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Set up project using scientific-python cookie
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ebrahimebrahim committed Dec 5, 2024
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13 changes: 13 additions & 0 deletions .copier-answers.yml
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# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
_commit: 2024.08.19
_src_path: gh:scientific-python/cookie
backend: hatch
email: [email protected]
full_name: Ebrahim Ebrahim
license: Apache
org: brain-microstructure-exploration-tools
project_name: abcdstats
project_short_description: Statistical analysis tools for use with ABCD neuroimaging
and tabular data
url: https://github.com/brain-microstructure-exploration-tools/abcdstats
vcs: true
1 change: 1 addition & 0 deletions .gitattributes
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.git_archival.txt export-subst
89 changes: 89 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://learn.scientific-python.org/development/

# Quick development

The fastest way to start with development is to use nox. If you don't have nox,
you can use `pipx run nox` to run it without installing, or `pipx install nox`.
If you don't have pipx (pip for applications), then you can install with
`pip install pipx` (the only case were installing an application with regular
pip is reasonable). If you use macOS, then pipx and nox are both in brew, use
`brew install pipx nox`.

To use, run `nox`. This will lint and test using every installed version of
Python on your system, skipping ones that are not installed. You can also run
specific jobs:

```console
$ nox -s lint # Lint only
$ nox -s tests # Python tests
$ nox -s docs -- --serve # Build and serve the docs
$ nox -s build # Make an SDist and wheel
```

Nox handles everything for you, including setting up an temporary virtual
environment for each run.

# 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]
```

If you have the
[Python Launcher for Unix](https://github.com/brettcannon/python-launcher), you
can instead do:

```bash
py -m venv .venv
py -m install -v -e .[dev]
```

# Pre-commit

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.

# Testing

Use pytest to run the unit checks:

```bash
pytest
```

# Coverage

Use pytest-cov to generate coverage reports:

```bash
pytest --cov=abcdstats
```

# Building docs

You can build the docs using:

```bash
nox -s docs
```

You can see a preview with:

```bash
nox -s docs -- --serve
```
11 changes: 11 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"
groups:
actions:
patterns:
- "*"
5 changes: 5 additions & 0 deletions .github/release.yml
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changelog:
exclude:
authors:
- dependabot
- pre-commit-ci
60 changes: 60 additions & 0 deletions .github/workflows/cd.yml
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name: CD

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

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

env:
# Many color libraries just need this to be set to any value, but at least
# one distinguishes color depth, where "3" -> "256-bit color".
FORCE_COLOR: 3

jobs:
dist:
name: Distribution build
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0

- uses: hynek/build-and-inspect-python-package@v2

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

steps:
- uses: actions/download-artifact@v4
with:
name: Packages
path: dist

- name: Generate artifact attestation for sdist and wheel
uses: actions/[email protected]
with:
subject-path: "dist/*"

- uses: pypa/gh-action-pypi-publish@release/v1
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/
71 changes: 71 additions & 0 deletions .github/workflows/ci.yml
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name: CI

on:
workflow_dispatch:
pull_request:
push:
branches:
- main

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

env:
# Many color libraries just need this to be set to any value, but at least
# one distinguishes color depth, where "3" -> "256-bit color".
FORCE_COLOR: 3

jobs:
pre-commit:
name: Format
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- uses: actions/setup-python@v5
with:
python-version: "3.x"
- uses: pre-commit/[email protected]
with:
extra_args: --hook-stage manual --all-files
- name: Run PyLint
run: pipx run nox -s pylint -- --output-format=github

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: ["3.8", "3.13"]
runs-on: [ubuntu-latest, windows-latest, macos-14]

include:
- python-version: "pypy-3.10"
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0

- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
allow-prereleases: true

- 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]
with:
token: ${{ secrets.CODECOV_TOKEN }}
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