.. raw:: html Contributing to Ziplign ======================= 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 .. raw:: html Table of Contents ----------------- - `I Have a Question <#i-have-a-question>`__ - `I Want To Contribute <#i-want-to-contribute>`__ - `Reporting Bugs <#reporting-bugs>`__ - `Suggesting Enhancements <#suggesting-enhancements>`__ - `Code Contributions <#code-contributions>`__ - `Improving The Documentation <#improving-the-documentation>`__ - `Styleguides <#styleguides>`__ - `Commit Messages <#commit-messages>`__ - `Join The Project Team <#join-the-project-team>`__ 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. 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 `__. - Provide as much context as you can about what you’re running into. - Provide the Ziplign version and your OS (Windows, MacOS etc), depending on what seems relevant. We will then take care of the issue as soon as possible. I Want To Contribute -------------------- .. rubric:: Legal Notice :name: 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 licence. Reporting Bugs ~~~~~~~~~~~~~~ .. raw:: html 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 <#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 `__. - 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: - OS, Platform and Version (Windows, Linux, macOS, x86, ARM) - Version of Ziplign - Possibly your input files and the output, or screenshots - Can you reliably reproduce the issue? And can you also reproduce it with older versions? .. raw:: html How Do I Submit a Good Bug Report? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 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 <#code-contributions>`__. Suggesting Enhancements ~~~~~~~~~~~~~~~~~~~~~~~ This section guides you through submitting an enhancement suggestion for Ziplign, **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. .. raw:: html 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. .. raw:: html 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 or screen recordings** which help you demonstrate the steps or point out the part which the suggestion is related to. You can use `LICEcap `__ to record GIFs on macOS and Windows, and the built-in `screen recorder in GNOME `__ or `SimpleScreenRecorder `__ on Linux. - **Explain why this enhancement would be useful** to most Ziplign users. You may also want to point out the other projects that solved it better and which could serve as inspiration. Code Contributions ~~~~~~~~~~~~~~~~~~ Ziplign is developed using the Godot engine and IDE available for free from here: https://godotengine.org/download/. It is available for Windows, MacOS and Linux. Please use the Godot IDE it to modify the code, and let it do the formatting (indendation etc). Test your changes using the “Run Project” button near the top right of the IDE. Please test the main functionality of Ziplign using the built-in test data. Run the project, select “New”, click the test data button at the top, and then “Start”. See the `test data `__ documentation for more details and screenshots. Once the test data are loaded, test all of the following still work, which is a basic check of the main functionality. It does not test everything. 1. All navigation buttons at the top left, and the cursor keys on the keyboard. 2. The main horizontal scroll bars at the top and bottom, to slide the genomes left and right. 3. Zooming using the buttons on the left and with the keys ``-``, ``+``, ``=``. Also, where possible, with a mouse wheel or trackpad pinch gesture. 4. Double-click on any BLAST match to check that the view jumps so that the match is on the left of the window. Reset the view by pressing ``=``. 5. Reverse complement buttons on the left. Check both the top and bottom genomes are correctly reverse complemented. 6. In the filter matches fields: - Set the minimum match length to 500bp. All but one of the matches should disappear. Put it back to 100bp. - Set the maximum match length to 500bp. One match should disappear. Put it back to 1000000bp. - Set the minimumum percent identity to 99. All but two matches should disappear. Put it back to 90. 7. Test saving/loading temporary views work. Press ``shift-1`` to save the current view in slot 1. Then move anywhere else and press ``1``. It should return to the saved view. 8. Check that searching works. Click on the magnifying glass icon on the left, near the bottom. Check the searches below. Clicking on each search result at the bottom left should highlight where it is in the genome. - Search for the sequence AGTCCAGAGTGGGGG. There should be two matches. - Search for “name” in the annotation. There should be several matches. 9. Return to the main menu (top left return button or press ``q``), and then check that the project can be saved to a file and then loaded from that file. If your code changes affect something not listed above, then obviously check the releveant functionality. Once you have made the changes and are happy everything works, submit a pull request. The GitHub documentation may help if this is your first pull request: https://docs.github.com/en/get-started/exploring-projects-on-github/contributing-to-open-source. Improving The Documentation ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Please raise a GitHub issue for suggestions, or pull requests with fixes are welcome! If you want to edit the documentation: - The documentation is in the folder ``docs/``. - Build a local copy of the documentation by running ``sphinx-build -b html -d _build/doctrees . OUT/html``. This assumes that sphinx is installed (on Ubuntu the package is python3-sphinx), and also the python package sphinx_rtd_theme (which is pip installable). - Submit a pull request with the changes .. raw:: html Attribution ----------- This guide is based on the `contributing.md `__!