Merge branch 'main' of...

Merge branch 'main' of ssh://git.scicore.unibas.ch:2222/zavolan_group/tools/terminal-fragment-selector

requirements.txt

+argparse
+biopython >= 1.78
+numpy >= 1.23.3
+pandas >= 1.4.4
\ No newline at end of file

setup.py

-From setup tools import setup, find_packages
+"""Set up project."""
+from setuptools import setup, find_packages
+from pathlib import Path
+
+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'
 
 setup(
-	name = “prog_for_life_science”, 
-	url = ‘ssh://git@git.scicore.unibas.ch:2222/zavolan_group/tools/terminal-fragment-selector.git’
-	author = ‘Hugo Madge Leon, Sunho Kim, Tanya Nandan’,
-	author_email = ‘kimsun@ethz.ch’,
-	License = ‘MIT’,
-	version = ‘1.0.0’,
-	packages = find_packages(),
-	install_requires= ['random','argparse 1.4.0','os.path', 'check_positive', 'arghelper 0.4.2', 'fragmentation_v2', 'numpy 1.23.4', 'pandas 1.5']
-)
\ No newline at end of file
+    name='terminal-fragment-selector',
+    version='0.1.1',
+    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
+)

terminal-fragment-selector/__init__.py

+"""Initialise package."""

terminal-fragment-selector/main.py → terminal-fragment-selector/cli.py

@@ -61,9 +61,7 @@ def file_validation(fasta_file: str,
     """
     with open(fasta_file, "r") as handle:
         fasta = SeqIO.parse(handle, "fasta")
-    try:
-        any(fasta)
-    except Exception:
+    if not any(fasta):
         logger.exception("Input FASTA file is either empty or \
             incorrect file type.")