Integration tests & github actions based CI

.github/workflows/linux.yml

@@ -0,0 +1,22 @@
+name: Build and Test
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-20.04
+    env:
+      BOOST_LIBDIR: /usr/lib/x86_64-linux-gnu/
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install dependencies
+        run: sudo apt-get update && sudo apt-get install -y --no-install-recommends --no-install-suggests g++ python-dev python3-dev python3-pip maven libnuma-dev libc-dev python3-venv  openmpi-bin libopenmpi-dev flex bison libomp-dev gsl-bin libgsl0-dev libboost-all-dev imagemagick-6.q16 inkscape
+      - name: build cpp
+        run: make all
+      - name: test
+        run: cd bin && ./test.sh

bin/test.sh

@@ -13,8 +13,10 @@ pip install pypng
 pip install pytest
 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

@@ -0,0 +1,88 @@
+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():
+    command = "np_shape_lab -R 10 -q 600 -c 0.005 -t 1 -v 1 -b 40 -s 40 -S 25000 -D 4 -F n"
+    command_list = command.split();
+    exec_command(command_list, cwd="..")
+    df = pd.read_csv('outfiles/area.dat', sep=r"\s+", header=None)
+    t = df.iat[-1, 1]
+    assert math.isclose(t, 15.675, rel_tol=1e-1)
+
+    df = pd.read_csv('outfiles/energy_in_parts_kE_bE_sE_tE_ljE_esE.dat', sep=r"\s+", header=None)
+    t = df.iat[-1, 4]
+    assert math.isclose(t, 380.971, rel_tol=1e-1)
+
+
+def test_example_two():
+    command = "np_shape_lab -R 10 -q 600 -c 0.01 -t 1 -v 1 -b 40 -s 40 -S 25000 -D 4 -F n"
+    command_list = command.split();
+    exec_command(command_list, cwd="..")
+    df = pd.read_csv('outfiles/area.dat', sep=r"\s+", header=None)
+    t = df.iat[-1, 1]
+    assert math.isclose(t, 13.2595, rel_tol=1e-2)
+
+    df = pd.read_csv('outfiles/energy_in_parts_kE_bE_sE_tE_ljE_esE.dat', sep=r"\s+", header=None)
+    t = df.iat[-1, 4]
+    assert math.isclose(t, 322.264, rel_tol=1e-1)
+
+
+def test_example_three():
+    command = "np_shape_lab -R 10 -q 600 -N 2 -p 0.5 -c 0.005 -t 1 -v 1 -b 40 -s 40 -S 25000 -D 4 -F n"
+    command_list = command.split();
+    exec_command(command_list, cwd="..")
+    df = pd.read_csv('outfiles/area.dat', sep=r"\s+", header=None)
+    t = df.iat[-1, 1]
+    assert math.isclose(t, 12.5275, rel_tol=1e-2)
+
+    df = pd.read_csv('outfiles/energy_in_parts_kE_bE_sE_tE_ljE_esE.dat', sep=r"\s+", header=None)
+    t = df.iat[-1, 4]
+    assert math.isclose(t, 304.473, rel_tol=1e-1)
+
+
+def test_example_four():
+    command = "np_shape_lab -R 10 -q 0 -c 0.005 -t 0 -v 0 -b 1 -s 1000 -S 25000 -D 4 -F n -B y"
+    command_list = command.split();
+    exec_command(command_list, cwd="..")
+    df = pd.read_csv('outfiles/area.dat', sep=r"\s+", header=None)
+    t = df.iat[-1, 1]
+    assert math.isclose(t, 12.3795, rel_tol=1e-2)
+
+    df = pd.read_csv('outfiles/energy_in_parts_kE_bE_sE_tE_ljE_esE.dat', sep=r"\s+", header=None)
+    t = df.iat[-1, 3]
+    assert math.isclose(t, 5.87409, rel_tol=1e-1)
+
+def test_example_five():
+    command = "np_shape_lab -R 10 -q 600 -N 2 -p 0.5 -c 0.005 -t 1 -v 1 -b 40 -s 40 -S 25000 -D 4 -F n -H y"
+    command_list = command.split();
+    exec_command(command_list, cwd="..")
+    df = pd.read_csv('outfiles/area.dat', sep=r"\s+", header=None)
+    t = df.iat[-1, 1]
+    assert math.isclose(t, 12.5099, rel_tol=1e-2)
+
+    df = pd.read_csv('outfiles/energy_in_parts_kE_bE_sE_tE_ljE_esE.dat', sep=r"\s+", header=None)
+    t = df.iat[-1, 4]
+    assert math.isclose(t, 304.044, rel_tol=1e-1)
+
+

bin/test/npshape_test.py

@@ -1,5 +1,5 @@
 import testbook
-import os
+import os, shutil
 import svgwrite
 import png
 
@@ -32,3 +32,26 @@ def test_convert_SVG_PNG(tb):
     assert os.path.exists("test/resources/output.png") == 1
     os.remove("test/resources/output.png")
 
+#@testbook.testbook('npshape-frontend.ipynb', execute=True)
+#def test_create_out_dirs(tb):
+#    func = tb.ref("createOutDirs")
+#    func()
+#    assert os.path.exists("outfiles")
+#    assert os.path.exists("simulation_snapshots")
+#    assert os.path.exists("snapshot_png")
+#    shutil.rmtree('outfiles', True)
+#    shutil.rmtree('simulation_snapshots', True)
+#    shutil.rmtree('snapshot_png', True)
+
+#@testbook.testbook('npshape-frontend.ipynb', execute=True)
+#def test_paramerter_append(tb):
+#    func = tb.ref("appendParameters")
+#    params = 'Maximum Surface Charge(Q in e) is 1\nNumber of patches used: 1\n' \
+#             'Patch size (p) is 1\nSurface Charge(Q in e) is 1\nBending Modulus is ' \
+#             '1\nStretching Modulus is 1\nSalt Concentration (M) is 1\n'
+#    out = func(1, 1, 1, 1, 1, 1, 1, 4)
+#    assert params == out
+
+
+
+