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Removed old "version added" directives (#13)
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ianmkenney committed Oct 17, 2023
1 parent 0b4ee8e commit 5eda30e
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -19,7 +19,7 @@ The rules for this file:
## [Unreleased]

### Authors
<!-- GitHub usernames of contributors to this release -->
- ianmkenney

### Added
<!-- New added features -->
Expand All @@ -35,3 +35,4 @@ The rules for this file:

### Removed
<!-- Removed features -->

44 changes: 0 additions & 44 deletions waterdynamics/waterdynamics.py
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Expand Up @@ -24,10 +24,6 @@
"""Water dynamics analysis --- :mod:`waterdynamics.waterdynamics`
=======================================================================
:Author: Alejandro Bernardin
:Year: 2014-2015
:Copyright: GNU Public License v3
This module provides functions to analyze water dynamics trajectories and water
interactions with other molecules. The functions in this module are: water
orientational relaxation (WOR) :footcite:p:`Yeh1999`, hydrogen bond lifetimes (HBL)
Expand Down Expand Up @@ -396,12 +392,6 @@ class WaterOrientationalRelaxation(object):
frame where analysis ends
dtmax : int
Maximum dt size, `dtmax` < `tf` or it will crash.
.. versionadded:: 0.11.0
.. versionchanged:: 1.0.0
Changed `selection` keyword to `select`
"""

def __init__(self, universe, select, t0, tf, dtmax, nproc=1):
Expand Down Expand Up @@ -498,7 +488,6 @@ def _getMeanOnePoint(self, universe, selection1, selection_str, dt,
"""
This function gets one point of the plot C_vec vs t. It uses the
_getOneDeltaPoint() function to calculate the average.
"""
repInd = self._repeatedIndex(selection1, dt, totalFrames)
sumsdt = 0
Expand Down Expand Up @@ -588,12 +577,6 @@ class AngularDistribution(object):
axis : {'x', 'y', 'z'} (optional)
Axis to create angle with the vector (HH, OH or dipole) and calculate
cosine theta ['z'].
.. versionadded:: 0.11.0
.. versionchanged:: 1.0.0
Changed `selection` keyword to `select`
"""

def __init__(self, universe, select, bins=40, nproc=1, axis="z"):
Expand Down Expand Up @@ -742,12 +725,6 @@ class MeanSquareDisplacement(object):
frame where analysis ends
dtmax : int
Maximum dt size, `dtmax` < `tf` or it will crash.
.. versionadded:: 0.11.0
.. versionchanged:: 1.0.0
Changed `selection` keyword to `select`
"""

def __init__(self, universe, select, t0, tf, dtmax, nproc=1):
Expand Down Expand Up @@ -814,7 +791,6 @@ def _getMeanOnePoint(self, universe, selection1, selection_str, dt,
"""
This function gets one point of the plot C_vec vs t. It's uses the
_getOneDeltaPoint() function to calculate the average.
"""
repInd = self._repeatedIndex(selection1, dt, totalFrames)
sumsdt = 0
Expand Down Expand Up @@ -907,21 +883,6 @@ class SurvivalProbability(object):
to the `stop` keyword passed to :meth:`SurvivalProbability.run`. Unlike
other :mod:`waterdynamics` final frame definitions
which are `inclusive`.
.. versionadded:: 0.11.0
.. versionchanged:: 1.0.0
Using the MDAnalysis.lib.correlations.py to carry out the intermittency
and autocorrelation calculations.
Changed `selection` keyword to `select`.
Removed support for the deprecated `t0`, `tf`, and `dtmax` keywords.
These should instead be passed to :meth:`SurvivalProbability.run` as
the `start`, `stop`, and `tau_max` keywords respectively.
The `stop` keyword as passed to :meth:`SurvivalProbability.run` has now
changed behaviour and will act in an `exclusive` manner (instead of it's
previous `inclusive` behaviour),
.. versionchanged:: 2.7.0
Updated docs to align with discrete autocorrelation function.
"""

def __init__(self, universe, select, verbose=False):
Expand Down Expand Up @@ -977,11 +938,6 @@ def run(self, tau_max=20, start=None, stop=None, step=None, residues=False,
sp_timeseries_data: list
raw datapoints from which the average is taken (sp_timeseries).
Time dependancy and distribution can be extracted.
.. versionchanged:: 1.0.0
To math other analysis methods, the `stop` keyword is now exclusive
rather than inclusive.
"""

start, stop, step = self.universe.trajectory.check_slice_indices(
Expand Down

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