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Kushagar gargKushagar garg
Kushagar garg
authored and
Kushagar garg
committed
STYLE: Apply black formatting
1 parent df196ee commit e1ee51d

1 file changed

Lines changed: 55 additions & 24 deletions

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  • testsuite/MDAnalysisTests/coordinates

‎testsuite/MDAnalysisTests/coordinates/base.py‎

Lines changed: 55 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -131,7 +131,7 @@ def test_distances(self):
131131
assert_allclose(
132132
d,
133133
self.ref_distances["endtoend"],
134-
atol=10**(-self.prec),
134+
atol=10 ** (-self.prec),
135135
rtol=0,
136136
err_msg="distance between M1:N and G214:C",
137137
)
@@ -322,21 +322,26 @@ def test_get_writer_2(self, ref, reader, tmpdir):
322322
assert_equal(W.n_atoms, 100)
323323

324324
def test_dt(self, ref, reader):
325-
assert_allclose(reader.dt, ref.dt, atol=10**(-ref.prec), rtol=0)
325+
assert_allclose(reader.dt, ref.dt, atol=10 ** (-ref.prec), rtol=0)
326326

327327
def test_ts_dt_matches_reader(self, reader):
328328
assert_equal(reader.ts.dt, reader.dt)
329329

330330
def test_total_time(self, ref, reader):
331-
assert_allclose(reader.totaltime, ref.totaltime, atol=10**(-ref.prec), rtol=0)
331+
assert_allclose(
332+
reader.totaltime, ref.totaltime, atol=10 ** (-ref.prec), rtol=0
333+
)
332334

333335
def test_first_dimensions(self, ref, reader):
334336
reader.rewind()
335337
if ref.dimensions is None:
336338
assert reader.ts.dimensions is None
337339
else:
338340
assert_allclose(
339-
reader.ts.dimensions, ref.dimensions, atol=10**(-ref.prec), rtol=0
341+
reader.ts.dimensions,
342+
ref.dimensions,
343+
atol=10 ** (-ref.prec),
344+
rtol=0,
340345
)
341346

342347
def test_changing_dimensions(self, ref, reader):
@@ -346,7 +351,10 @@ def test_changing_dimensions(self, ref, reader):
346351
assert reader.ts.dimensions is None
347352
else:
348353
assert_allclose(
349-
reader.ts.dimensions, ref.dimensions, atol=10**(-ref.prec), rtol=0
354+
reader.ts.dimensions,
355+
ref.dimensions,
356+
atol=10 ** (-ref.prec),
357+
rtol=0,
350358
)
351359
reader[1]
352360
if ref.dimensions_second_frame is None:
@@ -355,8 +363,8 @@ def test_changing_dimensions(self, ref, reader):
355363
assert_allclose(
356364
reader.ts.dimensions,
357365
ref.dimensions_second_frame,
358-
atol=10**(-ref.prec),
359-
rtol=0
366+
atol=10 ** (-ref.prec),
367+
rtol=0,
360368
)
361369

362370
def test_volume(self, ref, reader):
@@ -392,7 +400,7 @@ def test_iter_auxiliary(self, ref, reader):
392400
auxstep.data,
393401
ref.aux_highf_all_data[i],
394402
atol=1e-7,
395-
rtol = 0,
403+
rtol=0,
396404
err_msg="Auxiliary data does not match for "
397405
"step {}".format(i),
398406
)
@@ -457,7 +465,7 @@ def test_transformations_iter(self, ref, transformed):
457465
for i, ts in enumerate(transformed):
458466
idealcoords = ref.iter_ts(i).positions + v1 + v2
459467
assert_allclose(
460-
ts.positions, idealcoords, atol=10**(-ref.prec), rtol=0
468+
ts.positions, idealcoords, atol=10 ** (-ref.prec), rtol=0
461469
)
462470

463471
def test_transformations_2iter(self, ref, transformed):
@@ -469,11 +477,13 @@ def test_transformations_2iter(self, ref, transformed):
469477
for i, ts in enumerate(transformed):
470478
idealcoords.append(ref.iter_ts(i).positions + v1 + v2)
471479
assert_allclose(
472-
ts.positions, idealcoords[i], atol=10**(-ref.prec), rtol=0
480+
ts.positions, idealcoords[i], atol=10 ** (-ref.prec), rtol=0
473481
)
474482

475483
for i, ts in enumerate(transformed):
476-
assert_allclose(ts.positions, idealcoords[i], atol=10**(-ref.prec), rtol=0)
484+
assert_allclose(
485+
ts.positions, idealcoords[i], atol=10 ** (-ref.prec), rtol=0
486+
)
477487

478488
def test_transformations_slice(self, ref, transformed):
479489
# Are the transformations applied when iterating over a slice of the trajectory?
@@ -482,7 +492,7 @@ def test_transformations_slice(self, ref, transformed):
482492
for i, ts in enumerate(transformed[2:3:1]):
483493
idealcoords = ref.iter_ts(ts.frame).positions + v1 + v2
484494
assert_allclose(
485-
ts.positions, idealcoords, atol=10**(-ref.prec), rtol=0
495+
ts.positions, idealcoords, atol=10 ** (-ref.prec), rtol=0
486496
)
487497

488498
def test_transformations_switch_frame(self, ref, transformed):
@@ -494,25 +504,40 @@ def test_transformations_switch_frame(self, ref, transformed):
494504
first_ideal = ref.iter_ts(0).positions + v1 + v2
495505
if len(transformed) > 1:
496506
assert_allclose(
497-
transformed[0].positions, first_ideal, atol=10**(-ref.prec), rtol=0
507+
transformed[0].positions,
508+
first_ideal,
509+
atol=10 ** (-ref.prec),
510+
rtol=0,
498511
)
499512
second_ideal = ref.iter_ts(1).positions + v1 + v2
500513
assert_allclose(
501-
transformed[1].positions, second_ideal, atol=10**(-ref.prec), rtol=0
514+
transformed[1].positions,
515+
second_ideal,
516+
atol=10 ** (-ref.prec),
517+
rtol=0,
502518
)
503519

504520
# What if we comeback to the previous frame?
505521
assert_allclose(
506-
transformed[0].positions, first_ideal, atol=10**(-ref.prec), rtol=0
522+
transformed[0].positions,
523+
first_ideal,
524+
atol=10 ** (-ref.prec),
525+
rtol=0,
507526
)
508527

509528
# How about we switch the frame to itself?
510529
assert_allclose(
511-
transformed[0].positions, first_ideal, atol=10**(-ref.prec), rtol=0
530+
transformed[0].positions,
531+
first_ideal,
532+
atol=10 ** (-ref.prec),
533+
rtol=0,
512534
)
513535
else:
514536
assert_allclose(
515-
transformed[0].positions, first_ideal, atol=10**(-ref.prec), rtol=0
537+
transformed[0].positions,
538+
first_ideal,
539+
atol=10 ** (-ref.prec),
540+
rtol=0,
516541
)
517542

518543
def test_transformation_rewind(self, ref, transformed):
@@ -523,7 +548,10 @@ def test_transformation_rewind(self, ref, transformed):
523548
ideal_coords = ref.iter_ts(0).positions + v1 + v2
524549
transformed.rewind()
525550
assert_allclose(
526-
transformed[0].positions, ideal_coords, atol=10**(-ref.prec), rtol=0
551+
transformed[0].positions,
552+
ideal_coords,
553+
atol=10 ** (-ref.prec),
554+
rtol=0,
527555
)
528556

529557
def test_transformations_copy(self, ref, transformed):
@@ -540,7 +568,7 @@ def test_transformations_copy(self, ref, transformed):
540568
for i, ts in enumerate(new):
541569
ideal_coords = ref.iter_ts(i).positions + v1 + v2
542570
assert_allclose(
543-
ts.positions, ideal_coords, atol=10**(-ref.prec), rtol=0
571+
ts.positions, ideal_coords, atol=10 ** (-ref.prec), rtol=0
544572
)
545573

546574
def test_add_another_transformations_raises_ValueError(self, transformed):
@@ -816,7 +844,10 @@ def test_write_different_box(self, ref, universe, tmpdir):
816844
for ts_ref, ts_w in zip(universe.trajectory, written):
817845
universe.dimensions[:3] += 1
818846
assert_allclose(
819-
universe.dimensions, ts_w.dimensions, atol=10**(-ref.prec), rtol = 0
847+
universe.dimensions,
848+
ts_w.dimensions,
849+
atol=10 ** (-ref.prec),
850+
rtol=0,
820851
)
821852

822853
def test_write_trajectory_atomgroup(self, ref, reader, universe, tmpdir):
@@ -859,7 +890,7 @@ def test_write_selection(
859890
assert_allclose(
860891
copy_ts._pos,
861892
sel.atoms.positions,
862-
atol=10**(-ref.prec),
893+
atol=10 ** (-ref.prec),
863894
rtol=0,
864895
err_msg="coordinate mismatch between original and written "
865896
"trajectory at frame {} (orig) vs {} (copy)".format(
@@ -940,7 +971,7 @@ def assert_timestep_almost_equal(A, B, decimal=6, verbose=True):
940971
assert_allclose(
941972
A.positions,
942973
B.positions,
943-
atol=10**(-decimal),
974+
atol=10 ** (-decimal),
944975
rtol=0,
945976
err_msg="Timestep positions",
946977
verbose=verbose,
@@ -957,7 +988,7 @@ def assert_timestep_almost_equal(A, B, decimal=6, verbose=True):
957988
assert_allclose(
958989
A.velocities,
959990
B.velocities,
960-
atol=10**(-decimal),
991+
atol=10 ** (-decimal),
961992
rtol=0,
962993
err_msg="Timestep velocities",
963994
verbose=verbose,
@@ -974,7 +1005,7 @@ def assert_timestep_almost_equal(A, B, decimal=6, verbose=True):
9741005
assert_allclose(
9751006
A.forces,
9761007
B.forces,
977-
atol=10**(-decimal),
1008+
atol=10 ** (-decimal),
9781009
rtol=0,
9791010
err_msg="Timestep forces",
9801011
verbose=verbose,

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