docs: conceptual data-model overview (D2) - #27
Merged
Conversation
New docs/concepts/data-model.md — the end-to-end mental model for TCRi: the hierarchical generative model (clonotype prior p_c -> local p_ct per clone x covariate -> per-cell phenotype = classifier logits + log prior), the objects register_model writes to .uns/.obsm/.obs (with shapes), the ct_to_c / ct_to_cov / ct_array indexing, point-estimate vs posterior sampling, how the joint distribution feeds the entropy/MI/flux metrics, and the three temperatures. - index.md: add concepts/data-model to the toctree (after quickstart). - conf.py: enable MyST dollarmath so $...$ math renders. Builds clean (0 warnings); cross-references resolve; math renders via mathjax. Closes Notion D2. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
nceglia
marked this pull request as ready for review
June 8, 2026 04:15
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Adds
docs/concepts/data-model.md— the end-to-end mental model a new user needs before the API reference. Covers:p_c→ localp_ct(per clone×covariate) → per-cell phenotype =softmax(classifier logits + log p_ct), on top of the scVI/VampPrior latent.register_modelwrites — a table of every.uns/.obsm/.obskey with meaning + shape (tcri_p_ct,X_tcri_logits,X_tcri_probabilities, thect_*arrays, …).ct_to_c/ct_to_cov/ct_array) shown concretely, plus the filtered-view gotcha (the add utils to setup.py #4 guard).Also:
index.md: page added to the toctree (after quickstart).conf.py: enable MySTdollarmathso$…$renders.Verification
python -m sphinx -b html docs <out>→ build succeeded, 0 warnings.register_model,joint_distribution*) resolve; math renders via MathJax; page is in the sidebar toctree.Independent of the open theme PR (#26) — different
conf.pyregions, merges cleanly either order.Closes Notion D2.
🤖 Generated with Claude Code