Notebooks gallery#
Browse the notebooks before downloading them. Annotation and comparison use the small offline inputs from Examples gallery; all tables come from the installed CLI. The annotation and comparison notebooks have no committed execution outputs. The precursor tutorial retains its curated illustration outputs; documentation builds never execute notebooks.
Annotation and comparison#
Raw repertoires to annotation tables
Four single-chain rows and two pairs. Follow source identities, competing labels and the incomplete pair through the exported tables.
Offline · synthetic inputsCompare two CLI geometries
Run stem4 and vcdr12 with exact exclusion, join detailed pMHC evidence, and inspect score differences on matched query identities.
Keep the notebooks beside inputs in examples. Open them from the
repository root or examples directory, with a kernel that has vdjmatch
installed. Each run creates a fresh temporary output directory and invokes
sys.executable -m vdjmatch.cli with a 120-second timeout. See Examples gallery
for raw input downloads and shell commands.
Precursor frequency#
Precursor frequency for an epitope
Explore generation probability, union mass, unseen junctions and the conversion from repertoire mass to cell counts.
Measured precursor frequencies
Read the validation data, model conventions and setup for the interactive compendium.
The precursor workflow is separate from antigen annotation. Its setup and reference-data requirements are described in Validation data: measured precursor frequencies.
Run the complete gallery#
Use an isolated environment containing the published package and notebook tools. From the repository root:
uv venv .venv-gallery
uv pip install --python .venv-gallery/bin/python --index-url https://pypi.org/simple --no-cache -r examples/requirements-notebooks.txt
.venv-gallery/bin/python examples/check_gallery.py NEW_GALLERY_OUTPUT_DIRECTORY
This executes both shell examples, all three Jupyter notebooks with fresh kernels, and the marimo compendium. It records results and executed outputs in the new directory and returns a failure status if any workflow fails. The precursor tutorial uses four native threads and fetches its pinned public Hugging Face snapshot; the compendium uses one native thread and fetches its documented tables and reference. Documentation builds still do not execute notebooks.