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Modernize project (#231)
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cthoyt authored Aug 20, 2024
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6 changes: 3 additions & 3 deletions .bumpversion.cfg
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Expand Up @@ -19,9 +19,9 @@ values =
[bumpverion:part:build]
values = [0-9A-Za-z-]+

[bumpversion:file:setup.cfg]
search = version = {current_version}
replace = version = {new_version}
[bumpversion:file:pyproject.toml]
search = version = "{current_version}"
replace = version = "{new_version}"

[bumpversion:file:docs/source/conf.py]
search = release = "{current_version}"
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25 changes: 25 additions & 0 deletions .cruft.json
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@@ -0,0 +1,25 @@
{
"template": "https://github.com/cthoyt/cookiecutter-snekpack",
"commit": "761b8bdf58def4a53d7ef159a5717088505cf080",
"checkout": null,
"context": {
"cookiecutter": {
"package_name": "y0",
"package_name_stylized": "Y0",
"short_description": "Causal inference in Python.",
"author_name": "Charles Tapley Hoyt",
"author_email": "cthoyt@gmail.com",
"github_organization_name": "y0-causal-inference",
"github_repository_name": "y0",
"command_line_interface": true,
"gitlab": false,
"runner": "tox",
"__runner": "tox -e",
"__runner_pip": "tox tox-uv",
"__runner_tests": "py",
"__gh_slug": "y0-causal-inference/y0",
"_template": "https://github.com/cthoyt/cookiecutter-snekpack"
}
},
"directory": null
}
132 changes: 132 additions & 0 deletions .github/CODE_OF_CONDUCT.md
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@@ -0,0 +1,132 @@
# Contributor Covenant Code of Conduct

## Our Pledge

We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, caste, color, religion, or sexual
identity and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.

## Our Standards

Examples of behavior that contributes to a positive environment for our
community include:

* Demonstrating empathy and kindness toward other people
* Being respectful of differing opinions, viewpoints, and experiences
* Giving and gracefully accepting constructive feedback
* Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
* Focusing on what is best not just for us as individuals, but for the overall
community

Examples of unacceptable behavior include:

* The use of sexualized language or imagery, and sexual attention or advances of
any kind
* Trolling, insulting or derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or email address,
without their explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting

## Enforcement Responsibilities

Community leaders are responsible for clarifying and enforcing our standards of
acceptable behavior and will take appropriate and fair corrective action in
response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.

Community leaders have the right and responsibility to remove, edit, or reject
comments, commits, code, wiki edits, issues, and other contributions that are
not aligned to this Code of Conduct, and will communicate reasons for moderation
decisions when appropriate.

## Scope

This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official e-mail address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement at
cthoyt@gmail.com.
All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the
reporter of any incident.

## Enforcement Guidelines

Community leaders will follow these Community Impact Guidelines in determining
the consequences for any action they deem in violation of this Code of Conduct:

### 1. Correction

**Community Impact**: Use of inappropriate language or other behavior deemed
unprofessional or unwelcome in the community.

**Consequence**: A private, written warning from community leaders, providing
clarity around the nature of the violation and an explanation of why the
behavior was inappropriate. A public apology may be requested.

### 2. Warning

**Community Impact**: A violation through a single incident or series of
actions.

**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or permanent
ban.

### 3. Temporary Ban

**Community Impact**: A serious violation of community standards, including
sustained inappropriate behavior.

**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No public or
private interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, is allowed during this period.
Violating these terms may lead to a permanent ban.

### 4. Permanent Ban

**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.

**Consequence**: A permanent ban from any sort of public interaction within the
community.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.1, available at
[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].

Community Impact Guidelines were inspired by
[Mozilla's code of conduct enforcement ladder][Mozilla CoC].

For answers to common questions about this code of conduct, see the FAQ at
[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
[https://www.contributor-covenant.org/translations][translations].

[homepage]: https://www.contributor-covenant.org
[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
[Mozilla CoC]: https://github.com/mozilla/diversity
[FAQ]: https://www.contributor-covenant.org/faq
[translations]: https://www.contributor-covenant.org/translations
47 changes: 26 additions & 21 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,8 @@ This project uses the [GitHub Flow](https://guides.github.com/introduction/flow)
model for code contributions. Follow these steps:

1. [Create a fork](https://help.github.com/articles/fork-a-repo) of the upstream
repository at [`y0-causal-inference/y0`](https://github.com/y0-causal-inference/y0)
repository
at [`y0-causal-inference/y0`](https://github.com/y0-causal-inference/y0)
on your GitHub account (or in one of your organizations)
2. [Clone your fork](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository)
with `git clone https://github.com/<your namespace here>/y0.git`
Expand All @@ -19,7 +20,8 @@ model for code contributions. Follow these steps:

### Merge Model

This repository uses [squash merges](https://docs.github.com/en/github/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/about-pull-request-merges#squash-and-merge-your-pull-request-commits)
This repository
uses [squash merges](https://docs.github.com/en/github/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/about-pull-request-merges#squash-and-merge-your-pull-request-commits)
to group all related commits in a given pull request into a single commit upon
acceptance and merge into the main branch. This has several benefits:

Expand All @@ -30,21 +32,21 @@ acceptance and merge into the main branch. This has several benefits:

### Code Style

This project uses `tox` for running code quality checks. Start by installing
it` with `pip install tox tox-uv`.

This project encourages the use of optional static typing. It
uses [`mypy`](http://mypy-lang.org/) as a type checker
and [`sphinx_autodoc_typehints`](https://github.com/agronholm/sphinx-autodoc-typehints)
to automatically generate documentation based on type hints. You can check if
uses [`mypy`](http://mypy-lang.org/) as a type checker. You can check if
your code passes `mypy` with `tox -e mypy`.

This project uses [`black`](https://github.com/psf/black) to automatically
enforce a consistent code style. You can apply `black` and other pre-configured
linters with `tox -e lint`.
This project uses [`ruff`](https://docs.astral.sh/ruff/) to automatically
enforce a consistent code style. You can apply `ruff format` and other pre-configured
formatters with `tox -e format`.

This project uses [`flake8`](https://flake8.pycqa.org) and several plugins for
This project uses [`ruff`](https://docs.astral.sh/ruff/) and several plugins for
additional checks of documentation style, security issues, good variable
nomenclature, and more (
see [`tox.ini`](tox.ini) for a list of flake8 plugins). You can check if your
code passes `flake8` with `tox -e flake8`.
nomenclature, and more (see `pyproject.toml` for a list of Ruff plugins). You can check if your
code passes `ruff check` with `tox -e lint`.

Each of these checks are run on each commit using GitHub Actions as a continuous
integration service. Passing all of them is required for accepting a
Expand All @@ -56,7 +58,7 @@ comment, and we will help you.

Python's builtin `print()` should not be used (except when writing to files),
it's checked by the
[`flake8-print`](https://github.com/jbkahn/flake8-print) plugin to `flake8`. If
[`flake8-print` (T20)](https://docs.astral.sh/ruff/rules/#flake8-print-t20) plugin to `ruff`. If
you're in a command line setting or `main()` function for a module, you can use
`click.echo()`. Otherwise, you can use the builtin `logging` module by adding
`logger = logging.getLogger(__name__)` below the imports at the top of your
Expand All @@ -65,8 +67,9 @@ file.
### Documentation

All public functions (i.e., not starting with an underscore `_`) must be
documented using the [sphinx documentation format](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html#the-sphinx-docstring-format).
The [`darglint`](https://github.com/terrencepreilly/darglint) plugin to `flake8`
documented using
the [sphinx documentation format](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html#the-sphinx-docstring-format).
The [`darglint2`](https://github.com/akaihola/darglint2) tool
reports on functions that are not fully documented.

This project uses [`sphinx`](https://www.sphinx-doc.org) to automatically build
Expand All @@ -78,8 +81,8 @@ build it locally with `tox -e docs`.

Functions in this repository should be unit tested. These can either be written
using the `unittest` framework in the `tests/` directory or as embedded
doctests. You can check that the unit tests pass with `tox -e py` and that the
doctests pass with `tox -e doctests`. These tests are required to pass for
doctests. You can check that the unit tests pass with `tox -e py`
and that the doctests pass with `tox -e doctests`. These tests are required to pass for
accepting a contribution.

### Syncing your fork
Expand All @@ -93,19 +96,21 @@ $ git remote add y0-causal-inference https://github.com/y0-causal-inference/y0.g
```

Then, you can merge upstream code into your branch. You can also use the GitHub
UI to do this by following [this tutorial](https://docs.github.com/en/github/collaborating-with-pull-requests/working-with-forks/syncing-a-fork).
UI to do this by
following [this tutorial](https://docs.github.com/en/github/collaborating-with-pull-requests/working-with-forks/syncing-a-fork).

### Python Version Compatibility

This project aims to support all versions of Python that have not passed their
end-of-life dates. After end-of-life, the version will be removed from the Trove
qualifiers in the [`setup.cfg`](setup.cfg) and from the GitHub Actions testing
qualifiers in the `pyproject.toml` and from the GitHub Actions testing
configuration.

See https://endoflife.date/python for a timeline of Python release and
end-of-life dates.

## Acknowledgements
## Acknowledgements

These code contribution guidelines are derived from the [cthoyt/cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)
These code contribution guidelines are derived from
the [cthoyt/cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)
Python package template. They're free to reuse and modify as long as they're properly acknowledged.
79 changes: 79 additions & 0 deletions .github/workflows/cruft.yml
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# from https://cruft.github.io/cruft/#automating-updates-with-github-actions

name: Update repository with Cruft

permissions:
contents: write
pull-requests: write

on:
workflow_dispatch:
schedule:
- cron: "0 2 * * 1" # Every Monday at 2am

jobs:
update:
runs-on: ubuntu-latest
strategy:
fail-fast: true
matrix:
include:
- add-paths: .
body: Use this to merge the changes to this repository.
branch: cruft/update
commit-message: "chore: accept new Cruft update"
title: New updates detected with Cruft
- add-paths: .cruft.json
body: Use this to reject the changes in this repository.
branch: cruft/reject
commit-message: "chore: reject new Cruft update"
title: Reject new updates detected with Cruft
steps:
- uses: actions/checkout@v3

- uses: actions/setup-python@v4
with:
python-version: "3.10"

- name: Install Cruft
run: pip3 install cruft

- name: Check if update is available
continue-on-error: false
id: check
run: |
CHANGES=0
if [ -f .cruft.json ]; then
if ! cruft check; then
CHANGES=1
fi
else
echo "No .cruft.json file"
fi
echo "has_changes=$CHANGES" >> "$GITHUB_OUTPUT"
- name: Run update if available
if: steps.check.outputs.has_changes == '1'
run: |
git config --global user.email "you@example.com"
git config --global user.name "GitHub"
cruft update --skip-apply-ask --refresh-private-variables
git restore --staged .
- name: Create pull request
if: steps.check.outputs.has_changes == '1'
uses: peter-evans/create-pull-request@v4
with:
token: ${{ secrets.GITHUB_TOKEN }}
add-paths: ${{ matrix.add-paths }}
commit-message: ${{ matrix.commit-message }}
branch: ${{ matrix.branch }}
delete-branch: true
branch-suffix: timestamp
title: ${{ matrix.title }}
body: |
This is an autogenerated PR. ${{ matrix.body }}
[Cruft](https://cruft.github.io/cruft/) has detected updates from the Cookiecutter repository.
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