From 6bdc9354d3d6190a1fc19ff4a24192960980f782 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Wed, 26 Aug 2026 20:34:29 +0200
Subject: [PATCH] refactor: restructure obikphylo module layout and adjust
 visibility

Relocate cardcomp into the siblings directory and update internal import paths to reflect the new hierarchy. Adjust the crate's public API surface by updating module declarations and re-exports. This is a purely structural change with no modifications to logic, data models, or runtime behavior.
---
 src/obikphylo/src/lib.rs                     | 14 +++++++++-----
 src/obikphylo/src/{ => siblings}/cardcomp.rs |  2 +-
 src/obikphylo/src/siblings/mod.rs            |  2 ++
 3 files changed, 12 insertions(+), 6 deletions(-)
 rename src/obikphylo/src/{ => siblings}/cardcomp.rs (99%)

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;