pyaging 0.3.0__tar.gz → 0.3.1__tar.gz

{pyaging-0.3.0 → pyaging-0.3.1}/Makefile

@@ -1,6 +1,6 @@
 .PHONY: lint format update build install update-clocks-notebooks update-all-clocks verify-hf-auth verify-hf-data-repo-public create-hf-data-repo upload-clocks-to-hf upload-static-data-to-hf process-tutorials test test-tutorials docs version commit tag release release-slim
 
-VERSION ?= v0.3.0
+VERSION ?= v0.3.1
 HF_REPO_ID ?= lucascamillomd/pyaging-data
 HF_REPO_OWNER ?= lucascamillomd
 HF_STATIC_DIR ?= hf_static_data
@@ -101,7 +101,7 @@ docs:
 	@echo "Building documentation..."
 	cp tutorials/*.ipynb docs/source/tutorials
 	cp clocks/notebooks/*.ipynb docs/source/clock_notebooks
-	@cd docs && make html || { echo "Documentation build failed"; exit 1; }
+	uv run make -C docs html
 
 version:
 	@echo "Updating version in pyproject.toml to $(VERSION)..."

{pyaging-0.3.0 → pyaging-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyaging
-Version: 0.3.0
+Version: 0.3.1
 Summary: A Python-based compendium of GPU-optimized aging clocks.
 Project-URL: homepage, https://github.com/lucascamillomd/pyaging
 Project-URL: repository, https://github.com/lucascamillomd/pyaging
@@ -41,15 +41,13 @@ Description-Content-Type: text/markdown
 
 ##
 
-[![test](https://github.com/lucascamillomd/pyaging/actions/workflows/test.yml/badge.svg)](https://github.com/lucascamillomd/pyaging/actions/workflows/test.yml)
-[![build](https://github.com/lucascamillomd/pyaging/actions/workflows/build.yml/badge.svg)](https://github.com/lucascamillomd/pyaging/actions/workflows/build.yml)
-[![publish](https://github.com/lucascamillomd/pyaging/actions/workflows/publish.yml/badge.svg)](https://github.com/lucascamillomd/pyaging/actions/workflows/publish.yml)
-[![release](https://github.com/lucascamillomd/pyaging/actions/workflows/release.yml/badge.svg)](https://github.com/lucascamillomd/pyaging/actions/workflows/release.yml)
-[![documentation](https://readthedocs.org/projects/pyaging/badge/?version=latest)](https://pyaging.readthedocs.io/en/latest/)
+[![CI](https://github.com/lucascamillomd/pyaging/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/lucascamillomd/pyaging/actions/workflows/ci.yml)
+[![Release](https://github.com/lucascamillomd/pyaging/actions/workflows/release.yml/badge.svg)](https://github.com/lucascamillomd/pyaging/actions/workflows/release.yml)
+[![Documentation](https://readthedocs.org/projects/pyaging/badge/?version=latest)](https://pyaging.readthedocs.io/en/latest/)
 [![DOI](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtae200-blue.svg)](https://doi.org/10.1093/bioinformatics/btae200)
-[![upload](https://img.shields.io/pypi/v/pyaging?logo=PyPI)](https://pypi.org/project/pyaging/) 
-[![download](https://static.pepy.tech/badge/pyaging)](https://pepy.tech/project/pyaging)
-[![star](https://img.shields.io/github/stars/lucascamillomd/pyaging?logo=GitHub&color=red)](https://github.com/lucascamillomd/pyaging/stargazers)
+[![PyPI](https://img.shields.io/pypi/v/pyaging?logo=pypi)](https://pypi.org/project/pyaging/)
+[![Downloads](https://static.pepy.tech/badge/pyaging)](https://pepy.tech/project/pyaging)
+[![Stars](https://img.shields.io/github/stars/lucascamillomd/pyaging.svg?label=stars&style=flat&logo=github&color=red)](https://github.com/lucascamillomd/pyaging/stargazers)
 
 ## 🐍 **pyaging**: a Python-based compendium of GPU-optimized aging clocks
 
@@ -83,4 +81,4 @@ To cite `pyaging`, please use the following:
     url = {https://doi.org/10.1093/bioinformatics/btae200},
     eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae200/57218155/btae200.pdf},
 }
-```
+```

{pyaging-0.3.0 → pyaging-0.3.1}/README.md

@@ -4,15 +4,13 @@
 
 ##
 
-[![test](https://github.com/lucascamillomd/pyaging/actions/workflows/test.yml/badge.svg)](https://github.com/lucascamillomd/pyaging/actions/workflows/test.yml)
-[![build](https://github.com/lucascamillomd/pyaging/actions/workflows/build.yml/badge.svg)](https://github.com/lucascamillomd/pyaging/actions/workflows/build.yml)
-[![publish](https://github.com/lucascamillomd/pyaging/actions/workflows/publish.yml/badge.svg)](https://github.com/lucascamillomd/pyaging/actions/workflows/publish.yml)
-[![release](https://github.com/lucascamillomd/pyaging/actions/workflows/release.yml/badge.svg)](https://github.com/lucascamillomd/pyaging/actions/workflows/release.yml)
-[![documentation](https://readthedocs.org/projects/pyaging/badge/?version=latest)](https://pyaging.readthedocs.io/en/latest/)
-[![DOI](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtae200-blue.svg)](https://doi.org/10.1093/bioinformatics/btae200)
-[![upload](https://img.shields.io/pypi/v/pyaging?logo=PyPI)](https://pypi.org/project/pyaging/) 
-[![download](https://static.pepy.tech/badge/pyaging)](https://pepy.tech/project/pyaging)
-[![star](https://img.shields.io/github/stars/lucascamillomd/pyaging?logo=GitHub&color=red)](https://github.com/lucascamillomd/pyaging/stargazers)
+[![CI](https://github.com/lucascamillomd/pyaging/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/lucascamillomd/pyaging/actions/workflows/ci.yml)
+[![Release](https://github.com/lucascamillomd/pyaging/actions/workflows/release.yml/badge.svg)](https://github.com/lucascamillomd/pyaging/actions/workflows/release.yml)
+[![Documentation](https://readthedocs.org/projects/pyaging/badge/?version=latest)](https://pyaging.readthedocs.io/en/latest/)
+[![DOI](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtae200-blue.svg)](https://doi.org/10.1093/bioinformatics/btae200)
+[![PyPI](https://img.shields.io/pypi/v/pyaging?logo=pypi)](https://pypi.org/project/pyaging/)
+[![Downloads](https://static.pepy.tech/badge/pyaging)](https://pepy.tech/project/pyaging)
+[![Stars](https://img.shields.io/github/stars/lucascamillomd/pyaging.svg?label=stars&style=flat&logo=github&color=red)](https://github.com/lucascamillomd/pyaging/stargazers)
 
 ## 🐍 **pyaging**: a Python-based compendium of GPU-optimized aging clocks
 
@@ -46,4 +44,4 @@ To cite `pyaging`, please use the following:
     url = {https://doi.org/10.1093/bioinformatics/btae200},
     eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae200/57218155/btae200.pdf},
 }
-```
+```

{pyaging-0.3.0 → pyaging-0.3.1}/clocks/huggingface/README.md

@@ -20,8 +20,8 @@ This public repository contains the model weights and data files used by
 - Root-level example files support the pyaging tutorials.
 - `supporting_files/` contains dependencies used to construct or document clocks.
 
-Files used by the Python package are intentionally stored at the repository root so
-`hf_hub_download(..., local_dir="pyaging_data")` preserves existing flat local paths.
+Files used by the Python package are intentionally stored at the repository root and
+downloaded through the standard Hugging Face cache.
 The `main` branch is the live data release and may change independently of the Python
 package version.
 

{pyaging-0.3.0 → pyaging-0.3.1}/clocks/notebooks/camilloh3k27ac.ipynb

@@ -148,10 +148,10 @@
     "model.metadata[\"clock_name\"] = 'camilloh3k27ac'\n",
     "model.metadata[\"data_type\"] = 'histone mark'\n",
     "model.metadata[\"species\"] = 'Homo sapiens'\n",
-    "model.metadata[\"year\"] = 2023\n",
+    "model.metadata[\"year\"] = 2025\n",
     "model.metadata[\"approved_by_author\"] = '✅'\n",
-    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cells.\\\" bioRxiv (2023): 2023-08.\"\n",
-    "model.metadata[\"doi\"] = 'https://doi.org/10.1101/2023.08.21.554165'\n",
+    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cell types.\\\" Science Advances 11.1 (2025): eadk9373.\"\n",
+    "model.metadata[\"doi\"] = 'https://doi.org/10.1126/sciadv.adk9373'\n",
     "model.metadata[\"research_only\"] = None\n",
     "model.metadata[\"notes\"] = \"Chronological-age predictor built with a deep neural network from genome-wide H3K27ac ChIP-seq signal, a mark of active enhancers and promoters, as part of a pan-tissue family of histone-mark aging clocks spanning human tissues and cell types.\"\n",
     "model.metadata[\"tissue\"] = 'Multi-tissue (82 human tissue/cell types, ENCODE ChIP-seq biosamples, n=359 for H3K27ac)'\n",
@@ -160,7 +160,7 @@
     "model.metadata[\"model_type\"] = 'PCA + elastic net'\n",
     "model.metadata[\"platform\"] = 'ChIP-seq'\n",
     "model.metadata[\"population\"] = 'Humans, multiple tissues/cell types, embryonic through 90+ years, ~equal sex split'\n",
-    "model.metadata[\"journal\"] = 'bioRxiv (Cold Spring Harbor Laboratory)'\n",
+    "model.metadata[\"journal\"] = 'Science Advances'\n",
     "model.metadata[\"last_author\"] = 'Ritambhara Singh'\n",
     "model.metadata[\"n_features\"] = 1275\n",
     "model.metadata[\"citations\"] = 4\n",
@@ -438,10 +438,10 @@
       "training: True\n",
       "metadata: {'approved_by_author': '✅',\n",
       " 'citation': 'de Lima Camillo, Lucas Paulo, et al. \"Histone mark age of human '\n",
-      "             'tissues and cells.\" bioRxiv (2023): 2023-08.',\n",
+      "             'tissues and cells.\" Science Advances 11.1 (2025): eadk9373.',\n",
       " 'clock_name': 'camilloh3k27ac',\n",
       " 'data_type': 'histone mark',\n",
-      " 'doi': 'https://doi.org/10.1101/2023.08.21.554165',\n",
+      " 'doi': 'https://doi.org/10.1126/sciadv.adk9373',\n",
       " 'notes': None,\n",
       " 'research_only': None,\n",
       " 'species': 'Homo sapiens',\n",

{pyaging-0.3.0/docs/source/clock_notebooks → pyaging-0.3.1/clocks/notebooks}/camilloh3k27me3.ipynb

@@ -148,10 +148,10 @@
     "model.metadata[\"clock_name\"] = 'camilloh3k27me3'\n",
     "model.metadata[\"data_type\"] = 'histone mark'\n",
     "model.metadata[\"species\"] = 'Homo sapiens'\n",
-    "model.metadata[\"year\"] = 2023\n",
+    "model.metadata[\"year\"] = 2025\n",
     "model.metadata[\"approved_by_author\"] = '✅'\n",
-    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cells.\\\" bioRxiv (2023): 2023-08.\"\n",
-    "model.metadata[\"doi\"] = 'https://doi.org/10.1101/2023.08.21.554165'\n",
+    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cell types.\\\" Science Advances 11.1 (2025): eadk9373.\"\n",
+    "model.metadata[\"doi\"] = 'https://doi.org/10.1126/sciadv.adk9373'\n",
     "model.metadata[\"research_only\"] = None\n",
     "model.metadata[\"notes\"] = \"Chronological-age predictor built with a deep neural network from genome-wide H3K27me3 ChIP-seq signal, a Polycomb-associated repressive mark, as part of a pan-tissue family of histone-mark aging clocks spanning human tissues and cell types.\"\n",
     "model.metadata[\"tissue\"] = 'Multi-tissue (pan-tissue human tissues and cell types, ~82 tissues/biosamples; ENCODE ChIP-seq)'\n",
@@ -160,7 +160,7 @@
     "model.metadata[\"model_type\"] = 'PCA + elastic net'\n",
     "model.metadata[\"platform\"] = 'ChIP-seq'\n",
     "model.metadata[\"population\"] = 'Pan-age humans (embryonic to elderly), pan-tissue'\n",
-    "model.metadata[\"journal\"] = 'bioRxiv (Cold Spring Harbor Laboratory)'\n",
+    "model.metadata[\"journal\"] = 'Science Advances'\n",
     "model.metadata[\"last_author\"] = 'Ritambhara Singh'\n",
     "model.metadata[\"n_features\"] = 922\n",
     "model.metadata[\"citations\"] = 4\n",
@@ -438,10 +438,10 @@
       "training: True\n",
       "metadata: {'approved_by_author': '✅',\n",
       " 'citation': 'de Lima Camillo, Lucas Paulo, et al. \"Histone mark age of human '\n",
-      "             'tissues and cells.\" bioRxiv (2023): 2023-08.',\n",
+      "             'tissues and cells.\" Science Advances 11.1 (2025): eadk9373.',\n",
       " 'clock_name': 'camilloh3k27me3',\n",
       " 'data_type': 'histone mark',\n",
-      " 'doi': 'https://doi.org/10.1101/2023.08.21.554165',\n",
+      " 'doi': 'https://doi.org/10.1126/sciadv.adk9373',\n",
       " 'notes': None,\n",
       " 'research_only': None,\n",
       " 'species': 'Homo sapiens',\n",

{pyaging-0.3.0 → pyaging-0.3.1}/clocks/notebooks/camilloh3k36me3.ipynb

@@ -148,10 +148,10 @@
     "model.metadata[\"clock_name\"] = 'camilloh3k36me3'\n",
     "model.metadata[\"data_type\"] = 'histone mark'\n",
     "model.metadata[\"species\"] = 'Homo sapiens'\n",
-    "model.metadata[\"year\"] = 2023\n",
+    "model.metadata[\"year\"] = 2025\n",
     "model.metadata[\"approved_by_author\"] = '✅'\n",
-    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cells.\\\" bioRxiv (2023): 2023-08.\"\n",
-    "model.metadata[\"doi\"] = 'https://doi.org/10.1101/2023.08.21.554165'\n",
+    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cell types.\\\" Science Advances 11.1 (2025): eadk9373.\"\n",
+    "model.metadata[\"doi\"] = 'https://doi.org/10.1126/sciadv.adk9373'\n",
     "model.metadata[\"research_only\"] = None\n",
     "model.metadata[\"notes\"] = \"Chronological-age predictor built with a deep neural network from genome-wide H3K36me3 ChIP-seq signal, a mark of transcribed gene bodies, as part of a pan-tissue family of histone-mark aging clocks spanning human tissues and cell types.\"\n",
     "model.metadata[\"tissue\"] = 'multi-tissue (human tissues and cell lines; ENCODE H3K36me3 ChIP-seq)'\n",
@@ -160,7 +160,7 @@
     "model.metadata[\"model_type\"] = 'PCA + elastic net'\n",
     "model.metadata[\"platform\"] = 'ChIP-seq'\n",
     "model.metadata[\"population\"] = 'humans; pan-tissue, broad age range'\n",
-    "model.metadata[\"journal\"] = 'bioRxiv (Cold Spring Harbor Laboratory)'\n",
+    "model.metadata[\"journal\"] = 'Science Advances'\n",
     "model.metadata[\"last_author\"] = 'Ritambhara Singh'\n",
     "model.metadata[\"n_features\"] = 870\n",
     "model.metadata[\"citations\"] = 4\n",
@@ -438,10 +438,10 @@
       "training: True\n",
       "metadata: {'approved_by_author': '✅',\n",
       " 'citation': 'de Lima Camillo, Lucas Paulo, et al. \"Histone mark age of human '\n",
-      "             'tissues and cells.\" bioRxiv (2023): 2023-08.',\n",
+      "             'tissues and cells.\" Science Advances 11.1 (2025): eadk9373.',\n",
       " 'clock_name': 'camilloh3k36me3',\n",
       " 'data_type': 'histone mark',\n",
-      " 'doi': 'https://doi.org/10.1101/2023.08.21.554165',\n",
+      " 'doi': 'https://doi.org/10.1126/sciadv.adk9373',\n",
       " 'notes': None,\n",
       " 'research_only': None,\n",
       " 'species': 'Homo sapiens',\n",

{pyaging-0.3.0/docs/source/clock_notebooks → pyaging-0.3.1/clocks/notebooks}/camilloh3k4me1.ipynb

@@ -148,10 +148,10 @@
     "model.metadata[\"clock_name\"] = 'camilloh3k4me1'\n",
     "model.metadata[\"data_type\"] = 'histone mark'\n",
     "model.metadata[\"species\"] = 'Homo sapiens'\n",
-    "model.metadata[\"year\"] = 2023\n",
+    "model.metadata[\"year\"] = 2025\n",
     "model.metadata[\"approved_by_author\"] = '✅'\n",
-    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cells.\\\" bioRxiv (2023): 2023-08.\"\n",
-    "model.metadata[\"doi\"] = 'https://doi.org/10.1101/2023.08.21.554165'\n",
+    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cell types.\\\" Science Advances 11.1 (2025): eadk9373.\"\n",
+    "model.metadata[\"doi\"] = 'https://doi.org/10.1126/sciadv.adk9373'\n",
     "model.metadata[\"research_only\"] = None\n",
     "model.metadata[\"notes\"] = \"Chronological-age predictor built with a deep neural network from genome-wide H3K4me1 ChIP-seq signal, a mark of enhancers, as part of a pan-tissue family of histone-mark aging clocks spanning human tissues and cell types.\"\n",
     "model.metadata[\"tissue\"] = 'Multi-tissue (ENCODE human tissues and cell types; H3K4me1 ChIP-seq data, part of a larger dataset of 1,814 human samples across 82 tissues/cell types for 7 histone marks)'\n",
@@ -160,7 +160,7 @@
     "model.metadata[\"model_type\"] = 'PCA + elastic net'\n",
     "model.metadata[\"platform\"] = 'ChIP-seq'\n",
     "model.metadata[\"population\"] = 'Human, pan-tissue; ages spanning embryonic/fetal stages to 90+ years'\n",
-    "model.metadata[\"journal\"] = 'bioRxiv (Cold Spring Harbor Laboratory)'\n",
+    "model.metadata[\"journal\"] = 'Science Advances'\n",
     "model.metadata[\"last_author\"] = 'Ritambhara Singh'\n",
     "model.metadata[\"n_features\"] = 892\n",
     "model.metadata[\"citations\"] = 4\n",
@@ -438,10 +438,10 @@
       "training: True\n",
       "metadata: {'approved_by_author': '✅',\n",
       " 'citation': 'de Lima Camillo, Lucas Paulo, et al. \"Histone mark age of human '\n",
-      "             'tissues and cells.\" bioRxiv (2023): 2023-08.',\n",
+      "             'tissues and cells.\" Science Advances 11.1 (2025): eadk9373.',\n",
       " 'clock_name': 'camilloh3k4me1',\n",
       " 'data_type': 'histone mark',\n",
-      " 'doi': 'https://doi.org/10.1101/2023.08.21.554165',\n",
+      " 'doi': 'https://doi.org/10.1126/sciadv.adk9373',\n",
       " 'notes': None,\n",
       " 'research_only': None,\n",
       " 'species': 'Homo sapiens',\n",

{pyaging-0.3.0/docs/source/clock_notebooks → pyaging-0.3.1/clocks/notebooks}/camilloh3k4me3.ipynb

@@ -148,10 +148,10 @@
     "model.metadata[\"clock_name\"] = 'camilloh3k4me3'\n",
     "model.metadata[\"data_type\"] = 'histone mark'\n",
     "model.metadata[\"species\"] = 'Homo sapiens'\n",
-    "model.metadata[\"year\"] = 2023\n",
+    "model.metadata[\"year\"] = 2025\n",
     "model.metadata[\"approved_by_author\"] = '✅'\n",
-    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cells.\\\" bioRxiv (2023): 2023-08.\"\n",
-    "model.metadata[\"doi\"] = 'https://doi.org/10.1101/2023.08.21.554165'\n",
+    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cell types.\\\" Science Advances 11.1 (2025): eadk9373.\"\n",
+    "model.metadata[\"doi\"] = 'https://doi.org/10.1126/sciadv.adk9373'\n",
     "model.metadata[\"research_only\"] = None\n",
     "model.metadata[\"notes\"] = \"Chronological-age predictor built with a deep neural network from genome-wide H3K4me3 ChIP-seq signal, a mark of active promoters, as part of a pan-tissue family of histone-mark aging clocks spanning human tissues and cell types.\"\n",
     "model.metadata[\"tissue\"] = 'Multi-tissue (82 human tissue/cell types; ENCODE ChIP-seq samples, n=359)'\n",
@@ -160,7 +160,7 @@
     "model.metadata[\"model_type\"] = 'PCA + elastic net'\n",
     "model.metadata[\"platform\"] = 'ChIP-seq'\n",
     "model.metadata[\"population\"] = 'Humans, pan-age (embryonic to 90+ years), ~equal male/female'\n",
-    "model.metadata[\"journal\"] = 'bioRxiv (Cold Spring Harbor Laboratory)'\n",
+    "model.metadata[\"journal\"] = 'Science Advances'\n",
     "model.metadata[\"last_author\"] = 'Ritambhara Singh'\n",
     "model.metadata[\"n_features\"] = 1240\n",
     "model.metadata[\"citations\"] = 4\n",
@@ -438,10 +438,10 @@
       "training: True\n",
       "metadata: {'approved_by_author': '✅',\n",
       " 'citation': 'de Lima Camillo, Lucas Paulo, et al. \"Histone mark age of human '\n",
-      "             'tissues and cells.\" bioRxiv (2023): 2023-08.',\n",
+      "             'tissues and cells.\" Science Advances 11.1 (2025): eadk9373.',\n",
       " 'clock_name': 'camilloh3k4me3',\n",
       " 'data_type': 'histone mark',\n",
-      " 'doi': 'https://doi.org/10.1101/2023.08.21.554165',\n",
+      " 'doi': 'https://doi.org/10.1126/sciadv.adk9373',\n",
       " 'notes': None,\n",
       " 'research_only': None,\n",
       " 'species': 'Homo sapiens',\n",

{pyaging-0.3.0/docs/source/clock_notebooks → pyaging-0.3.1/clocks/notebooks}/camilloh3k9ac.ipynb

@@ -148,10 +148,10 @@
     "model.metadata[\"clock_name\"] = 'camilloh3k9ac'\n",
     "model.metadata[\"data_type\"] = 'histone mark'\n",
     "model.metadata[\"species\"] = 'Homo sapiens'\n",
-    "model.metadata[\"year\"] = 2023\n",
+    "model.metadata[\"year\"] = 2025\n",
     "model.metadata[\"approved_by_author\"] = '✅'\n",
-    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cells.\\\" bioRxiv (2023): 2023-08.\"\n",
-    "model.metadata[\"doi\"] = 'https://doi.org/10.1101/2023.08.21.554165'\n",
+    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cell types.\\\" Science Advances 11.1 (2025): eadk9373.\"\n",
+    "model.metadata[\"doi\"] = 'https://doi.org/10.1126/sciadv.adk9373'\n",
     "model.metadata[\"research_only\"] = None\n",
     "model.metadata[\"notes\"] = \"Chronological-age predictor built with a deep neural network from genome-wide H3K9ac ChIP-seq signal, a mark of active promoters, as part of a pan-tissue family of histone-mark aging clocks spanning human tissues and cell types.\"\n",
     "model.metadata[\"tissue\"] = 'Multi-tissue (human tissues and cell types; ENCODE ChIP-seq)'\n",
@@ -160,7 +160,7 @@
     "model.metadata[\"model_type\"] = 'PCA + elastic net'\n",
     "model.metadata[\"platform\"] = 'ChIP-seq'\n",
     "model.metadata[\"population\"] = 'Pan-age humans (fetal/embryonic to elderly)'\n",
-    "model.metadata[\"journal\"] = 'bioRxiv (Cold Spring Harbor Laboratory)'\n",
+    "model.metadata[\"journal\"] = 'Science Advances'\n",
     "model.metadata[\"last_author\"] = 'Ritambhara Singh'\n",
     "model.metadata[\"n_features\"] = 102\n",
     "model.metadata[\"citations\"] = 4\n",
@@ -438,10 +438,10 @@
       "training: True\n",
       "metadata: {'approved_by_author': '✅',\n",
       " 'citation': 'de Lima Camillo, Lucas Paulo, et al. \"Histone mark age of human '\n",
-      "             'tissues and cells.\" bioRxiv (2023): 2023-08.',\n",
+      "             'tissues and cells.\" Science Advances 11.1 (2025): eadk9373.',\n",
       " 'clock_name': 'camilloh3k9ac',\n",
       " 'data_type': 'histone mark',\n",
-      " 'doi': 'https://doi.org/10.1101/2023.08.21.554165',\n",
+      " 'doi': 'https://doi.org/10.1126/sciadv.adk9373',\n",
       " 'notes': None,\n",
       " 'research_only': None,\n",
       " 'species': 'Homo sapiens',\n",

{pyaging-0.3.0/docs/source/clock_notebooks → pyaging-0.3.1/clocks/notebooks}/camilloh3k9me3.ipynb

@@ -148,10 +148,10 @@
     "model.metadata[\"clock_name\"] = 'camilloh3k9me3'\n",
     "model.metadata[\"data_type\"] = 'histone mark'\n",
     "model.metadata[\"species\"] = 'Homo sapiens'\n",
-    "model.metadata[\"year\"] = 2023\n",
+    "model.metadata[\"year\"] = 2025\n",
     "model.metadata[\"approved_by_author\"] = '✅'\n",
-    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cells.\\\" bioRxiv (2023): 2023-08.\"\n",
-    "model.metadata[\"doi\"] = 'https://doi.org/10.1101/2023.08.21.554165'\n",
+    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cell types.\\\" Science Advances 11.1 (2025): eadk9373.\"\n",
+    "model.metadata[\"doi\"] = 'https://doi.org/10.1126/sciadv.adk9373'\n",
     "model.metadata[\"research_only\"] = None\n",
     "model.metadata[\"notes\"] = \"Chronological age predictor built from H3K9me3 histone-mark ChIP-seq signal, using this heterochromatin-associated modification profiled across diverse human tissues and cell types to estimate age via regularized regression on gene-level features.\"\n",
     "model.metadata[\"tissue\"] = 'Multi-tissue (pan-tissue human tissues and cell types, from ENCODE H3K9me3 ChIP-seq)'\n",
@@ -160,7 +160,7 @@
     "model.metadata[\"model_type\"] = 'PCA + elastic net'\n",
     "model.metadata[\"platform\"] = 'ChIP-seq'\n",
     "model.metadata[\"population\"] = 'Humans, pan-tissue, wide age range (embryonic to 90+ years)'\n",
-    "model.metadata[\"journal\"] = 'bioRxiv (Cold Spring Harbor Laboratory)'\n",
+    "model.metadata[\"journal\"] = 'Science Advances'\n",
     "model.metadata[\"last_author\"] = 'Ritambhara Singh'\n",
     "model.metadata[\"n_features\"] = 341\n",
     "model.metadata[\"citations\"] = 4\n",
@@ -438,10 +438,10 @@
       "training: True\n",
       "metadata: {'approved_by_author': '✅',\n",
       " 'citation': 'de Lima Camillo, Lucas Paulo, et al. \"Histone mark age of human '\n",
-      "             'tissues and cells.\" bioRxiv (2023): 2023-08.',\n",
+      "             'tissues and cells.\" Science Advances 11.1 (2025): eadk9373.',\n",
       " 'clock_name': 'camilloh3k9me3',\n",
       " 'data_type': 'histone mark',\n",
-      " 'doi': 'https://doi.org/10.1101/2023.08.21.554165',\n",
+      " 'doi': 'https://doi.org/10.1126/sciadv.adk9373',\n",
       " 'notes': None,\n",
       " 'research_only': None,\n",
       " 'species': 'Homo sapiens',\n",

{pyaging-0.3.0 → pyaging-0.3.1}/clocks/notebooks/camillopanhistone.ipynb

@@ -148,10 +148,10 @@
     "model.metadata[\"clock_name\"] = 'camillopanhistone'\n",
     "model.metadata[\"data_type\"] = 'histone mark'\n",
     "model.metadata[\"species\"] = 'Homo sapiens'\n",
-    "model.metadata[\"year\"] = 2023\n",
+    "model.metadata[\"year\"] = 2025\n",
     "model.metadata[\"approved_by_author\"] = '✅'\n",
-    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cells.\\\" bioRxiv (2023): 2023-08.\"\n",
-    "model.metadata[\"doi\"] = 'https://doi.org/10.1101/2023.08.21.554165'\n",
+    "model.metadata[\"citation\"] = \"de Lima Camillo, Lucas Paulo, et al. \\\"Histone mark age of human tissues and cell types.\\\" Science Advances 11.1 (2025): eadk9373.\"\n",
+    "model.metadata[\"doi\"] = 'https://doi.org/10.1126/sciadv.adk9373'\n",
     "model.metadata[\"research_only\"] = None\n",
     "model.metadata[\"notes\"] = \"Pan-tissue, pan-histone-mark age predictor that integrates ChIP-seq signal from multiple histone modifications across diverse human tissues, demonstrating that age is broadly encoded across the epigenome with accuracy comparable to DNA-methylation clocks.\"\n",
     "model.metadata[\"tissue\"] = 'multi-tissue (82 distinct human tissues; also validated on primary cell types)'\n",
@@ -160,7 +160,7 @@
     "model.metadata[\"model_type\"] = 'PCA + elastic net'\n",
     "model.metadata[\"platform\"] = 'ChIP-seq'\n",
     "model.metadata[\"population\"] = 'humans, pan-tissue, wide age range (embryonic to 90+ years)'\n",
-    "model.metadata[\"journal\"] = 'bioRxiv (Cold Spring Harbor Laboratory)'\n",
+    "model.metadata[\"journal\"] = 'Science Advances'\n",
     "model.metadata[\"last_author\"] = 'Ritambhara Singh'\n",
     "model.metadata[\"n_features\"] = 3739\n",
     "model.metadata[\"citations\"] = 4\n",
@@ -438,10 +438,10 @@
       "training: True\n",
       "metadata: {'approved_by_author': '✅',\n",
       " 'citation': 'de Lima Camillo, Lucas Paulo, et al. \"Histone mark age of human '\n",
-      "             'tissues and cells.\" bioRxiv (2023): 2023-08.',\n",
+      "             'tissues and cells.\" Science Advances 11.1 (2025): eadk9373.',\n",
       " 'clock_name': 'camillopanhistone',\n",
       " 'data_type': 'histone mark',\n",
-      " 'doi': 'https://doi.org/10.1101/2023.08.21.554165',\n",
+      " 'doi': 'https://doi.org/10.1126/sciadv.adk9373',\n",
       " 'notes': None,\n",
       " 'research_only': None,\n",
       " 'species': 'Homo sapiens',\n",

{pyaging-0.3.0 → pyaging-0.3.1}/docs/_static/clock_explorer.css

@@ -57,6 +57,9 @@
 .ce-scroll { max-height: 72vh; overflow: auto; border: 1px solid var(--ce-border); border-radius: 10px; }
 .ce-table { width: 100%; border-collapse: collapse; white-space: nowrap; }
 .ce-table th, .ce-table td { padding: 9px 12px; text-align: left; border-bottom: 1px solid var(--ce-border); }
+.ce-table .ce-col-clock { min-width: 15rem; font-weight: 600; }
+.ce-table .ce-col-approval, .ce-table .ce-col-num, .ce-table .ce-col-short { width: 1%; }
+.ce-table .ce-col-long { min-width: 11rem; }
 .ce-table thead th { position: sticky; top: 0; background: var(--ce-surface); cursor: pointer; user-select: none;
   font-weight: 600; z-index: 1; }
 .ce-table thead th.sort-asc::after { content: " ▲"; color: var(--ce-primary); }
@@ -64,6 +67,11 @@
 .ce-num { text-align: right; font-variant-numeric: tabular-nums; }
 .ce-row { cursor: pointer; }
 .ce-row:hover { background: var(--ce-surface); }
+.ce-approval { display: inline-flex; align-items: center; border-radius: 999px; padding: 2px 8px;
+  font-size: 0.72rem; font-weight: 600; }
+.ce-approval.is-approved { color: #166534; background: #dcfce7; }
+.ce-approval.is-pending { color: var(--ce-muted); background: var(--ce-surface); border: 1px solid var(--ce-border); }
+html[data-theme="dark"] .ce-approval.is-approved { color: #bbf7d0; background: #14532d; }
 .ce-expander-col { width: 26px; }
 .ce-caret { display: inline-block; transition: transform 0.15s ease; color: var(--ce-muted); }
 .ce-caret.open { transform: rotate(90deg); color: var(--ce-primary); }

{pyaging-0.3.0 → pyaging-0.3.1}/docs/_static/clock_explorer.js

@@ -12,38 +12,41 @@
     data_type: "Data type", species: "Species", platform: "Platform",
     model_type: "Model type", unit: "Unit", tissue: "Tissue",
     last_author: "Last author", journal: "Journal", predicts: "Predicts",
-    population: "Population", approved_by_author: "Approval",
+    population: "Population", approved_by_author: "Verified",
   };
   var COLUMNS = [
-    { key: "clock_name", label: "Clock", def: true },
-    { key: "data_type", label: "Data type", def: true },
-    { key: "species", label: "Species", def: true },
-    { key: "predicts", label: "Predicts", def: true },
-    { key: "model_type", label: "Model", def: true },
-    { key: "platform", label: "Platform", def: true },
-    { key: "citations", label: "Citations", def: true, num: true },
-    { key: "year", label: "Year", def: true, num: true },
-    { key: "n_features", label: "N features", def: false, num: true },
-    { key: "unit", label: "Unit", def: false },
-    { key: "tissue", label: "Tissue", def: false },
-    { key: "population", label: "Population", def: false },
-    { key: "last_author", label: "Last author", def: false },
-    { key: "journal", label: "Journal", def: false },
+    { key: "clock_name", label: "Clock", def: true, cls: "ce-col-clock" },
+    { key: "approved_by_author", label: "Verified", def: true, cls: "ce-col-approval" },
+    { key: "data_type", label: "Data type", def: true, cls: "ce-col-short" },
+    { key: "species", label: "Species", def: true, cls: "ce-col-short" },
+    { key: "year", label: "Year", def: true, num: true, cls: "ce-col-num" },
+    { key: "citations", label: "Citations", def: true, num: true, cls: "ce-col-num" },
+    { key: "n_features", label: "N features", def: true, num: true, cls: "ce-col-num" },
+    { key: "unit", label: "Unit", def: true, cls: "ce-col-short" },
+    { key: "model_type", label: "Model", def: true, cls: "ce-col-long" },
+    { key: "platform", label: "Platform", def: true, cls: "ce-col-long" },
+    { key: "predicts", label: "Predicts", def: true, cls: "ce-col-long" },
+    { key: "tissue", label: "Tissue", def: true, cls: "ce-col-long" },
+    { key: "population", label: "Population", def: true, cls: "ce-col-long" },
+    { key: "last_author", label: "Last author", def: true, cls: "ce-col-long" },
+    { key: "journal", label: "Journal", def: true, cls: "ce-col-long" },
   ];
   var DETAIL_FIELDS = [
     ["predicts", "Predicts"], ["unit", "Unit"], ["tissue", "Tissue"],
     ["platform", "Platform"], ["population", "Population"], ["model_type", "Model type"],
     ["n_features", "N features"], ["year", "Year"], ["citations", "Citations"],
     ["last_author", "Last author"], ["journal", "Journal"], ["species", "Species"],
-    ["data_type", "Data type"], ["approved_by_author", "Approved by author"],
+    ["data_type", "Data type"], ["approved_by_author", "Verified"],
   ];
   // Every sortable table column is offered in the quick-sort dropdown so a
   // column-header click always has a matching option and render() can re-sync
   // the dropdown instead of leaving it showing a stale key.
-  var SORT_OPTIONS = COLUMNS.map(function (c) { return { key: c.key, label: c.label }; });
+  var SORT_OPTIONS = [{ key: "default", label: "Verified first, then name" }].concat(
+    COLUMNS.map(function (c) { return { key: c.key, label: c.label }; })
+  );
 
   var state = {
-    clocks: [], selected: {}, search: "", sortKey: "citations", sortDir: "desc",
+    clocks: [], selected: {}, search: "", sortKey: "default", sortDir: "asc",
     view: "table", cols: null, expanded: {},
   };
   var mount, body, sortSelEl, sortDirBtn, viewToggleBtns;
@@ -60,9 +63,15 @@
     return COLUMNS.filter(function (c) { return state.cols[c.key]; });
   }
   function visible() {
-    return core.sortClocks(core.filterClocks(state.clocks, state.selected, state.search), state.sortKey, state.sortDir);
+    var filtered = core.filterClocks(state.clocks, state.selected, state.search);
+    return state.sortKey === "default" ? core.defaultOrder(filtered) : core.sortClocks(filtered, state.sortKey, state.sortDir);
   }
   function fmt(v) { return v == null || v === "" ? "—" : String(v); }
+  function columnClass(col) { return (col.num ? "ce-num " : "") + (col.cls || ""); }
+  function approvalBadge(value) {
+    var verified = String(value || "").toLowerCase() === "by authors";
+    return el("span", "ce-approval " + (verified ? "is-approved" : "is-pending"), verified ? "By authors" : "Not yet");
+  }
 
   // ---------- filter bar ----------
   function boxKey(f, value) { return f + " " + value; }
@@ -224,6 +233,7 @@
     sortDirBtn = el("button", "ce-btn ce-sortdir", state.sortDir === "desc" ? "▼" : "▲");
     sortDirBtn.type = "button";
     sortDirBtn.title = "Toggle sort direction";
+    sortDirBtn.setAttribute("aria-label", "Toggle sort direction");
     sortDirBtn.addEventListener("click", function () {
       state.sortDir = state.sortDir === "desc" ? "asc" : "desc";
       render();
@@ -299,7 +309,7 @@
     var thead = el("thead"), htr = el("tr");
     htr.appendChild(el("th", "ce-expander-col", ""));
     cols().forEach(function (col) {
-      var th = el("th", col.num ? "ce-num" : null, col.label);
+      var th = el("th", columnClass(col), col.label);
       if (state.sortKey === col.key) th.classList.add(state.sortDir === "desc" ? "sort-desc" : "sort-asc");
       th.addEventListener("click", function () {
         if (state.sortKey === col.key) state.sortDir = state.sortDir === "desc" ? "asc" : "desc";
@@ -318,8 +328,8 @@
       exp.appendChild(el("span", "ce-caret" + (state.expanded[c.clock_name] ? " open" : ""), "▸"));
       tr.appendChild(exp);
       cols().forEach(function (col) {
-        var td = el("td", col.num ? "ce-num" : null);
-        td.appendChild(document.createTextNode(fmt(c[col.key])));
+        var td = el("td", columnClass(col));
+        td.appendChild(col.key === "approved_by_author" ? approvalBadge(c[col.key]) : document.createTextNode(fmt(c[col.key])));
         tr.appendChild(td);
       });
       tr.addEventListener("click", function () {
@@ -369,6 +379,11 @@
     var countEl = document.getElementById("ce-count");
     if (countEl) countEl.textContent = rows.length + " / " + state.clocks.length + " clocks";
     if (sortDirBtn) sortDirBtn.textContent = state.sortDir === "desc" ? "▼" : "▲";
+    if (sortDirBtn) {
+      sortDirBtn.disabled = state.sortKey === "default";
+      sortDirBtn.title = state.sortKey === "default" ? "Default order is verified first, then name" : "Toggle sort direction";
+      sortDirBtn.setAttribute("aria-label", sortDirBtn.title);
+    }
     if (sortSelEl) {
       var hasKey = false;
       SORT_OPTIONS.forEach(function (o) { if (o.key === state.sortKey) hasKey = true; });

{pyaging-0.3.0 → pyaging-0.3.1}/docs/_static/clock_explorer_core.js

@@ -72,6 +72,15 @@
     });
   }
 
+  function defaultOrder(clocks) {
+    return clocks.slice().sort(function (a, b) {
+      var aVerified = String(a.approved_by_author || "").toLowerCase() === "by authors" ? 0 : 1;
+      var bVerified = String(b.approved_by_author || "").toLowerCase() === "by authors" ? 0 : 1;
+      if (aVerified !== bVerified) return aVerified - bVerified;
+      return String(a.clock_name || "").toLowerCase().localeCompare(String(b.clock_name || "").toLowerCase());
+    });
+  }
+
   function toCSV(clocks, columns) {
     function esc(v) {
       if (v == null) return "";
@@ -88,7 +97,7 @@
   var api = {
     FACET_FIELDS: FACET_FIELDS, NUMERIC: NUMERIC,
     computeFacets: computeFacets, filterClocks: filterClocks,
-    sortClocks: sortClocks, toCSV: toCSV,
+    sortClocks: sortClocks, defaultOrder: defaultOrder, toCSV: toCSV,
   };
   if (typeof module !== "undefined" && module.exports) module.exports = api;
   root.ClockExplorerCore = api;