v1.4.1: version bump

CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 message: "Please cite this software and data release when using the package."
 title: "Z-Screen Program Package"
 type: dataset
-version: 1.4.0
+version: 1.4.1
 date-released: 2026-08-29
 authors:
   - name: "Zafrens, Inc."

MANIFEST.json

@@ -1,12 +1,12 @@
 {
   "schema_version": "1.0",
   "package_name": "Z-Screen Program Package",
-  "package_version": "1.4.0",
+  "package_version": "1.4.1",
   "generated": "2026-08-29",
   "manifest_path": "provenance/file_manifest.csv",
-  "manifest_sha256": "3171526a3803dc76a2cfc9e671b668f97c2074c300843af2e394f31df8009b5b",
+  "manifest_sha256": "4e2a9ae19b5c932e1d8690d101a7bed5ff846935a9db7b2bc82f66abdc2fd571",
   "manifested_file_count": 296,
-  "manifested_bytes": 5304838164,
+  "manifested_bytes": 5304838166,
   "self_hash_policy": "MANIFEST.json and provenance/file_manifest.csv are excluded from file_manifest.csv to avoid circular self-hashing; MANIFEST.json records the CSV digest.",
   "distribution_status": "Software Apache-2.0; data and weights CC-BY-4.0 (see LICENSE.md)"
 }

README.md

@@ -10,7 +10,7 @@ tags:
 
 # Z-Screen Program Package
 
-Version 1.4.0, 2026-08-29. A standalone data and reference-model
+Version 1.4.1, 2026-08-29. A standalone data and reference-model
 package centered on the shared program layer of the Z-Screen
 combinatorial chemistry screens: per-compound 32-dimensional
 program-usage vectors and harmonized 6,000-gene response surfaces
@@ -19,7 +19,7 @@ basis they are defined against, an evaluation-grade reference model,
 and five annexes (imaging, therapeutic hypotheses, chemistry,
 same-well, phenomimicry).
 
-> **New in v1.4 (2026-08-29).** The CRISPR-knockout comparison has
+> **New in v1.4.1 (2026-08-29).** The CRISPR-knockout comparison has
 > been expanded into a full annex, **`annex_phenomimicry/`**: every
 > compound signature is now scored against 43 knockout signature sets
 > from 10 public perturb-seq datasets (~18.8k target genes, ~8M

provenance/file_manifest.csv

@@ -1,11 +1,11 @@
 relative_path,semantic_role,bytes,sha256,media_type
-CITATION.cff,citation,1050,52aa357ef6b8f31d0874cd3f5982878e55ffd2aaaef3a51d34faac21c532125b,application/yaml
+CITATION.cff,citation,1050,65db64029db7d13086c0a967cb07c8acaf0368b4973639051a19a3381b412ddd,application/yaml
 LICENSE.md,license,1547,d3bd5ec69d5f100a63a232b4098109822ac2a7ec01074088a08c82f329e1fd24,text/markdown
 LICENSES/Apache-2.0.txt,license,11371,fd4dad34b816594978238a024e7e8924a343648bd9f699b04fc0f07f0035128d,text/plain
 LICENSES/CC-BY-4.0.txt,license,18526,d427828b01b5573e01f275071ca1dcdb57961e4562efb42ec16ace5757edfb37,text/plain
 LICENSE_OR_DATA_USE.md,license_hold,410,325e49d3fc5e821f2368654a64babb066e9840f9040e714e96d294ae2620b9cc,text/markdown
 NOTICE,license,260,374c9a42ff72beeb49b92951dc45c3adc8df105a297e5fb9a9243c607b7403d1,text/plain
-README.md,front_doc,7140,3b1d381ec14310a81c80d6ca0c0aace0cdde2f06187bd1c9314fb34b4eb220fe,text/markdown
+README.md,front_doc,7142,5ab4c1035e7274d942c9e66ec99a1ce2e427af5a2f76f000507f76e228c6e86d,text/markdown
 START_HERE.md,front_doc,9425,f647b1b794b67ed57b1bf45e119c0b91f393f1962e752b5d6c6e635e85fde87a,text/markdown
 annex_chemistry/README.md,annex_readme,11632,90d11e0b8ff21808d4e2c9338a48189757bf6beed0a59131f1b99da4051514dd,text/markdown
 annex_chemistry/activity_cliffs.csv,chemistry_table,95455,20f59ef82e91e846995f31b3ff77f5dae7c4aa210cccac149df01a5118f64628,text/csv
@@ -281,7 +281,7 @@ models/context_token_trunk_reference_eval_v1_seed2.pt,reference_checkpoint,19317
 models/golden_predictions.json,golden_predictions,32499,5cc9d73393de87642bf766699bd405b872fc8fdca9193fdfa7ca8bce6329cbe2,application/json
 models/model_def.py,model_definition,7163,18ca256cd90e223672e0899b31e841b5c1ac4a7d4f62634825e4a02324bbc8a0,text/x-python
 models/predict.py,model_inference,7588,57c295082ad4a34b94a011276f4d06cee48a6cbee5a7e00c2e2787fe121bb438,text/x-python
-pyproject.toml,packaging_meta,651,5ad3f4a14628de01e115e4fd7702548f2878bbdeade3930ee1c5a2b566ef14fa,application/toml
+pyproject.toml,packaging_meta,651,9921d9ae9d6c575ec2152570a45c9c50392d44f818cf4ef0fcfb1f9b14475f30,application/toml
 src/zscreen_program_package/__init__.py,loader_source,303,612db22b176fea486f53ea686d740439480ff296b9bc63130be8f2c8f69749c1,text/x-python
 src/zscreen_program_package/cli.py,verifier_source,1012,acf126fb9bac8ea7527d008a4b28f65b2ea1efe6901d9de162d0cbd1d5173030,text/x-python
 src/zscreen_program_package/data.py,loader_source,4584,be25156809015f72d48fab56414b0d927a8e3bf22822fc860e9106468890b7bd,text/x-python

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "zscreen-program-package"
-version = "1.4.0"
+version = "1.4.1"
 description = "Shared program layer of the Z-Screen screens: usages, harmonized surfaces, pinned basis, reference model, and annexes"
 readme = "README.md"
 requires-python = ">=3.11"