diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 00000000..aaa339ce --- /dev/null +++ b/.github/CONTRIBUTING.md @@ -0,0 +1,69 @@ +# Contributing to REEV + +We love your input! +We want to make contributing to this project as easy and transparent as possible, whether it's: + +- Reporting a bug +- Discussing the current state of the code +- Submitting a fix +- Proposing new features +- Becoming a maintainer + +## We Develop with GiHhub + +We use GitHub to host code, to track issues and feature requests, as well as accept pull requests. + +## We Use [GitHub Flow](https://docs.github.com/en/get-started/quickstart/github-flow), So All Code Changes Happen Through Pull Requests + +Pull requests are the best way to propose changes to the codebase (we use [GitHub Flow](https://docs.github.com/en/get-started/quickstart/github-flowl)). +We actively welcome your pull requests: + +1. Fork the repo and create your branch from `main`. +2. If you've added code that should be tested, add tests. +3. If you've changed APIs, update the documentation. +4. Ensure the test suite passes. +5. Make sure your code lints. +6. Use [conventional ommits](https://www.conventionalcommits.org/en/v1.0.0/) for your commit messages. +7. Issue that pull request! + +## Any contributions you make will be under the MIT Software License + +In short, when you submit code changes, your submissions are understood to be under the same [MIT License](http://choosealicense.com/licenses/mit/) that covers the project. +Feel free to contact the maintainers if that's a concern. + +## Report bugs using GitHub's [issues](https://github.com/bihealth/reev/issues) + +We use GitHub issues to track public bugs. +Report a bug by [opening a new issue](https://github.com/bihealth/reev/issues/new/choose); it's that easy! + +## Write bug reports with detail, background, and sample code + +[This is an example](http://stackoverflow.com/q/12488905/180626) of a bug report that we found, and we think it's not a bad model. +Here's [another example from Craig Hockenberry](http://www.openradar.me/11905408), an app developer whom we respect. + +**Great Bug Reports** tend to have: + +- A quick summary and/or background +- Steps to reproduce + - Be specific! + - Give sample code if you can. [Above stackoverflow question](http://stackoverflow.com/q/12488905/180626) includes sample code that *anyone* with a base R setup can run to reproduce what the reporter was seeing +- What you expected would happen +- What actually happens +- Notes (possibly including why you think this might be happening, or stuff you tried that didn't work) + +People *love* thorough bug reports. +We're not even kidding. + +## Use a Consistent Coding Style + +We use black for Python code and prettier for JavaScript code. +You can find plenty examples in the code base and our continuous integration will enforce the style guides. +You can use the `make lint` target to check your code style locally. + +## License + +By contributing, you agree that your contributions will be licensed under its MIT License. + +## References + +This document was adapted from the open-source contribution guidelines for [Facebook's Draft](https://github.com/facebook/draft-js/blob/a9316a723f9e918afde44dea68b5f9f39b7d9b00/CONTRIBUTING.md) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 00000000..776284f3 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,14 @@ + diff --git a/LICENSE b/LICENSE index d6456956..98222b68 100644 --- a/LICENSE +++ b/LICENSE @@ -1,202 +1,21 @@ - - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/docs/CODE_OF_CONDUCT.md b/docs/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..f845da88 --- /dev/null +++ b/docs/CODE_OF_CONDUCT.md @@ -0,0 +1,128 @@ +# 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 +cubi@bih-charite.de. +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. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +https://www.contributor-covenant.org/faq. Translations are available at +https://www.contributor-covenant.org/translations. diff --git a/docs/SECURITY.md b/docs/SECURITY.md new file mode 100644 index 00000000..b18152ce --- /dev/null +++ b/docs/SECURITY.md @@ -0,0 +1,13 @@ +# Security Policy + +## Supported Versions + +We assume that we will host the primary REEV site and other deployments will be behind local firewalls. +In general, we thus only provide support for the latest reease of the software. +If you need any further support, please contact us at [cubi@bih-charite.de](mailto:cubi@bih-charite.de). + +## Reporting a Vulnerability + +Please report (suspected) security vulnerabilities to **[cubi@bih-charite.de](mailto:cubi@bih-charite.de)**. +You will receive a response from us within two working days. +If the issue is confirmed, we will release a patch as soon as possible depending on complexity but historically within a few days.