I was trying to practice Episode 07 - Python Testing And when I reached the build_bond_list test, invoking the command pytest -v and it throws an Exception:
(molssi_best_practices) radifar->mymolpy$ pytest -v
====================================================== test session starts ======================================================
platform linux -- Python 3.7.7, pytest-5.4.3, py-1.8.2, pluggy-0.13.1 -- /home/radifar/anaconda3/envs/molssi_best_practices/bin/python
cachedir: .pytest_cache
rootdir: /media/radifar/radifar-dsl/Python/molssi-best-practice/mymolpy
plugins: cov-2.10.0
collected 4 items
mymolpy/tests/test_measure.py::test_calculate_distance PASSED [ 25%]
mymolpy/tests/test_measure.py::test_calculate_angle PASSED [ 50%]
mymolpy/tests/test_molecule.py::test_build_bond_list FAILED [ 75%]
mymolpy/tests/test_mymolpy.py::test_mymolpy_imported PASSED [100%]
=========================================================== FAILURES ============================================================
_____________________________________________________ test_build_bond_list ______________________________________________________
def test_build_bond_list():
coordinates = np.array([
[1, 1, 1],
[2.4, 1, 1],
[-0.4, 1, 1],
[1, 1, 2.4],
[1, 1, -0.4]
])
> bonds = mymolpy.build_bond_list(coordinates)
mymolpy/tests/test_molecule.py:18:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
mymolpy/molecule.py:15: in build_bond_list
distance = calculate_distance(coordinates[atom1], coordinates[atom2])
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
rA = array([1., 1., 1.]), rB = array([1., 1., 1.])
def calculate_distance(rA, rB):
"""Calculate the distance between two points.
Parameters
----------
rA, rB : np.ndarray
The coordinates of each point.
Returns
-------
distance : float
The distance between the two points.
Examples
--------
>>> r1 = np.array([0, 0, 0])
>>> r2 = np.array([0, 0.1, 0])
>>> calculate_distance(r1, r2)
0.1
"""
if isinstance(rA, np.ndarray) is False or isinstance(rB, np.ndarray) is False:
raise TypeError("rA and rB must be numpy arrays")
dist_vec = (rA - rB)
distance = np.linalg.norm(dist_vec)
if distance == 0.0:
> raise Exception("Two atoms are located in the same point in space")
E Exception: Two atoms are located in the same point in space
mymolpy/measure.py:35: Exception
==================================================== short test summary info ====================================================
FAILED mymolpy/tests/test_molecule.py::test_build_bond_list - Exception: Two atoms are located in the same point in space
================================================== 1 failed, 3 passed in 0.46s ==================================================Btw, my package name is mymolpy instead of molecool, and here is my mymolpy/tests/test_molecule.py
"""
Unit and regression test for the molecule module
"""
import mymolpy
import numpy as np
def test_build_bond_list():
coordinates = np.array([
[1, 1, 1],
[2.4, 1, 1],
[-0.4, 1, 1],
[1, 1, 2.4],
[1, 1, -0.4]
])
bonds = mymolpy.build_bond_list(coordinates)
assert len(bonds) == 4
for bond_length in bonds.values():
assert bond_length == 1.4Here is my mymolpy/molecule.py
"""
Miscelaneous function related to molecule
"""
from .measure import calculate_distance
def build_bond_list(coordinates, max_bond=1.5, min_bond=0):
# Find the bonds in a molecule (set of coordinates) based on distance criteria.
bonds = {}
num_atoms = len(coordinates)
for atom1 in range(num_atoms):
for atom2 in range(atom1, num_atoms):
distance = calculate_distance(coordinates[atom1], coordinates[atom2])
if distance > min_bond and distance < max_bond:
bonds[(atom1, atom2)] = distance
return bondsAnd then I tried to debug mymolpy/molecule.py as follows (Notice that I'm adding +1 after atom1 in the inner for loop):
"""
Miscelaneous function related to molecule
"""
from .measure import calculate_distance
def build_bond_list(coordinates, max_bond=1.5, min_bond=0):
# Find the bonds in a molecule (set of coordinates) based on distance criteria.
bonds = {}
num_atoms = len(coordinates)
for atom1 in range(num_atoms):
for atom2 in range(atom1+1, num_atoms):
distance = calculate_distance(coordinates[atom1], coordinates[atom2])
if distance > min_bond and distance < max_bond:
bonds[(atom1, atom2)] = distance
return bondsAnd the test run perfectly!
(molssi_best_practices) radifar->mymolpy$ pytest -v
====================================================== test session starts ======================================================
platform linux -- Python 3.7.7, pytest-5.4.3, py-1.8.2, pluggy-0.13.1 -- /home/radifar/anaconda3/envs/molssi_best_practices/bin/python
cachedir: .pytest_cache
rootdir: /media/radifar/radifar-dsl/Python/molssi-best-practice/mymolpy
plugins: cov-2.10.0
collected 4 items
mymolpy/tests/test_measure.py::test_calculate_distance PASSED [ 25%]
mymolpy/tests/test_measure.py::test_calculate_angle PASSED [ 50%]
mymolpy/tests/test_molecule.py::test_build_bond_list PASSED [ 75%]
mymolpy/tests/test_mymolpy.py::test_mymolpy_imported PASSED [100%]
======================================================= 4 passed in 0.36s =======================================================
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