Add testing, travis and codecov

.gitignore

@@ -6,3 +6,5 @@
 
 # Python egg metadata, regenrated from source files in setuptools
 /*.egg-info
+.cache/
+.coverage

.travis.yml

@@ -0,0 +1,28 @@
+sudo: false
+
+language: python
+
+python:
+  - "3.5"
+  - "3.6"
+
+before_install:
+  - export DISPLAY=:99.0
+  - sh -e /etc/init.d/xvfb start
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+
+install:
+  - conda install --yes python=$TRAVIS_PYTHON_VERSION --file requirements/conda_requirements.txt
+  - pip install -r requirements/pypi_requirements.txt
+  - pip install -r requirements/test_requirements.txt
+  - python setup.py install
+
+script: pytest --pep8 --cov=./
+
+notifications:
+  email: false
+
+after_success:
+  - codecov

codecov.yml

@@ -0,0 +1,24 @@
+codecov:
+  branch: master
+
+coverage:
+  precision: 2
+  round: down
+  range: "50...100"
+
+  status:
+    project:
+      default:
+        target: auto
+        threshold: null
+        branches: null
+
+    patch:
+      default:
+        target: auto
+        branches: null
+
+comment:
+  layout: "header, diff, changes, sunburst, uncovered"
+  branches: null
+  behavior: default

requirements/conda_requirements.txt

@@ -0,0 +1,3 @@
+numpy
+scipy
+matplotlib

requirements/pypi_requirements.txt

@@ -0,0 +1,2 @@
+gitpython
+tqdm

requirements/rtd_requirements.txt

@@ -0,0 +1 @@
+numpydoc

requirements/test_requirements.txt

@@ -0,0 +1,8 @@
+codecov
+coverage
+pep8
+pytest
+pytest-cache
+pytest-cov
+pytest-pep8
+gitpython

test/unit/test_RandomWalk.py

@@ -0,0 +1,83 @@
+import porespy as ps
+import pytrax as pt
+import scipy as sp
+import os
+import matplotlib.pyplot as plt
+
+
+class SimulationTest():
+    def setup_class(self):
+        self.l = 100
+        self.im = ps.generators.overlapping_spheres(shape=[self.l, self.l],
+                                                    radius=5,
+                                                    porosity=0.5)
+        self.blobs = ps.generators.blobs([self.l, self.l, self.l])
+        self.rw = pt.RandomWalk(self.blobs)
+        self.blobs_2d = ps.generators.blobs([self.l, self.l]).astype(int)
+        self.rw_2d = pt.RandomWalk(self.blobs_2d, seed=True)
+
+    def test_random_walk(self):
+        self.rw.run(nt=1000, nw=100, stride=1)
+        assert sp.shape(self.rw.real_coords) == (1000, 100, 3)
+
+    def test_plot_msd(self):
+        self.rw.plot_msd()
+        pass
+
+    def test_random_walk_2d(self):
+        self.rw_2d.run(nt=1000, nw=100, same_start=True, stride=100)
+        assert sp.shape(self.rw_2d.real_coords) == (10, 100, 2)
+
+    def test_plot_walk_2d(self):
+        self.rw_2d.plot_walk_2d(data='w')
+        assert hasattr(self.rw_2d, 'im_big')
+        assert sp.sum(self.rw_2d.im_big > self.rw_2d.nw) == 0
+        plt.close('all')
+
+    def test_export(self):
+        cwd = os.getcwd()
+        self.rw_2d.export_walk(sub='temp', image=self.rw_2d.im, sample=10)
+        subdir = os.path.join(cwd, 'temp')
+        assert os.path.exists(subdir)
+        file_list = os.listdir(subdir)
+        # 10 coordinate files based on the stride and number of steps + image
+        assert len(file_list) == 11
+        # Delete all files and folder
+        for file in file_list:
+            fp = os.path.join(subdir, file)
+            os.remove(fp)
+        os.rmdir(subdir)
+
+    def test_seed(self):
+        # rw_2d was initialized with seed = True, this should mean running it
+        # repeatedly produces the same movements
+        self.rw_2d.run(nt=1000, nw=100, same_start=True)
+        temp_coords = self.rw_2d.real_coords.copy()
+        self.rw_2d.run(nt=1000, nw=100, same_start=True)
+        assert sp.allclose(self.rw_2d.real_coords, temp_coords)
+
+    def test_axial_density_plot(self):
+        self.rw.axial_density_plot(time=0, axis=0)
+        plt.close('all')
+
+    def test_rw_analytics(self):
+        w_list = [10, 100]
+        t_list = [10, 100]
+        self.rw_2d.run_analytics(w_list, t_list, fname='test.csv')
+        cwd = os.getcwd()
+        fpath = os.path.join(cwd, 'test.csv')
+        assert os.path.exists(fpath)
+        os.remove(fpath)
+        plt.close('all')
+
+if __name__ == '__main__':
+    t = SimulationTest()
+    t.setup_class()
+    t.test_random_walk()
+    t.test_plot_msd()
+    t.test_random_walk_2d()
+    t.test_plot_walk_2d()
+    t.test_export()
+    t.test_seed()
+    t.test_axial_density_plot()
+    t.test_rw_analytics()