refactor: update CLI

README.md

@@ -29,8 +29,7 @@ Output:
 To install package, run
 
 ```
-pip install -r requirements.txt
-pip install -r requirements_dev.txt
+pip install .
 ```
 
 

setup.py

 """Set up project."""
-from setuptools import setup, find_packages
 from pathlib import Path
+from setuptools import setup, find_packages
 
 project_root_dir = Path(__file__).parent.resolve()
 with open(project_root_dir / "requirements.txt",
           "r", encoding="utf-8") as f:
     INSTALL_REQUIRES = f.read().splitlines()
 
-url = 'https://git.scicore.unibas.ch/zavolan_group/tools/terminal-fragment-selector'
+URL = ('https://git.scicore.unibas.ch/zavolan_group/'
+       'tools/terminal-fragment-selector')
 
 setup(
     name='terminal-fragment-selector',
     version='0.1.1',
-    url=url,
+    url=URL,
     license='MIT',
     author='Hugo Madge Leon, Sunho Kim, Tanya Nandan',
     author_email='hmadge@ethz.ch',
     description='Terminal fragment selector',
     packages=find_packages(),
-    install_requires=INSTALL_REQUIRES
+    install_requires=INSTALL_REQUIRES,
+    entry_points={
+        'console_scripts': [
+            'terminal-fragment-selector=term_frag_sel.cli:main'
+            ]
+        }
 )

term_frag_sel/cli.py

@@ -18,13 +18,15 @@ logging.basicConfig(
 logger = logging.getLogger("main")
 
 
-def main(args: argparse.Namespace):
+def main():
     """Use CLI arguments to fragment sequences and output text file \
     with selected terminal fragments.
 
     Args:
         args (parser): list of arguments from CLI.
     """
+    args = parse_arguments()
+
     if not isinstance(args, argparse.Namespace):
         raise TypeError("Input should be argparse.Namespace")
 
@@ -38,8 +40,10 @@ def main(args: argparse.Namespace):
     logger.info("Fragmentation of %s...", args.fasta)
     splits = np.arange(0, len(list(fasta))+args.size, args.size)
 
-    for i, split in enumerate(splits):
-        fasta_dict = fasta[split:splits[i+1]]
+    for i in range(len(splits) - 1):
+        split = splits[i]
+        keys = list(fasta.keys())[split:splits[i+1]]
+        fasta_dict = {key: fasta[key] for key in keys}
         term_frags = fragmentation(fasta_dict, seq_counts,
                                    args.mean, args.std)
 
@@ -132,6 +136,4 @@ if __name__ == '__main__':
         level=logging.INFO,
     )
     logger = logging.getLogger(__name__)
-
-    arguments = parse_arguments()
-    main(arguments)
+    main()

term_frag_sel/utils.py

@@ -23,5 +23,4 @@ def check_positive(value: str) -> int:
     except ValueError as exc:
         raise argparse.ArgumentTypeError(f"""Expected positive integer,
                                          got: {value}""") from exc
-    else:
-        return ivalue
+    return ivalue

tests/test_cli.py

@@ -27,5 +27,5 @@ def test_file():
 
 def test_main():
     """Test main() function."""
-    with pytest.raises(TypeError):
-        main("")
+    with pytest.raises(SystemExit):
+        main()