Integration test

bin/test.sh

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+#!/bin/bash
+
+python3 -m venv ENV
+
+source ENV/bin/activate
+
+pip install hublib
+pip install jupyterlab
+pip install testbook
+pip install widgetsnbextension
+pip install svgwrite
+pip install pypng
+pip install pytest
+pip install scipy
+pip install tensorflow
+pip install keras
+pip install pandas
+pip install scikit-learn
+pip install matplotlib
+pip install ipywidgets
+pip install pandas
+jupyter nbextension enable --py widgetsnbextension
+
+export ENVIRON_CONFIG_DIRS=","
+export PATH=$PATH:$PWD
+pytest test || exit 1

bin/test/integration_test.py

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+import pytest
+import subprocess
+import sys
+import threading
+import pandas as pd
+import math
+
+def exec_command(command, cwd=None):
+    process = subprocess.Popen(command,
+                               stdout=subprocess.PIPE,
+                               universal_newlines=True)
+    while True:
+        output = process.stdout.readline()
+        print(output.strip())
+        # Do something else
+        return_code = process.poll()
+        if return_code is not None:
+            print('RETURN CODE', return_code)
+            # Process has finished, read rest of the output
+            for output in process.stdout.readlines():
+                print(output.strip())
+            break
+
+
+def test_example_one():
+    exec_command(['md_simulation_confined_ions', '-T', '0.001', '-Z', '3', '-p', '1', '-n', '-1', '-c', '.5', '-d', '0.474', '-a', '0.627', '-i', '0', '-S', '10000'], cwd="..")
+    df = pd.read_csv('outfiles/energy.dat', sep=r"\s+", header=None)
+    t = df.iat[-1, 6]
+    assert math.isclose(t, 2310.45, rel_tol=1e-1)
+
+
+
+
+
+