Publishing GTDB Tk

Publishing GTDB-Tk

Note: The majority of processes are automated and are triggered when a release is created.

Getting ready for release

Step 1: Increment version

Note: GTDB-Tk uses semantic versioning (i.e. major.minor.patch).

• Update __version__ in gtdbtk/__init__.py

Step 2: Update documentation

• Update documentation changelog in docs/src/changelog.rst

Step 2: Run GTDB-Tk unit tests

Step 3: Test GTDB-Tk installation

• python setup.py sdist
• conda create -n GTDBTK_TEST --clone gtdbtk-dev
• conda activate GTDBTK_TEST
• pip install dist/*

Step 4: Create a new release

• Create a new release (tag and name should match the new version)
• Include the changelog.rst information in the description.

Note: This will trigger CI to do the following:

• DockerHub - will build a new image based on the version (~10 mins)
• GitHub Actions - will build the PyPI package and upload it.
• Bioconda - will automatically open a new PR which will need to be approved and merged.

Step 5: Update github.io

Add an announcement for the new release in Announcements.html (gh_page branch of GTDB-Tk).

Publishing GTDB-Tk reference data

Run

python GTDBTk/scripts/verify_official_package.py --package_directory ~/release<n>/ --output_file gtdbtk.r<n>_data.tar.gz

The script will check all files and generate a targz file at the end of the process