
rev: "0.50" | ||
hooks: | ||
- id: check-manifest | ||
args: [--no-build-isolation] | ||
additional_dependencies: [setuptools-scm] | ||
- repo: https://github.com/codespell-project/codespell | ||
# Configuration for codespell is in pyproject.toml | ||
rev: v2.3.0 | ||
hooks: | ||
- id: codespell | ||
additional_dependencies: | ||
- tomli |
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include LICENSE | ||
include README.md | ||
exclude .pre-commit-config.yaml | ||
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recursive-exclude * __pycache__ | ||
recursive-exclude * *.py[co] | ||
recursive-exclude docs * | ||
recursive-exclude tests * |
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from importlib.metadata import PackageNotFoundError, version | ||
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try: | ||
__version__ = version("aeon_sleap_processing") | ||
except PackageNotFoundError: | ||
# package is not installed | ||
pass |
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[project] | ||
name = "aeon_sleap_processing" | ||
authors = [ | ||
{ name = "Jai Bhagat", email = "[email protected]" }, | ||
{ name = "Goncalo Lopes", email = "[email protected]" }, | ||
{ name = "Chang Huan Lo", email = "[email protected]" }, | ||
{ name = "Anaya Pouget", email = "[email protected]"}, | ||
] | ||
description = "Project Aeon computational data pipeline for post-process refinement of SLEAP data using zoomed in cameras." | ||
readme = "README.md" | ||
requires-python = ">=3.9.0" | ||
dynamic = ["version"] | ||
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dependencies = [] | ||
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license = {text = "BSD-3-Clause"} | ||
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classifiers = [ | ||
"Development Status :: 2 - Pre-Alpha", | ||
"Programming Language :: Python", | ||
"Programming Language :: Python :: 3", | ||
"Programming Language :: Python :: 3.9", | ||
"Programming Language :: Python :: 3.10", | ||
"Programming Language :: Python :: 3.11", | ||
"Operating System :: OS Independent", | ||
"License :: OSI Approved :: BSD License", | ||
] | ||
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[project.optional-dependencies] | ||
dev = [ | ||
"pytest", | ||
"pytest-cov", | ||
"coverage", | ||
"tox", | ||
"mypy", | ||
"pre-commit", | ||
"ruff", | ||
"setuptools_scm", | ||
] | ||
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[build-system] | ||
requires = [ | ||
"setuptools>=45", | ||
"wheel", | ||
"setuptools_scm[toml]>=6.2", | ||
] | ||
build-backend = "setuptools.build_meta" | ||
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[tool.setuptools] | ||
include-package-data = true | ||
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[tool.setuptools.packages.find] | ||
include = ["aeon_sleap_processing*"] | ||
exclude = ["tests*"] | ||
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[tool.pytest.ini_options] | ||
addopts = "--cov=aeon_sleap_processing" | ||
filterwarnings = [ | ||
"error", | ||
] | ||
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[tool.setuptools_scm] | ||
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[tool.check-manifest] | ||
ignore = [ | ||
".yaml", | ||
"tox.ini", | ||
"tests/", | ||
"tests/test_unit/", | ||
"tests/test_integration/", | ||
] | ||
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[tool.ruff] | ||
line-length = 79 | ||
exclude = ["__init__.py", "build", ".eggs"] | ||
lint.select = [ | ||
"E", # pycodestyle errors | ||
"F", # Pyflakes | ||
"I", # isort | ||
# You can see what all the rules do here: https://docs.astral.sh/ruff/rules/ | ||
# Some additional ruff rules that might be useful (uncomment to enable) | ||
#"UP", # pyupgrade | ||
#"B", # flake8 bugbear | ||
#"SIM", # flake8 simplify | ||
#"C90", # McCabe complexity | ||
] | ||
fix = true | ||
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[tool.ruff.format] | ||
docstring-code-format = true # Also format code in docstrings (e.g. examples) | ||
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[tool.tox] | ||
legacy_tox_ini = """ | ||
[tox] | ||
envlist = py{39,310,311} | ||
isolated_build = True | ||
[gh-actions] | ||
python = | ||
3.9: py39 | ||
3.10: py310 | ||
3.11: py311 | ||
[testenv] | ||
extras = | ||
dev | ||
commands = | ||
pytest -v --color=yes --cov=aeon_sleap_processing --cov-report=xml | ||
""" | ||
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[tool.codespell] | ||
skip = '.git' | ||
check-hidden = true |
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def test_placeholder(): | ||
assert True |