Merge develop

.github/workflows/gh-ci.yaml

@@ -14,7 +14,7 @@ defaults:
     shell: bash -l {0}
 
 env:
-  MDA_CONDA_MIN_DEPS: "pip pytest mmtf-python biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
+  MDA_CONDA_MIN_DEPS: "pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib 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_PIP_MIN_DEPS: 'coveralls coverage<5 pytest-cov pytest-xdist'
   MDA_PIP_EXTRA_DEPS: 'duecredit parmed'

.readthedocs.yml

@@ -0,0 +1,24 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in with Sphinx
+sphinx:
+  configuration: package/doc/sphinx/source/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  install:
+    - method: pip
+      path: package
+
+conda:
+  environment: maintainer/conda/environment.yml

azure-pipelines.yml

@@ -49,7 +49,7 @@ jobs:
       hypothesis
       matplotlib
       numpy
-      pytest
+      pytest==6.1.2
       pytest-cov
       pytest-xdist
       scikit-learn

maintainer/conda/environment.yml

@@ -0,0 +1,34 @@
+name: mda-dev
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - chemfiles
+  - codecov
+  - cython
+  - griddataformats
+  - gsd
+  - h5py==2.10.0
+  - hypothesis
+  - joblib>=0.12
+  - matplotlib==3.2.2
+  - mmtf-python
+  - mock
+  - networkx
+  - numpy>=1.17.3
+  - psutil
+  - pytest
+  - python==3.7
+  - scikit-learn
+  - scipy
+  - pip
+  - sphinx==1.8.5
+  - tidynamics>=1.0.0
+  - tqdm>=4.43.0
+  - sphinxcontrib-bibtex
+  - sphinx_rtd_theme
+  - pip:
+      - duecredit
+      - parmed
+      - msmb_theme==1.2.0
+      - sphinx-sitemap==1.0.2

package/AUTHORS

@@ -151,7 +151,10 @@ Chronological list of authors
   - Nicholas Craven
   - Mieczyslaw Torchala
   - Haochuan Chen
-
+  - Karthikeyan Singaravelan
+2021
+  - Aditya Kamath
+
 External code
 -------------
 

package/CHANGELOG

@@ -16,11 +16,13 @@ The rules for this file:
 ??/??/?? tylerjereddy, richardjgowers, IAlibay, hmacdope, orbeckst, cbouy,
          lilyminium, daveminh, jbarnoud, yuxuanzhuang, VOD555, ianmkenney,
          calcraven，xiki-tempula, mieczyslaw, manuel.nuno.melo, PicoCentauri,
-         hanatok, rmeli
+         hanatok, rmeli, aditya-kamath, tirkarthi
 
   * 2.0.0
 
 Fixes
+  * atommethods (_get_prev/next_residues_by_resid) returns empty residue group 
+    when given empty residue group (Issue #3089)
   * MOL2 files without bonds can now be read and written (Issue #3057)
   * Write `CONECT` record only once in multi-model PDB files (Issue #3018)
   * Add '.nc' as a recognised extension for the NCDFWriter (Issue #3030)
@@ -75,8 +77,14 @@ Fixes
     (Issue #2934)
   * Fix tests for analysis.bat that could fail when run in parallel and that
     would create a test artifact (Issue #2979, PR #2981)
+  * Fix syntax warning over comparison of literals using is (Issue #3066)
 
 Enhancements
+  * Added automatic selection class generation for TopologyAttrs,
+    FloatRangeSelection, and BoolSelection (Issues #2925, #2875; PR #2927)
+  * Added 'to' operator, negatives, scientific notation, and arbitrary
+    whitespace for ranges (Issue #3054, PR #2927)
+  * Added `atol` and `rtol` keywords for float comparison (PR #2927)
   * Improved performance of the ParmEd converter (Issue #3028, PR #3029)
   * Improved analysis class docstrings, and added missing classes to the 
     `__all__` list (PR #2998)
@@ -112,7 +120,7 @@ Enhancements
     'protein' selection (#2751 PR #2755)
   * Added an RDKit converter that works for any input with all hydrogens
     explicit in the topology (Issue #2468, PR #2775)
-
+  
 Changes
   * Continuous integration uses mamba rather than conda to install the
     dependencies (PR #2983)

package/MDAnalysis/analysis/legacy/x3dna.py

@@ -423,7 +423,7 @@ def plot(self, **kwargs):
             ax.set_xlabel(r"Nucleic Acid Number")
             param = self.profiles.values()[0].dtype.names[k]
             if param in ["Shear", "Stretch", "Stagger", "Rise", "Shift", "Slide"]:
-                ax.set_ylabel("{0!s} ($\AA$)".format((param)))
+                ax.set_ylabel(r"{!s} ($\AA$)".format(param))
             else:
                 ax.set_ylabel("{0!s} (deg)".format((param)))
             ax.figure.savefig("{0!s}.png".format((param)))

package/MDAnalysis/analysis/rms.py

@@ -745,27 +745,37 @@ def __init__(self, atomgroup, **kwargs):
            u = mda.Universe(TPR, XTC, in_memory=True)
            protein = u.select_atoms("protein")
 
-           # 1) need a step to center and make whole: this trajectory
-           #    contains the protein being split across periodic boundaries
-           #
-           # TODO
+           # 1) the current trajectory contains a protein split across
+           #    periodic boundaries, so we first make the protein whole and
+           #    center it in the box using on-the-fly transformations
+           import MDAnalysis.transformations as trans
+
+           not_protein = u.select_atoms('not protein')
+           transforms = [trans.unwrap(protein),
+                         trans.center_in_box(protein, wrap=True),
+                         trans.wrap(not_protein)]
+           u.trajectory.add_transformations(*transforms)
 
            # 2) fit to the initial frame to get a better average structure
            #    (the trajectory is changed in memory)
-           prealigner = align.AlignTraj(u, select="protein and name CA", in_memory=True).run()
+           prealigner = align.AlignTraj(u, u, select="protein and name CA",
+                                        in_memory=True).run()
 
            # 3) reference = average structure
-           reference_coordinates = u.trajectory.timeseries(asel=protein).mean(axis=1)
-           # make a reference structure (need to reshape into a 1-frame "trajectory")
-           reference = mda.Merge(protein).load_new(
-                       reference_coordinates[:, None, :], order="afc")
+           ref_coordinates = u.trajectory.timeseries(asel=protein).mean(axis=1)
+           # make a reference structure (need to reshape into a 1-frame
+           # "trajectory")
+           reference = mda.Merge(protein).load_new(ref_coordinates[:, None, :],
+                                                   order="afc")
 
         We created a new universe ``reference`` that contains a single frame
         with the averaged coordinates of the protein.  Now we need to fit the
         whole trajectory to the reference by minimizing the RMSD. We use
         :class:`MDAnalysis.analysis.align.AlignTraj`::
 
-           aligner = align.AlignTraj(u, reference, select="protein and name CA", in_memory=True).run()
+           aligner = align.AlignTraj(u, reference,
+                                     select="protein and name CA",
+                                     in_memory=True).run()
 
         The trajectory is now fitted to the reference (the RMSD is stored as
         `aligner.rmsd` for further inspection). Now we can calculate the RMSF::

package/MDAnalysis/coordinates/GMS.py

@@ -202,7 +202,7 @@ def _read_next_timestep(self, ts=None):
                     line) is not None):
                     flag = 2
                     continue
-                if (flag == 2) and (re.match(r'^\s*[-]+\s*', line) is not None):
+                if (flag == 2) and (re.match(r'^\s*-+\s*', line) is not None):
                     flag = 3
                     continue
                 if flag == 3 and counter < self.n_atoms:

package/MDAnalysis/core/groups.py

@@ -2606,7 +2606,9 @@ def ts(self):
 
     # As with universe.select_atoms, needing to fish out specific kwargs
     # (namely, 'updating') doesn't allow a very clean signature.
-    def select_atoms(self, sel, *othersel, **selgroups):
+
+    def select_atoms(self, sel, *othersel, periodic=True, rtol=1e-05,
+                     atol=1e-08, updating=False, **selgroups):
         """Select atoms from within this Group using a selection string.
 
         Returns an :class:`AtomGroup` sorted according to their index in the
@@ -2623,6 +2625,12 @@ def select_atoms(self, sel, *othersel, **selgroups):
         periodic : bool (optional)
           for geometric selections, whether to account for atoms in different
           periodic images when searching
+        atol : float, optional
+            The absolute tolerance parameter for float comparisons.
+            Passed to :func:``numpy.isclose``.
+        rtol : float, optional
+            The relative tolerance parameter for float comparisons.
+            Passed to :func:``numpy.isclose``.
         updating : bool (optional)
           force the selection to be re evaluated each time the Timestep of the
           trajectory is changed.  See section on **Dynamic selections** below.
@@ -2893,17 +2901,15 @@ def select_atoms(self, sel, *othersel, **selgroups):
            Removed flags affecting default behaviour for periodic selections;
            periodic are now on by default (as with default flags)
         .. versionchanged:: 2.0.0
-            Added the *smarts* selection.
+            Added the *smarts* selection. Added `atol` and `rtol` keywords
+            to select float values.
         """
 
         if not sel:
             warnings.warn("Empty string to select atoms, empty group returned.",
                           UserWarning)
             return self[[]]
 
-        periodic = selgroups.pop('periodic', True)
-
-        updating = selgroups.pop('updating', False)
         sel_strs = (sel,) + othersel
 
         for group, thing in selgroups.items():
@@ -2912,7 +2918,9 @@ def select_atoms(self, sel, *othersel, **selgroups):
                                 "You provided {} for group '{}'".format(
                                     thing.__class__.__name__, group))
 
-        selections = tuple((selection.Parser.parse(s, selgroups, periodic=periodic)
+        selections = tuple((selection.Parser.parse(s, selgroups,
+                                                   periodic=periodic,
+                                                   atol=atol, rtol=rtol)
                             for s in sel_strs))
         if updating:
             atomgrp = UpdatingAtomGroup(self, selections, sel_strs)