From 05a5fd9860d40172a98002cc139824e88ac3e5a1 Mon Sep 17 00:00:00 2001
From: Thomas Wemyss <twemyss@users.noreply.github.com>
Date: Thu, 26 Nov 2020 12:55:48 +0000
Subject: [PATCH] Add CLI entry point to module (Addresses
 UCL-RITS/rse-classwork-2020#144)

---
 sagital_average/__init__.py                   |  1 +
 sagital_average/brain_sample.csv              | 20 +++++++++++++++++++
 sagital_average/command.py                    | 12 +++++++++++
 .../requirements.txt                          |  0
 .../sagital_brain.py                          | 14 -------------
 .../tests/test_average.py                     |  0
 sagital_brain/__init__.py                     |  0
 setup.py                                      |  5 +++++
 8 files changed, 38 insertions(+), 14 deletions(-)
 create mode 100644 sagital_average/__init__.py
 create mode 100644 sagital_average/brain_sample.csv
 create mode 100644 sagital_average/command.py
 rename {sagital_brain => sagital_average}/requirements.txt (100%)
 rename {sagital_brain => sagital_average}/sagital_brain.py (50%)
 rename {sagital_brain => sagital_average}/tests/test_average.py (100%)
 delete mode 100644 sagital_brain/__init__.py

diff --git a/sagital_average/__init__.py b/sagital_average/__init__.py
new file mode 100644
index 0000000..829850f
--- /dev/null
+++ b/sagital_average/__init__.py
@@ -0,0 +1 @@
+from .sagital_brain import run_averages
\ No newline at end of file
diff --git a/sagital_average/brain_sample.csv b/sagital_average/brain_sample.csv
new file mode 100644
index 0000000..d0b9035
--- /dev/null
+++ b/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
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+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
diff --git a/sagital_average/command.py b/sagital_average/command.py
new file mode 100644
index 0000000..29e6aa1
--- /dev/null
+++ b/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)
\ No newline at end of file
diff --git a/sagital_brain/requirements.txt b/sagital_average/requirements.txt
similarity index 100%
rename from sagital_brain/requirements.txt
rename to sagital_average/requirements.txt
diff --git a/sagital_brain/sagital_brain.py b/sagital_average/sagital_brain.py
similarity index 50%
rename from sagital_brain/sagital_brain.py
rename to sagital_average/sagital_brain.py
index 063d63a..b33870c 100755
--- a/sagital_brain/sagital_brain.py
+++ b/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)
diff --git a/sagital_brain/tests/test_average.py b/sagital_average/tests/test_average.py
similarity index 100%
rename from sagital_brain/tests/test_average.py
rename to sagital_average/tests/test_average.py
diff --git a/sagital_brain/__init__.py b/sagital_brain/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/setup.py b/setup.py
index 090b6a5..4f16d5a 100644
--- a/setup.py
+++ b/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'
+    ]}
 )
\ No newline at end of file