set up cli parser to take energy cutoff

primingsitepredictor/cli.py

@@ -5,17 +5,29 @@ Created on Mon Nov 14 14:49:50 2022
 @author: baerma
 """
 import argparse
+import logging
 
+def create_parser():
+    parser = argparse.ArgumentParser(
+    prog = 'Priming site predictor',
+    description = 'Takes a cutoff energy and the predicts location of priming sites of transcripts',
+    epilog = 'To predict or not to predict')
+    parser.add_argument('energycutoff', type=float, help='a float as energy Cutoff')
+    #parser.add_argument('transcripts', help='fastafile containing transcripts') #What type is that? fasta? Actually doesn't make sense here
+    args = parser.parse_args()
+    energy_cutoff = args.energycutoff
+    return energy_cutoff
+#possibly make a class out of this although I think it's an overkill
 
-parser = argparse.ArgumentParser(description='Process some integers.')
-parser.add_argument('integers', metavar='N', type=int, nargs='+',
-                    help='an integer for the accumulator')
-parser.add_argument('--sum', dest='accumulate', action='store_const',
-                    const=sum, default=max,
-                    help='sum the integers (default: find the max)')
-
-args = parser.parse_args()
-print(args.accumulate(args.integers))
-
-
+def letsgo():
+    energy_cutoff = create_parser()
+    print(f"Your energy cutoff is {energy_cutoff}")
 
+if __name__ == '__main__':
+    logging.basicConfig(
+        format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
+        level=logging.INFO,
+    )
+    LOG = logging.getLogger(__name__)
+    letsgo()
+    #here we would point to the main module and parse the energy cutoff

setup.py

@@ -10,6 +10,6 @@ setup(
     packages = ['primingsitepredictor'],
     entry_points = {
         'console_scripts': [
-            'psp = primingsitepredictor.main:main'
+            'primingsitepredictor = primingsitepredictor.cli:letsgo'
         ]
     })