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test core_fast added [Issue #28] #30

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test core_fast added [Issue #28] #30

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3 changes: 1 addition & 2 deletions membrane_curvature/lib/mods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,8 +75,7 @@ def dict2pickle(name, dict_):
pickle.dump(dict_, pk, protocol=pickle.HIGHEST_PROTOCOL)


def core_fast(traj, jump, n_cells, leaflets, lipid_types, lipid_ref,
box_size, max_width, prefix):
def core_fast(traj, jump, n_cells, leaflets, lipid_types, lipid_ref, max_width, prefix):
"""
Runs core_fast_leaflet for each leaflet

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34 changes: 16 additions & 18 deletions membrane_curvature/tests/test_mdakit_membcurv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,9 @@

import pytest
import sys
import math
import os
import mdtraj as md # This will be gone after refactoring
import itertools as it
from ..lib.mods import core_fast_leaflet, curvature, mean_curvature, gaussian_curvature, dict2pickle
from ..lib.mods import core_fast_leaflet, curvature, mean_curvature, gaussian_curvature, dict2pickle, core_fast
import numpy as np
from numpy.testing import assert_almost_equal
import MDAnalysis as mda
Expand Down Expand Up @@ -188,27 +186,13 @@ def md_ref_beads():
return md_ref_beads


def test_membrane_curvature_imported():
"""Sample test, will always pass so long as import statement worked"""
assert "membrane_curvature" in sys.modules


def test_dict_to_pickle(tmpdir):
name = 'test_pickle_output'
dict_ = {'A': 1, 'B': 2, 'C': 3}
with tmpdir.as_cwd():
dict2pickle(name, dict_)
unpickled = pickle.load(open(name + '.pickle', 'rb'))
assert dict_ == unpickled


def test_gaussian_curvature():
K_test = gaussian_curvature(MEMBRANE_CURVATURE_DATA['z_ref'])
for k, k_test in zip(MEMBRANE_CURVATURE_DATA['gaussian_curvature'], K_test):
assert_almost_equal(k, k_test)


def test_mean_curvature():
def test_mean_curvature():
H_test = mean_curvature(MEMBRANE_CURVATURE_DATA['z_ref'])
for h, h_test in zip(MEMBRANE_CURVATURE_DATA['mean_curvature'], H_test):
assert_almost_equal(h, h_test)
Expand All @@ -224,6 +208,17 @@ def test_core_fast_leaflet(md_ref_beads, mdtraj_po4):
assert_almost_equal(z, z_test)


def test_core_fast(md_ref_beads, mdtraj_po4):
jump = 1
n_cells = 10
max_width = 19
z_calc = np.zeros([n_cells, n_cells])
core_fast_leaflet(z_calc, "upper", mdtraj_po4, jump, n_cells, ["POPC"], md_ref_beads, max_width)
core_fast(mdtraj_po4, jump, n_cells, ["upper"], ["POPC"], md_ref_beads, max_width, 'test')
for z, z_test in zip(MEMBRANE_CURVATURE_DATA['z_avg_coords'], z_calc):
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In unit testing we typically try to validate a single function in at least one test. Could you add tests where you check the functionality of core_fast and core_fast_leaflet separately in addition to this one?

assert_almost_equal(z, z_test)


def test_curvature(md_ref_beads, mdtraj_po4):
jump = 1
n_cells = 10
Expand All @@ -239,3 +234,6 @@ def test_curvature(md_ref_beads, mdtraj_po4):

for k, k_test in zip(MEMBRANE_CURVATURE_DATA['gaussian_from_z_avg'][lf], K_test[lf]):
assert_almost_equal(k, k_test)