WIP: Master merge

maintainer/change_release.sh

@@ -19,11 +19,11 @@ die () {
 
 findcommand() {
     for name in $*; do
-    path=$(which $name)
-    if [ -n "$path" ]; then
-        echo $path
-        return 0
-    fi
+        path=$(which $name)
+        if [ -n "$path" ]; then
+            echo $path
+            return 0
+        fi
     done
     die "None of the commands $* found." 2
 }
@@ -74,12 +74,12 @@ echo "Using sed = $SED"
 echo "Setting RELEASE/__version__ in MDAnalysis to $RELEASE"
 
 git grep -E -l 'RELEASE.*[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?' $FILES  \
-   | xargs -I FILE $SED '/RELEASE/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?/'${RELEASE}'/' -i.bak FILE
+   | xargs -I FILE $SED -e '/RELEASE/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?/'${RELEASE}'/' -i .bak FILE
 
 git grep -E -l '__version__ *=.*[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?'  $FILES \
-   | xargs -I FILE $SED '/__version__/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?/'${RELEASE}'/' -i.bak FILE
+   | xargs -I FILE $SED -e '/__version__/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?/'${RELEASE}'/' -i .bak FILE
 
 git grep -E -l 'version:.*[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?'  $FILES \
-   | xargs -I FILE $SED '/version:/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?/'${RELEASE}'/' -i.bak FILE
+   | xargs -I FILE $SED -e '/version:/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?/'${RELEASE}'/' -i .bak FILE
 
 git status

maintainer/conda/MDAnalysis/meta.yaml

@@ -1,12 +1,12 @@
 package:
   name: mdanalysis
   # This has to be changed after a release
-  version: "0.19.1dev"
+  version: "2.0.0-dev0"
 
 source:
    git_url: https://github.com/MDAnalysis/mdanalysis
-   git_branch: develop
-   # git_tag: release-0.15.0
+   # git_branch: develop
+   git_tag: release-0.19.1
 
 # specify the subversion of the conda package. Defaults to 0. If you make
 # changes to the conda package alone with out an increase in the source package

package/AUTHORS

@@ -150,6 +150,7 @@ Chronological list of authors
   - Edis Jakupovic
   - Nicholas Craven
   - Mieczyslaw Torchala
+  - Ramon Crehuet
   - Haochuan Chen
   - Karthikeyan Singaravelan
 2021
@@ -167,6 +168,7 @@ Chronological list of authors
   - Sulay Shah
   - Alexander Yang
 
+
 External code
 -------------
 

package/CHANGELOG

@@ -330,6 +330,115 @@ Deprecations
     read it from the input TRZ trajectory.
 
 
+05/01/21  IAlibay
+
+  * 1.1.1
+
+Fixes
+  * Remove absolute paths from package upload to pypi.
+
+
+04/28/21  richardjgowers, IAlibay, tylerjereddy, xiki-tempula, lilyminium,
+          zemanj, PicoCentauri
+
+  * 1.1.0
+
+Fixes
+  * Removes use of absolute paths in setup.py to avoid Windows installation
+    failures (Issue #3129)
+  * Adds test for crashes caused by small box NSGrid searches (Issue #2670)
+  * Replaces decreated NumPy type aliases and fixes NEP 34 explicit ragged
+    array warnings (PR #3139, backports PRs #2845 and #2834)
+  * Fixed several issues with NSGrid and triclinic boxes not finding some pairs.
+    (Issues #2229 #2345 #2919, PR #2937).
+  * Removed deprecation warning from numpy in hbond_autocorrel
+    (Issue #2987 PR #3242)
+  * Fixed bug in exclusion matrix of hbond_autocorrel (PR #3242)
+
+Changes
+  * Maximum pinned versions in setup.py removed for python 3.6+ (PR #3139)
+
+Deprecations
+  * ParmEdConverter no longer accepts Timestep objects at all
+    (Issue #3031, PR #3172)
+  * NCDFWriter `scale_factor` writing will change in version 2.0 to
+    better match AMBER outputs (Issue #2327)
+  * Deprecated using the last letter of the segid as the
+    chainID when writing PDB files (Issue #3144)
+  * Deprecated tempfactors and bfactors being separate
+    TopologyAttrs, with a warning (PR #3161)
+  * hbonds.WaterBridgeAnalysis will be removed in 2.0.0 and
+    replaced with hydrogenbonds.WaterBridgeAnalysis (#3111)
+  * TPRParser indexing resids from 0 by default is deprecated.
+    From 2.0 TPRParser will index resids from 1 by default.
+
+
+Enhancements
+  * Added `get_connections` method to get bonds, angles, dihedrals, etc.
+    with or without atoms outside the group (Issues #1264, #2821, PR #3160)
+  * Added `tpr_resid_from_one` keyword to select whether TPRParser
+    indexes resids from 0 or 1 (Issue #2364, PR #3153)
+
+
+01/17/21 richardjgowers, IAlibay, orbeckst, tylerjereddy, jbarnoud,
+         yuxuanzhuang, lilyminium, VOD555, p-j-smith, bieniekmateusz,
+         calcraven, ianmkenney, rcrehuet, manuel.nuno.melo, hanatok
+
+  * 1.0.1
+
+Fixes
+  * Due to issues with the reliability/accuracy of `nsgrid`, this method is
+    currently not recommended for use. It has also been removed as an option
+    from lib.capped_distance and lib.self_capped_distance. Please use PKDTree
+    instead (Issue #2930)
+  * Development status changed from beta to mature (Issue #2773)
+  * pip installation only requests Python 2.7-compatible packages (#2736)
+  * Testsuite does not use any more matplotlib.use('agg') (#2191)
+  * The methods provided by topology attributes now appear in the
+    documentation (Issue #1845)
+  * AtomGroup.center now works correctly for compounds + unwrapping
+    (Issue #2984)
+  * In ChainReader, read_frame does not trigger change of iterating position.
+    (Issue #2723, PR #2815)
+  * empty_atomgroup.select_atoms('name *') now returns an empty
+    AtomGroup instead of TypeError (Issue #2765)
+  * TRZReader now checks `n_atoms` on reading. (Issue #2817, PR #2820)
+  * TRZWriter now writes `n_atoms` to the file. (Issue #2817, PR #2820)
+  * rdf.InterRDF_s density keyword documented and now gives correct results for
+    density=True; the keyword was available since 0.19.0 but with incorrect
+    semantics and not documented and did not produce correct results (Issue
+    #2811, PR #2812)
+  * In hydrogenbonds.hbond_analysis.HydrogenbondAnalysis an AttributeError
+    was thrown when finding D-H pairs via the topology if `hydrogens` was an
+    empty AtomGroup (Issue #2848)
+  * Fixed reading in masses and charges from a hoomdxml file
+    (Issue #2888, PR #2889)
+  * Fixed performance regression on select_atoms for string selections (#2751)
+  * Fixed the DMSParser, allowing the creation of multiple segids sharing
+    residues with identical resids (Issue #1387, PR #2872)
+  * Fixed missing space between floats in helanal output files (PR #2733)
+  * ensure that unistd.h is included on macOS when compiling ENCORE's spe.c
+    (Issue #2934)
+
+Enhancements
+  * Improved performance of the ParmEd converter (Issue #3028, PR #3029)
+  * Improved performances when parsing TPR files (PR #2804)
+
+Changes (not affecting users)
+  * Continuous integration uses mamba rather than conda to install the
+    dependencies (PR #2983)
+
+Deprecations
+  * waterdynamics.HydrogenBondLifetimes will be removed in 2.0.0 and
+    replaced with hydrogenbonds.HydrogenBondAnalysis.lifetime() (#2547)
+  * lib.util.echo() will be removed in 2.0.0
+  * core.universe.as_Universe() will be removed in 2.0.0
+  * analysis.leaflets.LeafletFinder() will not accept a filename any more,
+    only a Universe, in 2.0.0
+  * analysis.helanal will be removed in 2.0.0 and replaced by
+    analysis.helix_analysis (PR #2622)
+
+
 06/09/20 richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira,
          PicoCentauri, davidercruz, jbarnoud, RMeli, IAlibay, mtiberti, CCook96,
          Yuan-Yu, xiki-tempula, HTian1997, Iv-Hristov, hmacdope, AnshulAngaria,
@@ -356,7 +465,7 @@ Fixes
   * n_components correctly selects PCA components (Issue #2623)
   * Use internal residue indices instead of resids for similarity and connectivity
     selections (Issues #2669 and #2672, PR #2673)
-  * Checks for cryo-em 1 A^3 default CRYST1 record,
+  * Checks for cryo-em 1 A^3 default CRYST1 record, 
     disabling setting of box dimensions if found (Issue #2599)
   * mdamath.angles now returns np.pi instead of -np.pi in cases of
     lower bound roundoff errors. (Issue #2632, PR #2634)
@@ -381,7 +490,7 @@ Fixes
   * Clarifies density_from_Universe docs and adds user warning (Issue #2372)
   * Fix upstream deprecation of `matplotlib.axis.Tick` attributes in
     `MDAnalysis.analysis.psa`
-  * PDBWriter now uses first character of segid as ChainID (Issue #2224)
+  * PDBWriter now uses last character of segid as ChainID (Issue #2224)
   * Adds a more detailed warning when attempting to read chamber-style parm7
     files (Issue #2475)
   * ClusterCollection.get_ids now returns correctly (Issue #2464)
@@ -395,6 +504,7 @@ Fixes
     than one format (Issue #2353)
   * PDBQTParser now gives icode TopologyAttrs (Issue #2361)
   * GROReader and GROWriter now can handle boxes with box vectors >1000nm
+    (Issue #2371)
   * Guess atom element with uppercase name
   * TopologyGroup no longer reshapes the type, guessed, and order properties
     (Issue #2392)
@@ -417,7 +527,7 @@ Fixes
 Enhancements
   * Added support for FHI-AIMS input files (PR #2705)
   * vastly improved support for 32-bit Windows (PR #2696)
-  * Added methods to compute the root-mean-square-inner-product of subspaces
+  * Added methods to compute the root-mean-square-inner-product of subspaces 
     and the cumulative overlap of a vector in a subspace for PCA (PR #2613)
   * Added .frames and .times arrays to AnalysisBase (Issue #2661)
   * Added elements attribute to PDBParser (Issue #2553, #2647)
@@ -464,7 +574,7 @@ Enhancements
 
 Changes
   * Unused `MDAnalysis.lib.mdamath._angle` has been removed (Issue #2650)
-  * Refactored dihedral selections and Ramachandran.__init__ to speed up
+  * Refactored dihedral selections and Ramachandran.__init__ to speed up 
     dihedral selections for faster tests (Issue #2671, PR #2706)
   * Removes the deprecated `t0`, `tf`, and `dtmax` from
     :class:Waterdynamics.SurvivalProbability. Instead the `start`, `stop` and
@@ -527,7 +637,6 @@ Changes
     function calls. (Issue #782)
 
 Deprecations
-  * analysis.helanal is deprecated in 1.0 (remove in 2.0)
   * analysis.hole is deprecated in 1.0 (remove in 2.0)
   * analysis.hbonds.HydrogenBondAnalysis is deprecated in 1.0 (remove in 2.0)
   * analysis.density.density_from_Universe() (remove in 2.0)
@@ -536,6 +645,7 @@ Deprecations
   * Writer.write_next_timestep is deprecated, use write() instead (remove in 2.0)
   * Writer.write(Timestep) is deprecated, use either a Universe or AtomGroup
 
+
 09/05/19 IAlibay, richardjgowers
 
   * 0.20.1
@@ -908,7 +1018,6 @@ Testsuite
   * Unit tests for unwanted side effects when importing MDAnalysis
   * MDAnalysis.visualization is now tested
 
-
 01/24/18 richardjgowers, rathann, orbeckst, tylerjereddy, mtiberti, kain88-de,
          jbarnoud, nestorwendt, mmattaNU, jmborr, sobuelow, sseyler, rcortini,
          xiki-tempula, manuel.nuno.melo
@@ -1018,6 +1127,9 @@ Fixes
   * Fixed dtype of numpy arrays to accomodate 32 bit architectures (Issue #1362)
   * Groups are hashable on python 3 (Issue #1397)
 
+Changes
+  * scipy and matplotlib are now required dependencies (Issue #1159)
+
 
 Changes
   * scipy and matplotlib are now required dependencies (Issue #1159)

package/MANIFEST.in

@@ -12,4 +12,4 @@ global-exclude *.pyc
 global-exclude *.pyo
 global-exclude *.pyd
 global-exclude *~
-global-exclude .git
+global-exclude .git

package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py

@@ -768,7 +768,8 @@ def count_by_time(self):
         indices /= self.step
 
         counts = np.zeros_like(self.frames)
-        counts[indices.astype(int)] = tmp_counts
+        counts[indices.astype(np.intp)] = tmp_counts
+
         return counts
 
     def count_by_type(self):
@@ -786,8 +787,8 @@ def count_by_type(self):
         acceptor atoms in a hydrogen bond.
         """
 
-        d = self.u.atoms[self.results.hbonds[:, 1].astype(int)]
-        a = self.u.atoms[self.results.hbonds[:, 3].astype(int)]
+        d = self.u.atoms[self.hbonds[:, 1].astype(np.intp)]
+        a = self.u.atoms[self.hbonds[:, 3].astype(np.intp)]
 
         tmp_hbonds = np.array([d.resnames, d.types, a.resnames, a.types],
                               dtype=str).T
@@ -815,9 +816,9 @@ def count_by_ids(self):
         in a hydrogen bond.
         """
 
-        d = self.u.atoms[self.results.hbonds[:, 1].astype(int)]
-        h = self.u.atoms[self.results.hbonds[:, 2].astype(int)]
-        a = self.u.atoms[self.results.hbonds[:, 3].astype(int)]
+        d = self.u.atoms[self.hbonds[:, 1].astype(np.intp)]
+        h = self.u.atoms[self.hbonds[:, 2].astype(np.intp)]
+        a = self.u.atoms[self.hbonds[:, 3].astype(np.intp)]
 
         tmp_hbonds = np.array([d.ids, h.ids, a.ids]).T
         hbond_ids, ids_counts = np.unique(tmp_hbonds, axis=0,

package/MDAnalysis/analysis/leaflet.py

@@ -118,8 +118,8 @@ class LeafletFinder(object):
     consecutively, starting at 0. To obtain the atoms in the input structure
     use :meth:`LeafletFinder.groups`::
 
-       u_PDB = mda.Universe(PDB)
-       L = LeafletFinder(u_PDB, 'name P*')
+       u = mda.Universe(PDB)
+       L = LeafletFinder(u, 'name P*')
        leaflet0 = L.groups(0)
        leaflet1 = L.groups(1)
 

package/MDAnalysis/analysis/waterdynamics.py

@@ -942,7 +942,7 @@ class SurvivalProbability(object):
        Using the MDAnalysis.lib.correlations.py to carry out the intermittency
        and autocorrelation calculations.
        Changed `selection` keyword to `select`.
-       Removed support for the deprecated `t0`, `tf`, and `dtmax` keywords. 
+       Removed support for the deprecated `t0`, `tf`, and `dtmax` keywords.
        These should instead be passed to :meth:`SurvivalProbability.run` as
        the `start`, `stop`, and `tau_max` keywords respectively.
        The `stop` keyword as passed to :meth:`SurvivalProbability.run` has now

package/MDAnalysis/coordinates/PDB.py

@@ -539,6 +539,9 @@ class PDBWriter(base.WriterBase):
     .. versionchanged:: 2.0.0
         Add the `redindex` argument. Setting this keyword to ``True``
         (the default) preserves the behavior in earlier versions of MDAnalysis.
+        The PDB writer checks for a valid chainID entry instead of using the
+        last character of segid. Should a chainID not be present, or not
+        conform to the PDB standard, the default value of  'X' is used.
 
     """
     fmt = {

package/MDAnalysis/coordinates/TRJ.py

@@ -823,6 +823,18 @@ class NCDFWriter(base.WriterBase):
     .. _`Issue #506`:
        https://github.com/MDAnalysis/mdanalysis/issues/506#issuecomment-225081416
 
+    Raises
+    ------
+    FutureWarning
+        When writing. The :class:`NCDFWriter` currently does not write any
+        `scale_factor` values for the data variables. Whilst not in breach
+        of the AMBER NetCDF standard, this behaviour differs from that of
+        most AMBER writers, especially for velocities which usually have a
+        `scale_factor` of 20.455. In MDAnalysis 2.0, the :class:`NCDFWriter`
+        will enforce `scale_factor` writing to either match user inputs (either
+        manually defined or via the :class:`NCDFReader`) or those as written by
+        AmberTools's :program:`sander` under default operation.
+
     See Also
     --------
     :class:`NCDFReader`
@@ -882,6 +894,13 @@ def __init__(self,
         self.has_forces = kwargs.get('forces', False)
         self.curr_frame = 0
 
+        # warn users of upcoming changes
+        wmsg = ("In MDAnalysis v2.0, `scale_factor` writing will change ("
+                "currently these are not written), to better match the way "
+                "they are written by AMBER programs. See NCDFWriter docstring "
+                "for more details.")
+        warnings.warn(wmsg, FutureWarning)
+
     def _init_netcdf(self, periodic=True):
         """Initialize netcdf AMBER 1.0 trajectory.
 

package/MDAnalysis/coordinates/TRZ.py

@@ -140,7 +140,7 @@ class TRZReader(base.ReaderBase):
        Extra data (Temperature, Energies, Pressures, etc) now read
        into ts.data dictionary.
        Now passes a weakref of self to ts (ts._reader).
-    .. versionchanged:: 2.0.0
+    .. versionchanged:: 1.0.1
        Now checks for the correct `n_atoms` on reading
        and can raise :exc:`ValueError`.
     """