Development

CI/CD

Scripts that help ensure the tool's quality. Extra dependencies need to be installed in order to run Truvari's CI/CD scripts.

pip install pylint anybadge coverage

Check code formatting with

python repo_utils/pylint_maker.py

We use autopep8 (via vim-autopep8) for formatting.

Test the code and generate a coverage report with

bash repo_utils/truvari_ssshtests.sh

Truvari leverages github actions to perform these checks when new code is pushed to the repository. We've noticed that the actions sometimes hangs through no fault of the code. If this happens, cancel and resubmit the job. Once FuncTests are successful, it uploads an artifact of the coverage html report which you can download to see a line-by-line accounting of test coverage.

git flow

To organize the commits for the repository, we use git-flow. Therefore, develop is the default branch, the latest tagged release is on master, and new, in-development features are within feature/<name>

When contributing to the code, be sure you're working off of develop and have run git flow init.

versioning

Truvari uses Semantic Versioning. As of v3.0.0, a single version is kept in the code under truvari/__init__.__version__. We try to keep the suffix -dev on the version in the develop branch. When cutting a new release, we either replace the suffix with -rc if we've built a release candidate that may need more testing/development. Once we've committed to a full release that will be pushed to PyPi, no suffix is placed on the version.

docs

The github wiki serves the documentation most relevant to the develop/ branch. When cutting a new release, we freeze and version the wiki's documentation with the helper utility docs/freeze_wiki.sh.

conda

The package management we maintain is via PyPi so that the command pip install truvari is available. There is a very old version of Truvari that was uploaded to conda that we'll eventually look into maintaining. In the meantime, we recommend reading this when using conda and trying to use Truvari's documented installation procedure.

docker

A Dockerfile exists to build an image of Truvari. To make a Docker image, clone the repository and run

docker build -t truvari .

You can then run Truvari through docker using

docker run -v `pwd`:/data -it truvari

Where pwd can be whatever directory you'd like to mount in the docker to the path /data/, which is the working directory for the Truvari run. You can provide parameters directly to the entry point.

docker run -v `pwd`:/data -it truvari anno svinfo -i example.vcf.gz

If you'd like to interact within the docker container for things like running the CI/CD scripts

docker run -v `pwd`:/data --entrypoint /bin/bash -it truvari

You'll now be inside the container and can run FuncTests or run Truvari directly

bash repo_utils/truvari_ssshtests.sh
truvari anno svinfo -i example.vcf.gz

Truvari SDK

Many of the helper methods/objects are documented such that developers can reuse truvari in their own code. To see developer documentation, visit readthedocs.

Documentation can also be seen using

import truvari
help(truvari)