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Test new python versions #880

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merged 23 commits into from
Oct 28, 2021
Merged

Test new python versions #880

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f5a40ef
test new python versions
mikemhenry Oct 21, 2021
bb8a1ee
need python 3.10 not 3.1
mikemhenry Oct 21, 2021
8b30e50
make matrix easier to understand
mikemhenry Oct 25, 2021
fb1eade
fix yaml
mikemhenry Oct 25, 2021
4c5186b
fix matrix var issue
mikemhenry Oct 25, 2021
018ba9e
hardcode os
mikemhenry Oct 25, 2021
04f9be3
don't need OS in yaml
mikemhenry Oct 25, 2021
a0a2789
fixing yaml syntax
mikemhenry Oct 25, 2021
45e15de
Merge branch 'master' into feat/test_new_python_versions
mikemhenry Oct 25, 2021
58b01cb
see if setting these versions will fix the issues
mikemhenry Oct 25, 2021
7d7b9e5
now lets see which package fixed this
mikemhenry Oct 25, 2021
641f3a3
I think this is it
mikemhenry Oct 25, 2021
8f14631
not sure if this will work, bash scripting is not my strenght
mikemhenry Oct 25, 2021
9aab034
install nightly build correctly this time
mikemhenry Oct 25, 2021
8c92cf1
make sure to install even if it exits in env
mikemhenry Oct 25, 2021
df4693a
dropping python 3.10 testing
mikemhenry Oct 25, 2021
dbcb41c
lets see if conda will install the dev version
mikemhenry Oct 26, 2021
da6a676
lets see if this gets us the right openmm nightly
mikemhenry Oct 26, 2021
c4444ec
remove pin to test test fix
mikemhenry Oct 26, 2021
b03bd8f
fix tests to check across pcb
mikemhenry Oct 27, 2021
a25628f
fix silly name error
mikemhenry Oct 27, 2021
318d493
mistake in logic for error checking
mikemhenry Oct 27, 2021
92c1648
force installing from omnia
mikemhenry Oct 27, 2021
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5 changes: 4 additions & 1 deletion perses/tests/test_coordinate_numba.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,10 @@ def test_openmm_dihedral():
msg += '_internal_to_cartesian generated positions for: {}\n'.format(phi)
msg += 'OpenMM: {}\n'.format(openmm_phi)
msg += 'positions: {}'.format(positions)
assert np.linalg.norm(openmm_phi - phi) < TORSION_TOLERANCE, msg

delta = abs(openmm_phi - phi)
error = min(delta, 2*np.pi - delta)
assert error < TORSION_TOLERANCE, msg
Comment on lines +105 to +108
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If these changes work, we should include some kind of Fixes #879 in the PR, I suppose.


# Check that _cartesian_to_internal agrees
rtp, detJ = geometry_engine._cartesian_to_internal(xyz_atom1, bond_position, angle_position, torsion_position)
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6 changes: 5 additions & 1 deletion perses/tests/test_geometry_engine.py
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Expand Up @@ -609,7 +609,11 @@ def test_torsion_scan():
for i, phi in enumerate(phis):
xyz_ge = xyzs[i]
r_new, theta_new, phi_new = _get_internal_from_omm(xyz_ge, testsystem.positions[1], testsystem.positions[2], testsystem.positions[3])
if np.abs(phi_new - phi) > TOLERANCE:

delta = abs(phi_new - phi)
error = min(delta, 2*np.pi-delta)

if error < TORSION_TOLERANCE:
raise Exception("Torsion scan did not match OpenMM torsion")
if np.abs(r_new - r) > TOLERANCE or np.abs(theta_new - theta) > TOLERANCE:
raise Exception("Theta or r was disturbed in torsion scan.")
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