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Deprecate hole2 class in favour of MDAKit #4200

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Jul 16, 2023
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Deprecate hole2 class in favour of MDAKit #4200

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e1da8fb
Deprecated hole2 class
IAlibay Jul 16, 2023
fee090d
update changelog
IAlibay Jul 16, 2023
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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 @@ -38,6 +38,8 @@ Changes
(PR #4174, Issue #3819)

Deprecations
* The hole2 module is deprecated in favour of the the MDAKit:
https://github.com/MDAnalysis/hole2-mdakit (Issue #4179, PR #4200)
* MDAnalysis no longer officially supports 32 bit installations (they are
no longer tested in our continuous integration pipelines). Note: whilst
no code changes have been made to disable 32 bit, although it is known that
Expand Down
15 changes: 15 additions & 0 deletions package/MDAnalysis/analysis/hole2/hole.py
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Expand Up @@ -33,6 +33,7 @@
import matplotlib.pyplot as plt
from collections import OrderedDict

from MDAnalysis.lib.util import deprecate
from ...exceptions import ApplicationError
from ..base import AnalysisBase
from ...lib import util
Expand All @@ -46,6 +47,9 @@
logger = logging.getLogger(__name__)


@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"))
def hole(pdbfile,
infile_text=None,
infile=None,
Expand Down Expand Up @@ -429,6 +433,11 @@
are now stored in a :class:`MDAnalysis.analysis.base.Results`
instance.

.. deprecated:: 2.6.0
This class has been moved to the MDAKit
`hole2-mdakit <https://github.com/MDAnalysis/hole2-mdakit>`_ and will
be removed for the core MDAnalysis library in version 3.0

"""

input_file = '{prefix}hole{i:03d}.inp'
Expand Down Expand Up @@ -478,6 +487,12 @@
write_input_files=False):
super(HoleAnalysis, self).__init__(universe.universe.trajectory,
verbose=verbose)

wmsg = ("This class has been moved to the MDAKit `hole2-mdakit` "

Check warning on line 491 in package/MDAnalysis/analysis/hole2/hole.py

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package/MDAnalysis/analysis/hole2/hole.py#L491 

Added line #L491 was not covered by tests
"(https://github.com/MDAnalysis/hole2-mdakit) and will be "
"removed in version 3.0.")
warnings.warn(wmsg, DeprecationWarning)

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Added line #L494 was not covered by tests

if output_level > 3:
msg = 'output_level ({}) needs to be < 3 in order to extract a HOLE profile!'
warnings.warn(msg.format(output_level))
Expand Down
49 changes: 34 additions & 15 deletions testsuite/MDAnalysisTests/analysis/test_hole2.py
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Expand Up @@ -110,8 +110,9 @@ class TestHole(object):

def test_correct_input(self, tmpdir):
with tmpdir.as_cwd():
hole2.hole(self.filename, random_seed=self.random_seed,
infile='hole.inp')
with pytest.warns(DeprecationWarning, match="to the MDAKit"):
hole2.hole(self.filename, random_seed=self.random_seed,
infile='hole.inp')

infile = str(tmpdir.join('hole.inp'))
with open(infile, 'r') as f:
Expand All @@ -135,9 +136,10 @@ def test_input_options(self, tmpdir):
cog = u.select_atoms('protein').center_of_geometry()

with tmpdir.as_cwd():
hole2.hole(self.filename, random_seed=self.random_seed,
infile='hole.inp', cpoint=cog,
ignore_residues=[])
with pytest.warns(DeprecationWarning, match="to the MDAKit"):
hole2.hole(self.filename, random_seed=self.random_seed,
infile='hole.inp', cpoint=cog,
ignore_residues=[])

infile = str(tmpdir.join('hole.inp'))
with open(infile, 'r') as f:
Expand All @@ -159,7 +161,9 @@ def test_input_options(self, tmpdir):

def test_correct_profile_values(self, tmpdir):
with tmpdir.as_cwd():
profiles = hole2.hole(self.filename, random_seed=self.random_seed)
with pytest.warns(DeprecationWarning, match="to the MDAKit"):
profiles = hole2.hole(self.filename,
random_seed=self.random_seed)

values = list(profiles.values())
assert_equal(len(values), 1,
Expand Down Expand Up @@ -195,11 +199,13 @@ def test_correct_profile_values(self, tmpdir):

# assert_equal(len(profiles), int(keep_frames/step))

@pytest.mark.filterwarnings("ignore: `hole` is deprecated")
def test_application_error(self, tmpdir):
with tmpdir.as_cwd():
with pytest.raises(ApplicationError):
hole2.hole(self.filename, dcd=DCD)

@pytest.mark.filterwarnings("ignore: `hole` is deprecated")
def test_output_level(self, tmpdir):
with tmpdir.as_cwd():
with pytest.warns(UserWarning, match="needs to be < 3"):
Expand All @@ -210,9 +216,10 @@ def test_output_level(self, tmpdir):

def test_keep_files(self, tmpdir):
with tmpdir.as_cwd():
hole2.hole(self.filename, random_seed=self.random_seed,
infile='hole.inp',
keep_files=False)
with pytest.warns(DeprecationWarning, match="to the MDAKit"):
hole2.hole(self.filename, random_seed=self.random_seed,
infile='hole.inp',
keep_files=False)
sphpdbs = tmpdir.join('*.sph')
assert len(glob.glob(str(sphpdbs))) == 0
outfiles = tmpdir.join('*.out')
Expand Down Expand Up @@ -243,7 +250,8 @@ def universe(self):
@pytest.fixture()
def hole(self, universe, tmpdir):
with tmpdir.as_cwd():
h = hole2.HoleAnalysis(universe)
with pytest.warns(DeprecationWarning, match='This class has been'):
h = hole2.HoleAnalysis(universe)
h.run(start=self.start, stop=self.stop,
random_seed=self.random_seed)
return h
Expand Down Expand Up @@ -274,21 +282,25 @@ class TestOSError:
def universe(self):
return mda.Universe(MULTIPDB_HOLE)

@pytest.mark.filterwarnings("ignore: `hole` is deprecated")
def test_hole_method_oserror(self):
errmsg = exe_err.format(name='dummy_path', kw='executable')
with pytest.raises(OSError, match=errmsg):
h = hole2.hole(PDB_HOLE, executable='dummy_path')

@pytest.mark.filterwarnings("ignore: This class has been moved")
def test_hole_oserror(self, universe):
errmsg = exe_err.format(name='dummy_path', kw='executable')
with pytest.raises(OSError, match=errmsg):
h = hole2.HoleAnalysis(universe, executable='dummy_path')

@pytest.mark.filterwarnings("ignore: This class has been moved")
def test_sos_triangle_oserror(self, universe):
errmsg = exe_err.format(name='dummy_path', kw='sos_triangle')
with pytest.raises(OSError, match=errmsg):
h = hole2.HoleAnalysis(universe, sos_triangle='dummy_path')

@pytest.mark.filterwarnings("ignore: This class has been moved")
def test_sph_process_oserror(self, universe):
errmsg = exe_err.format(name='dummy_path', kw='sph_process')
with pytest.raises(OSError, match=errmsg):
Expand Down Expand Up @@ -316,6 +328,7 @@ def test_min_radius(self, hole):
assert_almost_equal(hole.min_radius(), values,
err_msg="min_radius() array not correct")

@pytest.mark.filterwarnings("ignore: This class has been moved")
def test_context_manager(self, universe, tmpdir):
with tmpdir.as_cwd():
with hole2.HoleAnalysis(universe) as h:
Expand All @@ -336,14 +349,16 @@ def test_context_manager(self, universe, tmpdir):
vmd_file = tmpdir.join('hole.vmd')
assert len(glob.glob(str(vmd_file))) == 1

@pytest.mark.filterwarnings("ignore: This class has been moved")
@pytest.mark.parametrize("start,stop,step", [
(1, 9, 2), (1, None, 3), (5, -2, None)])
def test_nonzero_start_surface(self, universe, tmpdir,
start, stop, step,
surface="hole.vmd"):
# Issue 3476
with tmpdir.as_cwd():
h = hole2.HoleAnalysis(universe)
with pytest.warns(DeprecationWarning, match='This class has been'):
h = hole2.HoleAnalysis(universe)
h.run(start=start, stop=stop, step=step)
h.create_vmd_surface(filename=surface)

Expand All @@ -358,6 +373,7 @@ def test_nonzero_start_surface(self, universe, tmpdir,
np.arange(len(universe.trajectory[start:stop:step])),
err_msg="wrong frame indices in VMD surface file")

@pytest.mark.filterwarnings("ignore: This class has been moved")
def test_output_level(self, tmpdir, universe):
with tmpdir.as_cwd():
with pytest.warns(UserWarning, match='needs to be < 3'):
Expand All @@ -373,10 +389,11 @@ def test_cpoint_geometry(self, tmpdir, universe):
protein = universe.select_atoms('protein')
cogs = [protein.center_of_geometry() for ts in universe.trajectory]
with tmpdir.as_cwd():
h = hole2.HoleAnalysis(universe,
select='protein',
cpoint='center_of_geometry',
write_input_files=True)
with pytest.warns(DeprecationWarning, match='This class has been'):
h = hole2.HoleAnalysis(universe,
select='protein',
cpoint='center_of_geometry',
write_input_files=True)
h.run(start=self.start,
stop=self.stop, random_seed=self.random_seed)

Expand Down Expand Up @@ -469,6 +486,7 @@ def test_plot3D_rmax(self, hole, frames, profiles):
assert_almost_equal(z, radius)
assert line.get_label() == str(frame)

@pytest.mark.filterwarnings("ignore: This class has been moved")
def test_none_filename(self, tmpdir):
universe_none_filename = mda.Universe(PDB_HOLE, in_memory=True)
universe_none_filename.trajectory.filename = None
Expand Down Expand Up @@ -722,6 +740,7 @@ def universe():

@pytest.mark.skipif(rlimits_missing,
reason="Test skipped because platform does not allow setting rlimits")
@pytest.mark.filterwarnings("ignore: This class has been moved")
def test_hole_module_fd_closure(self, universe, tmpdir):
"""test open file descriptors are closed (MDAnalysisTests.analysis.test_hole.TestHoleModule): Issue 129"""
# If Issue 129 isn't resolved, this function will produce an OSError on
Expand Down
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