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histogramdd normed argument replaced by density #3976

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merged 7 commits into from
Dec 23, 2022
Merged

histogramdd normed argument replaced by density #3976

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histogramdd normed argument replaced by density
IAlibay Dec 20, 2022
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more normed->density changes
IAlibay Dec 20, 2022
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add changelog entry
IAlibay Dec 20, 2022
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Bugfix entry
IAlibay Dec 21, 2022
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changelog typo
IAlibay Dec 23, 2022
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pin numpy for 32bit in azure pipelines
IAlibay Dec 23, 2022
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ne not not
IAlibay Dec 23, 2022
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2 changes: 2 additions & 0 deletions package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,8 @@ The rules for this file:
* 2.5.0

Fixes
* np.histogramdd calls in :class:`DensityAnalysis` now pass the `density`
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@MDAnalysis/coredevs please look at discord for this one - in my opinion we probably should do a 2.4.2 release since this has effectively killed the DensityAnalysis code. However, how we do bugfix releases really should be discussed.

TLDR; I'm pushing for us to be able to do bugfixes from a separate feature branch than develop. That way PRs can keep rolling into develop without breaking semver if we need to do a bugfix release.

argument rather than the numpy 1.24 removed `density` (PR #3976)

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6 changes: 3 additions & 3 deletions package/MDAnalysis/analysis/density.py
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Expand Up @@ -463,7 +463,7 @@ def _prepare(self):
bins = BINS['Nbins']
# create empty grid with the right dimensions (and get the edges)
grid, edges = np.histogramdd(np.zeros((1, 3)), bins=bins,
range=arange, normed=False)
range=arange, density=False)
grid *= 0.0
self._grid = grid
self._edges = edges
Expand All @@ -473,7 +473,7 @@ def _prepare(self):
def _single_frame(self):
h, _ = np.histogramdd(self._atomgroup.positions,
bins=self._bins, range=self._arange,
normed=False)
density=False)
# reduce (proposed change #2542 to match the parallel version in pmda.density)
# return self._reduce(self._grid, h)
#
Expand Down Expand Up @@ -644,7 +644,7 @@ class Density(Grid):

If the input histogram consists of counts per cell then the
:meth:`Density.make_density` method converts the grid to a physical density. For
a probability density, divide it by :meth:`Density.grid.sum` or use ``normed=True``
a probability density, divide it by :meth:`Density.grid.sum` or use ``density=True``
right away in :func:`~numpy.histogramdd`.

The user *should* set the *parameters* keyword (see docs for the
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