pav3 3.0.0.dev3__tar.gz → 3.0.0.dev4__tar.gz

{pav3-3.0.0.dev3/src/pav3.egg-info → pav3-3.0.0.dev4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pav3
-Version: 3.0.0.dev3
+Version: 3.0.0.dev4
 Summary: Assembly-based variant discovery
 License-Expression: MIT
 Requires-Python: >=3.12
@@ -38,7 +38,7 @@ pip install pav3
 To run PAV, use the `pav3` command after setting up configuration files.
 
 ```
-pav3
+python -m pav3
 ```
 
 

{pav3-3.0.0.dev3 → pav3-3.0.0.dev4}/README.md

@@ -16,7 +16,7 @@ pip install pav3
 To run PAV, use the `pav3` command after setting up configuration files.
 
 ```
-pav3
+python -m pav3
 ```
 
 

{pav3-3.0.0.dev3 → pav3-3.0.0.dev4}/pyproject.toml

@@ -26,11 +26,11 @@ dependencies = [
 ]
 
 [project.scripts]
-pav3 = "pav3.cli.cli:main"
+pav3 = "pav3.cli:main"
 
 [pav.urls]
 Homepage = "https://github.com/BeckLaboratory/pav"
-#Documentation = "https://pav3.readthedocs.io"
+Documentation = "https://pav3.readthedocs.io"
 Repository = "https://github.com/BeckLaboratory/pav"
 Issues = "https://github.com/BeckLaboratory/pav/issues"
 Changelog = "https://github.com/BeckLaboratory/pav/blob/master/CHANGELOG.md"
@@ -51,7 +51,6 @@ classifiers = [
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.12",
-    "Private :: Do Not Upload",  # Temporary until published
 ]
 
 authors = [
@@ -96,9 +95,8 @@ build-backend = "setuptools.build_meta"
 include-package-data = true
 
 [tool.setuptools.packages.find]
-namespaces = true
 where = ["src"]
-include = ["pav3", "data", "workflow"]
+include = ["pav3"]
 exclude = ["*__pycache__"]
 
 [tool.setuptools.package-data]

pav3-3.0.0.dev4/src/pav3/__init__.py

@@ -0,0 +1,60 @@
+"""PAV Python library routines."""
+
+__version__ = '3.0.0.dev4'
+
+__all__ = [
+    'align',
+    'anno',
+    'call',
+    'cli',
+    'lgsv',
+    'anno',
+    'const',
+    'inv',
+    'io',
+    'kde',
+    'params',
+    'pipeline',
+    'region',
+    'schema',
+    'seq',
+    'util',
+]
+
+__license__ = 'MIT License'
+__author__ = 'Peter Audano'
+__copyright__ = 'Copyright (c) 2024 Peter Audano'
+__credits__ = ['Peter Audano']
+__maintainer__ = 'Peter Audano'
+__email__ = 'peter.audano@jax.org'
+__status__ = 'Development'
+
+__license_spdx__ = 'MIT'
+
+__license_text__ = """MIT License
+
+Copyright (c) 2024 Peter Audano
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+
+import importlib
+
+for name in __all__:
+    globals()[name] = importlib.import_module(f'.{name}', package=__name__)

pav3-3.0.0.dev4/src/pav3/__main__.py

@@ -0,0 +1,6 @@
+"""Support for direct pav3 execution."""
+
+from .cli import main
+
+if __name__ == '__main__':
+    main()

pav3-3.0.0.dev4/src/pav3/align/__init__.py

@@ -0,0 +1,17 @@
+"""Alignment handling routines."""
+
+import importlib
+
+__all__ = [
+    'features',
+    'lcmodel',
+    'lift',
+    'op',
+    'records',
+    'score',
+    'tables',
+    'trim',
+]
+
+for name in __all__:
+    globals()[name] = importlib.import_module(f'.{name}', package=__name__)