Merge pull request #45 from pyiron/unittests

Switch from pytest to unittest

.coveragerc

@@ -0,0 +1,5 @@
+# .coveragerc to control coverage.py
+[run]
+source = pylammpsmpi
+omit = pylammpsmpi/_version.py
+concurrency = multiprocessing

.github/workflows/pythonpackage.yml → .github/workflows/unittests.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: [3.6, 3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2
@@ -28,13 +28,6 @@ jobs:
     - run: conda --version
     - run: which python
     - run: conda config --set always_yes yes --set changeps1 no
-    - run: conda install -c conda-forge lammps mpi4py openmpi pytest numpy distributed dask-jobqueue
+    - run: conda install -c conda-forge lammps mpi4py openmpi coveralls codacy-coverage coverage numpy distributed dask-jobqueue
     - run: pip install -e .
-    - run: python -m pytest tests/
-    - run: python setup.py sdist
-    - name: publish package on pypi
-      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-       user: ${{ secrets.pypi_username }}
-       password: ${{ secrets.pypi_password }}
+    - run: coverage run -m unittest discover tests

.travis.yml

@@ -11,11 +11,16 @@ matrix:
         - bash miniconda.sh -b -p $HOME/miniconda
         - conda info -a
         - conda config --set always_yes yes --set changeps1 no
-        - conda install -c conda-forge lammps mpi4py openmpi pytest numpy distributed dask-jobqueue
+        - conda install -c conda-forge lammps mpi4py openmpi coveralls codacy-coverage coverage numpy distributed dask-jobqueue
         - conda update -q conda
         - pip install -e .
       script:
-        - python -m pytest tests/
+        - coverage run -m unittest discover tests
+        - coverage combine
+      after_success:
+        - coveralls
+        - coverage xml
+        - python-codacy-coverage -r coverage.xml
       deploy:
         - provider: pypi
           user: pyiron

README.md

@@ -1,4 +1,5 @@
 # `PyLammpsMPI`
+[![Build Status](https://travis-ci.org/pyiron/pylammpsmpi.svg?branch=master)](https://travis-ci.org/pyiron/pylammpsmpi)
 
 ## Install with pip 
 

tests/test_pylammpsmpi_cluster.py

@@ -1,75 +1,85 @@
-import pytest
+# coding: utf-8
+# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+# Distributed under the terms of "New BSD License", see the LICENSE file.
+
+import unittest
 import os
 import numpy as np
 from pylammpsmpi import LammpsLibrary
 from dask.distributed import Client, LocalCluster
 
-cluster = LocalCluster(n_workers=1, threads_per_worker=2)
-client = Client(cluster)
-
-lmp = LammpsLibrary(cores=2, mode='dask', client=client)
-lmp.file("tests/in.simple")
-
-def test_extract_atom():
-
-    f = lmp.extract_atom("f")
-    assert len(f) == 256
-    assert np.round(f[0][0], 2) == -0.26
-
-    ids = lmp.extract_atom("id")
-    assert len(ids) == 256
-
-def test_gather_atoms():
-
-    f = lmp.gather_atoms("f")
-    assert len(f) == 256
-    #this checks if info was gathered from
-    #all processors
-    assert np.round(f[-22][0], 2) == 0.31
-
-    ids = lmp.extract_atom("id")
-    assert len(ids) == 256
-
-def test_extract_box():
-
-    box = lmp.extract_box()
-    assert len(box) == 7
-
-    assert box[0][0] == 0.0
-    assert np.round(box[1][0], 2) == 6.72
-
-    lmp.reset_box([0.0,0.0,0.0], [8.0,8.0,8.0], 0.0,0.0,0.0)
-    box = lmp.extract_box()
-    assert box[0][0] == 0.0
-    assert np.round(box[1][0], 2) == 8.0
-
-
-def test_extract_fix():
-
-    x = lmp.extract_fix("2", 0, 1, 1)
-    assert np.round(x, 2) == -2.61
-
-def test_extract_variable():
-
-    x = lmp.extract_variable("tt", "all", 0)
-    assert np.round(x, 2) == 1.13
-
-    x = lmp.extract_variable("fx", "all", 1)
-    assert len(x) == 128
-    assert np.round(x[0], 2) == -0.26
-
-def test_scatter_atoms():
 
-    f = lmp.gather_atoms("f")
-    val = np.random.randint(0, 100)
-    f[1][0] = val
-    lmp.scatter_atoms("f", f)
-    f1 = lmp.gather_atoms("f")
-    assert f1[1][0] == val
+class TestLocalLammpsLibrary(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        execution_path = os.path.dirname(os.path.abspath(__file__))
+        cluster = LocalCluster(n_workers=1, threads_per_worker=2)
+        client = Client(cluster)
+        cls.lmp = LammpsLibrary(cores=2, mode='dask', client=client)
+        cls.lmp.file(os.path.join(execution_path, "in.simple"))
+
+    @classmethod
+    def tearDownClass(cls):
+        cls.lmp.close()
+
+    def test_extract_atom(self):
+        f = self.lmp.extract_atom("f")
+        self.assertEqual(len(f), 256)
+        self.assertEqual(np.round(f[0][0], 2), -0.26)
+
+        ids = self.lmp.extract_atom("id")
+        self.assertEqual(len(ids), 256)
+
+    def test_gather_atoms(self):
+        f = self.lmp.gather_atoms("f")
+        self.assertEqual(len(f), 256)
+        # this checks if info was gathered from
+        # all processors
+        self.assertEqual(np.round(f[-22][0], 2), 0.31)
+
+        ids = self.lmp.extract_atom("id")
+        self.assertEqual(len(ids), 256)
+
+    def test_extract_box(self):
+        box = self.lmp.extract_box()
+        self.assertEqual(len(box), 7)
+
+        self.assertEqual(box[0][0], 0.0)
+        self.assertEqual(np.round(box[1][0], 2), 6.72)
+
+        self.lmp.reset_box([0.0,0.0,0.0], [8.0,8.0,8.0], 0.0,0.0,0.0)
+        box = self.lmp.extract_box()
+        self.assertEqual(box[0][0], 0.0)
+        self.assertEqual(np.round(box[1][0], 2), 8.0)
+
+    def test_extract_fix(self):
+        x = self.lmp.extract_fix("2", 0, 1, 1)
+        self.assertEqual(np.round(x, 2), -2.61)
+
+    def test_extract_variable(self):
+        x = self.lmp.extract_variable("tt", "all", 0)
+        self.assertEqual(np.round(x, 2), 1.13)
+
+        x = self.lmp.extract_variable("fx", "all", 1)
+        self.assertEqual(len(x), 128)
+        self.assertEqual(np.round(x[0], 2), -0.26)
+
+    def test_scatter_atoms(self):
+        f = self.lmp.gather_atoms("f")
+        val = np.random.randint(0, 100)
+        f[1][0] = val
+        self.lmp.scatter_atoms("f", f)
+        f1 = self.lmp.gather_atoms("f")
+        self.assertEqual(f1[1][0], val)
+
+        f = self.lmp.gather_atoms("f", ids=[1,2])
+        val = np.random.randint(0, 100)
+        f[1][1] = val
+        self.lmp.scatter_atoms("f", f, ids=[1,2])
+        f1 = self.lmp.gather_atoms("f", ids=[1,2])
+        self.assertEqual(f1[1][1], val)
+
+
+if __name__ == "__main__":
+    unittest.main()
 
-    f = lmp.gather_atoms("f", ids=[1,2])
-    val = np.random.randint(0, 100)
-    f[1][1] = val
-    lmp.scatter_atoms("f", f, ids=[1,2])
-    f1 = lmp.gather_atoms("f", ids=[1,2])
-    assert f1[1][1] == val

tests/test_pylammpsmpi_local.py

@@ -1,71 +1,82 @@
-import pytest
-import os
+# coding: utf-8
+# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+# Distributed under the terms of "New BSD License", see the LICENSE file.
+
+import unittest
 import numpy as np
+import os
 from pylammpsmpi import LammpsLibrary
 
-lmp = LammpsLibrary(cores=2, mode='local')
-lmp.file("tests/in.simple")
-
-def test_extract_atom():
-
-    f = lmp.extract_atom("f")
-    assert len(f) == 256
-    assert np.round(f[0][0], 2) == -0.26
 
-    ids = lmp.extract_atom("id")
-    assert len(ids) == 256
+class TestLocalLammpsLibrary(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        execution_path = os.path.dirname(os.path.abspath(__file__))
+        cls.lmp = LammpsLibrary(cores=2, mode='local')
+        cls.lmp.file(os.path.join(execution_path, "in.simple"))
 
-def test_gather_atoms():
+    @classmethod
+    def tearDownClass(cls):
+        cls.lmp.close()
 
-    f = lmp.gather_atoms("f")
-    assert len(f) == 256
-    #this checks if info was gathered from
-    #all processors
-    assert np.round(f[-22][0], 2) == 0.31
+    def test_extract_atom(self):
+        f = self.lmp.extract_atom("f")
+        self.assertEqual(len(f), 256)
+        self.assertEqual(np.round(f[0][0], 2), -0.26)
 
-    ids = lmp.extract_atom("id")
-    assert len(ids) == 256
+        ids = self.lmp.extract_atom("id")
+        self.assertEqual(len(ids), 256)
 
-def test_extract_box():
+    def test_gather_atoms(self):
+        f = self.lmp.gather_atoms("f")
+        self.assertEqual(len(f), 256)
+        # this checks if info was gathered from
+        # all processors
+        self.assertEqual(np.round(f[-22][0], 2), 0.31)
 
-    box = lmp.extract_box()
-    assert len(box) == 7
+        ids = self.lmp.extract_atom("id")
+        self.assertEqual(len(ids), 256)
 
-    assert box[0][0] == 0.0
-    assert np.round(box[1][0], 2) == 6.72
+    def test_extract_box(self):
 
-    lmp.reset_box([0.0,0.0,0.0], [8.0,8.0,8.0], 0.0,0.0,0.0)
-    box = lmp.extract_box()
-    assert box[0][0] == 0.0
-    assert np.round(box[1][0], 2) == 8.0
+        box = self.lmp.extract_box()
+        self.assertEqual(len(box), 7)
 
+        self.assertEqual(box[0][0], 0.0)
+        self.assertEqual(np.round(box[1][0], 2), 6.72)
 
-def test_extract_fix():
+        self.lmp.reset_box([0.0, 0.0, 0.0], [8.0, 8.0, 8.0], 0.0, 0.0, 0.0)
+        box = self.lmp.extract_box()
+        self.assertEqual(box[0][0], 0.0)
+        self.assertEqual(np.round(box[1][0], 2), 8.0)
 
-    x = lmp.extract_fix("2", 0, 1, 1)
-    assert np.round(x, 2) == -2.61
+    def test_extract_fix(self):
+        x = self.lmp.extract_fix("2", 0, 1, 1)
+        self.assertEqual(np.round(x, 2), -2.61)
 
-def test_extract_variable():
+    def test_extract_variable(self):
+        x = self.lmp.extract_variable("tt", "all", 0)
+        self.assertEqual(np.round(x, 2), 1.13)
+        x = self.lmp.extract_variable("fx", "all", 1)
+        self.assertEqual(len(x), 128)
+        self.assertEqual(np.round(x[0], 2), -0.26)
 
-    x = lmp.extract_variable("tt", "all", 0)
-    assert np.round(x, 2) == 1.13
+    def test_scatter_atoms(self):
 
-    x = lmp.extract_variable("fx", "all", 1)
-    assert len(x) == 128
-    assert np.round(x[0], 2) == -0.26
+        f = self.lmp.gather_atoms("f")
+        val = np.random.randint(0, 100)
+        f[1][0] = val
+        self.lmp.scatter_atoms("f", f)
+        f1 = self.lmp.gather_atoms("f")
+        self.assertEqual(f1[1][0], val)
 
-def test_scatter_atoms():
+        f = self.lmp.gather_atoms("f", ids=[1, 2])
+        val = np.random.randint(0, 100)
+        f[1][1] = val
+        self.lmp.scatter_atoms("f", f, ids=[1, 2])
+        f1 = self.lmp.gather_atoms("f", ids=[1, 2])
+        self.assertEqual(f1[1][1], val)
 
-    f = lmp.gather_atoms("f")
-    val = np.random.randint(0, 100)
-    f[1][0] = val
-    lmp.scatter_atoms("f", f)
-    f1 = lmp.gather_atoms("f")
-    assert f1[1][0] == val
 
-    f = lmp.gather_atoms("f", ids=[1,2])
-    val = np.random.randint(0, 100)
-    f[1][1] = val
-    lmp.scatter_atoms("f", f, ids=[1,2])
-    f1 = lmp.gather_atoms("f", ids=[1,2])
-    assert f1[1][1] == val
+if __name__ == "__main__":
+    unittest.main()