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Add DepWarnings to X3DNA code and docs #4333

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merged 5 commits into from
Nov 5, 2023
Merged

Add DepWarnings to X3DNA code and docs #4333

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ce38f07
add depwarnings to X3DNA
hmacdope Nov 5, 2023
dff31c1
3.0.0 -> 3.0
hmacdope Nov 5, 2023
d8c3842
Revert "3.0.0 -> 3.0"
hmacdope Nov 5, 2023
64b9a25
changelog
hmacdope Nov 5, 2023
a7615ce
use decorator
hmacdope Nov 5, 2023
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3 changes: 2 additions & 1 deletion package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ The rules for this file:

-------------------------------------------------------------------------------
??/??/?? IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith,
richardjgowers, lilyminium, ALescoulie
richardjgowers, lilyminium, ALescoulie, hmacdope

* 2.7.0

Expand Down Expand Up @@ -55,6 +55,7 @@ Changes
`analysis.nucleicacids.WatsonCrickDist.results.distances` (Issue #3720, PR #3735)

Deprecations
* X3DNA has been deprecated and will be removed in 3.0.0 (Issue #3788)
* coordinates.base.ConverterBase has been deprecated and will be removed in 3.0.0;
use converters.base.ConvertBase instead (Issue #3404)
* In `nucleicacids.WatsonCrickDist`, accepting lists of `Residue` objects was deprecated
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14 changes: 14 additions & 0 deletions package/MDAnalysis/analysis/legacy/x3dna.py
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Expand Up @@ -162,7 +162,10 @@ def mean_std_from_x3dnaPickle(profile):
stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt,
roll, twist]``.

.. deprecated:: 2.7.0
X3DNA will be removed in 3.0.0.
"""
warnings.warn("X3DNA module is deprecated and will be removed in MDAnalysis 3.0, see #3788", category=DeprecationWarning)
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we have a decorator for this - please see

mdanalysis/package/MDAnalysis/analysis/hole2/hole.py

Lines 50 to 52 in 5fa0d27

@deprecate(release="2.6.0", remove="3.0.0",
message=("This method has been moved to the MDAKit hole2-mdakit: "
"https://github.com/MDAnalysis/hole2-mdakit"))
for an example

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ah ta.

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RE: 1 if the code is not usable and we are removing it i don't really want to invest any energy in finding out why / how. Is it okay just to put the warnings in as is? Let me know wither way.

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@hmacdope - my point here is "what's the point in putting in a warning if it won't even work locally". If you can get the warnings locally then it's fine, otherwise I'd just add in the docstring changes and call it a day.

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@hmacdope hmacdope Nov 5, 2023 •
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@IAlibay Okay you can get the warnings on before whatever is broken, at least it may warn the (possibly 0) people that have a niche setup that this works for this that it will be removed.

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Thanks for testing this locally, that's probably good enough.

if profile.x3dna_param is False:
bp_shear, bp_stretch, bp_stagger, bp_rise, bp_shift, bp_slide, bp_buckle, bp_prop, bp_open, bp_tilt, bp_roll,\
bp_twist = [], [], [], [], [], [], [], [], [], [], [], []
Expand Down Expand Up @@ -247,6 +250,9 @@ class BaseX3DNA(object):

for each nucleic acid pair.

.. deprecated:: 2.7.0
X3DNA will be removed in 3.0.0.

.. _X3DNA: http://x3dna.org

"""
Expand Down Expand Up @@ -472,6 +478,9 @@ class X3DNA(BaseX3DNA):

.. versionadded:: 0.8

.. deprecated:: 2.7.0
X3DNA will be removed in 3.0.0.

.. _`X3DNA docs`: http://forum.x3dna.org/
"""

Expand Down Expand Up @@ -504,6 +513,7 @@ def __init__(self, filename, **kwargs):
--------
:class:`X3DNAtraj`
"""
warnings.warn("X3DNA module is deprecated and will be removed in MDAnalysis 3.0, see #3788", category=DeprecationWarning)
# list of temporary files, to be cleaned up on __del__
self.tempfiles = [
"auxiliary.par", "bestpairs.pdb", "bp_order.dat", "bp_helical.par", "cf_7methods.par",
Expand Down Expand Up @@ -717,6 +727,9 @@ class X3DNAtraj(BaseX3DNA):
universe and feed it to X3DNA. By default it sequentially creates a PDB for
each frame and runs X3DNA on the frame.


.. deprecated:: 2.7.0
X3DNA will be removed in 3.0.0.
"""

def __init__(self, universe, **kwargs):
Expand Down Expand Up @@ -753,6 +766,7 @@ def __init__(self, universe, **kwargs):
:class:`X3DNA`

"""
warnings.warn("X3DNA module is deprecated and will be removed in MDAnalysis 3.0, see #3788")
self.universe = universe
self.selection = kwargs.pop("selection", "nucleic")

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