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Contributing to AIgarMIC

First off, thanks for taking the time to contribute!

All types of contributions are encouraged and valued. See the 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
  • Cite the project or associated validation work
  • Mention the project at local meetups and tell your friends/colleagues

Table of Contents

Code of Conduct

This project and everyone participating in it is governed by the AIgarMIC Code of Conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to [email protected].

I Have a Question

If you want to ask a question, we assume that you have read the available Documentation.

Before you ask a question, it is best to search for existing 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.

If you then still feel the need to ask a question and need clarification, we recommend the following:

  • Start a topic in the Discussions section (alternatively, email the lead developer at [email protected]).
  • Provide as much context as you can about what you're running into.
  • Provide project and platform versions (especially tensorflow and keras versions), 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. If you are looking for support, you might want to check this section).
  • 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.
  • Collect information about the bug:
    • Stack trace (Traceback)
    • OS, Platform and Version (Windows, Linux, macOS, x86, ARM)
    • Version of python, tensorflow and keras
    • 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 [email protected].

We use GitHub issues to track bugs and errors. If you run into an issue with the project:

  • Open an Issue. (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.

Suggesting Enhancements

This section guides you through submitting an enhancement suggestion for AIgarMIC, 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 carefully and find out if the functionality is already covered, maybe by an individual configuration.
  • Perform a search 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.
  • Consider whether the enhancement can be satisfied by using alternative software, such as cellprofiler (for agar plate image manipulation), or AMR (for analysis and processing of minimum inhibitory concentration results). Generally, AIgarMIC enhancements that are alternatively feasible using such software will only be considered if they have a significant positive impact on minimum inhibitory concentration analysis routine workflows.

How Do I Submit a Good Enhancement Suggestion?

Enhancement suggestions are tracked as GitHub 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 to record GIFs on macOS and Windows, and this tool or this tool on Linux.
  • Explain why this enhancement would be useful to most AIgarMIC 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

Installation instructions and developer notes for AIgarMIC can be found in the documentation. We suggest using PyCharm as the IDE for development, although this is optional. For development purposes, we recommend:

Contribute to AIgarMIC by following these general steps:

  1. Fork the project locally,
  2. Create a new branch that will contain your feature/bug fix,
  3. Make your updates,
  4. If the branch contains new feature/s functionality, add testing code to the tests directory (we use pytest as the testing framework),
  5. Ensure that the full testing suite passes (including ones requiring optional assets) -- see developer notes for more information on testing,
  6. Check that build process succeeds (we use poetry for dependency management and building), again see developer notes for more information,
  7. Update documentation (if appropriate) and check that doctest passes,
  8. Commit your changes and push to your fork,
  9. Create a pull request to the main branch of the AIgarMIC repository.

Improving The Documentation

For documentation, we use reStructuredText. Source files are stored in the docs directory. The documentation is built using sphinx. Documentation source code can be updated using the same contribution process as for code. Please try to keep the documentation free of excessive laboratory jargon, and provide examples using the optional assets wherever possible.

Styleguides

AIgarMIC follows the PEP 8 style guide, although convention and refactor recommendations are not enforced. Please see developer notes for more information on checking PEP 8 compliance.

In addition, these are some specific style guides for AIgarMIC:

  • User-accessible or API-level classes and functions/methods should have a sphinx compliant reStructuredText docstring.
  • Comments should be used sparingly
  • Maximum line length is 120 characters
  • Use of type hints in functions/methods
  • Import and no-member errors related to tensorflow, keras and openCV are known and can be ignored inline using: # pylint: disable=import-error,no-member

Join The Project Team and Collaborations

If you are interested in joining the team or a formal collaboration, please email the lead developer, Alessandro Gerada at: [email protected].

Attribution

This guide is based on the contributing-gen. Make your own!