Implements gso tests for #53, fixed bug in cloning Coordinates and La…

…ndscapePosition

lightdock/gso/coordinates.py

@@ -15,7 +15,7 @@ class Coordinates(object):
     dimensions of the solution space used in the objective function."""
 
     def __init__(self, values):
-        self._values = values
+        self._values = values.copy()
         self.dimension = len(self._values)
 
     def __getitem__(self, index):
@@ -42,7 +42,7 @@ def __ne__(self, other):
 
     def clone(self):
         """Get a copy of the current coordinate"""
-        return Coordinates(self._values * 1)
+        return Coordinates(self._values)
 
     def __add__(self, other):
         """Adds two coordinates"""

lightdock/gso/parameters.py

@@ -13,9 +13,9 @@ def __init__(self, file_name=None):
         self._config = ConfigParser()
         try:
             if file_name:
-                self._config.readfp(open(file_name))
+                self._config.read_file(open(file_name))
             else:
-                self._config.readfp(
+                self._config.read_file(
                     open(Path(os.environ["LIGHTDOCK_CONF_PATH"]) / "glowworm.conf")
                 )
         except Exception as e:

lightdock/gso/searchspace/landscape.py

@@ -21,7 +21,7 @@ class LandscapePosition(object):
 
     def __init__(self, objective_function, coordinates, step=DEFAULT_STEP_SIZE):
         self.objective_function = objective_function
-        self.coordinates = coordinates
+        self.coordinates = coordinates.clone()
         self.step = step
 
     def evaluate_objective_function(self):
@@ -42,7 +42,7 @@ def __ne__(self, other):
     def clone(self):
         """Creates a copy of this landscape position"""
         return LandscapePosition(
-            self.objective_function, self.coordinates.clone(), self.step
+            self.objective_function, self.coordinates, self.step
         )
 
     def __add__(self, other):

lightdock/test/gso/searchspace/test_docking_landscape.py

@@ -1,10 +1,8 @@
 """Tests for DockingLandscapePosition class"""
 
-import os
-from pathlib import Path
-import shutil
-from nose.tools import assert_almost_equal
+import pytest
 import numpy as np
+from pathlib import Path
 from lightdock.gso.searchspace.landscape import DockingLandscapePosition
 from lightdock.gso.coordinates import Coordinates
 from lightdock.scoring.mj3h.driver import MJ3h, MJ3hAdapter
@@ -15,28 +13,14 @@
 
 
 class TestDockingLandscapePosition:
-    def __init__(self):
+    def setup_class(self):
         self.path = Path(__file__).absolute().parent
-        self.test_path = self.path / "scratch_docking_landscape"
         self.golden_data_path = self.path / "golden_data"
         atoms, _, chains = parse_complex_from_file(
             self.golden_data_path / "1PPErec.pdb"
         )
         self.receptor = Complex(chains, atoms)
 
-    def setup(self):
-        try:
-            shutil.rmtree(self.test_path)
-        except OSError:
-            pass
-        os.mkdir(self.test_path)
-
-    def teardown(self):
-        try:
-            shutil.rmtree(self.test_path)
-        except OSError:
-            pass
-
     def test_clone(self):
         atoms, _, chains = parse_complex_from_file(
             self.golden_data_path / "1PPElig.pdb"
@@ -59,8 +43,8 @@ def test_clone(self):
 
         landscape_position_2.translation[0] = 5.0
 
-        assert_almost_equal(5.0, landscape_position_2.translation[0])
-        assert_almost_equal(0.0, landscape_position_1.translation[0])
+        assert 5.0 == pytest.approx(landscape_position_2.translation[0])
+        assert 0.0 == pytest.approx(landscape_position_1.translation[0])
 
     def test_repr(self):
         atoms, _, chains = parse_complex_from_file(
@@ -91,7 +75,7 @@ def test_evaluate_objective_function_no_movement(self):
             scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model
         )
 
-        assert_almost_equal(2.02, landscape_position.evaluate_objective_function())
+        assert 2.02 == pytest.approx(landscape_position.evaluate_objective_function())
 
     def test_evaluate_objective_function_rotation_y_axis_180(self):
         atoms, _, chains = parse_complex_from_file(
@@ -105,7 +89,7 @@ def test_evaluate_objective_function_rotation_y_axis_180(self):
             scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model
         )
 
-        assert_almost_equal(-1.4, landscape_position.evaluate_objective_function())
+        assert -1.4 == pytest.approx(landscape_position.evaluate_objective_function())
 
     def test_evaluate_objective_function_rotation_y_axis_180_translation_10(self):
         atoms, _, chains = parse_complex_from_file(
@@ -119,7 +103,7 @@ def test_evaluate_objective_function_rotation_y_axis_180_translation_10(self):
             scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model
         )
 
-        assert_almost_equal(6.39, landscape_position.evaluate_objective_function())
+        assert 6.39 == pytest.approx(landscape_position.evaluate_objective_function())
 
     def test_distance2_same_landscape_position(self):
         atoms, _, chains = parse_complex_from_file(
@@ -135,7 +119,7 @@ def test_distance2_same_landscape_position(self):
         landscape_position2 = DockingLandscapePosition(
             scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model
         )
-        assert_almost_equal(0.0, landscape_position1.distance2(landscape_position2))
+        assert 0.0 == pytest.approx(landscape_position1.distance2(landscape_position2))
 
     def test_distance2_10A_translation_x(self):
         atoms, _, chains = parse_complex_from_file(
@@ -156,8 +140,8 @@ def test_distance2_10A_translation_x(self):
             adapter2.receptor_model,
             adapter2.ligand_model,
         )
-        assert_almost_equal(100.0, landscape_position1.distance2(landscape_position2))
-        assert_almost_equal(10.0, landscape_position1.distance(landscape_position2))
+        assert 100.0 == pytest.approx(landscape_position1.distance2(landscape_position2))
+        assert 10.0 == pytest.approx(landscape_position1.distance(landscape_position2))
 
     def test_distance2_minus_10A_translation_y(self):
         atoms, _, chains = parse_complex_from_file(
@@ -178,8 +162,8 @@ def test_distance2_minus_10A_translation_y(self):
             adapter2.receptor_model,
             adapter2.ligand_model,
         )
-        assert_almost_equal(100.0, landscape_position1.distance2(landscape_position2))
-        assert_almost_equal(10.0, landscape_position1.distance(landscape_position2))
+        assert 100.0 == pytest.approx(landscape_position1.distance2(landscape_position2))
+        assert 10.0 == pytest.approx(landscape_position1.distance(landscape_position2))
 
     def test_move_step_rot_full_step_trans_half(self):
         atoms, _, chains = parse_complex_from_file(

lightdock/test/gso/searchspace/test_j1.py

@@ -1,12 +1,12 @@
 """Tests for J1 function"""
 
+import pytest
 from lightdock.gso.searchspace.benchmark_ofunctions import J1
 from lightdock.gso.coordinates import Coordinates
-from nose.tools import assert_almost_equals
 
 
 class TestJ1:
-    def __init__(self):
+    def setup_class(self):
         self.expected_values = [
             [
                 6.671280296717448e-05,
@@ -49,7 +49,4 @@ def test_compute_J1_matrix(self):
         j1 = J1()
         for i in range(5):
             for j in range(5):
-                assert_almost_equals(
-                    self.expected_values[i][j],
-                    j1(Coordinates([-3.0 + j * 1.5, -3.0 + i * 1.5])),
-                )
+                assert self.expected_values[i][j] == pytest.approx(j1(Coordinates([-3.0 + j * 1.5, -3.0 + i * 1.5])))

lightdock/test/gso/searchspace/test_j2.py

@@ -1,12 +1,12 @@
 """Tests for J2 function"""
 
+import pytest
 from lightdock.gso.searchspace.benchmark_ofunctions import J2
 from lightdock.gso.coordinates import Coordinates
-from nose.tools import assert_almost_equals
 
 
 class TestJ2:
-    def __init__(self):
+    def setup_class(self):
         self.expected_values = [
             [50, 51.25, 25, 51.25, 50],
             [51.25, 52.5, 26.25, 52.5, 51.25],
@@ -19,7 +19,4 @@ def test_compute_J1_matrix(self):
         j2 = J2()
         for i in range(5):
             for j in range(5):
-                assert_almost_equals(
-                    self.expected_values[i][j],
-                    j2(Coordinates([-5.0 + j * 2.5, -5.0 + i * 2.5])),
-                )
+                assert self.expected_values[i][j] == pytest.approx(j2(Coordinates([-5.0 + j * 2.5, -5.0 + i * 2.5])))

lightdock/test/gso/searchspace/test_j3.py

@@ -1,12 +1,12 @@
 """Tests for J3 function"""
 
+import pytest
 from lightdock.gso.searchspace.benchmark_ofunctions import J3
 from lightdock.gso.coordinates import Coordinates
-from nose.tools import assert_almost_equals
 
 
 class TestJ3:
-    def __init__(self):
+    def setup_class(self):
         self.expected_values = [
             [
                 3.80536808724531,
@@ -49,7 +49,4 @@ def test_compute_J1_matrix(self):
         j3 = J3()
         for i in range(5):
             for j in range(5):
-                assert_almost_equals(
-                    self.expected_values[i][j],
-                    j3(Coordinates([-10.0 + j * 5.0, -10.0 + i * 5.0])),
-                )
+                assert self.expected_values[i][j] == pytest.approx(j3(Coordinates([-10.0 + j * 5.0, -10.0 + i * 5.0])))

lightdock/test/gso/searchspace/test_j4.py

@@ -1,12 +1,12 @@
 """Tests for J4 function"""
 
+import pytest
 from lightdock.gso.searchspace.benchmark_ofunctions import J4
 from lightdock.gso.coordinates import Coordinates
-from nose.tools import assert_almost_equals
 
 
 class TestJ4:
-    def __init__(self):
+    def setup_class(self):
         self.expected_values = [
             [29, 28, 27, 26, 25, 25],
             [28, 27, 26, 25, 24, 24],
@@ -20,7 +20,4 @@ def test_compute_J1_matrix(self):
         j4 = J4()
         for i in range(6):
             for j in range(6):
-                assert_almost_equals(
-                    self.expected_values[i][j],
-                    j4(Coordinates([-2.0 + j * 0.8, -2.0 + i * 0.8])),
-                )
+                assert self.expected_values[i][j] == pytest.approx(j4(Coordinates([-2.0 + j * 0.8, -2.0 + i * 0.8])))

lightdock/test/gso/searchspace/test_j5.py

@@ -1,12 +1,12 @@
 """Tests for J5 function"""
 
-from nose.tools import assert_equals
+import pytest
 from lightdock.gso.searchspace.benchmark_ofunctions import J5
 from lightdock.gso.coordinates import Coordinates
 
 
 class TestJ5:
-    def __init__(self):
+    def setup_class(self):
         self.expected_values = [
             [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
             [1, 1, 1, -1, -1, 1, 1, 1, 1, 1, -1, -1, 1, 1, 1],
@@ -29,7 +29,4 @@ def test_compute_J1_matrix(self):
         j5 = J5()
         for i in range(15):
             for j in range(15):
-                assert_equals(
-                    self.expected_values[i][j],
-                    j5(Coordinates([-6.24 + j * 0.89143, -6.24 + i * 0.89143])),
-                )
+                assert self.expected_values[i][j] == pytest.approx(j5(Coordinates([-6.24 + j * 0.89143, -6.24 + i * 0.89143])))

lightdock/test/gso/searchspace/test_landscape.py

@@ -1,14 +1,14 @@
 """Tests for LandscapePosition class"""
 
+import pytest
 from math import sqrt
 from lightdock.gso.coordinates import Coordinates
 from lightdock.gso.searchspace.landscape import LandscapePosition
 from lightdock.gso.searchspace.benchmark_ofunctions import J1
-from nose.tools import assert_almost_equals
 
 
 class TestLandscapePosition:
-    def __init__(self):
+    def setup_class(self):
         self.objective_function = J1()
         self.coordinates1 = Coordinates([0.0, 0.0])
         self.coordinates2 = Coordinates([1.0, 1.0])
@@ -19,9 +19,7 @@ def __init__(self):
     def test_LandscapePosition_with_J1(self):
         landscape_point = LandscapePosition(self.objective_function, self.coordinates1)
 
-        assert_almost_equals(
-            0.9810118431238463, landscape_point.evaluate_objective_function()
-        )
+        assert 0.9810118431238463 == pytest.approx(landscape_point.evaluate_objective_function())
 
     def test_LandscapePosition_with_J1_matrix(self):
         expected_values = [
@@ -66,9 +64,7 @@ def test_LandscapePosition_with_J1_matrix(self):
             for j in range(5):
                 coord = Coordinates([-3.0 + i * 1.5, -3.0 + j * 1.5])
                 landscape_point = LandscapePosition(self.objective_function, coord)
-                assert_almost_equals(
-                    expected_values[j][i], landscape_point.evaluate_objective_function()
-                )
+                assert expected_values[j][i] == pytest.approx(landscape_point.evaluate_objective_function())
 
     def test_equals(self):
         landscape_point1 = LandscapePosition(self.objective_function, self.coordinates1)
@@ -150,18 +146,18 @@ def test_distance_J1(self):
         landscape_point1 = LandscapePosition(self.objective_function, self.coordinates2)
         landscape_point2 = LandscapePosition(self.objective_function, self.coordinates1)
 
-        assert_almost_equals(sqrt(2.0), landscape_point1.distance(landscape_point2))
+        assert sqrt(2.0) == pytest.approx(landscape_point1.distance(landscape_point2))
 
     def test_distance2_J1(self):
         landscape_point1 = LandscapePosition(self.objective_function, self.coordinates2)
         landscape_point2 = LandscapePosition(self.objective_function, self.coordinates1)
 
-        assert_almost_equals(2.0, landscape_point1.distance2(landscape_point2))
+        assert 2.0 == pytest.approx(landscape_point1.distance2(landscape_point2))
 
     def test_norm(self):
         landscape_point1 = LandscapePosition(self.objective_function, self.coordinates2)
 
-        assert_almost_equals(sqrt(2.0), landscape_point1.norm())
+        assert sqrt(2.0) == pytest.approx(landscape_point1.norm())
 
     def test_move_using_default_step(self):
         landscape_point1 = LandscapePosition(self.objective_function, self.coordinates1)

lightdock/test/gso/searchspace/test_ofunction.py

@@ -1,11 +1,11 @@
 """Tests for ObjectiveFunction interface"""
 
+import pytest
 from lightdock.gso.searchspace.ofunction import ObjectiveFunction
-from nose.tools import raises
 
 
 class TestObjectiveFunction:
-    @raises(NotImplementedError)
     def test_call(self):
-        function = ObjectiveFunction()
-        function(coordinates=[])
+        with pytest.raises(NotImplementedError):
+            function = ObjectiveFunction()
+            function(coordinates=[])

lightdock/test/gso/test_boundaries.py

@@ -5,7 +5,7 @@
 
 
 class TestBoundingBox:
-    def __init__(self):
+    def setup_class(self):
         self.dimension1 = Boundary(0, 1)
         self.dimension2 = Boundary(0, 5)