Issues

load_dataset is not deterministic: set-ordered class blocks, and a regex character class that can gap canonical residues
breimanntools/aaanalysis#588 · opened on Sep 18, 2026 · v1.2
Docstring style drift: version history and feature rationale have moved into the docstrings
breimanntools/aaanalysis#581 · opened on Sep 18, 2026 · v1.2
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Gate the docs build: fail when the docutils error count rises
breimanntools/aaanalysis#571 · opened on Sep 17, 2026 · v1.2
Wrap external explainability tooling around the package's models
breimanntools/aaanalysis#558 · opened on Sep 16, 2026 · v1.4
Decide whether external per-amino-acid scales should load as a scale set
breimanntools/aaanalysis#557 · opened on Sep 16, 2026 · v1.4
Ingest an external descriptor matrix as a feature matrix
breimanntools/aaanalysis#556 · opened on Sep 16, 2026 · v1.4
Adapter recipe notebooks for the upstream bridges that already have code
breimanntools/aaanalysis#555 · opened on Sep 16, 2026 · v1.4
P9 Interpretability: audit against the rubric
breimanntools/aaanalysis#554 · opened on Sep 16, 2026 · v1.2
P6 Compositional vs positional: audit against the rubric
breimanntools/aaanalysis#553 · opened on Sep 16, 2026 · v1.2
P10 Validation: audit against the rubric and close the gaps
breimanntools/aaanalysis#552 · opened on Sep 16, 2026 · v1.2
P8 Prediction: visualize the three label settings and the honest-evaluation hook
breimanntools/aaanalysis#551 · opened on Sep 16, 2026 · v1.2
P7 Select and reduce features: show the signature before and after reduction
breimanntools/aaanalysis#550 · opened on Sep 16, 2026 · v1.2
P5 Engineer features: visualize the sequence and numerical arms
breimanntools/aaanalysis#549 · opened on Sep 16, 2026 · v1.2
P4 Prediction levels: show residue, domain and protein side by side
breimanntools/aaanalysis#548 · opened on Sep 16, 2026 · v1.2
Bound total peak memory and make chunked CPP runs resumable (out-of-core)
breimanntools/aaanalysis#546 · opened on Sep 16, 2026 · v1.5
Reject non-finite values in the shared numeric range validator
breimanntools/aaanalysis#545 · opened on Sep 16, 2026 · v1.2
Add a reliability-aware optimization layer to SeqOpt (DyRAMO-style adaptive applicability domain, optimizer-agnostic)
breimanntools/aaanalysis#522 · opened on Aug 11, 2026 · v1.2
API-consistency pass on the new prediction/design tier (stabilize the experimental classes)
breimanntools/aaanalysis#510 · opened on Jul 22, 2026 · v1.2
pipe: parity anchor for predict_samples, the ≤10-line KPI, and param-coverage gating for ap notebooks
breimanntools/aaanalysis#509 · opened on Jul 22, 2026 · v1.2
epic: v2 unified architecture (TaskSpec/DataSpec, typed result objects, namespaces, migration tooling)
breimanntools/aaanalysis#499 · opened on Jul 18, 2026 · v2.X
[Potential] Add cross-modal explanation alignment (CPP / PLM / structure / conservation)
breimanntools/aaanalysis#498 · opened on Jul 18, 2026 · v2.X
[Potential] Add an experimental-feedback result schema (predicted candidate to assay outcome)
breimanntools/aaanalysis#497 · opened on Jul 18, 2026 · v2.X
[Potential] Add a scientific lineage graph (dataset to features to model to explanation to design)
breimanntools/aaanalysis#496 · opened on Jul 18, 2026 · v2.X
[Potential] Add dataset-shift / drift diagnostics (reference vs target distributions)
breimanntools/aaanalysis#495 · opened on Jul 18, 2026 · v2.X
[Potential] Add an optional-dependency compatibility matrix in CI
breimanntools/aaanalysis#494 · opened on Jul 18, 2026 · v1.5
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