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
+//! (currently [`distance`]) moves here incrementally.
-//! 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};

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

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;