consenrich 0.4.0b3__tar.gz → 0.7.10rc6__tar.gz

consenrich-0.7.10rc6/MANIFEST.in

@@ -0,0 +1,4 @@
+include README.md
+recursive-include src/consenrich *.pyx *.c
+recursive-include src/consenrich/data *.bed *.sizes
+

{consenrich-0.4.0b3/src/consenrich.egg-info → consenrich-0.7.10rc6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: consenrich
-Version: 0.4.0b3
+Version: 0.7.10rc6
 Summary: Genome-wide estimation of signals hidden in noisy multi-sample HTS datasets
 Author-email: "Nolan H. Hamilton" <nolan.hamilton@unc.edu>
 Requires-Python: >=3.11
@@ -14,6 +14,7 @@ Requires-Dist: pysam>=0.23.3
 Requires-Dist: pybedtools>=0.11.2
 Requires-Dist: PyYAML>=6.0.2
 Requires-Dist: PyWavelets>=1.9.0
+Requires-Dist: matplotlib
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
@@ -34,14 +35,20 @@ Dynamic: requires-python
 
 # Consenrich
 
-Consenrich is an adaptive linear filter for genome-wide estimation of signals hidden in
-noisy multi-sample HTS datasets. Consenrich supports a variety of functional genomics assays including ATAC-seq, DNase-seq, ChIP-seq, CUT&RUN, etc.
+Consenrich is an adaptive linear state estimator that yields genome-wide, uncertainty-calibrated signal tracks from noisy multi-sample cohorts' epigenetic HTS data.
 
-![Simplified Schematic of Consenrich.](docs/images/noise.png)
+<p align="center">
+  <img src="docs/images/noise.png" alt="Simplified Schematic of Consenrich." width="600">
+</p>
+
+
+Special emphasis is placed on computational efficiency, model interpretability, and practical utility for downstream tasks that require well-resolved genome-wide signal estimates and uncertainty quantification across samples, such as:
+
+* Consensus detection of open chromatin regions, TF binding, histone modification, etc.
+* Candidate prioritization for differential analyses, functional validation, integrative modeling, etc.
 
 [**See the Documentation**](https://nolan-h-hamilton.github.io/Consenrich/) for usage examples, installation details, configuration options, and an API reference.
 
----
 
 ## Manuscript Preprint and Citation
 

consenrich-0.7.10rc6/README.md

@@ -0,0 +1,31 @@
+# Consenrich
+
+Consenrich is an adaptive linear state estimator that yields genome-wide, uncertainty-calibrated signal tracks from noisy multi-sample cohorts' epigenetic HTS data.
+
+<p align="center">
+  <img src="docs/images/noise.png" alt="Simplified Schematic of Consenrich." width="600">
+</p>
+
+
+Special emphasis is placed on computational efficiency, model interpretability, and practical utility for downstream tasks that require well-resolved genome-wide signal estimates and uncertainty quantification across samples, such as:
+
+* Consensus detection of open chromatin regions, TF binding, histone modification, etc.
+* Candidate prioritization for differential analyses, functional validation, integrative modeling, etc.
+
+[**See the Documentation**](https://nolan-h-hamilton.github.io/Consenrich/) for usage examples, installation details, configuration options, and an API reference.
+
+
+## Manuscript Preprint and Citation
+
+**BibTeX Citation**
+
+```bibtex
+@article {Hamilton2025,
+	author = {Hamilton, Nolan H and Huang, Yu-Chen E and McMichael, Benjamin D and Love, Michael I and Furey, Terrence S},
+	title = {Genome-Wide Uncertainty-Moderated Extraction of Signal Annotations from Multi-Sample Functional Genomics Data},
+	year = {2025},
+	doi = {10.1101/2025.02.05.636702},
+	publisher = {Cold Spring Harbor Laboratory},
+	journal = {bioRxiv}
+}
+```

{consenrich-0.4.0b3 → consenrich-0.7.10rc6}/pyproject.toml

@@ -10,7 +10,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "consenrich"
-version = "0.4.0b3"
+version = "0.7.10rc6"
 description = "Genome-wide estimation of signals hidden in noisy multi-sample HTS datasets"
 authors = [{ name="Nolan H. Hamilton", email="nolan.hamilton@unc.edu" }]
 readme = "README.md"
@@ -24,7 +24,8 @@ dependencies = [
     "pysam>=0.23.3",
     "pybedtools>=0.11.2",
     "PyYAML>=6.0.2",
-    "PyWavelets>=1.9.0"
+    "PyWavelets>=1.9.0",
+    "matplotlib",
 ]
 
 [project.optional-dependencies]
@@ -44,11 +45,14 @@ docs = [
 package-dir = {"" = "src"}
 include-package-data = true
 
+[tool.setuptools.package-data]
+consenrich = ["src/consenrich/data/**"]
+
 [project.scripts]
 consenrich = "consenrich.consenrich:main"
 
 [tool.cibuildwheel]
-build = " cp311-* cp312-* cp313-*"
+build = "cp311-* cp312-* cp313-*"
 skip  = "*-musllinux_*"
 
 

{consenrich-0.4.0b3 → consenrich-0.7.10rc6}/setup.py

@@ -4,16 +4,21 @@ from Cython.Build import cythonize
 import pysam
 import numpy
 
+
 def get_includes():
     class Includes:
         def __iter__(self):
             import pysam
             import numpy
-            return iter(pysam.get_include()+[numpy.get_include()])
+
+            return iter(pysam.get_include() + [numpy.get_include()])
+
         def __getitem__(self, i):
             return list(self)[i]
+
     return Includes()
 
+
 extensions = [
     Extension(
         "consenrich.cconsenrich",
@@ -25,19 +30,30 @@ extensions = [
             "-fno-trapping-math",
             "-fno-math-errno",
             "-mtune=generic",
+            "-fopenmp",
         ],
+        extra_link_args=["-fopenmp"],
     )
 ]
 
 setup(
     name="consenrich",
-    version="0.4.0b3",
+    version="0.7.10rc6",
     packages=find_packages(where="src"),
     include_package_data=True,
     package_dir={"": "src"},
     ext_modules=cythonize(extensions, language_level="3"),
-    install_requires=["cython>=3.0", "numpy>=2.1", "pandas>=2.3", "scipy>=1.15",
-                      "pysam>=0.23.3", "pybedtools>=0.11.2", "PyYAML>=6.0.2", "PyWavelets>=1.9.0"],
+    install_requires=[
+        "cython>=3.0",
+        "numpy>=2.1",
+        "pandas>=2.3",
+        "scipy>=1.15",
+        "pysam>=0.23.3",
+        "pybedtools>=0.11.2",
+        "PyYAML>=6.0.2",
+        "PyWavelets>=1.9.0",
+        "matplotlib",
+    ],
     python_requires=">=3.11",
     zip_safe=False,
 )