diff --git a/src/obikphylo/src/lib.rs b/src/obikphylo/src/lib.rs index 653c2cb3..d45e5a4b 100644 --- a/src/obikphylo/src/lib.rs +++ b/src/obikphylo/src/lib.rs @@ -5,13 +5,17 @@ //! //! Starts with [`siblings`] (family presence-mask annex, SNP distance, //! cardinality, pseudo-alignment); further phylo-domain functionality -//! (currently `obikindex::distance`/`obikindex::cardcomp`) moves here -//! incrementally. +//! (currently [`distance`]) moves here incrementally. +//! +//! `siblings` is temporarily disconnected (commented out below) while +//! `obikindex`'s stateless audit is being caught up with piece by piece — +//! see the project memory on this. `cardcomp` already moved into +//! `siblings/` (it's sibling-specific) and is unaffected by the +//! disconnection itself compiling; it just isn't reachable from outside +//! this crate until `siblings` comes back. -mod cardcomp; mod distance; mod matrix_store; -pub mod siblings; +// pub mod siblings; // temporarily disconnected — see module doc above. -pub use cardcomp::{cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix}; pub use distance::{DistanceMetric, DistanceOutput}; diff --git a/src/obikphylo/src/cardcomp.rs b/src/obikphylo/src/siblings/cardcomp.rs similarity index 99% rename from src/obikphylo/src/cardcomp.rs rename to src/obikphylo/src/siblings/cardcomp.rs index e89d7b27..dbc87e3d 100644 --- a/src/obikphylo/src/cardcomp.rs +++ b/src/obikphylo/src/siblings/cardcomp.rs @@ -17,7 +17,7 @@ //! since TNT/PhyG search *unrooted* trees) if the cost matrix is //! symmetric, the discrete-parsimony analogue of CTMC reversibility. -use crate::siblings::{BasePairTally, CardinalityTally}; +use super::{BasePairTally, CardinalityTally}; /// Row-stochastic 5×5 cardinality transition probabilities (`0..=4`), /// diagonal included ("stay at the same cardinality"), from diff --git a/src/obikphylo/src/siblings/mod.rs b/src/obikphylo/src/siblings/mod.rs index bbd03b59..2a59b795 100644 --- a/src/obikphylo/src/siblings/mod.rs +++ b/src/obikphylo/src/siblings/mod.rs @@ -45,6 +45,7 @@ mod alignment; mod build; mod cache; +mod cardcomp; mod cardinality; mod distance; mod entropy; @@ -62,6 +63,7 @@ mod tests; pub use alignment::{SnpAlignment, SnpAlignmentExt}; pub use build::SiblingAnnexBuildExt; +pub use cardcomp::{cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix}; pub use cardinality::{CardinalityExt, CardinalityTally}; pub use distance::{BasePairTally, DistanceExt, RawSnpDistanceOutput}; pub use entropy::ShannonEntropyExt;