Skip to content

Commit 47c336f

Browse files
blakeawblakeaw
committed
Merge branch 'version-0.1.0'
2 parents 2f533af + 5af98a1 commit 47c336f

60 files changed

Lines changed: 7575 additions & 0 deletions

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

‎.coveragerc‎

Lines changed: 9 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,9 @@
1+
# .coveragerc
2+
3+
[run]
4+
source = qspy
5+
6+
[report]
7+
omit =
8+
*/tests/*
9+
*/site-packages/*

‎CHANGELOG.md‎

Lines changed: 24 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
1+
# Change Log
2+
All notable changes to this project will be documented in this file.
3+
4+
The format is based on [Keep a Changelog](http://keepachangelog.com/)
5+
and this project adheres to [Semantic Versioning](http://semver.org/).
6+
7+
## [0.1.0] - 2025-07-03
8+
9+
### Added
10+
- Initial development version of the package, prepared for release.
11+
12+
------
13+
14+
## Entry format
15+
16+
## [Unreleased] - yyyy-mm-dd
17+
18+
N/A
19+
20+
### Added
21+
22+
### Changed
23+
24+
### Fixed

‎CODE_OF_CONDUCT.md‎

Lines changed: 131 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,131 @@
1+
2+
# Contributor Covenant Code of Conduct
3+
4+
[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md)
5+
6+
## Our Pledge
7+
8+
We as members, contributors, and leaders pledge to make participation in our
9+
community a harassment-free experience for everyone, regardless of age, body
10+
size, visible or invisible disability, ethnicity, sex characteristics, gender
11+
identity and expression, level of experience, education, socio-economic status,
12+
nationality, personal appearance, race, caste, color, religion, or sexual
13+
identity and orientation.
14+
15+
We pledge to act and interact in ways that contribute to an open, welcoming,
16+
diverse, inclusive, and healthy community.
17+
18+
## Our Standards
19+
20+
Examples of behavior that contributes to a positive environment for our
21+
community include:
22+
23+
- Demonstrating empathy and kindness toward other people
24+
- Being respectful of differing opinions, viewpoints, and experiences
25+
- Giving and gracefully accepting constructive feedback
26+
- Accepting responsibility and apologizing to those affected by our mistakes,
27+
and learning from the experience
28+
- Focusing on what is best not just for us as individuals, but for the overall
29+
community
30+
31+
Examples of unacceptable behavior include:
32+
33+
- The use of sexualized language or imagery, and sexual attention or advances of
34+
any kind
35+
- Trolling, insulting or derogatory comments, and personal or political attacks
36+
- Public or private harassment
37+
- Publishing others' private information, such as a physical or email address,
38+
without their explicit permission
39+
- Other conduct which could reasonably be considered inappropriate in a
40+
professional setting
41+
42+
## Enforcement Responsibilities
43+
44+
Community leaders are responsible for clarifying and enforcing our standards of
45+
acceptable behavior and will take appropriate and fair corrective action in
46+
response to any behavior that they deem inappropriate, threatening, offensive,
47+
or harmful.
48+
49+
Community leaders have the right and responsibility to remove, edit, or reject
50+
comments, commits, code, wiki edits, issues, and other contributions that are
51+
not aligned to this Code of Conduct, and will communicate reasons for moderation
52+
decisions when appropriate.
53+
54+
## Scope
55+
56+
This Code of Conduct applies within all community spaces, and also applies when
57+
an individual is officially representing the community in public spaces.
58+
Examples of representing our community include using an official email address,
59+
posting via an official social media account, or acting as an appointed
60+
representative at an online or offline event.
61+
62+
## Enforcement
63+
64+
Instances of abusive, harassing, or otherwise unacceptable behavior may be
65+
reported to the community leaders responsible for enforcement at
66+
[INSERT CONTACT METHOD].
67+
All complaints will be reviewed and investigated promptly and fairly.
68+
69+
All community leaders are obligated to respect the privacy and security of the
70+
reporter of any incident.
71+
72+
## Enforcement Guidelines
73+
74+
Community leaders will follow these Community Impact Guidelines in determining
75+
the consequences for any action they deem in violation of this Code of Conduct:
76+
77+
### 1. Correction
78+
79+
**Community Impact**: Use of inappropriate language or other behavior deemed
80+
unprofessional or unwelcome in the community.
81+
82+
**Consequence**: A private, written warning from community leaders, providing
83+
clarity around the nature of the violation and an explanation of why the
84+
behavior was inappropriate. A public apology may be requested.
85+
86+
### 2. Warning
87+
88+
**Community Impact**: A violation through a single incident or series of
89+
actions.
90+
91+
**Consequence**: A warning with consequences for continued behavior. No
92+
interaction with the people involved, including unsolicited interaction with
93+
those enforcing the Code of Conduct, for a specified period of time. This
94+
includes avoiding interactions in community spaces as well as external channels
95+
like social media. Violating these terms may lead to a temporary or permanent
96+
ban.
97+
98+
### 3. Temporary Ban
99+
100+
**Community Impact**: A serious violation of community standards, including
101+
sustained inappropriate behavior.
102+
103+
**Consequence**: A temporary ban from any sort of interaction or public
104+
communication with the community for a specified period of time. No public or
105+
private interaction with the people involved, including unsolicited interaction
106+
with those enforcing the Code of Conduct, is allowed during this period.
107+
Violating these terms may lead to a permanent ban.
108+
109+
### 4. Permanent Ban
110+
111+
**Community Impact**: Demonstrating a pattern of violation of community
112+
standards, including sustained inappropriate behavior, harassment of an
113+
individual, or aggression toward or disparagement of classes of individuals.
114+
115+
**Consequence**: A permanent ban from any sort of public interaction within the
116+
community.
117+
118+
## Attribution
119+
120+
This Code of Conduct is adapted from the
121+
[Contributor Covenant](https://www.contributor-covenant.org/), version 2.1,
122+
available at
123+
<https://www.contributor-covenant.org/version/2/1/code_of_conduct/>.
124+
125+
Community Impact Guidelines were inspired by
126+
[Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/inclusion).
127+
128+
For answers to common questions about this code of conduct, see the FAQ at
129+
<https://www.contributor-covenant.org/faq/>. Translations are available at
130+
<https://www.contributor-covenant.org/translations/>.
131+

‎CONTRIBUTING.md‎

Lines changed: 66 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,66 @@
1+
# Before getting started
2+
3+
Thank you for contributing! Bug reports, feature requests, bug fixes or other contributions are all welcomed.
4+
5+
## Coding conventions
6+
7+
GitHub is used to host code, track issues, and accept pull requests. This project uses [semantic versioning](https://semver.org/) and keeps a [CHANGELOG](./CHANGELOG.md). Google style docstrings are used, and [Ruff formatting](https://docs.astral.sh/ruff/formatter/) is applied to code. For new functions, it is requested that type annotations be included in the function definition.
8+
9+
10+
# How to contribute
11+
12+
13+
## Issues
14+
15+
One great non-code way to contribute is to open an issue.
16+
17+
### Types of Issues
18+
19+
Here are the different types of Issues you can contribute:
20+
21+
* :bug: **Bug Reports**: Problem, errors, or other issues where the code is not working as expected. Please use the `bug` label.
22+
* :bulb: **Feauture Request/Suggestion**: Request or suggest some new functionality or an update/change to existing functionality. Please use the `enhancement` label.
23+
24+
### Creating a new issue
25+
26+
You can open issues here: [https://github.com/Borealis-BioModeling/qspy/issues](https://github.com/Borealis-BioModeling/qspy/issues).
27+
28+
However, before creating a new issue, please check the existing issues first to see if your issue or a similar one has already been raised. If it has, please add a comment to the existing issue rather than creating a new duplicate issue; e.g., with a bug report commenting with something like "I am also experiencing this problem" along with any additional context about your specific environment and package versions should suffice.
29+
30+
For all Bug Report issues, please provide context, including the environment and relevant package versions, code snippets for the offending code/use when applicable, a description of the expected outcome, and the actual outcome with associated error messages when applicable.
31+
32+
### Support
33+
34+
If you have support questions you can email them to [blakeaw1102@gmail.com](mailto:blakeaw1102@gmail.com)
35+
36+
## Pull Requests
37+
38+
If you want to contribute code that fixes bugs or adds new features you can fork the repository and open a pull request as described below.
39+
40+
However, before doing so, please ask first. You can do so by commenting on the relevant Issue. This helps prevent duplicated or wasted efforts.
41+
42+
Note that for automated testing and coverage analysis requires the following:
43+
[pytest](https://docs.pytest.org/en/stable/getting-started.html), [Coverage.py](https://coverage.readthedocs.io/en/7.6.10/install.html), and [nose](https://nose.readthedocs.io/en/latest/).
44+
```
45+
pip install pytest coverage nose
46+
```
47+
48+
PR contribution steps:
49+
50+
1. [Fork the repo](https://github.com/Borealis-BioModeling/qspy/fork)
51+
2. Create a new branch, e.g.:
52+
* **Bug Fix:** `fix/issue-number`, e.g. `fix/11`
53+
* **New Feature** `feature/new-feature`, e.g. `feature/foo-bar`
54+
3. For feature additions, please include additional tests for the new feature.
55+
4. Run all the tests using pytest: `python -m pytest` - or also with coverage (Coverage.py) analysis: `coverage run -m pytest`
56+
5. Once your branch passes all the tests, commit your changes, e.g. `git commit -am 'Add the new-feature feature.'`
57+
7. Push the branch to your fork, e.g. `git push origin feature/new-feature`
58+
8. Create a new [Pull request](https://github.com/Borealis-BioModeling/qspy/pulls). Reference any relevant Issues in the PR description.
59+
60+
Please note that any code contributions will be licensed according to this project's [LICENSE](./LICENSE).
61+
62+
## Code of Conduct
63+
64+
All contributions will be considered based solely on their quality and fit with the overall direction of the project.
65+
66+
All contributors are expected to be kind and respectful to one another. Behavior that is harmful to your fellow contributors is not acceptable.

‎CONTRIBUTORS.md‎

Lines changed: 15 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,15 @@
1+
# QSPy Contributors
2+
3+
Thank you to everyone who has contributed to the success of this project!
4+
5+
## Core Contributors
6+
7+
* **Blake A. Wilson** (@blakeaw) - Lead Developer, Project Maintainer
8+
9+
## Valued Contributors
10+
11+
* **Your name could be here** (@contributor) - Bug fixes, Documentation improvements, etc.
12+
13+
## Special Thanks
14+
15+
* **PySB Developers and Contributors** - QSPy is built on top of [PySB](https://pysb.org/), so wouldn't be possible without the hard work of PySB developers and contributors!

0 commit comments

Comments
 (0)