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nvictus committed Jun 17, 2023
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4 changes: 4 additions & 0 deletions .git_archival.txt
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node: $Format:%H$
node-date: $Format:%cI$
describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
ref-names: $Format:%D$
1 change: 1 addition & 0 deletions .gitattributes
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.git_archival.txt export-subst
65 changes: 65 additions & 0 deletions .github/CONTRIBUTING.md
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See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed
description of best practices for developing scientific packages.

[spc-dev-intro]: https://scientific-python-cookie.readthedocs.io/guide/intro

# Setting up a development environment manually

You can set up a development environment by running:

```bash
python3 -m venv .venv
source ./.venv/bin/activate
pip install -v -e .[dev]
```

or just

```bash
hatch shell
```

# Post setup

You should prepare pre-commit, which will help you by checking that commits pass
required checks:

```bash
pip install pre-commit # or brew install pre-commit on macOS
pre-commit install # Will install a pre-commit hook into the git repo
```

You can also/alternatively run `pre-commit run` (changes only) or
`pre-commit run --all-files` to check even without installing the hook.

This project uses pre-commit for all style checking. Install pre-commit and run:

```bash
pre-commit run -a
```

to check all files.

# Testing

Use pytest to run the unit checks:

```bash
pytest
```

# Coverage

Use pytest-cov to generate coverage reports:

```bash
pytest --cov=dask-ngs
```

# Building docs

You can build the docs using:

```bash
hatch docs
```
7 changes: 7 additions & 0 deletions .github/dependabot.yml
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version: 2
updates:
# Maintain dependencies for GitHub Actions
- package-ecosystem: "github-actions"
directory: "/"
schedule:
interval: "weekly"
105 changes: 105 additions & 0 deletions .github/workflows/ci.yml
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name: CI

on:
workflow_dispatch:
pull_request:
push:
branches:
- main
release:
types:
- published

concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true

env:
FORCE_COLOR: 3

jobs:
pre-commit:
name: Format
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- uses: actions/setup-python@v4
with:
python-version: "3.x"
- uses: pre-commit/[email protected]
with:
extra_args: --hook-stage manual --all-files

checks:
name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
runs-on: ${{ matrix.runs-on }}
needs: [pre-commit]
strategy:
fail-fast: false
matrix:
python-version: ["3.7", "3.11"]
runs-on: [ubuntu-latest, macos-latest, windows-latest]

steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0

- uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}

- name: Install package
run: python -m pip install .[test]

- name: Test package
run: >-
python -m pytest -ra --cov --cov-report=xml --cov-report=term
--durations=20
- name: Upload coverage report
uses: codecov/[email protected]

dist:
needs: [pre-commit]
name: Distribution build
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0

- name: Build sdist and wheel
run: pipx run build

- uses: actions/upload-artifact@v3
with:
path: dist

- name: Check products
run: pipx run twine check dist/*

publish:
needs: [dist]
name: Publish to PyPI
environment: pypi
permissions:
id-token: write
runs-on: ubuntu-latest
if: github.event_name == 'release' && github.event.action == 'published'

steps:
- uses: actions/download-artifact@v3
with:
name: artifact
path: dist

- uses: pypa/gh-action-pypi-publish@release/v1
if: github.event_name == 'release' && github.event.action == 'published'
with:
# Remember to tell (test-)pypi about this repo before publishing
# Remove this line to publish to PyPI
repository-url: https://test.pypi.org/legacy/
158 changes: 158 additions & 0 deletions .gitignore
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# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# 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

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
cover/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
# For a library or package, you might want to ignore these files since the code is
# intended to run in multiple environments; otherwise, check them in:
# .python-version

# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock

# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# setuptools_scm
src/*/_version.py


# ruff
.ruff_cache/

# OS specific stuff
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db

# Common editor files
*~
*.swp
49 changes: 49 additions & 0 deletions .pre-commit-config.yaml
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ci:
autoupdate_commit_msg: "chore: update pre-commit hooks"
autofix_commit_msg: "style: pre-commit fixes"

repos:
- repo: https://github.com/psf/black
rev: "23.3.0"
hooks:
- id: black-jupyter

- repo: https://github.com/pre-commit/pre-commit-hooks
rev: "v4.4.0"
hooks:
- id: check-added-large-files
- id: check-case-conflict
- id: check-merge-conflict
- id: check-symlinks
- id: check-yaml
- id: debug-statements
- id: end-of-file-fixer
- id: mixed-line-ending
- id: name-tests-test
args: ["--pytest-test-first"]
- id: requirements-txt-fixer
- id: trailing-whitespace

- repo: https://github.com/pre-commit/pygrep-hooks
rev: "v1.10.0"
hooks:
- id: rst-backticks
- id: rst-directive-colons
- id: rst-inline-touching-normal

- repo: https://github.com/asottile/blacken-docs
rev: "1.13.0"
hooks:
- id: blacken-docs
additional_dependencies: [black==23.3.0]

- repo: https://github.com/charliermarsh/ruff-pre-commit
rev: "v0.0.264"
hooks:
- id: ruff
args: ["--fix", "--show-fixes"]

- repo: https://github.com/codespell-project/codespell
rev: "v2.2.4"
hooks:
- id: codespell
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