Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
You can contribute in many ways:
Types of Contributions¶
Report bugs at https://github.com/charite/jannovar/issues
If you are reporting a bug, please include:
- Your operating system name and version.
- Any details about your local setup that might be helpful in troubleshooting.
- Detailed steps to reproduce the bug.
Look through the Github issues for bugs. If you want to start working on a bug then please write short message on the issue tracker to prevent duplicate work.
Look through the Github issues for features. If you want to start working on an issue then please write short message on the issue tracker to prevent duplicate work.
Jannovar could always use more documentation, whether as part of the official vcfpy docs, in docstrings, or even on the web in blog posts, articles, and such.
Jannovar uses Sphinx for the user manual (that you are currently reading). See doc_guidelines on how the documentation reStructuredText is used. See doc_setup on creating a local setup for building the documentation.
The best way to send feedback is to file an issue at https://github.com/charite/jannovar/issues
If you are proposing a feature:
- Explain in detail how it would work.
- Keep the scope as narrow as possible, to make it easier to implement.
- Remember that this is a volunteer-driven project, and that contributions are welcome :)
For the documentation, please adhere to the following guidelines:
- Put each sentence on its own line, this makes tracking changes through Git SCM easier.
- Provide hyperlink targets, at least for the first two section levels.
- Use the section structure from below.
.. heading_1: ========= Heading 1 ========= .. heading_2: --------- Heading 2 --------- .. heading_3: Heading 3 ========= .. heading_4: Heading 4 --------- .. heading_5: Heading 5 ~~~~~~~~~ .. heading_6: Heading 6 :::::::::
For building the documentation, you have to install the Python program Sphinx. This is best done in a virtual environment. The following assumes you have a working Python 3 setup.
Use the following steps for installing Sphinx and the dependencies for building the Jannovar documentation:
$ cd jannovar/manual $ virtualenv -p python3 .venv $ source .venv/bin/activate $ pip install --upgrade -r requirements.txt
Use the following for building the documentation.
The first two lines is only required for loading the virtualenv.
Afterwards, you can always use
make html for building.
$ cd jannovar/manual $ source .venv/bin/activate $ make html # rebuild for changed files only $ make clean && make html # force rebuild
Ready to contribute? First, create your Java/Documentation development setup as described in install_from_source/doc_setup.
Fork the Jannovar repo on GitHub.
Clone your fork locally:
$ git clone firstname.lastname@example.org:your_name_here/jannovar.git
Create a branch for local development:
$ git checkout -b name-of-your-bugfix-or-feature
Now you can make your changes locally.
When you’re done making your changes, make sure that the build runs through. For Java:
$ mvn package
$ make clean && make html
Commit your changes and push your branch to GitHub:
$ git add . $ git commit -m "Your detailed description of your changes." $ git push origin name-of-your-bugfix-or-feature
Submit a pull request through the GitHub website.
Pull Request Guidelines¶
Before you submit a pull request, check that it meets these guidelines:
- The pull request should include tests.
- If the pull request adds functionality, the docs should be updated.
- Describe your changes in the