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Developer Notes

General Procedures

Versioning:
  • Follows semantic versioning (major.minor.patch)
  • Pre-release candidates (major.minor.path.dev0)
Contributing:
  • Always use PRs and add tests when appropriate
  • Merges will be considered after travis-ci passes
  • Please add updates to CHANGES.rst which will be used for release notes
Local Tests:
  • python setup.py build
  • python setup.py install
  • nosetests
  • check py2 and py3 environments if possible

Deployment

PypI Release:

  • First make sure your PyPI config is properly setup:

    [distutils]
index-servers =
  pypi
  pypitest

[pypi]
repository=https://upload.pypi.org/legacy/
username=<NAME>
password=<PASS>

[pypitest]
repository=https://test.pypi.org/legacy/
username=<NAME>
password=<PASS>

  • All releases are uploaded to PyPI using twine(python3):

    # test
python setup.py sdist
twine upload dist/* -r pypitest
pip install -U --pre -i https://test.pypi.org/legacy/  starseqr

# final
python setup.py sdist
twine upload dist/* -r pypi
pip install -U starseqr
Github:
  • tag v0.x.x
  • name STAR-SEQRv0.x.x
  • add changes from CHANGES.rst
Docker:

  • Update release in docker/Dockerfile

  • The following scripts get the version tag from the package and tag the docker image:

    sudo bash build_docker.sh
sudo bash push_docker.sh
DNANEXUS:
  • Make any updates to /devtools/dnanexus/dxapp.json and /devtools/dnanexus/src/starseqr.py
  • cd devtools/dnanexus
  • dx source env
  • dx login
  • dx build --app starseqr
  • dx api app-starseqr/0.0.x publish "{"makeDefault": true}"
Bioconda:
  • cd into bioconda-recipes
  • git checkout -b starseqr:vx.x.x
  • modify code including version, url, md5
  • vim recipes/starseqr/meta.yaml
  • ./simulate-travis.py --disable-docker
  • git push origin starseqr:vx.x.x
  • login to github and do pull request