# Contributing to pyCellPhenoX First off, thanks for taking the time to contribute! ❤️ All types of contributions are encouraged and valued. See the [Table of Contents](#table-of-contents) for different ways to help and details about how this project handles them. Please make sure to read the relevant section before making your contribution. It will make it a lot easier for us maintainers and smooth out the experience for all involved. The community looks forward to your contributions. 🎉 > And if you like the project, but just don't have time to contribute, that's fine. There are other easy ways to support the project and show your appreciation, which we would also be very happy about: > - Star the project > - Tweet about it > - Refer this project in your project's readme > - Mention the project at local meetups and tell your friends/colleagues ## Table of Contents - [Code of Conduct](#code-of-conduct) - [I Have a Question](#i-have-a-question) - [I Want To Contribute](#i-want-to-contribute) - [Reporting Bugs](#reporting-bugs) - [Suggesting Enhancements](#suggesting-enhancements) - [Styleguides](#style-guides) - [Documentation](#documentation) - [Dev Environments](#dev-environments) - [Code Quality](#code-quality) - [Formatting](#formatting) - [Linting](#linting) - [Documentation Style Guide](#documentation-style-guide) - [Commit Messages](#commit-messages) - [Attribution](#attribution) ## Code of Conduct This project and everyone participating in it is governed by the [pyCellPhenoX Code of Conduct](https://github.com/fanzhanglab/pyCellPhenoXblob/master/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to . ## I Have a Question > If you want to ask a question, we assume that you have read the available [Documentation](https://pyCellPhenoX.readthedocs.io). Before you ask a question, it is best to search for existing [Issues](https://github.com/fanzhanglab/pyCellPhenoX/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue. It is also advisable to search the internet for answers first. If you then still feel the need to ask a question and need clarification, we recommend the following: - Open an [Issue](https://github.com/fanzhanglab/pyCellPhenoX/issues/new). - Provide as much context as you can about what you're running into. - Provide project and platform versions (nodejs, npm, etc), depending on what seems relevant. We will then take care of the issue as soon as possible. ## I Want To Contribute > ### Legal Notice > When contributing to this project, you must agree that you have authored 100% of the content, that you have the necessary rights to the content and that the content you contribute may be provided under the project license. ### Reporting Bugs #### Before Submitting a Bug Report A good bug report shouldn't leave others needing to chase you up for more information. Therefore, we ask you to investigate carefully, collect information and describe the issue in detail in your report. Please complete the following steps in advance to help us fix any potential bug as fast as possible. - Make sure that you are using the latest version. - Determine if your bug is really a bug and not an error on your side e.g. using incompatible environment components/versions (Make sure that you have read the [documentation](https://pyCellPhenoX.readthedocs.io). If you are looking for support, you might want to check [this section](#i-have-a-question)). - To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the [bug tracker](https://github.com/fanzhanglab/pyCellPhenoXissues?q=label%3Abug). - Also make sure to search the internet (including Stack Overflow) to see if users outside of the GitHub community have discussed the issue. - Collect information about the bug: - Stack trace (Traceback) - OS, Platform and Version (Windows, Linux, macOS, x86, ARM) - Version of the interpreter, compiler, SDK, runtime environment, package manager, depending on what seems relevant. - Possibly your input and the output - Can you reliably reproduce the issue? And can you also reproduce it with older versions? #### How Do I Submit a Good Bug Report? > You must never report security related issues, vulnerabilities or bugs including sensitive information to the issue tracker, or elsewhere in public. Instead sensitive bugs must be sent by email to . We use GitHub issues to track bugs and errors. If you run into an issue with the project: - Open an [Issue](https://github.com/fanzhanglab/pyCellPhenoX/issues/new). (Since we can't be sure at this point whether it is a bug or not, we ask you not to talk about a bug yet and not to label the issue.) - Explain the behavior you would expect and the actual behavior. - Please provide as much context as possible and describe the *reproduction steps* that someone else can follow to recreate the issue on their own. This usually includes your code. For good bug reports you should isolate the problem and create a reduced test case. - Provide the information you collected in the previous section. Once it's filed: - The project team will label the issue accordingly. - A team member will try to reproduce the issue with your provided steps. If there are no reproduction steps or no obvious way to reproduce the issue, the team will ask you for those steps and mark the issue as `needs-repro`. Bugs with the `needs-repro` tag will not be addressed until they are reproduced. - If the team is able to reproduce the issue, it will be marked `needs-fix`, as well as possibly other tags (such as `critical`), and the issue will be left to be [implemented by someone](#your-first-code-contribution). ### Suggesting Enhancements This section guides you through submitting an enhancement suggestion for pyCellPhenoX, **including completely new features and minor improvements to existing functionality**. Following these guidelines will help maintainers and the community to understand your suggestion and find related suggestions. #### Before Submitting an Enhancement - Make sure that you are using the latest version. - Read the [documentation](https://pyCellPhenoX.readthedocs.io) carefully and find out if the functionality is already covered, maybe by an individual configuration. - Perform a [search](https://github.com/fanzhanglab/pyCellPhenoX/issues) to see if the enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one. - Find out whether your idea fits with the scope and aims of the project. It's up to you to make a strong case to convince the project's developers of the merits of this feature. Keep in mind that we want features that will be useful to the majority of our users and not just a small subset. If you're just targeting a minority of users, consider writing an add-on/plugin library. #### How Do I Submit a Good Enhancement Suggestion? Enhancement suggestions are tracked as [GitHub issues](https://github.com/fanzhanglab/pyCellPhenoX/issues). - Use a **clear and descriptive title** for the issue to identify the suggestion. - Provide a **step-by-step description of the suggested enhancement** in as many details as possible. - **Describe the current behavior** and **explain which behavior you expected to see instead** and why. At this point you can also tell which alternatives do not work for you. - You may want to **include screenshots and animated GIFs** which help you demonstrate the steps or point out the part which the suggestion is related to. You can use [this tool](https://www.cockos.com/licecap/) to record GIFs on macOS and Windows, and [this tool](https://github.com/colinkeenan/silentcast) or [this tool](https://github.com/GNOME/byzanz) on Linux. - **Explain why this enhancement would be useful** to most pyCellPhenoX users. You may also want to point out the other projects that solved it better and which could serve as inspiration. ## Your first code contribution We welcome contributions! Follow these steps to contribute: ### 1. Fork, Clone, and Branch - Fork the repository and clone it to your local machine. ```bash git clone https://github.com/fanzhanglab/pyCellPhenoX.git cd pyCellPhenoX ``` Please branch from the `main` branch given we have set up branch protections. ``` bash git checkout -b your-branch-name ``` ### 2. Make Your Changes - Make sure your code follows the project standards. - Format your Python code with Black: ``` bash black your_file.py ``` ### 3. Commit and Push Commit your changes with a meaningful message: ```bash git commit -m "Description of your changes" ``` Push your changes: ``` bash git push origin your-branch-name ``` ### 4. Submit a Pull Request Submit a pull request and explain the changes you've made. ## Style Guides ### Documentation We use [sphinx](https://www.sphinx-doc.org/en/master/index.html) for autodocumentation of docstrings, using the [napoleon extenstion](https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html) to parse [NumPy style docstrings](https://numpydoc.readthedocs.io/en/latest/format.html), implemented with a [furo](https://pradyunsg.me/furo/) theme. We host our documentation on [readthedocs.org](https://readthedocs.org/) at [https://pyCellPhenoX.readthedocs.io/en/](https://pyCellPhenoX.readthedocs.io/en/). To build and test changes to the docs locally, run the following command: ```bash sphinx-build -b html docs build ``` See [`docs/conf.py`](../conf.py) for full documentation configuration. ### Dev environments #### Local devcontainer Instructions for setting up a local development environment using VSCode DevContainers: 1. Install [VSCode](https://code.visualstudio.com/download) 2. Install the [Remote - Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers) extension 3. Open the repository in VSCode 4. Click on the green "Reopen in Container" button in the lower left corner of the window 5. Wait for the container to build and install the required dependencies ## Code Quality Please follow the below quality guides to the best of your abilities. If you have configured your [dev environment](#dev-environments) as described above, the formatting and linting rules will also be enforced automatically using the installed [pre-commit](https://pre-commit.com/) hooks. ### Formatting We use [black](https://black.readthedocs.io/en/stable/) for formatting Python code, and [prettier](https://prettier.io/) for formatting markdown, json and yaml files. We include `black` in the poetry dev dependencies so it can be run manually using `black format` Prettier (which is not python-based) is not included in the poetry dev dependencies, but can be installed and run manually. Alternately, both `black format` and `prettier` will be run automatically at commit time with the pre-commit hooks installed. ### Linting For python code linting, we also use [black](https://black.readthedocs.io/en/stable/), which can perform same linting checks as Flake8. You can use the command `black --check your_file.py` or `black path/to/your/directory` to check for linting errors. We also include some commented-out rules in that section that we are working towards enabling in the future. All linting checks will also be run automatically at commit time with the pre-commit hooks as described above. ### Documentation style guide We use the [numpy documentation style guide](https://numpydoc.readthedocs.io/en/latest/format.html). When writing markdown documentation, please also ensure that each sentence is on a new line. ### Commit messages pyCellPhenoX uses [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/) standard for commit messages to aid in automatic changelog generation. We prepare commit messages that follow this standard using [commitizen](https://commitizen-tools.github.io/commitizen/), which comes with the poetry dev dependencies. ## Attribution This guide is based on the **contributing-gen**. [Make your own](https://github.com/bttger/contributing-gen)!