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Unpin parmed w/ numpy v2 #4883

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Unpin parmed w/ numpy v2 #4883

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6dfa3d6
Update ParmEd.py
IAlibay Jan 7, 2025
9a614d5
Update test_parmed.py
IAlibay Jan 7, 2025
c2202f7
Update util.py
IAlibay Jan 7, 2025
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21 changes: 6 additions & 15 deletions package/MDAnalysis/converters/ParmEd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,6 @@

from ..guesser.tables import SYMB2Z
import numpy as np
from numpy.lib import NumpyVersion

from . import base
from ..coordinates.base import SingleFrameReaderBase
Expand Down Expand Up @@ -171,21 +170,13 @@
obj : AtomGroup or Universe or :class:`Timestep`
"""
try:
# TODO: remove this guard when parmed has a release
# that supports NumPy 2
if NumpyVersion(np.__version__) < "2.0.0":
import parmed as pmd
else:
raise ImportError
import parmed as pmd
except ImportError:
if NumpyVersion(np.__version__) >= "2.0.0":
ermsg = "ParmEd is not compatible with NumPy 2.0+"
else:
ermsg = (
"ParmEd is required for ParmEdConverter but is not "
"installed. Try installing it with \n"
"pip install parmed"
)
ermsg = (

Check warning on line 175 in package/MDAnalysis/converters/ParmEd.py

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package/MDAnalysis/converters/ParmEd.py#L175 

Added line #L175 was not covered by tests
"ParmEd is required for ParmEdConverter but is not "
"installed. Try installing it with \n"
"pip install parmed"
)
raise ImportError(errmsg)
try:
# make sure to use atoms (Issue 46)
Expand Down
10 changes: 2 additions & 8 deletions testsuite/MDAnalysisTests/converters/test_parmed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,9 +23,7 @@
import pytest
import MDAnalysis as mda

import numpy as np
from numpy.testing import assert_allclose, assert_equal
from numpy.lib import NumpyVersion

from MDAnalysisTests.coordinates.base import _SingleFrameReader
from MDAnalysisTests.coordinates.reference import RefAdKSmall
Expand All @@ -43,12 +41,8 @@
PRM_UreyBradley,
)

# TODO: remove this guard when parmed has a release
# that support NumPy 2
if NumpyVersion(np.__version__) < "2.0.0":
pmd = pytest.importorskip("parmed")
else:
pmd = pytest.importorskip("parmed_skip_with_numpy2")

pmd = pytest.importorskip("parmed")


class TestParmEdReaderGRO:
Expand Down
7 changes: 0 additions & 7 deletions testsuite/MDAnalysisTests/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,6 @@
import pytest

from numpy.testing import assert_warns
import numpy as np
from numpy.lib import NumpyVersion


def block_import(package):
Expand Down Expand Up @@ -114,11 +112,6 @@ def import_not_available(module_name):
msg="skip test as module_name could not be imported")

"""
# TODO: remove once these packages have a release
# with NumPy 2 support
if NumpyVersion(np.__version__) >= "2.0.0":
if module_name == "parmed":
return True
try:
test = importlib.import_module(module_name)
except ImportError:
Expand Down
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