Add CLI entry point to module (Addresses UCL-RITS/rse-classwork-2020#144

)

sagital_average/__init__.py

@@ -0,0 +1 @@
+from .sagital_brain import run_averages

sagital_average/brain_sample.csv

@@ -0,0 +1,20 @@
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1

sagital_average/command.py

@@ -0,0 +1,12 @@
+from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
+import sagital_brain
+
+def process():
+    parser = ArgumentParser(description="Calculates the average for each sagital-horizontal plane.",
+                            formatter_class=ArgumentDefaultsHelpFormatter)
+    parser.add_argument('file_input', nargs='?', default="brain_sample.csv",
+                        help="Input CSV file with the results from scikit-brain binning algorithm.")
+    parser.add_argument('--file_output', '-o', default="brain_average.csv",
+                        help="Name of the output CSV file.")
+    arguments = parser.parse_args()
+    sagital_brain.run_averages(arguments.file_input, arguments.file_output)

sagital_brain/sagital_brain.py → sagital_average/sagital_brain.py

@@ -1,7 +1,3 @@
-#!/usr/local/python3
-
-from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
-
 import numpy as np
 
 def run_averages(file_input='brain_sample.csv', file_output='brain_average.csv'):
@@ -23,13 +19,3 @@ def run_averages(file_input='brain_sample.csv', file_output='brain_average.csv')
     np.savetxt(file_output, averages, fmt='%.1f', delimiter=',')
 
 
-if __name__ == "__main__":
-    parser = ArgumentParser(description="Calculates the average for each sagital-horizontal plane.",
-                            formatter_class=ArgumentDefaultsHelpFormatter)
-    parser.add_argument('file_input', nargs='?', default="brain_sample.csv",
-                        help="Input CSV file with the results from scikit-brain binning algorithm.")
-    parser.add_argument('--file_output', '-o', default="brain_average.csv",
-                        help="Name of the output CSV file.")
-    arguments = parser.parse_args()
-
-    run_averages(arguments.file_input, arguments.file_output)

setup.py

@@ -4,4 +4,9 @@
     name="Sagital Brain",
     version="0.1.0",
     packages=find_packages(),
+    install_requires=['numpy', 'pytest'],
+    entry_points={
+        'console_scripts': [
+            'sagital_brain = sagital_brain.command:process'
+    ]}
 )