Contributing

Get Started!

Ready to contribute? Here's how to set up sequencing_report_service for local development.

Clone the project repo:

$ git clone git@gitlab.snpseq.medsci.uu.se:shared/sequencing-report-service.git

Install your local copy into a virtualenv. Create a virtual environment with Conda and install the project there:

$ conda create -n sequencing_report_service python=3.7
$ source activate sequencing_report_service
$ python setup.py develop

Create a branch for local development (if these are attached to a Jira ticket include the ticket number in branch name:
```
$ git checkout -b name-of-your-bugfix-or-feature
```
Now you can make your changes locally.
When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:
```
$ flake8 sequencing_report_service tests
$ python setup.py test or py.test
$ tox
```
To get flake8 and tox, just pip install them into your virtualenv.

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

Before you submit a merge request, check that it meets these guidelines:

The pull request should include tests.
If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.

To run a subset of tests:

$ py.test tests.test_sequencing_report_service

A reminder for the maintainers on how to deploy. Make sure all your changes are committed (including an entry in HISTORY.rst). Then run:

$ bumpversion patch # possible: major / minor / patch
$ git push
$ git push --tags

TODO Add docs on continuous deployment here.