Merge branch 'develop' into get_connections_develop

.disabled-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==2.10.0"
+    - 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_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - PIP_DEPENDENCIES="duecredit parmed"

.github/workflows/gh-ci.yaml

@@ -15,7 +15,7 @@ defaults:
 
 env:
   MDA_CONDA_MIN_DEPS: "pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov"
-  MDA_CONDA_EXTRA_DEPS: "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==2.10.0"
+  MDA_CONDA_EXTRA_DEPS: "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"
   MDA_PIP_MIN_DEPS: 'coveralls coverage<5 pytest-cov pytest-xdist'
   MDA_PIP_EXTRA_DEPS: 'duecredit parmed'
 

azure-pipelines.yml

@@ -35,6 +35,9 @@ jobs:
         Python38-64bit-full:
           PYTHON_VERSION: '3.8'
           PYTHON_ARCH: 'x64'
+        Python39-64bit-full:
+          PYTHON_VERSION: '3.9'
+          PYTHON_ARCH: 'x64'
   steps:
   - task: UsePythonVersion@0
     inputs:
@@ -44,7 +47,7 @@ jobs:
   - script: python -m pip install --upgrade pip setuptools wheel
     displayName: 'Install tools'
   - script: >-
-      python -m pip install
+      python -m pip install --only-binary=h5py
       cython
       hypothesis
       matplotlib
@@ -54,11 +57,10 @@ jobs:
       pytest-xdist
       scikit-learn
       scipy
-      h5py==2.10.0
+      h5py
       tqdm
     displayName: 'Install dependencies'
   # TODO: recent rdkit is not on PyPI
-  # NOTE: h5py pinned because of gh-3019
   - script: >-
       python -m pip install
       biopython

maintainer/conda/environment.yml

@@ -8,7 +8,7 @@ dependencies:
   - cython
   - griddataformats
   - gsd
-  - h5py==2.10.0
+  - h5py
   - hypothesis
   - joblib>=0.12
   - matplotlib==3.2.2
@@ -31,4 +31,4 @@ dependencies:
       - duecredit
       - parmed
       - msmb_theme==1.2.0
-      - sphinx-sitemap==1.0.2
+      - sphinx-sitemap==1.0.2

package/AUTHORS

@@ -157,6 +157,10 @@ Chronological list of authors
   - Leonardo Barneschi
   - Henrik Jäger
   - Jan Stevens
+  - Orion Cohen
+  - Dimitrios Papageorgiou
+  - Hannah Pollak
+  - Estefania Barreto-Ojeda
 
 External code
 -------------

package/CHANGELOG

@@ -17,11 +17,15 @@ The rules for this file:
          lilyminium, daveminh, jbarnoud, yuxuanzhuang, VOD555, ianmkenney,
          calcraven，xiki-tempula, mieczyslaw, manuel.nuno.melo, PicoCentauri,
          hanatok, rmeli, aditya-kamath, tirkarthi, LeonardoBarneschi, hejamu,
-         biogen98
+         biogen98, orioncohen, z3y50n, hp115, ojeda-e
 
   * 2.0.0
 
 Fixes
+  * Helix_analysis coverage raised to 100% and `from __future__ import`
+    removed (Issue #3209) 
+  * Fixed 'sphzone', 'sphlayer', 'cyzone', and 'cylayer' to return empty if the
+   zone/layer is empty, consistent with 'around' (Issue #2915)
   * A Universe created from an ROMol with no atoms returns now a Universe 
     with 0 atoms (Issue #3142)
   * ValueError raised when empty atomgroup is given to DensityAnalysis
@@ -90,6 +94,8 @@ Enhancements
   * Added intra_bonds, intra_angles, intra_dihedrals etc. to return only
     the connections involving atoms within the AtomGroup, instead of
     including atoms outside the AtomGroup (Issue #1264, #2821, PR #3200)
+  * Add `set_dimensions` transformation class for setting constant 
+    box dimensions for all timesteps in trajectory (Issue #2691)
   * Added a ValueError raised when not given a gridcenter while
     providing grid dimensions to DensityAnalysis, also added
     check for NaN in the input (Issue #3148, PR #3154)
@@ -144,6 +150,7 @@ Enhancements
 
 
 Changes
+  * Fixed inaccurate docstring inside the RMSD class (Issue #2796, PR #3134) 
   * TPRParser now loads TPR files with `tpr_resid_from_one=True` by default,
     which starts TPR resid indexing from 1 (instead of 0 as in 1.x) (Issue #2364, PR #3152)
   * Introduces encore specific C compiler arguments to allow for lowering of

package/MDAnalysis/analysis/helix_analysis.py

@@ -78,7 +78,6 @@
     hel_xyz = hel.helix_analysis(u.atoms.positions, ref_axis=[0, 0, 1])
 
 """
-from __future__ import division, absolute_import
 
 import warnings
 import numpy as np

package/MDAnalysis/analysis/rms.py

@@ -380,7 +380,10 @@ def __init__(self, atomgroup, reference=None, select='all',
              corresponding atom in `select`, and assumes ``None`` for `groupselections`.
 
         weights_groupselections : False or list of {"mass", ``None`` or array_like} (optional)
-             1. ``False`` will apply imposed weights to `groupselections` from ``weights`` option.
+             1. ``False`` will apply imposed weights to `groupselections` from
+             ``weights`` option if ``weights`` is either ``"mass"`` or ``None``. 
+             Otherwise will assume a list of length equal to length of 
+             `groupselections` filled with ``None`` values.
 
              2. A list of {"mass", ``None`` or array_like} with the length of `groupselections`
              will apply the weights to `groupselections` correspondingly.

package/MDAnalysis/coordinates/H5MD.py

@@ -600,7 +600,7 @@ def _read_frame(self, frame):
             else:
                 raise NoDataError("Provide at least a position, velocity"
                                   " or force group in the h5md file.")
-        except ValueError:
+        except (ValueError, IndexError):
             raise IOError from None
 
         self._frame = frame

package/MDAnalysis/core/selection.py

@@ -217,6 +217,7 @@ def apply(self, group):
         return func(self, group)
     return apply
 
+
 class _Selectionmeta(type):
     def __init__(cls, name, bases, classdict):
         type.__init__(type, name, bases, classdict)
@@ -352,6 +353,8 @@ def __init__(self, parser, tokens):
     def apply(self, group):
         indices = []
         sel = self.sel.apply(group)
+        if len(sel) == 0:
+            return group[[]]
         box = self.validate_dimensions(group.dimensions)
         periodic = box is not None
         ref = sel.center_of_geometry().reshape(1, 3).astype(np.float32)
@@ -378,6 +381,8 @@ def __init__(self, parser, tokens):
     def apply(self, group):
         indices = []
         sel = self.sel.apply(group)
+        if len(sel) == 0:
+            return group[[]]
         box = self.validate_dimensions(group.dimensions)
         periodic = box is not None
         ref = sel.center_of_geometry().reshape(1, 3).astype(np.float32)
@@ -394,7 +399,8 @@ class CylindricalSelection(Selection):
     @return_empty_on_apply
     def apply(self, group):
         sel = self.sel.apply(group)
-
+        if len(sel) == 0:
+            return group[[]]
         # Calculate vectors between point of interest and our group
         vecs = group.positions - sel.center_of_geometry()
 

package/MDAnalysis/transformations/__init__.py

@@ -130,3 +130,4 @@ def wrapped(ts):
 from .positionaveraging import PositionAverager
 from .fit import fit_translation, fit_rot_trans
 from .wrap import wrap, unwrap
+from .boxdimensions import set_dimensions

package/MDAnalysis/transformations/boxdimensions.py

@@ -0,0 +1,87 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+#
+# MDAnalysis --- https://www.mdanalysis.org
+# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
+# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
+# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
+# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
+# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
+# doi: 10.25080/majora-629e541a-00e
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+
+"""\
+Set box dimensions --- :mod:`MDAnalysis.transformations.boxdimensions`
+=======================================================================
+
+Set dimensions of the simulation box to a constant vector across all timesteps.
+
+
+.. autoclass:: set_dimensions
+"""
+import numpy as np
+
+
+class set_dimensions:
+    """
+    Set simulation box dimensions.
+
+    Timestep dimensions are modified in place.
+
+    Example
+    -------
+
+    e.g. set simulation box dimensions to a vector containing unit cell
+    dimensions [*a*, *b*, *c*, *alpha*, *beta*, *gamma*], lengths *a*,
+    *b*, *c* are in the MDAnalysis length unit (Å), and angles are in degrees.
+
+    .. code-block:: python
+
+        dim = [2, 2, 2, 90, 90, 90]
+        transform = mda.transformations.boxdimensions.set_dimensions(dim)
+        u.trajectory.add_transformations(transform)
+
+    Parameters
+    ----------
+    dimensions: iterable of floats
+        vector that contains unit cell lengths and angles.
+        Expected shapes are (6, 0) or (1, 6)
+
+    Returns
+    -------
+    :class:`~MDAnalysis.coordinates.base.Timestep` object
+    """
+
+    def __init__(self, dimensions):
+        self.dimensions = dimensions
+
+        try:
+            self.dimensions = np.asarray(self.dimensions, np.float32)
+        except ValueError:
+            errmsg = (f'{self.dimensions} cannot be converted into '
+                       'np.float32 numpy.ndarray')
+            raise ValueError(errmsg)
+        try:
+            self.dimensions = self.dimensions.reshape(6, )
+        except ValueError:
+            errmsg = (f'{self.dimensions} array does not have valid box '
+                       'dimension shape.\nSimulation box dimensions are '
+                       'given by an float array of shape (6, ), '
+                       ' containing 3 lengths and 3 angles: '
+                       '[a, b, c, alpha, beta, gamma]')
+            raise ValueError(errmsg)
+
+    def __call__(self, ts):
+        ts.dimensions = self.dimensions
+        return ts

package/doc/sphinx/source/documentation_pages/trajectory_transformations.rst

@@ -233,4 +233,5 @@ Currently implemented transformations
    ./transformations/positionaveraging
    ./transformations/fit
    ./transformations/wrap
+   ./transformations/boxdimensions
 

package/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst

@@ -0,0 +1 @@
+.. automodule:: MDAnalysis.transformations.boxdimensions

testsuite/MDAnalysisTests/analysis/test_helix_analysis.py

@@ -20,7 +20,6 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
-from __future__ import absolute_import, division
 import re
 
 import numpy as np
@@ -397,6 +396,11 @@ def test_universe_from_origins(self, helanal):
         assert len(u.atoms) == len(helanal.atomgroups[0])-2
         assert len(u.trajectory) == 70
 
+    def test_universe_from_origins_except(self, psf_ca):
+        ha = hel.HELANAL(psf_ca, select='resnum 161-187')
+        with pytest.raises(ValueError, match=r'before universe_from_origins'):
+            u = ha.universe_from_origins()
+
     def test_multiple_atoms_per_residues(self):
         u = mda.Universe(XYZ)
         with pytest.warns(UserWarning) as rec:
@@ -430,6 +434,12 @@ def test_residue_gaps_no_split(self, psf_ca):
         assert 'has gaps in the residues' in warnmsg
         assert 'Splitting into' not in warnmsg
 
+    def test_len_groups_short(self, psf_ca):
+        sel = 'resnum 161-168'
+        with pytest.warns(UserWarning, match='Fewer than 9 atoms found'):
+            ha = hel.HELANAL(psf_ca, select=sel)
+            assert len(ha.atomgroups) < 9
+
     @pytest.mark.parametrize('ref_axis,screw_angles', [
         # input vectors zigzag between [-1, 0, 0] and [1, 0, 0]
         # global axis is z-axis

testsuite/MDAnalysisTests/core/test_atomselections.py

@@ -210,6 +210,10 @@ def test_cylayer(self, universe, selstr):
         sel = universe.select_atoms(selstr)
         assert_equal(len(sel), 88)
 
+    def test_empty_cylayer(self, universe):
+        empty = universe.select_atoms('cylayer 4.0 6.0 10 -10 name NOT_A_NAME')
+        assert_equal(len(empty), 0)
+
     @pytest.mark.parametrize('selstr', [
         'cyzone 6.0 10 -10 bynum 1281',
         'cyzone 6.0 10 -10 index 1280'
@@ -218,6 +222,10 @@ def test_cyzone(self, universe, selstr):
         sel = universe.select_atoms(selstr)
         assert_equal(len(sel), 166)
 
+    def test_empty_cyzone(self, universe):
+        empty = universe.select_atoms('cyzone 6.0 10 -10 name NOT_A_NAME')
+        assert_equal(len(empty), 0)
+
     def test_point(self, universe):
         ag = universe.select_atoms('point 5.0 5.0 5.0 3.5')
 
@@ -770,6 +778,10 @@ def test_sphlayer(self, u):
 
         assert idx == set(ag.indices)
 
+    def test_empty_sphlayer(self, u):
+        empty = u.select_atoms('sphlayer 2.4 6.0 name NOT_A_NAME')
+        assert len(empty) == 0
+
     def test_sphzone(self, u):
         r1 = u.select_atoms('resid 1')
         cog = r1.center_of_geometry().reshape(1, 3)
@@ -781,6 +793,10 @@ def test_sphzone(self, u):
 
         assert idx == set(ag.indices)
 
+    def test_empty_sphzone(self, u):
+        empty = u.select_atoms('sphzone 5.0 name NOT_A_NAME')
+        assert len(empty) == 0
+
     def test_point_1(self, u):
         # The example selection
         ag = u.select_atoms('point 5.0 5.0 5.0 3.5')