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Refactor/xspline update #43

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Oct 11, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/build.yml
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This was also a weird bug where updating python made the tests pass...

Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ jobs:

steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
- name: Set up Python 3.12.4
uses: actions/setup-python@v2
with:
python-version: 3.8
python-version: 3.12.4
- name: Install dependencies
run: python -m pip install .[dev] --upgrade pip
- name: Test with pytest
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10 changes: 10 additions & 0 deletions .pre-commit-config.yaml
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repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
rev: v0.4.2
hooks:
# Run the linter.
- id: ruff
args: [ --fix ]
# Run the formatter.
- id: ruff-format
2 changes: 0 additions & 2 deletions AUTHORS.rst

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16 changes: 16 additions & 0 deletions CHANGELOG.md
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## [0.1.0] - 2024-07-25

### Added
- pyproject

### Fixed
- updated to support xspline API changes since version 0.0.7

### Changes


## [0.0.0] - 2020-05-29

**0.0.0 - 05/29/2020**

- Repo creation
3 changes: 0 additions & 3 deletions CHANGELOG.rst

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111 changes: 111 additions & 0 deletions CODE_OF_CONDUCT.md
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# 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, 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
[INSERT CONTACT METHOD]. 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 2.0, available at
[https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0].

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

[v2.0]: https://www.contributor-covenant.org/version/2/0/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
81 changes: 0 additions & 81 deletions CODE_OF_CONDUCT.rst

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11 changes: 4 additions & 7 deletions CONTRIBUTING.rst → CONTRIBUTING.md
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@@ -1,5 +1,4 @@
Contributing
============
# Contributing

When contributing to this repository, please first discuss the change you wish
to make via issue, email, or any other method with the owners of this
Expand All @@ -8,15 +7,13 @@ repository before making a change.
Please note we have a code of conduct, please follow it in all your
interactions with the project.

Submitting Changes
------------------
## Submitting Changes

- Always make a new branch for your work.
- Patches should be small to facilitate easier review. Sometimes this will
result in many small PRs to land a single large feature.
- Larger changes should be discussed in the project's GitHub issues page.
- New features and significant bug fixes should be documented in the changelog.
- You must have legal permission to distribute any code you contribute to
``anml``, and it must be available under both the GNU
GPLv3 license.

`anml`, and it must be available under both the GNU
GPLv3 license.
4 changes: 2 additions & 2 deletions LICENSE
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@@ -1,6 +1,6 @@
BSD 2-Clause License

Copyright (c) 2022, IHME Math Sciences
Copyright (c) 2019-2024, IHME Math Sciences
All rights reserved.

Redistribution and use in source and binary forms, with or without
Expand All @@ -22,4 +22,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
12 changes: 0 additions & 12 deletions MANIFEST.in

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14 changes: 14 additions & 0 deletions README.md
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[![PyPI version](https://badge.fury.io/py/anml.svg)](https://badge.fury.io/py/anml)
![Python](https://img.shields.io/badge/python-3.6%2B-blue.svg)
[![Build Status](https://github.com/ihmeuw-msca/regmod/workflows/build/badge.svg)](https://github.com/ihmeuw-msca/regmod/actions)
[![GitHub](https://img.shields.io/github/license/ihmeuw-msca/anml)](./LICENSE)
[![docs](https://img.shields.io/badge/docs-here-green)](https://ihmeuw-msca.github.io/anml)
[![codecov](https://img.shields.io/codecov/c/github/ihmeuw-msca/anml)](https://codecov.io/gh/ihmeuw-msca/anml)
[![codacy](https://img.shields.io/codacy/grade/ae72a07785f5469eac234d1f6bdf555f)](https://app.codacy.com/gh/ihmeuw-msca/anml/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)


# anml: A Nonlinear Modeling Library

This is a nonlinear modeling library.

**NOTE** This repository is under construction. 🚧 ⚠️ 👷
11 changes: 0 additions & 11 deletions README.rst

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61 changes: 61 additions & 0 deletions pyproject.toml
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[build-system]
build-backend = "setuptools.build_meta"
requires = [
"setuptools>=61",
]

[project]
name = "anml"
version = "0.3.0"
description = "This is a nonlinear modeling library."
readme = "README.md"
license = { text = "BSD-2-Clause" }
requires-python = ">=3.6"
authors = [
{ name = "IHME Math Sciences", email = "ihme.math.sciences@gmail.com" },
]

dependencies =[
"numpy<2.0.0",
"pandas",
"scipy",
"xspline",
"click"
]

[project.urls]
homepage = "https://github.com/ihmeuw-msca/anml"

[tool.pytest.ini_options]
testpaths = ["tests", "integration"]
addopts = "-v -ra -q"
log_cli = true
log_cli_level = "INFO"
log_format = "%(asctime)s %(levelname)s %(message)s"
log_date_format = "%Y-%m-%d %H:%M:%S"
minversion = "6.0"
filterwarnings = "ignore"

[project.optional-dependencies]
docs = [
"sphinx>=3.0.0",
"sphinx-autodoc-typehints",
"furo",
"sphinx-click",
"IPython",
"matplotlib"
]
test = [
"pytest",
"pytest-mock"
]
dev = [
"sphinx>=3.0.0",
"sphinx-autodoc-typehints",
"furo",
"sphinx-click",
"IPython",
"matplotlib",
"pytest",
"pytest-mock"
]
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