pav3 3.0.0.dev14__tar.gz → 3.0.0.dev16__tar.gz

{pav3-3.0.0.dev14/src/pav3.egg-info → pav3-3.0.0.dev16}/PKG-INFO

@@ -1,15 +1,16 @@
 Metadata-Version: 2.4
 Name: pav3
-Version: 3.0.0.dev14
+Version: 3.0.0.dev16
 Summary: Assembly-based variant discovery
 License-Expression: MIT
 Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: agglovar>=0.0.1.dev8
+Requires-Dist: agglovar>=0.0.1.dev9
 Requires-Dist: biopython>=1.85
 Requires-Dist: fastexcel>=0.14.0
 Requires-Dist: frozendict>=2.4.6
+Requires-Dist: hmmlearn>=0.3.3
 Requires-Dist: intervaltree>=3.1.0
 Requires-Dist: numpy>=2.3.2
 Requires-Dist: polars[numpy,pandas,pyarrow]>=1.35.2
@@ -18,6 +19,8 @@ Requires-Dist: pysam>=0.23.3
 Requires-Dist: scipy>=1.16.1
 Requires-Dist: scipy-stubs==1.16.1.1
 Requires-Dist: snakemake>=9.9.0
+Provides-Extra: fig
+Requires-Dist: matplotlib>=3.10.8; extra == "fig"
 Dynamic: license-file
 
 <h1 align="center"><img width="300px" src="img/logo/PAVLogo_Full.png"/></h1>

{pav3-3.0.0.dev14 → pav3-3.0.0.dev16}/pyproject.toml

@@ -11,10 +11,11 @@ readme = "README.md"
 
 requires-python = ">=3.12"
 dependencies = [
-    "agglovar>=0.0.1.dev8",
+    "agglovar>=0.0.1.dev9",
     "biopython>=1.85",
     "fastexcel>=0.14.0",
     "frozendict>=2.4.6",
+    "hmmlearn>=0.3.3",
     "intervaltree>=3.1.0",
     "numpy>=2.3.2",
     "polars[numpy,pandas,pyarrow]>=1.35.2",
@@ -28,6 +29,11 @@ dependencies = [
 [project.scripts]
 pav3 = "pav3.cli:main"
 
+[project.optional-dependencies]
+fig = [
+    "matplotlib>=3.10.8",
+]
+
 [pav.urls]
 Homepage = "https://github.com/BeckLaboratory/pav"
 Documentation = "https://pav3.readthedocs.io"
@@ -82,10 +88,6 @@ dev = [
     "sphinx-rtd-theme>=3.0.2",
     "tox>=4.30.2",
 ]
-plot = [
-    "matplotlib>=3.10.6",
-]
-
 
 [build-system]
 requires = ["setuptools"]

{pav3-3.0.0.dev14 → pav3-3.0.0.dev16}/src/pav3/__init__.py

@@ -1,18 +1,18 @@
 """PAV Python library routines."""
 
-__version__ = '3.0.0.dev14'
+__version__ = '3.0.0.dev16'
 
 __all__ = [
     'align',
     'anno',
     'call',
     'cli',
-    'lgsv',
-    'anno',
     'const',
-    'inv',
+    'fig',
     'io',
+    'inv',
     'kde',
+    'lgsv',
     'params',
     'pipeline',
     'region',
@@ -20,6 +20,7 @@ __all__ = [
     'seq',
     'util',
     'vcf',
+    'workflow',
 ]
 
 __license__ = 'MIT License'