CONTRIBUTING.md

Making a new release

1. For a new major release, remove stuff (e.g. parameters, methods) deprecated in the previous cycle.
2. Update the __version__ string in bioblend/__init__.py .
3. Update CHANGELOG.md .
4. Commit the changes above, push to GitHub, and wait for Continuous Integration (CI) tests to pass.
5. Make a new release through the GitHub interface. A CI job will automatically upload the packages to PyPI.
6. Check and merge the automatic pull request to update the Bioconda package.

How to run BioBlend tests

1. Clone Galaxy to a directory outside of BioBlend source directory via git clone https://github.com/galaxyproject/galaxy.git

2. Change directory to your BioBlend source and run the tests via ./run_bioblend_tests.sh -g GALAXY_PATH [-r GALAXY_REV] [-e TOX_ENV] where GALAXY_PATH is the directory where the galaxy repository was cloned, GALAXY_REV is the branch or commit of Galaxy that you would like to test against (if different from the current state of your galaxy clone), and TOX_ENV is used to specify the Python version to use for BioBlend, e.g. py38 for Python 3.8.

   You can also add 2>&1 | tee log.txt to the command above to contemporarily view the test output and save it to the log.txt file.

3. If needed, you can temporarily increase the Galaxy job timeout used by BioBlend tests with e.g. export BIOBLEND_TEST_JOB_TIMEOUT=100, and re-run the tests.