Limit numpy thread usage for Transformation classes

.travis.yml

@@ -30,7 +30,7 @@ env:
     - SETUP_CMD="${PYTEST_FLAGS}"
     - BUILD_CMD="pip install -e package/ && (cd testsuite/ && python setup.py build)"
     - CONDA_MIN_DEPENDENCIES="mmtf-python biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
-    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py"
+    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py threadpoolctl"
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - PIP_DEPENDENCIES="duecredit parmed"

package/MDAnalysis/lib/util.py

@@ -202,6 +202,8 @@
 import functools
 from functools import wraps
 import textwrap
+from contextlib import ContextDecorator
+from threadpoolctl import threadpool_limits
 
 import mmtf
 import numpy as np
@@ -2353,3 +2355,11 @@ def check_box(box):
     if np.all(box[3:] == 90.):
         return 'ortho', box[:3]
     return 'tri_vecs', triclinic_vectors(box)
+
+
+class threadpool_limits_decorator(threadpool_limits, ContextDecorator):
+    def __enter__(self):
+        return self
+
+    def __exit__(self, *exc):
+        return False

package/MDAnalysis/transformations/fit.py

@@ -36,6 +36,7 @@
 
 from ..analysis import align
 from ..lib.transformations import euler_from_matrix, euler_matrix
+from ..lib.util import threadpool_limits_decorator
 
 
 class fit_translation(object):
@@ -207,6 +208,7 @@ def __init__(self, ag, reference, plane=None, weights=None):
         self.ref_com = self.ref.center(self.weights)
         self.ref_coordinates = self.ref.atoms.positions - self.ref_com
 
+    @threadpool_limits_decorator(limits=1)
     def __call__(self, ts):
         mobile_com = self.mobile.atoms.center(self.weights)
         mobile_coordinates = self.mobile.atoms.positions - mobile_com

package/MDAnalysis/transformations/rotate.py

@@ -36,6 +36,7 @@
 
 from ..lib.transformations import rotation_matrix
 from ..lib.util import get_weights
+from ..lib.util import threadpool_limits_decorator
 
 
 class rotateby(object):
@@ -162,6 +163,7 @@ def __init__(self,
         else:
             raise ValueError('A point or an AtomGroup must be specified')
 
+    @threadpool_limits_decorator(limits=1)
     def __call__(self, ts):
         if self.point is None:
             position = self.center_method()