py-mdanalysis: update to 0.15.0

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: py-mdanalysis: update to 0.15.0
From: Thomas Klausner <wiz%NetBSD.org@localhost>
Date: Sun, 11 Sep 2016 16:58:21 +0000
Module Name:	pkgsrc-wip
Committed By:	Thomas Klausner <wiz%NetBSD.org@localhost>
Pushed By:	wiz
Date:		Sun Sep 11 18:58:21 2016 +0200
Changeset:	14d1b5101c20d475b0d8affa88170e9e36a27cd5

Modified Files:
	py-mdanalysis/Makefile
	py-mdanalysis/PLIST
	py-mdanalysis/distinfo

Log Message:
py-mdanalysis: update to 0.15.0

This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.

  * 0.15.0

Metadata

  * link download_url to GitHub releases so that Depsy recognizes
    contributors (issue #749)
  * a __version__ variable is now exposed; it is built by setup.py from the
    AUTHORS file (Issue #784)

API Changes

  * rmsd doesn't superimpose by default anymore. The superposition
    is controlled by the 'superposition' keyword now. (see issue #562, #822)

Enhancements

  * Add conda build scripts (Issue #608)
  * Added read-only property giving Universe init kwargs (Issue #292)
  * Added 'crdbox' as AMBER Trj format extension (Issue #846)
  * Iteration and seeking in PDB files made faster (Issue #848)

Fixes
  * ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
  * rmsd now returns proper value when given array of weights (Issue #814)
  * change_release now finds number and dev (Issue #776)
  * units.py now correctly prints errors for unknown units.
  * test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
  * HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
  * MOL2 files without substructure section can now be read (Issue #816)
  * MOL2 files can be written without substructure section (Issue #816)
  * GRO files with an incomplete set of velocities can now be read (Issue #820)
  * Fixed Atom.position/velocity/force returning a view onto Timestep array
    (Issue #755)
  * PDB files can now read a CRYST entry if it happens before model headers
    (Issue #849)
  * Fixed HistoryReader returning 1 based frame indices (Issue #851)

Changes

  * Added zero_based indices for HBondsAnalysis. (Issue #807)
  * Generalized contact analysis class `Contacts` added. (Issue #702)
  * Removed Bio.PDBParser and sloppy structure builder and all of
    MDAnalysis.coordinates.pdb (Issue #777)
  * PDB parsers/readers/writers replaced by "permissive"/"primitive"
    counterparts (formerly known as PrimitivePDBReader); the
    'permissive' keyword for Universe is now ignored and only the
    native MDAnalysis PDBReader is being used (Issue #777)
  * PDBReader only opens a single file handle in its lifetime,
    previously opened & closed handle each frame (Issue #850)

Deprecations (Issue #599)
  * Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
    Writer/Parser (Issue #777)
  * Deprecated all `get_*` and `set_*` methods of Groups.
  * Deprecation warnings for accessing atom attributes from Residue,
    ResidueGroup, Segment, SegmentGroup. Will not be present or will
    give per-level results.
  * Deprecation warnings for accessing plural residue attributes from
    Residue or Segment (will disappear), or from SegmentGroup (will give
    per-Segment results).
  * Deprecation warnings for accessing plural segment attributes from Segment
    (will disappear).
  * Deprecated Atom number, pos, centroid, universe setter
  * Deprecated AtomGroup serials, write_selection
  * Deprecated Residue name, id
  * Deprecated Segment id, name
  * Deprecated as_Universe function; not needed
  * Deprecated ContactAnalysis and ContactAnalysis1 classes

02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
         manuel.nuno.melo, Balasubra, Saxenauts, mattihappy

  * 0.14.0

API Changes

  * Offsets files for Gromacs trajectory formats have been changed to a numpy
    style format '.npz'. Offsets files will be regenerated when you load a
    xtc/trr trajectory again. (Issue #441)
  * rotation_matrix now accepts array-likes as input

Enhancement

  * XDR file seeking errors now report system errno. (PR #678)
  * Offsets reading for xtc/trr files has been sped up. (Issue #441)
  * select_atoms now implicitly ORs multiple values after a keyword for
    many types of selections (Issue #345)
  * Performance improvements for the PDBReader of about 10%
  * LinearDensity analysis module added, which allows to compute linear mass
    and charge density profiles along the three cartesian axes of the cell.
    Works for orthorombic, fixed volume cells only. (Issue #670)
  * Trajectories can now be sliced using a boolean array (Issue #725)

Changes

  * xdrlib was rebranded libmdaxdr. (Issue #679)
  * xdrlib has been ported to cython. (Issue #441)
  * util.NamedStream no longer inherits from basestring (Issue #649)
  * Short TRZ titles are striped from trailing spaces. A friendlier error
    message is raised when the TRZ writer is asked to write a title longer
    than 80 characters. (Issue #689)
  * PDB doesn't save charge information anymore
  * coordinates.core.get_writer_for uses the user defined format if provided
    before trying to deduce the format from file extension. (Issue #712)

Fixes
  * Syntax error corrected in psa.py (Issue #738)
  * XDR file seeking and telling working again for large files (Issue #677).
  * ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
  * Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
  * The 'atom' selection keyword returns an empty selection rather than an
    error when no atoms are are found. (Issue #644)
  * nucleic selection will now detect nucleic residue names suffixed with 3 or 5
    (Issue #461)
  * Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
  * Fixed NCDFReader not reading dt (Issue #676)
  * Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
  * Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
  * Fixed cyzone selection failing in orthogonal systems (Issue #710)
  * Fixed Error in calculation of average grid density (Issue #716)
  * Fixed indexing an AtomGroup using a list of bools now working (Issue #729)

01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
         orbeckst, Balasubra

  * 0.13.0

API Changes

  * ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
  * XYZWriter can now be used as a container format for different protein models
    as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
    assumes that it is used as a container and won't give a warning if the
    number of atoms differs between frames.
  * GROWriter.fmt strings updated to use format style (Issue #494)
  * removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
    keyword for the functions in MDAnalysis.lib.distances (Issue #530)

Enhancement

  * ChainReader now reports times properly summed over sub-readers (Issue #522)
  * GRO file reading approximately 50% faster for large files (Issue #212)
  * GRO file writing now will write velocities where possible (Issue #494)
  * Added bonded selection (Issue #362)
  * Spherical layer and spherical zone selections now much faster (Issue #362)
  * new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
    to select "serial" or "OpenMP"-enabled versions of the code; the default
    is "serial" so old code will behave as before (see Issue #530)
  * Lammps data file parsing improved greatly.  Should now support all files,
    and triclinic geometry. (Issue #139)
  * Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
  * Added analysis.rdf, with InterRDF tool. (Issue #460)
  * Made Reader.check_slice_indices a public method (Issue #604)
  * analysis.helanal.helanal_main() now returns results as dict
  * Added keyword to update selection every frame in density calculation (Issue #584)
  * New keywords start, stop, step for density.density_from_Universe()
    to slice a trajectory.
  * MOL2Reader now reads molecule and substructure into ts.data
  * All subclasses of ProtoReader, Writer and TopologyReader are automatically
    added to the MDAnalysis directory of I/O (Issue #431)

Changes

  * built html doc files are no longer version controlled (Issue #491)
  * The lib._distances and lib_distances_openmp libraries now have a
    OPENMP_ENABLED boolean flag which indicates if openmp was used in
    compilation.  (Issue #530)
  * analysis.helanal.helanal_trajectory() and helanal_main() now use a
    logger at level INFO to output all their computed values instead
    of printing to stdout
  * default offset for ProgressMeter was changed from 0 to 1 (to match
    the change from 1- to 0-based ts.frame counting)
  * removed superfluous analysis.density.density_from_trajectory();
    use density_from_Universe(TOPOL, TRAJ) instead.
  * MOL2Writer.write now only writes a single frame (Issue #521)

Fixes

  * Fixed select_atoms requiring a trajectory be loaded (Issue #270)
  * AtomGroup timesteps no longer cached (Issue #606)
  * GROWriter now truncates atom numbers over 99999 (Issue #550)
  * AMBER netcdf writer now correctly uses float32 precision (Issue #518)
  * Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
    (Issue #533)
  * Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
  * Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
  * Fixed unpickling errors due to lingering dead universes. (Issue #487)
  * Fixed analysis.density modules requiring the defunct `skip` attribute
    on trajectories. (Issue #489)
  * ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
  * ten2eleven will now convert numatoms to n_atoms argument
    for writer() functions (Issue #470)
  * Fixed non-compliant Amber NCDFWriter (Issue #488)
  * Fixed many Timestep methods failing when positions weren't present
    (Issue #512)
  * Fixed PointSelection using KDTree (Issue #362)
  * Fixed GROParser getting tripped up by some file (Issue #548)
  * Fixed writing dx files from analysis.density.density_from_Universe()
    (Issue #544 and #410)
  * Fixed base.Reader._check_slice_indices not liking numpy ints
    (Issue #604)
  * Fixed broken analysis.helanal.helanal_trajectory() and
    helanal_main()
  * Fixed lib.util.greedy_splitext() (now returns full path)
  * Fixed MOL2Reader not reading molecule and substructure on init
    (Issue #521)
  * Fixed MOL2Writer rereading frames when writing them (Issue #521)
  * Fixed PDBWriter not writing occupancies from atoms (Issue #620)

10/08/15

  * 0.12.1 kain88-de, orbeckst, richardjgowers

API Changes

Enhancements

Changes

Fixes
  * Fixed OpenMP detection on Linux/OSX #459
  * Fixed reading of LAMMPS trajectory times: default unit ought
    to be fs and not ps
  * Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
    keyword argument Universe(..., dt=<dt>)
  * Fixed a bug in topology.core.guess_atom_element where a
    single digit atom name would raise an IndexError (#476)
  * Fixed numpy -> np in LeafletFinder

10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud

  * 0.12.0

API Changes

  * PrimitivePDBReader now imports occupancies into the `TimeStep` object.
    (Issue #396)
  * Atoms without a Universe now return NoDataError instead of
    AttributeError
  * AtomGroups of zero length or containing Atoms with no Universe raise
    a NoDataError when trying to access Universe
  * Atoms now keep a strong reference to Universe, meaning they
    do not become orphaned when the Universe goes out of scope (Issue #297)

Enhancements

  * `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
    `occupancies` properties (Issue #396)
  * XYZReader now supports frame indexing (Issue #428)
  * Reader objects can now be sliced using lists and arrays of indices
    (Issue #437)
  * `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
    neighbor plotting method (Issue #438)
  * New class `PSAPair` added to MDAnalysis.analysis.psa for handling
    Hausdorff pairs analysis (Issue #438)
  * `PSAnalysis` can now generate annotated heat maps (Issue #438)
  * Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
  * Additional getters added to `Path` and `PSAnalysis` (Issue #438)
  * MSD matrix function now globally available in MDAnalysis.analysis.psa
    (Issue #438)
  * Function for obtaining coordinate axes from numpy trajectories now
    globally available in MDAnalysis.analysis.psa (Issue #438)
  * TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
  * Setup.py now looks for some configuration values in a config file. Each
    config option can also be changed via environment variables if they are
    prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'

Changes
  * An AtomGroup with 0 atoms now yields an `IndexError` on call to
    `AtomGroup.write` (Issue #434)
  * `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
  * To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'

Fixes
  * Fixed minor issue in lib.mdamath.make_whole where if all bonds
    were correctly sized, it wouldn't notice that multiple fragments
    had been given. (Issue #445)
  * Fixed issue with PDB Topology parsing where if serials went
    over 100k, they wrapped to '***', breaking the parser (Issue #446)
  * Fixed AtomGroup.sequence() (Issue #451)
  * Fixed PrimitivePDBParser not detecting when resids had looped over
    10,000. The original resid is stored as Atom.resnum (Issue #454)
  * Fixed TPR topology parser to treat all bonded interactions available in
    Gromacs 5.1 (Issue #222 and #352, pull request #463).

09/07/15  tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
        manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
        gormanstock

  * 0.11.0

  This release brings large changes to many parts of the API and might
  break many existing scripts. For a full guide on the API changes,
  please see:

  https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide

  Migrating old scripts has been made easier with the introduction of
  the ten2eleven tool which is part of the package.
  Details on how to use this are available at:

  https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py

  API Changes

  * Changed AtomGroup counting methods to properties with different
    names: numberOfAtoms() to n_atoms, numberOfResidues() to
    n_residues, numberOfSegments() --> n_segments (Issue #376)
  * Changed trajectory reader numframes to n_frames (Issue #376)
  * Changed Timestep.numatoms to n_atoms (Issue #376)
  * Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
  * Changed atom.number attribute to atom.index (Issue #372)
  * Changed many AtomGroup methods to properties.  These are: indices,
    masses, charges, names, types, radii, resids, resnames, resnums,
    segids (Issue #372)
  * Timestep can now only init using an integer argument (which
    represents the number of atoms) (Issue #250)
  * Added from_timestep and from_coordinates construction methods
    to base.Timestep (Issue #250)
  * Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
    want to search in cartesian coordinates directly for nighboring
    points use the BioPython KDTree or scikit-learn Neighbors module.
    The AtomNeighborSearch class has been ported to use the BioPython
    KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
    MDAnalaysis.KDTree still exists in this version so load the
    NeighborSearch module but is deprecated and will be removed in
    1.0. (Issue #383)
  * Moved MDAnalysis.core.transformations to
    MDAnalysis.lib.transformations (Issue #287)
  * Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
  * Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
  * Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
  * Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
    (Issue #287)
  * Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
    (Issue #287)
  * Moved norm, normal, angle, stp and dihedral from lib.util to
    lib.mdamath (Issue #287)
  * AtomGroup.bond .angle .dihedral and .improper now return the
    corresponding TopologyObject rather than performing the calculation
    (Issue #373)
  * All TopologyObjects now have a "value" method to evaluate them
    (Issue #373)
  * TopologyGroup now has a "values" methods to evaluate all contained
    bonds (Issue #373)
  * MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
    (Issue #373)
  * TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
  * deprecated camelCase AtomGroup methods in favour of underscore_style
    (Issue #389)
  * deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
  * AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
    of equal size to AtomGroup (Issue #385)
  * ResidueGroup.segids now gives arrays of equal size to ResidueGroup
    (Issue #385)
  * AtomGroup setters `set_<property>` now plural for consistency with
    property names (Issue #385)
  * DCDReader no longer supports the "skip" keyword.  Use slicing
    on reader iteration to achieve same affect. (Issue #350)
  * All Readers have a default "dt" of 1.0 ps.  This applies also to
    single frame readers, these would previously raise an error on
    accessing dt. (Issue #350)
  * NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)

  Enhancements

  * Added the 'global' selection keyword (Issue #268)
  * Added Jmol selection writer (Issue #356)
  * Added reading of Hoomd XML files (Issue #333)
    These can only act as topology information for now
  * Tests can now detect memleaks on a per-test basis (Issue #323)
  * AtomGroups can now be pickled/unpickled (Issue #293)
  * Universes can have a __del__ method (not actually added) without
    leaking (Issue #297)
  * Added reading of DL_Poly format CONFIG and HISTORY files, these can
    both act as both Topology and Coordinate information (Issue #298)
  * Timestep objects now have __eq__ method (Issue #294)
  * coordinates.base.Timestep now can handle velocities and forces
    (Issue #294)
  * Waterdynamics analysis module added, including five analysis
    classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
    Angular Distribution, Mean Square Displacement and Survival
    Probability. Documentation and test are included. (Issue #300)
  * RMSF class added to rms analysis module
  * ProgressMeter now outputs every *interval* number of ``update``
    calls (Issue #313)
  * Created lib.mdamath for common mathematical functions. (Issue #287)
  * All Timesteps have the has_positions has_velocities and has_forces
    boolean flags (Issue #213)
  * Timesteps can now allocate velocities and forces if they weren't
    originally created with these through the use of the has_ flags.
    (Issue #213)
  * Timesteps now store 'dt' and 'time_offset' if passed to them by
    Reader to calculate time attribute (Issues #306 and #307)
  * MDAnalysis.selection: can also be written to a NamedStream
  * Added function lib.mdamath.make_whole to "unbreak" molecules
    over periodic boundaries. (Issue #355)
  * Added triclinic_dimensions to Timestep, returns representation of
    unit cell as triclinic vectors (Issue #276)
  * Added setter to bfactors property (Issue #372)
  * Added AtomGroup altLocs and serials properties with setters.
    (Issue #372)
  * MDAnalysis.core.AtomGroup.Merge now copies across bonding
    information (Issue #249)

  Changes

  * numpy >= 1.5 required
  * A ProtoReader class intermediate between IObase and Reader was added
    so specific Readers can be subclassed without __del__ (the
    ChainReader and SingleFrameReader), thus preventing memleaks
    (Issue #312).
  * Atoms (and all container classes thereof) are now bound to Universes
    only via weakrefs. If Universes are not explicitly kept in scope
    Atoms will become orphaned. (Issue #297)
  * Removed FormatError, now replaced by ValueError (Issue #294)
  * base.Reader now defines __iter__ and __iter__ removed from many
    Readers (now use base.Reader implementation) (Issue #350)
  * Timestep._x _y and _z are now read only (Issue #213)
  * moved MDAnalysis.selections.base.get_writer() to
    MDAnalysis.selections.get_writer() to break a circular import. This
    should not affect any code because
    MDAnalysis.selections.get_writer() already existed.
  * distances.contact_matrix now treats the particle distance with
    itself as a contact for sparse matrices and numpy arrays. The
    progress reporting for sparse calculations has been removed.
    (Issue #375)
  * TopologyObjects and TopologyGroup moved to core.topologyobjects
    module (Issue #373)
  * Consolidated coordinates.guess_format and topology.guess_format to
    lib.util.guess_format  (Issue #336)

  Fixes

  * All Writers now refer to time between written Timesteps as "dt",
    was previously "delta" in some Writers. (Issue #206)
  * Topology files can now be compressed (Issue #336)
  * Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
  * Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
    to refer to time elapsed between timesteps. (Issue #350 and #206)
  * Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
  * ChainReaders no longer cause memory leak (Issue #312)
  * analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
    static selections (Issue #296)
  * Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
  * relative imports are now banned in unit testing modules
    (Issue #189)
  * Fixed bug and added DivisionByZero exception in
    analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
  * Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
  * Fixed contact_matrix handles periodic boundary conditions correctly
    for sparse matrices. (Issue #375)
  * Fixed analysis.hole not using CPOINT (Issue #384)
  * Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
  * Fixed TopologyGroup.from_indices not guessing topology object class
    (Issue #409)
  * Fixed TopologyGroup.__contains__ failing if different instance of
    same bond was queried. (Issue #409)

06/01/15  richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
          sseyler
  * 0.10.0

  Enhancements

  * Improved performance of PDB Reading.  Up to 3x faster. (Issue #212)
  * Added the 'same ... as' selection keyword (Issue #217)
  * Added guess_bonds keyword argument to Universe creation.  This will attempt to
    guess all topology information on Universe creation. (Issue #245)
  * Added guess_bonds method to AtomGroup. (Issue #245)
  * All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
  * TopologyGroup now has alternate constructor method, .from_indices()
  * Added TopologyObject.indices property
  * Amber netCDF4 Reader will now read Forces (Issue #257)
  * Amber netCDF4 Writer will now write Velocities and Forces
  * Added Amber coordinate/restart file reader (Issue #262)
  * Structural superpositions (MDAnalysis.analysis.align) can work
    with partial matches of atoms.
  * new path similarity analysis module MDAnalysis.analysis.psa
  * AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
    works identically to numpy masks. (Issue #282)

  Changes

  * TopologyGroup can now have zero length, and will evaluate to False
    when empty.
  * Renamed TopologyGroup.dump_contents to "to_indices"
  * Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
  * PrimitivePDBReader now requires the numatoms keyword
  * Structural superpositions (MDAnalysis.analysis.align) use partial
    matches of atoms by default (use strict=True for old behavior)
  * Function rmsd() was removed from MDAnalysis.analysis.align name
    space and should be accessed as MDAnalysis.analysis.rms.rmsd()

  Fixes

  * bynum selections now work from AtomGroup instances (Issue #275)
  * Cylinder selections now work from AtomGroup instances and honor
    PBC (Issue #274)
  * NetCDFWriter previously always wrote velocities/forces if found
    in timestep, rather than following how the Writer was created.

04/20/15  tyler.je.reddy, richardjgowers, orbeckst
  * 0.9.2

  Enhancements

  * Can now set velocity from Atom object. (Issue 221)
  * Atom object now has force attribute for getting/setting forces (requires a
    trajectory with forces) (Issue 221)
  * Added wrap method. Wrap allows the centers of groups of atoms to be
    moved within the primary unit cell without breaking up the group. (Issue 190)

  Changes

  * The MDAnalysis project moved from Google Code to GitHub: the new
    website is http://www.mdanalysis.org and the new source code
    repository is at https://github.com/MDAnalysis/mdanalysis
  * "applications" were removed from the mdanalysis source code
    repository and now exist as independent repositories under
    https://github.com/MDAnalysis/
  * Using a non-existent atom name as an instant selector now raises
    AttributeError instead of SelectionError (Issue 220)

  Fixes

  * trajectory objects are now properly closed in unit tests (Issue 256)

03/27/15  manuel.nuno.melo, richardjgowers, comconadin
  * 0.9.1

  Enhancements

  * XYZ file format can be used without an associated topology file.
  * GAMESS output files can be read as trajectories for calculations of
    type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)

  Changes

  * removed undocumented MDAnalysis.builder module

  Fixes

  * TRR coordinate access via _y and _z now works properly (Issue 224)

03/15/15  richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
          bala.biophysics, dotsdl, sebastien.buchoux
  * 0.9.0

  Enhancements

  * offsets for XTC and TRR trajectories now stored and retrieved
    automatically; improves init times for large trajectories (Issue 208)
  * docs now use secure mathjax CDN (Issue 182)
  * minor improvements to helanal docstring
  * Support for reading altloc records in PDB files
  * Cap proteins with ACE and NMA terminal caps
  * MOL2 read and write support
  * 2D streamplot code no longer uses deprecated matplotlib.nxutils module
  * core.distances.calc_angles and calc_torsions now accept an optional box
    argument to consider periodic boundary conditions in their calculation
    (Issue 172)
  * TopologyGroup angles and torsions methods both have a pbc flag, (default
    False) to toggle consideration of periodic boundaries
  * XYZWriter (write simple XYZ trajectories)
  * TRZReader upgrades, seeking and numframes faster
  * PQRWriter (write PQR files)
  * HydrogenBond analysis: new keyword distance_type to alternatively
    look at the distance between heavy atoms (Issue 185)
  * TopologyGroup/TopologyDict system overhauled. (Issue 194)
  * TopologyObject class created, Bonds/Angles/etc nicer to work with.
  * Topology information is now loaded lazily into Universe, can be forced to
    load all with u.load_topology(). All topology information is now stored in
    .bonds .angles .torsions and .impropers attributes.
  * Added support for improper torsions.
  * AtomGroup now has .bonds .angles .torsions and .impropers attributes which
    retrieve relevant TopologyGroups
  * Increased performance of topology.core.guess_bonds greatly
  * Added topology.core.guess_angles guess_torsions and guess_improper_torsions
    which given accurate bond information can calculate the rest of the
    topology info.
  * Universe topology information is now settable after initialisation using lists of indices
    such as those provided by the guess_* functions.
  * Added LAMMPS data parser for topology files with the .data suffix. Can also
    read single frame coordinate & velocity information from these files.
    (Issue 139)
  * Added Fragments.  Fragments are continuously bonded groups of atoms.
    These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
    attributes.
    (Issue 190)
  * Added ability to remove items from Universe cache with _clear_caches.
  * Added ability to define dimensions from AtomGroup, Universe and Timestep for most
    formats.
    (Issue 203)
  * streamIO: many readers can directly use gzip- or bzip2 compressed
    files or a stream (such as cStringIO.StringIO) wrapped in
    util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
    GRO, MOL2, XYZ
  * Added hydrogen bonding time autocorrelation analysis module
    (analysis.hbonds.HydrogenBondAutoCorrel)
  * Added energy units to core.units (Issue 214)
  * New AtomGroup.split() method to produce a list of AtomGroups for each atom,
    residue, or segment
  * New AtomGroup.sequence() method to extract a protein sequence.
  * Can pass subclasses of Reader and Topology reader to Universe init to allow
    custom readers to be defined. (Issue 198)
  * Added Atom.bonded_atoms property.  This returns an AtomGroup of the Atoms
    that are bonded to a given Atom. (Issue 219)
  * Added atom selections to ContactAnalysis (Issue 169)

  Changes

  * DCD unitcell format changed: MDAnalysis will now read it as [A,
    gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
    C]. The new CHARMM box vector unitcell format is heuristically guessed.
    (see Issue 187 for a full discussion and implications).
  * __getstate__() and __setstate__() raise an NotImplementedError for
    Universe and AtomGroup; before they were silently accepted on
    pickling and a cryptic "TypeError: AtomGroup is not callable" was
    raised (see also Issue 173 for detailed explanation)
  * XTC/TRR reader raise IOError with errorcode EIO (instead of
    ENODATA) when the last frame is reached and EBADF (instead of
    EFAULT) for any other issues (partially addresses Issue 150,
    Windows compatibility)
  * Universe.bonds now returns a TopologyGroup not a list.  TopologyGroup can be
    iterated over; list(universe.bonds) should provide a fix to legacy code.
  * PQR reader will now set segid to a chainID if found in the PQR
    file (previously, the segid would always be set to 'SYSTEM').
  * util.anyopen() only returns the stream and not the tuple (stream,
    filename) anymore; it tries to set stream.name instead
  * topology reading now done via classes (similar to trajectory reading)
    rather than functions.
    (Issue 210)

  Fixes

  * fixed DCD triclinic unit cell reading and writing (although the new CHARMM
    format with the box matrix is not supported for writing) (Issue 187)
    ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
  * fixed creation of residues and segments in Merge()
  * resolves Issue 188 regarding Helanal Finish Argument
  * fixed Issue 184 (TPR files with double precision)
  * fixed Issue 199 (FutureWarning in pyqcprot)

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=14d1b5101c20d475b0d8affa88170e9e36a27cd5

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 py-mdanalysis/Makefile |  12 ++-
 py-mdanalysis/PLIST    | 242 ++++++++++++++++++++++++++++++++++++++-----------
 py-mdanalysis/distinfo |   7 +-
 3 files changed, 200 insertions(+), 61 deletions(-)

diffs:
diff --git a/py-mdanalysis/Makefile b/py-mdanalysis/Makefile
index 006a359..b247275 100644
--- a/py-mdanalysis/Makefile
+++ b/py-mdanalysis/Makefile
@@ -1,16 +1,22 @@
 # $NetBSD: Makefile,v 1.11 2014/05/09 07:38:48 thomasklausner Exp $
 
-DISTNAME=	MDAnalysis-0.8.0rc4
+DISTNAME=	MDAnalysis-0.15.0
 PKGNAME=	${PYPKGPREFIX}-${DISTNAME:tl}
 CATEGORIES=	biology
-MASTER_SITES=	http://mdanalysis.googlecode.com/files/
+MASTER_SITES=	${MASTER_SITE_PYPI:=M/MDAnalysis/}
 
 MAINTAINER=	jihbed.research%gmail.com@localhost
-HOMEPAGE=	http://code.google.com/p/mdanalysis/
+HOMEPAGE=	http://www.mdanalysis.org/
 COMMENT=   	Library to analyze and manipulate molecular dynamics trajectories
 LICENSE=	gnu-gpl-v2
 
 DEPENDS+=	${PYPKGPREFIX}-biopython>=1.63:../../wip/biopython
+DEPENDS+=	${PYPKGPREFIX}-networkx-[0-9]*:../../math/py-networkx
+DEPENDS+=	${PYPKGPREFIX}-six-[0-9]*:../../lang/py-six
+# also needs unpackaged GridDataFormats
+# TEST_DEPENDS
+BUILD_DEPENDS+=	${PYPKGPREFIX}-nose-[0-9]*:../../devel/py-nose
+# also needs unpackaged MDAnalysisTests for tests
 
 USE_LANGUAGES=	c c++
 
diff --git a/py-mdanalysis/PLIST b/py-mdanalysis/PLIST
index 7e512f7..337a258 100644
--- a/py-mdanalysis/PLIST
+++ b/py-mdanalysis/PLIST
@@ -1,23 +1,13 @@
-@comment $NetBSD: PLIST,v 1.3 2014/01/03 21:28:42 jihbed Exp $
+@comment $NetBSD$
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
 ${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
 ${PYSITELIB}/${EGG_INFODIR}/requires.txt
 ${PYSITELIB}/${EGG_INFODIR}/top_level.txt
-${PYSITELIB}/MDAnalysis/KDTree/CKDTree.py
-${PYSITELIB}/MDAnalysis/KDTree/CKDTree.pyc
-${PYSITELIB}/MDAnalysis/KDTree/CKDTree.pyo
-${PYSITELIB}/MDAnalysis/KDTree/KDTree.py
-${PYSITELIB}/MDAnalysis/KDTree/KDTree.pyc
-${PYSITELIB}/MDAnalysis/KDTree/KDTree.pyo
-${PYSITELIB}/MDAnalysis/KDTree/NeighborSearch.py
-${PYSITELIB}/MDAnalysis/KDTree/NeighborSearch.pyc
-${PYSITELIB}/MDAnalysis/KDTree/NeighborSearch.pyo
-${PYSITELIB}/MDAnalysis/KDTree/_CKDTree.so
-${PYSITELIB}/MDAnalysis/KDTree/__init__.py
-${PYSITELIB}/MDAnalysis/KDTree/__init__.pyc
-${PYSITELIB}/MDAnalysis/KDTree/__init__.pyo
+${PYSITELIB}/MDAnalysis/KDTree.py
+${PYSITELIB}/MDAnalysis/KDTree.pyc
+${PYSITELIB}/MDAnalysis/KDTree.pyo
 ${PYSITELIB}/MDAnalysis/__init__.py
 ${PYSITELIB}/MDAnalysis/__init__.pyc
 ${PYSITELIB}/MDAnalysis/__init__.pyo
@@ -27,6 +17,9 @@ ${PYSITELIB}/MDAnalysis/analysis/__init__.pyo
 ${PYSITELIB}/MDAnalysis/analysis/align.py
 ${PYSITELIB}/MDAnalysis/analysis/align.pyc
 ${PYSITELIB}/MDAnalysis/analysis/align.pyo
+${PYSITELIB}/MDAnalysis/analysis/base.py
+${PYSITELIB}/MDAnalysis/analysis/base.pyc
+${PYSITELIB}/MDAnalysis/analysis/base.pyo
 ${PYSITELIB}/MDAnalysis/analysis/contacts.py
 ${PYSITELIB}/MDAnalysis/analysis/contacts.pyc
 ${PYSITELIB}/MDAnalysis/analysis/contacts.pyo
@@ -39,9 +32,15 @@ ${PYSITELIB}/MDAnalysis/analysis/distances.pyo
 ${PYSITELIB}/MDAnalysis/analysis/gnm.py
 ${PYSITELIB}/MDAnalysis/analysis/gnm.pyc
 ${PYSITELIB}/MDAnalysis/analysis/gnm.pyo
-${PYSITELIB}/MDAnalysis/analysis/hbonds.py
-${PYSITELIB}/MDAnalysis/analysis/hbonds.pyc
-${PYSITELIB}/MDAnalysis/analysis/hbonds.pyo
+${PYSITELIB}/MDAnalysis/analysis/hbonds/__init__.py
+${PYSITELIB}/MDAnalysis/analysis/hbonds/__init__.pyc
+${PYSITELIB}/MDAnalysis/analysis/hbonds/__init__.pyo
+${PYSITELIB}/MDAnalysis/analysis/hbonds/hbond_analysis.py
+${PYSITELIB}/MDAnalysis/analysis/hbonds/hbond_analysis.pyc
+${PYSITELIB}/MDAnalysis/analysis/hbonds/hbond_analysis.pyo
+${PYSITELIB}/MDAnalysis/analysis/hbonds/hbond_autocorrel.py
+${PYSITELIB}/MDAnalysis/analysis/hbonds/hbond_autocorrel.pyc
+${PYSITELIB}/MDAnalysis/analysis/hbonds/hbond_autocorrel.pyo
 ${PYSITELIB}/MDAnalysis/analysis/helanal.py
 ${PYSITELIB}/MDAnalysis/analysis/helanal.pyc
 ${PYSITELIB}/MDAnalysis/analysis/helanal.pyo
@@ -51,36 +50,60 @@ ${PYSITELIB}/MDAnalysis/analysis/hole.pyo
 ${PYSITELIB}/MDAnalysis/analysis/leaflet.py
 ${PYSITELIB}/MDAnalysis/analysis/leaflet.pyc
 ${PYSITELIB}/MDAnalysis/analysis/leaflet.pyo
+${PYSITELIB}/MDAnalysis/analysis/lineardensity.py
+${PYSITELIB}/MDAnalysis/analysis/lineardensity.pyc
+${PYSITELIB}/MDAnalysis/analysis/lineardensity.pyo
 ${PYSITELIB}/MDAnalysis/analysis/nuclinfo.py
 ${PYSITELIB}/MDAnalysis/analysis/nuclinfo.pyc
 ${PYSITELIB}/MDAnalysis/analysis/nuclinfo.pyo
+${PYSITELIB}/MDAnalysis/analysis/polymer.py
+${PYSITELIB}/MDAnalysis/analysis/polymer.pyc
+${PYSITELIB}/MDAnalysis/analysis/polymer.pyo
+${PYSITELIB}/MDAnalysis/analysis/psa.py
+${PYSITELIB}/MDAnalysis/analysis/psa.pyc
+${PYSITELIB}/MDAnalysis/analysis/psa.pyo
+${PYSITELIB}/MDAnalysis/analysis/rdf.py
+${PYSITELIB}/MDAnalysis/analysis/rdf.pyc
+${PYSITELIB}/MDAnalysis/analysis/rdf.pyo
 ${PYSITELIB}/MDAnalysis/analysis/rms.py
 ${PYSITELIB}/MDAnalysis/analysis/rms.pyc
 ${PYSITELIB}/MDAnalysis/analysis/rms.pyo
+${PYSITELIB}/MDAnalysis/analysis/waterdynamics.py
+${PYSITELIB}/MDAnalysis/analysis/waterdynamics.pyc
+${PYSITELIB}/MDAnalysis/analysis/waterdynamics.pyo
 ${PYSITELIB}/MDAnalysis/analysis/x3dna.py
 ${PYSITELIB}/MDAnalysis/analysis/x3dna.pyc
 ${PYSITELIB}/MDAnalysis/analysis/x3dna.pyo
-${PYSITELIB}/MDAnalysis/builder/__init__.py
-${PYSITELIB}/MDAnalysis/builder/__init__.pyc
-${PYSITELIB}/MDAnalysis/builder/__init__.pyo
-${PYSITELIB}/MDAnalysis/builder/charmm.py
-${PYSITELIB}/MDAnalysis/builder/charmm.pyc
-${PYSITELIB}/MDAnalysis/builder/charmm.pyo
+${PYSITELIB}/MDAnalysis/authors.py
+${PYSITELIB}/MDAnalysis/authors.pyc
+${PYSITELIB}/MDAnalysis/authors.pyo
 ${PYSITELIB}/MDAnalysis/coordinates/CRD.py
 ${PYSITELIB}/MDAnalysis/coordinates/CRD.pyc
 ${PYSITELIB}/MDAnalysis/coordinates/CRD.pyo
 ${PYSITELIB}/MDAnalysis/coordinates/DCD.py
 ${PYSITELIB}/MDAnalysis/coordinates/DCD.pyc
 ${PYSITELIB}/MDAnalysis/coordinates/DCD.pyo
+${PYSITELIB}/MDAnalysis/coordinates/DLPoly.py
+${PYSITELIB}/MDAnalysis/coordinates/DLPoly.pyc
+${PYSITELIB}/MDAnalysis/coordinates/DLPoly.pyo
 ${PYSITELIB}/MDAnalysis/coordinates/DMS.py
 ${PYSITELIB}/MDAnalysis/coordinates/DMS.pyc
 ${PYSITELIB}/MDAnalysis/coordinates/DMS.pyo
+${PYSITELIB}/MDAnalysis/coordinates/GMS.py
+${PYSITELIB}/MDAnalysis/coordinates/GMS.pyc
+${PYSITELIB}/MDAnalysis/coordinates/GMS.pyo
 ${PYSITELIB}/MDAnalysis/coordinates/GRO.py
 ${PYSITELIB}/MDAnalysis/coordinates/GRO.pyc
 ${PYSITELIB}/MDAnalysis/coordinates/GRO.pyo
+${PYSITELIB}/MDAnalysis/coordinates/INPCRD.py
+${PYSITELIB}/MDAnalysis/coordinates/INPCRD.pyc
+${PYSITELIB}/MDAnalysis/coordinates/INPCRD.pyo
 ${PYSITELIB}/MDAnalysis/coordinates/LAMMPS.py
 ${PYSITELIB}/MDAnalysis/coordinates/LAMMPS.pyc
 ${PYSITELIB}/MDAnalysis/coordinates/LAMMPS.pyo
+${PYSITELIB}/MDAnalysis/coordinates/MOL2.py
+${PYSITELIB}/MDAnalysis/coordinates/MOL2.pyc
+${PYSITELIB}/MDAnalysis/coordinates/MOL2.pyo
 ${PYSITELIB}/MDAnalysis/coordinates/PDB.py
 ${PYSITELIB}/MDAnalysis/coordinates/PDB.pyc
 ${PYSITELIB}/MDAnalysis/coordinates/PDB.pyo
@@ -99,6 +122,9 @@ ${PYSITELIB}/MDAnalysis/coordinates/TRR.pyo
 ${PYSITELIB}/MDAnalysis/coordinates/TRZ.py
 ${PYSITELIB}/MDAnalysis/coordinates/TRZ.pyc
 ${PYSITELIB}/MDAnalysis/coordinates/TRZ.pyo
+${PYSITELIB}/MDAnalysis/coordinates/XDR.py
+${PYSITELIB}/MDAnalysis/coordinates/XDR.pyc
+${PYSITELIB}/MDAnalysis/coordinates/XDR.pyo
 ${PYSITELIB}/MDAnalysis/coordinates/XTC.py
 ${PYSITELIB}/MDAnalysis/coordinates/XTC.pyc
 ${PYSITELIB}/MDAnalysis/coordinates/XTC.pyo
@@ -116,31 +142,6 @@ ${PYSITELIB}/MDAnalysis/coordinates/core.py
 ${PYSITELIB}/MDAnalysis/coordinates/core.pyc
 ${PYSITELIB}/MDAnalysis/coordinates/core.pyo
 ${PYSITELIB}/MDAnalysis/coordinates/dcdtimeseries.so
-${PYSITELIB}/MDAnalysis/coordinates/pdb/__init__.py
-${PYSITELIB}/MDAnalysis/coordinates/pdb/__init__.pyc
-${PYSITELIB}/MDAnalysis/coordinates/pdb/__init__.pyo
-${PYSITELIB}/MDAnalysis/coordinates/pdb/extensions.py
-${PYSITELIB}/MDAnalysis/coordinates/pdb/extensions.pyc
-${PYSITELIB}/MDAnalysis/coordinates/pdb/extensions.pyo
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/TRR.py
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/TRR.pyc
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/TRR.pyo
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/XTC.py
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/XTC.pyc
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/XTC.pyo
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/__init__.py
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/__init__.pyc
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/__init__.pyo
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/_libxdrfile.so
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/core.py
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/core.pyc
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/core.pyo
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/libxdrfile.py
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/libxdrfile.pyc
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/libxdrfile.pyo
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/statno.py
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/statno.pyc
-${PYSITELIB}/MDAnalysis/coordinates/xdrfile/statno.pyo
 ${PYSITELIB}/MDAnalysis/core/AtomGroup.py
 ${PYSITELIB}/MDAnalysis/core/AtomGroup.pyc
 ${PYSITELIB}/MDAnalysis/core/AtomGroup.pyo
@@ -153,16 +154,21 @@ ${PYSITELIB}/MDAnalysis/core/Timeseries.pyo
 ${PYSITELIB}/MDAnalysis/core/__init__.py
 ${PYSITELIB}/MDAnalysis/core/__init__.pyc
 ${PYSITELIB}/MDAnalysis/core/__init__.pyo
-${PYSITELIB}/MDAnalysis/core/_transformations.so
-${PYSITELIB}/MDAnalysis/core/distances.so
+${PYSITELIB}/MDAnalysis/core/distances.py
+${PYSITELIB}/MDAnalysis/core/distances.pyc
+${PYSITELIB}/MDAnalysis/core/distances.pyo
 ${PYSITELIB}/MDAnalysis/core/log.py
 ${PYSITELIB}/MDAnalysis/core/log.pyc
 ${PYSITELIB}/MDAnalysis/core/log.pyo
-${PYSITELIB}/MDAnalysis/core/parallel/__init__.py
-${PYSITELIB}/MDAnalysis/core/parallel/__init__.pyc
-${PYSITELIB}/MDAnalysis/core/parallel/__init__.pyo
-${PYSITELIB}/MDAnalysis/core/parallel/distances.so
-${PYSITELIB}/MDAnalysis/core/qcprot.so
+${PYSITELIB}/MDAnalysis/core/parallel.py
+${PYSITELIB}/MDAnalysis/core/parallel.pyc
+${PYSITELIB}/MDAnalysis/core/parallel.pyo
+${PYSITELIB}/MDAnalysis/core/qcprot.py
+${PYSITELIB}/MDAnalysis/core/qcprot.pyc
+${PYSITELIB}/MDAnalysis/core/qcprot.pyo
+${PYSITELIB}/MDAnalysis/core/topologyobjects.py
+${PYSITELIB}/MDAnalysis/core/topologyobjects.pyc
+${PYSITELIB}/MDAnalysis/core/topologyobjects.pyo
 ${PYSITELIB}/MDAnalysis/core/transformations.py
 ${PYSITELIB}/MDAnalysis/core/transformations.pyc
 ${PYSITELIB}/MDAnalysis/core/transformations.pyo
@@ -172,6 +178,96 @@ ${PYSITELIB}/MDAnalysis/core/units.pyo
 ${PYSITELIB}/MDAnalysis/core/util.py
 ${PYSITELIB}/MDAnalysis/core/util.pyc
 ${PYSITELIB}/MDAnalysis/core/util.pyo
+${PYSITELIB}/MDAnalysis/exceptions.py
+${PYSITELIB}/MDAnalysis/exceptions.pyc
+${PYSITELIB}/MDAnalysis/exceptions.pyo
+${PYSITELIB}/MDAnalysis/lib/NeighborSearch.py
+${PYSITELIB}/MDAnalysis/lib/NeighborSearch.pyc
+${PYSITELIB}/MDAnalysis/lib/NeighborSearch.pyo
+${PYSITELIB}/MDAnalysis/lib/__init__.py
+${PYSITELIB}/MDAnalysis/lib/__init__.pyc
+${PYSITELIB}/MDAnalysis/lib/__init__.pyo
+${PYSITELIB}/MDAnalysis/lib/_transformations.so
+${PYSITELIB}/MDAnalysis/lib/c_distances.so
+${PYSITELIB}/MDAnalysis/lib/c_distances_openmp.so
+${PYSITELIB}/MDAnalysis/lib/distances.py
+${PYSITELIB}/MDAnalysis/lib/distances.pyc
+${PYSITELIB}/MDAnalysis/lib/distances.pyo
+${PYSITELIB}/MDAnalysis/lib/formats/__init__.py
+${PYSITELIB}/MDAnalysis/lib/formats/__init__.pyc
+${PYSITELIB}/MDAnalysis/lib/formats/__init__.pyo
+${PYSITELIB}/MDAnalysis/lib/formats/cython_util.so
+${PYSITELIB}/MDAnalysis/lib/formats/libmdaxdr.so
+${PYSITELIB}/MDAnalysis/lib/log.py
+${PYSITELIB}/MDAnalysis/lib/log.pyc
+${PYSITELIB}/MDAnalysis/lib/log.pyo
+${PYSITELIB}/MDAnalysis/lib/mdamath.py
+${PYSITELIB}/MDAnalysis/lib/mdamath.pyc
+${PYSITELIB}/MDAnalysis/lib/mdamath.pyo
+${PYSITELIB}/MDAnalysis/lib/qcprot.so
+${PYSITELIB}/MDAnalysis/lib/transformations.py
+${PYSITELIB}/MDAnalysis/lib/transformations.pyc
+${PYSITELIB}/MDAnalysis/lib/transformations.pyo
+${PYSITELIB}/MDAnalysis/lib/util.py
+${PYSITELIB}/MDAnalysis/lib/util.pyc
+${PYSITELIB}/MDAnalysis/lib/util.pyo
+${PYSITELIB}/MDAnalysis/migration/__init__.py
+${PYSITELIB}/MDAnalysis/migration/__init__.pyc
+${PYSITELIB}/MDAnalysis/migration/__init__.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/__init__.py
+${PYSITELIB}/MDAnalysis/migration/fixes/__init__.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/__init__.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agcountmethods.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agcountmethods.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agcountmethods.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agmethods.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agmethods.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agmethods.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agmethods2.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agmethods2.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agmethods2.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agsetterpluralization.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agsetterpluralization.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_agsetterpluralization.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_calctorsions.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_calctorsions.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_calctorsions.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_camelcase.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_camelcase.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_camelcase.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_framenumberingzerobased.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_framenumberingzerobased.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_framenumberingzerobased.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_mdaimports.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_mdaimports.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_mdaimports.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_numframes.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_numframes.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_numframes.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_selectatoms.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_selectatoms.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_selectatoms.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_torsionclasses.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_torsionclasses.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_torsionclasses.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_torsions.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_torsions.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_torsions.pyo
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_writer.py
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_writer.pyc
+${PYSITELIB}/MDAnalysis/migration/fixes/fix_writer.pyo
+${PYSITELIB}/MDAnalysis/migration/ten2eleven.py
+${PYSITELIB}/MDAnalysis/migration/ten2eleven.pyc
+${PYSITELIB}/MDAnalysis/migration/ten2eleven.pyo
+${PYSITELIB}/MDAnalysis/migration/test_dummy_old_MDA_code.py
+${PYSITELIB}/MDAnalysis/migration/test_dummy_old_MDA_code.pyc
+${PYSITELIB}/MDAnalysis/migration/test_dummy_old_MDA_code.pyo
+${PYSITELIB}/MDAnalysis/migration/test_dummy_torsion.py
+${PYSITELIB}/MDAnalysis/migration/test_dummy_torsion.pyc
+${PYSITELIB}/MDAnalysis/migration/test_dummy_torsion.pyo
 ${PYSITELIB}/MDAnalysis/selections/__init__.py
 ${PYSITELIB}/MDAnalysis/selections/__init__.pyc
 ${PYSITELIB}/MDAnalysis/selections/__init__.pyo
@@ -184,6 +280,9 @@ ${PYSITELIB}/MDAnalysis/selections/charmm.pyo
 ${PYSITELIB}/MDAnalysis/selections/gromacs.py
 ${PYSITELIB}/MDAnalysis/selections/gromacs.pyc
 ${PYSITELIB}/MDAnalysis/selections/gromacs.pyo
+${PYSITELIB}/MDAnalysis/selections/jmol.py
+${PYSITELIB}/MDAnalysis/selections/jmol.pyc
+${PYSITELIB}/MDAnalysis/selections/jmol.pyo
 ${PYSITELIB}/MDAnalysis/selections/pymol.py
 ${PYSITELIB}/MDAnalysis/selections/pymol.pyc
 ${PYSITELIB}/MDAnalysis/selections/pymol.pyo
@@ -199,18 +298,30 @@ ${PYSITELIB}/MDAnalysis/tests/datafiles.pyo
 ${PYSITELIB}/MDAnalysis/topology/CRDParser.py
 ${PYSITELIB}/MDAnalysis/topology/CRDParser.pyc
 ${PYSITELIB}/MDAnalysis/topology/CRDParser.pyo
+${PYSITELIB}/MDAnalysis/topology/DLPolyParser.py
+${PYSITELIB}/MDAnalysis/topology/DLPolyParser.pyc
+${PYSITELIB}/MDAnalysis/topology/DLPolyParser.pyo
 ${PYSITELIB}/MDAnalysis/topology/DMSParser.py
 ${PYSITELIB}/MDAnalysis/topology/DMSParser.pyc
 ${PYSITELIB}/MDAnalysis/topology/DMSParser.pyo
 ${PYSITELIB}/MDAnalysis/topology/ExtendedPDBParser.py
 ${PYSITELIB}/MDAnalysis/topology/ExtendedPDBParser.pyc
 ${PYSITELIB}/MDAnalysis/topology/ExtendedPDBParser.pyo
+${PYSITELIB}/MDAnalysis/topology/GMSParser.py
+${PYSITELIB}/MDAnalysis/topology/GMSParser.pyc
+${PYSITELIB}/MDAnalysis/topology/GMSParser.pyo
 ${PYSITELIB}/MDAnalysis/topology/GROParser.py
 ${PYSITELIB}/MDAnalysis/topology/GROParser.pyc
 ${PYSITELIB}/MDAnalysis/topology/GROParser.pyo
+${PYSITELIB}/MDAnalysis/topology/HoomdXMLParser.py
+${PYSITELIB}/MDAnalysis/topology/HoomdXMLParser.pyc
+${PYSITELIB}/MDAnalysis/topology/HoomdXMLParser.pyo
 ${PYSITELIB}/MDAnalysis/topology/LAMMPSParser.py
 ${PYSITELIB}/MDAnalysis/topology/LAMMPSParser.pyc
 ${PYSITELIB}/MDAnalysis/topology/LAMMPSParser.pyo
+${PYSITELIB}/MDAnalysis/topology/MOL2Parser.py
+${PYSITELIB}/MDAnalysis/topology/MOL2Parser.pyc
+${PYSITELIB}/MDAnalysis/topology/MOL2Parser.pyo
 ${PYSITELIB}/MDAnalysis/topology/PDBParser.py
 ${PYSITELIB}/MDAnalysis/topology/PDBParser.pyc
 ${PYSITELIB}/MDAnalysis/topology/PDBParser.pyo
@@ -232,9 +343,15 @@ ${PYSITELIB}/MDAnalysis/topology/TOPParser.pyo
 ${PYSITELIB}/MDAnalysis/topology/TPRParser.py
 ${PYSITELIB}/MDAnalysis/topology/TPRParser.pyc
 ${PYSITELIB}/MDAnalysis/topology/TPRParser.pyo
+${PYSITELIB}/MDAnalysis/topology/XYZParser.py
+${PYSITELIB}/MDAnalysis/topology/XYZParser.pyc
+${PYSITELIB}/MDAnalysis/topology/XYZParser.pyo
 ${PYSITELIB}/MDAnalysis/topology/__init__.py
 ${PYSITELIB}/MDAnalysis/topology/__init__.pyc
 ${PYSITELIB}/MDAnalysis/topology/__init__.pyo
+${PYSITELIB}/MDAnalysis/topology/base.py
+${PYSITELIB}/MDAnalysis/topology/base.pyc
+${PYSITELIB}/MDAnalysis/topology/base.pyo
 ${PYSITELIB}/MDAnalysis/topology/core.py
 ${PYSITELIB}/MDAnalysis/topology/core.pyc
 ${PYSITELIB}/MDAnalysis/topology/core.pyo
@@ -253,3 +370,18 @@ ${PYSITELIB}/MDAnalysis/topology/tpr/setting.pyo
 ${PYSITELIB}/MDAnalysis/topology/tpr/utils.py
 ${PYSITELIB}/MDAnalysis/topology/tpr/utils.pyc
 ${PYSITELIB}/MDAnalysis/topology/tpr/utils.pyo
+${PYSITELIB}/MDAnalysis/units.py
+${PYSITELIB}/MDAnalysis/units.pyc
+${PYSITELIB}/MDAnalysis/units.pyo
+${PYSITELIB}/MDAnalysis/version.py
+${PYSITELIB}/MDAnalysis/version.pyc
+${PYSITELIB}/MDAnalysis/version.pyo
+${PYSITELIB}/MDAnalysis/visualization/__init__.py
+${PYSITELIB}/MDAnalysis/visualization/__init__.pyc
+${PYSITELIB}/MDAnalysis/visualization/__init__.pyo
+${PYSITELIB}/MDAnalysis/visualization/streamlines.py
+${PYSITELIB}/MDAnalysis/visualization/streamlines.pyc
+${PYSITELIB}/MDAnalysis/visualization/streamlines.pyo
+${PYSITELIB}/MDAnalysis/visualization/streamlines_3D.py
+${PYSITELIB}/MDAnalysis/visualization/streamlines_3D.pyc
+${PYSITELIB}/MDAnalysis/visualization/streamlines_3D.pyo
diff --git a/py-mdanalysis/distinfo b/py-mdanalysis/distinfo
index 01d7a32..686d12e 100644
--- a/py-mdanalysis/distinfo
+++ b/py-mdanalysis/distinfo
@@ -1,5 +1,6 @@
 $NetBSD: distinfo,v 1.3 2014/01/03 21:28:42 jihbed Exp $
 
-SHA1 (MDAnalysis-0.8.0rc4.tar.gz) = 890a862b3a982a67226cf138935316335dc15325
-RMD160 (MDAnalysis-0.8.0rc4.tar.gz) = 306102a81a430aaf4d1fcbfdfbeb9702342f721b
-Size (MDAnalysis-0.8.0rc4.tar.gz) = 5107532 bytes
+SHA1 (MDAnalysis-0.15.0.tar.gz) = 579e7d8ad92a410ed2e886bbb1d5ed7fef5d5590
+RMD160 (MDAnalysis-0.15.0.tar.gz) = b06d6ef3d2ab33cb94b8a074be2e1e9c0b43af3e
+SHA512 (MDAnalysis-0.15.0.tar.gz) = 5aea6c8b2aa0d900fe408b3e5d0b51d6204201e2c4e6ad681d57836f7828f4178c162bf59622dcd34ac3d86a285c4826dc8756efe495e9bf8eb51cdd0891f792
+Size (MDAnalysis-0.15.0.tar.gz) = 2238589 bytes
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