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[Review Needed]Pytest Style core/test_atomgroup.py #1635

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merged 3 commits into from Sep 5, 2017

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@utkbansal utkbansal commented Aug 20, 2017

Fixes #

Changes made in this Pull Request:

PR Checklist

  • Tests?
  • Docs?
  • CHANGELOG updated?
  • Issue raised/referenced?
@richardjgowers richardjgowers self-assigned this Aug 21, 2017
def test_getitem_str(self):
ag1 = self.universe.atoms['HT1']
dih_prec = 2
# def setUp(self):

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ag.wrap(compound='fragments')

cen = np.vstack([f.center_of_mass() for f in ag.fragments])

assert_equal(self._in_box(cen), True)
assert_equal(self._in_box(cen, u), True)

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@richardjgowers

richardjgowers Aug 21, 2017
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just use assert

ag.wrap(compound='segments')

cen = np.vstack([s.atoms.center_of_mass() for s in ag.segments])

assert_equal(self._in_box(cen), True)
assert_equal(self._in_box(cen, u), True)

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ag.wrap(compound='residues')

cen = np.vstack([r.atoms.center_of_mass() for r in ag.residues])

assert_equal(self._in_box(cen), True)
assert_equal(self._in_box(cen, u), True)

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ag.wrap(compound='group')

cen = ag.center_of_mass()

assert_equal(self._in_box(cen), True)
assert_equal(self._in_box(cen, u), True)

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ag.wrap(compound='atoms')

assert_equal(self._in_box(ag.positions), True)
assert_equal(self._in_box(ag.positions, u), True)

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assert_almost_equal,
assert_equal,
assert_array_almost_equal,
assert_array_equal,

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@richardjgowers

richardjgowers Aug 25, 2017
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we're not using assert_array_equal

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@utkbansal

utkbansal Aug 26, 2017
Author Member

@richardjgowers The dtype causes a mismatch in this case. How do I work around it?

E           AssertionError: 
E           Arrays are not almost equal to 7 decimals
E           
E           (mismatch 33.3333333333%)
E            x: array([ 2.6028271, -1.1962211,  0.       ], dtype=float32)
E            y: array([ 2.6028272, -1.1962211,  0.       ])

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@kain88-de

kain88-de Aug 27, 2017
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which test causes the dtype issue?

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@utkbansal

utkbansal Sep 1, 2017
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@richardjgowers @kain88-de In class TestAtomGroup

    def test_index_slice_empty(self, universe):
        u = universe
        assert_equal(u.atoms[0:0], [],
                           "making an empty AtomGroup failed")
@kain88-de kain88-de force-pushed the utkbansal:core-atom-grp branch from 1f11bc5 to 2a6a8c1 Sep 4, 2017
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@kain88-de kain88-de commented Sep 4, 2017

@richardjgowers can you have a look at the recent commit to remove assert_array_*. Thanks.

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@richardjgowers richardjgowers commented Sep 5, 2017

@kain88-de lgtm if it passes

@kain88-de kain88-de merged commit b138532 into MDAnalysis:develop Sep 5, 2017
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3 participants