Add NOTICE (third-party attribution); scrub internal paths from demo provenance; fix project URLs to ChatterjeeLab org

NOTICE

@@ -0,0 +1,25 @@
+SF-Cluster
+Copyright (c) 2026 Hanqun Cao
+
+This software builds on the following third-party work, which it depends on at
+runtime but does NOT redistribute. Each retains its own license and authorship.
+
+1. FrustrAI-Seq — per-residue frustration prediction model.
+   License: Apache-2.0.
+   Source:  https://github.com/leuschjanphilipp/FrustrAI-Seq
+   Weights: https://huggingface.co/leuschj/FrustrAI-Seq
+   SF-Cluster calls this model to compute the frustration features that guide
+   MSA subsampling. Install and weights are fetched from the upstream sources.
+
+2. ProtT5 (Rostlab/prot_t5_xl_half_uniref50-enc) — protein language model used
+   internally by FrustrAI-Seq.
+   Source:  https://huggingface.co/Rostlab/prot_t5_xl_half_uniref50-enc
+
+3. AF-Cluster (Wayment-Steele et al.) — the MSA-clustering method SF-Cluster is
+   compared against and conceptually extends.
+   License: MIT.
+   Source:  https://github.com/HWaymentSteele/AF_Cluster
+
+AlphaFold2 / ColabFold are used as the downstream structure predictor and are
+neither included nor wrapped by this package; install them separately under
+their own licenses.

examples/data/provenance.md

@@ -13,17 +13,14 @@ outputs.
 | `KaiB_fi_matrix.npy`  | (364, 91) float32      | Per-residue FI matrix. Row `i` corresponds to record `i` in the A3M. |
 | `KaiB_seq_ids.txt`    | 364 lines              | One short sequence ID per line, in the same order as the A3M / FI matrix. |
 
-## Source paths (private dev repo, read-only)
-
-- Filtered MSA:
-  `/data1/hanqun/SF-Design/SF-Cluster/data/processed/msa/KaiB/KaiB/KaiB_KaiBTE_91aa_UniProt_Q79V61_5to95_2QKE_chainB.filtered.a3m`
-  (depth 6821, L=91)
-- FI artifacts (per-subset):
-  `/data1/hanqun/SF-Design/SF-Cluster/results/frustai_artifacts/KaiB/diverse_sf/KaiB/{000..011}/`
-  with files `fi_matrix.npy` ((32, 91) float32), `metadata.json`,
-  `fi_residual_matrix.npy`, `entropy_matrix.npy`.
-- Source subset A3Ms (used to map FI rows → sequence IDs):
-  `/data1/hanqun/SF-Design/SF-Cluster/results/baseline_p8/diverse_sf/KaiB/KaiB/screen/diversesf_KaiB_KaiB_seed{000..011}.a3m`.
+## Provenance (internal source paths omitted)
+
+Derived from the SF-Cluster Phase II KaiB `diverse_sf` benchmark arm: the
+filtered KaiB MSA (depth 6821, L=91) and the per-subset FrustrAI-Seq FI
+artifacts (12 subsets, each a `(32, 91)` float32 `fi_matrix.npy` with
+`metadata.json`, `fi_residual_matrix.npy`, `entropy_matrix.npy`) mapped back to
+the 12 subset A3Ms to recover sequence IDs. Internal dev-repo paths are omitted
+from this public demo asset.
 
 ## Construction recipe
 

pyproject.toml

@@ -33,8 +33,8 @@ dev = ["pytest>=7.0"]
 sf-cluster = "sf_cluster.cli:main"
 
 [project.urls]
-Homepage = "https://github.com/hanqun-cao/sf-cluster"
-Issues = "https://github.com/hanqun-cao/sf-cluster/issues"
+Homepage = "https://github.com/ChatterjeeLab/SF-Cluster"
+Issues = "https://github.com/ChatterjeeLab/SF-Cluster/issues"
 
 [tool.setuptools.packages.find]
 where = ["src"]