Merge develop (#2)

* Add arbitrary TopologyAttr selection (MDAnalysis#2927) Fixes MDAnalysis#2925 Fixes MDAnalysis#2875 Fixes MDAnalysis#3054 Changes made in this Pull Request: - added a class factory to subclass `core.selection.Selection` for each TopologyAttr - added tokens to `core.selection.SameSelection` - added `FloatRangeSelection` and `BoolSelection` - added negatives, scientific notation and "to" delimiter for ranges * Add ReadTheDocs configuration for PR builds (MDAnalysis#3060) - Adds RTD configuration - Add `environment.yml` for package installation * Remove appveyor * Install MDAnalysis on ReadTheDocs via pip (MDAnalysis#3071) Install via `pip install package/` to build current docs on ReadTheDocs * try stringio * rm metals file * pin pytest * pin pytest on gh actions * Fixes RMSF docstring (Issue MDAnalysis#2806) (MDAnalysis#3033) Fixes the RMSF docstring's align command and adds transformation to make the results accurate * MAINT: simplify guessers regex (MDAnalysis#3085) * the `SYMBOLS` regex in `guessers.py` does not require any escape sequences because the metacharacters are inactive in the character class (this includes the range metacharacter when placed at the start or end of the character class) * MAINT: char class regex improve * avoid the overhead of a regex character class when that character class has only a single character (i.e., serves no purpose) * there is only one instance of this in MDA codebase discovered by my [scraping code](https://github.com/tylerjereddy/regex-improve) * for a longer explanation see my similar changes in NumPy codebase: numpy/numpy#18083 * Fix syntax warning over comparison of literals using is. * Quick fix for atommethods to return empty residue group (MDAnalysis#3089) Returns empty residue group for _get_prev_residues_by_resid and _get_next_residues_by_resid * Add to authors list. Co-authored-by: Lily Wang <[email protected]> Co-authored-by: IAlibay <[email protected]> Co-authored-by: Tyler Reddy <[email protected]> Co-authored-by: Lily Wang <[email protected]> Co-authored-by: Irfan Alibay <[email protected]> Co-authored-by: Oliver Beckstein <[email protected]> Co-authored-by: Karthikeyan Singaravelan <[email protected]> Co-authored-by: Aditya Kamath <[email protected]>
cbouy · Jan 12, 2021 · 09a05be · 09a05be
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diff --git a/.appveyor.yml b/.appveyor.yml
diff --git a/.github/workflows/gh-ci.yaml b/.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'

diff --git a/.readthedocs.yml b/.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
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -49,7 +49,7 @@ jobs:
       hypothesis
       matplotlib
       numpy
-      pytest
+      pytest==6.1.2
       pytest-cov
       pytest-xdist
       scikit-learn

diff --git a/maintainer/conda/environment.yml b/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
diff --git a/package/AUTHORS b/package/AUTHORS
@@ -151,7 +151,10 @@ Chronological list of authors
   - Nicholas Craven
   - Mieczyslaw Torchala
   - Haochuan Chen
-
+  - Karthikeyan Singaravelan
+2021
+  - Aditya Kamath
+
 External code
 -------------
 

diff --git a/package/CHANGELOG b/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)

diff --git a/package/MDAnalysis/analysis/legacy/x3dna.py b/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)))

diff --git a/package/MDAnalysis/analysis/rms.py b/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::

diff --git a/package/MDAnalysis/coordinates/GMS.py b/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:

diff --git a/package/MDAnalysis/core/groups.py b/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)