modernize package

Author: alpae

omark/__init__.py

@@ -15,9 +15,10 @@
 '''
 
 from datetime import date
+from importlib.metadata import version as omark_version
 
 __packagename__ = "omark"
-__version__ = "0.4.0"
+__version__ = omark_version("omark")
 __copyright__ = "(C) 2022-{:d} Yannis Nevers  <yannis.nevers@unil.ch>".format(
     date.today().year
 )

bin/omark omark/cli.pybin/omark renamed to omark/cli.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 '''
             OMArk - Quality assesment of coding-gene repertoire annotation
             (C) 2022 Yannis Nevers <yannis.nevers@unil.ch>
@@ -17,7 +15,7 @@
         '''
 
 import argparse
-import omark.omark as omark
+from . import omark
 
 def build_arg_parser():
     """Handle the parameter sent when executing the script from the terminal
@@ -48,8 +46,7 @@ def build_arg_parser():
     return parser
 
 
-if __name__=='__main__':
-	
+def main():
     parser = build_arg_parser()  
     arg = parser.parse_args()
     omark.launcher(arg)

pyproject.toml

@@ -0,0 +1,37 @@
+[project]
+name = "omark"
+version = "0.4.0"
+description = "OMArk - Proteome quality assesment based on OMAmer placements"
+readme = "README.md"
+license = "GPL-3.0-or-later"
+license-file = "LICENSE"
+requires-python = ">=3.9,<3.13"
+authors = [
+    { name  = "Yannis Nevers", email = "yannis.nevers@unil.ch"},
+]
+dependencies = [
+    "biopython >1.83,<2",
+    "ete3",
+    "jinja2",
+    "matplotlib",
+    "omamer>=2.1.0",
+]
+keywords = ["Proteome quality", "Sequence annotation", "Quality control", "Molecular evolution"]
+classifiers = [
+  "Development Status :: 5 - Production",
+  "Programming Language :: Python"
+]
+
+[project.urls]
+Homepage = "https://github.com/DessimozLab/omark"
+
+[project.scripts]
+omark = "omark.cli:main"
+
+[build-system]
+requires = ["uv_build>=0.9.14,<0.10.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+module-root = "./"
+data = ["omark/assets"]