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| # Contributor Covenant Code of Conduct | ||
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| ## Our Pledge | ||
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| We as members, contributors, and leaders pledge to make participation in our | ||
| project 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. | ||
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| We pledge to act and interact in ways that contribute to an open, welcoming, | ||
| diverse, inclusive, and healthy community. | ||
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| ## Our Standards | ||
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| Examples of behavior that contributes to a positive environment for our | ||
| community include: | ||
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| * 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 | ||
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| Examples of unacceptable behavior include: | ||
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| * 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 | ||
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| ## Enforcement Responsibilities | ||
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| 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. | ||
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| 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. | ||
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| ## Scope | ||
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| 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. | ||
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| ## Enforcement | ||
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| Instances of abusive, harassing, or otherwise unacceptable behavior may be | ||
| reported to the [project maintainer](lvulliard@cemm.oeaw.ac.at). | ||
| All complaints will be reviewed and investigated promptly and fairly. | ||
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| All community leaders are obligated to respect the privacy and security of the | ||
| reporter of any incident. | ||
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| ## Enforcement Guidelines | ||
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| Community leaders will follow these Community Impact Guidelines in determining | ||
| the consequences for any action they deem in violation of this Code of Conduct: | ||
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| ### 1. Correction | ||
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| **Community Impact**: Use of inappropriate language or other behavior deemed | ||
| unprofessional or unwelcome in the community. | ||
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| **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. | ||
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| ### 2. Warning | ||
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| **Community Impact**: A violation through a single incident or series of | ||
| actions. | ||
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| **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. | ||
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| ### 3. Temporary Ban | ||
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| **Community Impact**: A serious violation of community standards, including | ||
| sustained inappropriate behavior. | ||
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| **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. | ||
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| ### 4. Permanent Ban | ||
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| **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. | ||
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| **Consequence**: A permanent ban from any sort of public interaction within the | ||
| community. | ||
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| ## Attribution | ||
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| This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), | ||
| version 2.1, available at | ||
| <https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>. |
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| # How to contribute to BioProfiling.jl | ||
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| We gladly welcome all contributions to BioProfiling.jl! | ||
| This document presents the most constructive and ways to participate in this project. | ||
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| ## Code of Conduct | ||
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| Please follow our [code of conduct](CODE_OF_CONDUCT.md) when participating or contributing to this repository. | ||
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| ## Use of the Issues tab | ||
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| The project uses the [repository's issues](https://github.com/menchelab/BioProfiling.jl/issues) to track bugs and ideas for novel features and improvements. Feel free to participate, whether or not you have the time and expertise to **come up with a solution yourself**! Please do your best to make your issue clear, reproducible, and unique. In particular, do not forget the issue archive as it may have been addressed already. | ||
| This is also the perfect place to discuss your contribution ideas with the community before starting implementing them. This can save you and others time, by making sure the changes are relevant for the community and will be compatible with the rest of the codebase. | ||
| The most pressing issues are listed in the [Projects tab](https://github.com/menchelab/BioProfiling.jl/projects) so that they are adressed in the next release. Some issues might also be tagged as "good first issues" if they are expected to be relatively straightforward to implement and do not require an advanced understanding of the project's source code. | ||
| Finally, **if you are seeking help** on how to use BioProfiling.jl and did not find an answer in [the documentation](https://menchelab.github.io/BioProfiling.jl/dev/) or in [the example notebooks](https://github.com/menchelab/BioProfilingNotebooks), you are also welcome to create a new issue to ask your question! | ||
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| ## Code contributions | ||
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| For all code contributions, please [create a pull request](https://github.com/menchelab/BioProfiling.jl/pulls), either to the main branch for bug fixes and performance improvements or to a development branch, according to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). | ||
| To do so, **fork the project, create and checkout a branch, add and commit your changes, test your code locally, push your new branch and open a pull request**. Other contributors and maintainers will be able to review your changes and may ask you to make additional modifications so that your contribution fits nicely in the project, and eventually merge your code to the master or development branches. Thanks for even considering going through this process! | ||
| To ensure the code is functional and stays compatible with new versions of its dependencies, a [battery of tests](test/runtests.jl) is implemented. For all new features, such tests need to be added in the `test` folder before the PR can be merged. These tests will be automatically run via GitHub Actions when creating a pull request to the master branch. You can also test them locally as follows: | ||
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| ```julia | ||
| import Pkg | ||
| Pkg.activate("./") | ||
| Pkg.resolve() | ||
| Pkg.test() | ||
| ``` | ||
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| All tests should pass for the supported versions of Julia and the package's dependencies. | ||
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| ## Development environment | ||
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| BioProfiling.jl is intended to be compatible with a large set of environments as detailed in [Project.toml](Project.toml). If you need to setup a development environment, an easy solution is to start from the [latest Docker image designed to run the example notebooks](https://hub.docker.com/r/koalive/bioprofilingnotebooks), which comes with all dependencies installed. To avoid inteferences between the pre-installed version of BioProfiling.jl and your local version of the source code, you can remove the version installed in the container with the following lines: | ||
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| ```julia | ||
| import Pkg | ||
| Pkg.rm("BioProfiling") | ||
| ``` | ||
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| As mentioned in the [Code contributions section](#code-contributions), you can test your changes locally but you do not need to worry about breaking features as we use continuous integration to validate changes to the master branch. | ||
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| ## Contributors acknowledgment | ||
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| We really appreciate all contributions which make BioProfiling.jl more useful for the community! The package is [open source, provided for free and under the MIT license](LICENSE) and we offer our profound gratitude to the contributors, who will also be acknowledged in [the Credits section on the project's README](README.md#credits). |
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