replaced lib.transformations with transformations package

.github/actions/setup-deps/action.yaml

@@ -45,6 +45,8 @@ inputs:
     default: 'pytest'
   scipy:
     default: 'scipy'
+  transformations:
+    default: 'transformations'
   threadpoolctl:
     default: 'threadpoolctl'
   tqdm:

azure-pipelines.yml

@@ -88,6 +88,7 @@ jobs:
       pytest-timeout
       pytest-xdist
       scikit-learn
+      transformations
       tqdm
       threadpoolctl
       filelock

maintainer/conda/environment.yml

@@ -25,6 +25,7 @@ dependencies:
   - scipy
   - pip
   - sphinx <7.0
+  - transformations
   - tidynamics>=1.0.0
   - tqdm>=4.43.0
   - sphinxcontrib-bibtex

package/CHANGELOG

@@ -58,11 +58,15 @@ Enhancements
    MDAnalysisTest.util (PR #5038)
 
 Changes
+ * Replaced old vendored lib.transformations with import of the
+   transformations package (#5061)
  * Removed undocumented and unused attribute
    `analysis.lineardensity.LinearDensity.totalmass` (PR #5007)
  * Remove `default` channel from RTD conda env. (Issue # 5036, PR # 5037)   
 
 Deprecations
+* lib.transformations.rotaxis() moved to lib.mdamath.rotaxis()
+* lib.transformations to be removed in 3.0.0
 
 
 03/11/25 IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy,

package/MDAnalysis/analysis/base.py

@@ -122,7 +122,7 @@ class MyAnalysis(AnalysisBase):
         def get_supported_backends(cls):
             return ('serial', 'multiprocessing', 'dask',)
 
-        
+
         def _get_aggregator(self):
           return ResultsGroup(lookup={'timeseries': ResultsGroup.ndarray_vstack})
 
@@ -352,7 +352,7 @@ def _define_run_frames(
         Returns
         -------
         Union[slice, np.ndarray]
-            Appropriate slicer for the trajectory that would give correct iteraction
+            Appropriate slicer for the trajectory that would give correct iteration
             order via trajectory[slicer]
 
         Raises

package/MDAnalysis/core/groups.py

@@ -99,6 +99,8 @@
 import contextlib
 import warnings
 
+import transformations
+
 from .. import (
     _CONVERTERS,
     _TOPOLOGY_ATTRS,
@@ -114,7 +116,6 @@
     int_array_is_sorted,
 )
 from ..lib import distances
-from ..lib import transformations
 from ..lib import mdamath
 from .accessors import Accessor, ConverterWrapper
 from ..selections import get_writer as get_selection_writer_for
@@ -1518,7 +1519,7 @@ def transform(self, M):
 
         See Also
         --------
-        MDAnalysis.lib.transformations : module of all coordinate transforms
+        :mod:`transformations` : module of all coordinate transforms
 
         Notes
         -----
@@ -1551,7 +1552,7 @@ def translate(self, t):
 
         See Also
         --------
-        MDAnalysis.lib.transformations : module of all coordinate transforms
+        :mod:`transformations` : module of all coordinate transforms
 
         Notes
         -----
@@ -1601,7 +1602,7 @@ def rotate(self, R, point=(0, 0, 0)):
         See Also
         --------
         rotateby : rotate around given axis and angle
-        MDAnalysis.lib.transformations : module of all coordinate transforms
+        :mod:`transformations` : module of all coordinate transforms
 
         """
         R = np.asarray(R)
@@ -1651,7 +1652,7 @@ def rotateby(self, angle, axis, point=None):
 
         See Also
         --------
-        MDAnalysis.lib.transformations.rotation_matrix :
+        :mod:`transformations.rotation_matrix` :
             calculate :math:`\mathsf{R}`
 
         """

package/MDAnalysis/core/topologyattrs.py

@@ -66,7 +66,7 @@
     unique_int_1d,
     check_atomgroup_not_empty,
 )
-from ..lib import transformations, mdamath
+from ..lib import mdamath
 from ..exceptions import NoDataError, SelectionError
 from .topologyobjects import TopologyGroup
 from . import selection
@@ -2120,7 +2120,7 @@ def align_principal_axis(group, axis, vector):
         """
         p = group.principal_axes()[axis]
         angle = np.degrees(mdamath.angle(p, vector))
-        ax = transformations.rotaxis(p, vector)
+        ax = mdamath.rotaxis(p, vector)
         # print "principal[%d] = %r" % (axis, p)
         # print "axis = %r, angle = %f deg" % (ax, angle)
         return group.rotateby(angle, ax)
@@ -2290,7 +2290,7 @@ def dipole_vector(
         r"""Dipole vector of the group.
 
         .. math::
-            \boldsymbol{\mu} = \sum_{i=1}^{N} q_{i} ( \mathbf{r}_{i} - 
+            \boldsymbol{\mu} = \sum_{i=1}^{N} q_{i} ( \mathbf{r}_{i} -
             \mathbf{r}_{COM} )
 
         Computes the dipole vector of :class:`Atoms<Atom>` in the group.
@@ -2303,10 +2303,10 @@ def dipole_vector(
         a charged group the dipole moment can be later adjusted  with:
 
         .. math::
-            \boldsymbol{\mu}_{COC} = \boldsymbol{\mu}_{COM} + 
+            \boldsymbol{\mu}_{COC} = \boldsymbol{\mu}_{COM} +
             q_{ag}\mathbf{r}_{COM} - q_{ag}\boldsymbol{r}_{COC}
 
-        Where :math:`\mathbf{r}_{COM}` is the center of mass and 
+        Where :math:`\mathbf{r}_{COM}` is the center of mass and
         :math:`\mathbf{r}_{COC}` is the center of charge.
 
         Parameters
@@ -2330,7 +2330,7 @@ def dipole_vector(
             :class:`Atoms<Atom>` *belonging to the group* will be taken into
             account.
         center : {'mass', 'charge'}, optional
-            Choose whether the dipole vector is calculated at the center of 
+            Choose whether the dipole vector is calculated at the center of
             "mass" or the center of "charge", default is "mass".
 
         Returns
@@ -2421,8 +2421,8 @@ def dipole_moment(group, **kwargs):
         fragment can be obtained by setting the `compound` parameter
         accordingly.
 
-        Note that when there is a net charge, the magnitude of the dipole 
-        moment is dependent on the `center` chosen. 
+        Note that when there is a net charge, the magnitude of the dipole
+        moment is dependent on the `center` chosen.
         See :meth:`~dipole_vector`.
 
         Parameters
@@ -2446,7 +2446,7 @@ def dipole_moment(group, **kwargs):
             :class:`Atoms<Atom>` *belonging to the group* will be taken into
             account.
         center : {'mass', 'charge'}, optional
-            Choose whether the dipole vector is calculated at the center of 
+            Choose whether the dipole vector is calculated at the center of
             "mass" or the center of "charge", default is "mass".
 
         Returns
@@ -2492,23 +2492,23 @@ def quadrupole_tensor(
         tensor of the group:
 
         .. math::
-            \mathsf{Q} = \sum_{i=1}^{N} q_{i} ( \mathbf{r}_{i} - 
+            \mathsf{Q} = \sum_{i=1}^{N} q_{i} ( \mathbf{r}_{i} -
             \mathbf{r}_{COM} ) \otimes ( \mathbf{r}_{i} - \mathbf{r}_{COM} )
 
         The traceless quadrupole tensor, :math:`\hat{\mathsf{Q}}`, is then
         taken from:
 
         .. math::
-            \hat{\mathsf{Q}} = \frac{3}{2} \mathsf{Q} - \frac{1}{2} 
+            \hat{\mathsf{Q}} = \frac{3}{2} \mathsf{Q} - \frac{1}{2}
             tr(\mathsf{Q})
 
         Computes the quadrupole tensor of :class:`Atoms<Atom>` in the group.
         Tensor per :class:`Residue`, :class:`Segment`, molecule, or
         fragment can be obtained by setting the `compound` parameter
         accordingly.
 
-        Note that when there is an unsymmetrical plane in the molecule or 
-        group, the magnitude of the quadrupole tensor is dependent on the 
+        Note that when there is an unsymmetrical plane in the molecule or
+        group, the magnitude of the quadrupole tensor is dependent on the
         ``center`` (e.g., :math:`\mathbf{r}_{COM}`) chosen and cannot be translated.
 
         Parameters
@@ -2532,15 +2532,15 @@ def quadrupole_tensor(
             :class:`Atoms<Atom>` *belonging to the group* will be taken into
             account.
         center : {'mass', 'charge'}, optional
-            Choose whether the dipole vector is calculated at the center of 
+            Choose whether the dipole vector is calculated at the center of
             "mass" or the center of "charge", default is "mass".
 
         Returns
         -------
         numpy.ndarray
             Quadrupole tensor(s) of (compounds of) the group in :math:`eÅ^2`.
             If `compound` was set to ``'group'``, the output will be a single
-            tensor of shape ``(3,3)``. Otherwise, the output will be a 1d array 
+            tensor of shape ``(3,3)``. Otherwise, the output will be a 1d array
             of shape ``(n,3,3)`` where ``n`` is the number of compounds.
 
 
@@ -2623,20 +2623,20 @@ def __quadrupole_tensor(recenteredpos, charges):
 
     def quadrupole_moment(group, **kwargs):
         r"""Quadrupole moment of the group according to :footcite:p:`Gray1984`.
-         
+
         .. math::
             Q = \sqrt{\frac{2}{3}{\hat{\mathsf{Q}}}:{\hat{\mathsf{Q}}}}
 
-        where the quadrupole moment is calculated from the tensor double 
+        where the quadrupole moment is calculated from the tensor double
         contraction of the traceless quadropole tensor :math:`\hat{\mathsf{Q}}`
 
         Computes the quadrupole moment of :class:`Atoms<Atom>` in the group.
         Quadrupole per :class:`Residue`, :class:`Segment`, molecule, or
         fragment can be obtained by setting the `compound` parameter
         accordingly.
 
-        Note that when there is an unsymmetrical plane in the molecule or 
-        group, the magnitude of the quadrupole moment is dependant on the 
+        Note that when there is an unsymmetrical plane in the molecule or
+        group, the magnitude of the quadrupole moment is dependant on the
         ``center`` chosen and cannot be translated.
 
         Parameters
@@ -2660,7 +2660,7 @@ def quadrupole_moment(group, **kwargs):
             :class:`Atoms<Atom>` *belonging to the group* will be taken into
             account.
         center : {'mass', 'charge'}, optional
-            Choose whether the dipole vector is calculated at the center of 
+            Choose whether the dipole vector is calculated at the center of
             "mass" or the center of "charge", default is "mass".
 
         Returns

package/MDAnalysis/lib/__init__.py

@@ -39,9 +39,10 @@
     "nsgrid",
 ]
 
+
 from . import log
-from . import transformations
 from . import util
+from . import transformations
 from . import mdamath
 from . import distances  # distances relies on mdamath
 from . import NeighborSearch

package/MDAnalysis/lib/mdamath.py

@@ -43,6 +43,7 @@
 .. autofunction:: triclinic_box
 .. autofunction:: triclinic_vectors
 .. autofunction:: box_volume
+.. autofunction:: rotaxis
 
 
 Connectivity
@@ -455,3 +456,30 @@ def box_volume(dimensions: npt.ArrayLike) -> float:
         tri_vecs = triclinic_vectors(dim, dtype=np.float64)
         volume = tri_vecs[0, 0] * tri_vecs[1, 1] * tri_vecs[2, 2]
     return volume
+
+
+def rotaxis(a, b):
+    """Return the rotation axis to rotate vector a into b.
+
+    Parameters
+    ----------
+    a, b : array_like
+        two vectors
+
+    Returns
+    -------
+    c : np.ndarray
+        vector to rotate a into b
+
+
+    Note
+    ----
+    If a == b this will always return [1, 0, 0]
+
+    .. versionchanged:: 2.10.0
+       Moved from (removed) lib.transformations to lib.mdamath
+    """
+    if np.allclose(a, b):
+        return np.array([1, 0, 0])
+    c = np.cross(a, b)
+    return c / np.linalg.norm(c)