Removed some use of deprecated methods #825
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| coordinates = deprecate(coordinates, | ||
| message="{}; use `positions` property instead".format(_SIXTEEN_DEPRECATION)) | ||
| .. deprecated:: 0.7.6 | ||
| In new scripts use :meth:`AtomGroup.get_positions` preferrably. |
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Perhaps change this note, or add a new deprecation note.
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@richardjgowers looks like you honestly broke the tests. |
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Oops! I've been conferencing but I'll get on it, the warnings are annoying. On Sat, 16 Apr 2016 19:41 kain88-de, [email protected] wrote:
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@richardjgowers do you know how to filter the output of the test for deprecation messages? |
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@kain88-de not sure what you mean, I didn't really have a sophisticated approach here. Might be fixed now |
| @@ -69,13 +69,13 @@ | |||
| The same is mostly true for :class:`Residue` instances although they are | |||
| derived from :class:`Atom` instances: all :class:`Atom` objects with the same | |||
| :attr:`Atom.resid` are bundled into a single :class:`Residue` with | |||
| :class:`Residue.id` = *resid*. This means that just changing, say, the residue | |||
| :class:`Residue.resid` = *resid*. This means that just changing, say, the residue | |||
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Thanks for doing these. I completely forgot to check all the docs for old usage patterns.
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Looks good to me. @kain88-de want to give it a glance before we merge, since I'm a bit too close for completely clear eyes? |
Should remove a lot of dep warnings that come up from within the code WRT positions/velocities/forces