Issue 782 removeflags

package/CHANGELOG

@@ -96,6 +96,10 @@ Changes
   * Removed `MDAnalysis.migration` (Issue #2490, PR #2496)
   * The fasta2select now always assumes that the gap character in a sequence
     is "-" (Issue #2448, PR #2457)
+  * Removed core.flags.  Default behaviour (eg pbc, units) now defaults to
+    the default setting of the flag before removal.  If you were using flags
+    you will now have to supply the flag setting as keyword arguments to
+    function calls. (Issue #782)
 
 Deprecations
   * analysis.hbonds.HydrogenBondAnalysis is deprecated in 1.0 (remove in 2.0)

package/MDAnalysis/analysis/density.py

@@ -212,10 +212,6 @@ class Density(Grid):
         - *density*: unit of the density if ``isDensity=True`` or ``None``
           otherwise; the default is "Angstrom^{-3}" for densities
           (meaning :math:`\text{Å}^{-3}`).
-
-        (Actually, the default unit is the value of
-        ``MDAnalysis.core.flags['length_unit']``; in most
-        cases this is "Angstrom".)
     metadata : dict
         a user defined dictionary of arbitrary values associated with the
         density; the class does not touch :attr:`Density.metadata` but
@@ -325,7 +321,7 @@ class Density(Grid):
     """
 
     def __init__(self, *args, **kwargs):
-        length_unit = MDAnalysis.core.flags['length_unit']
+        length_unit = 'Angstrom'
 
         parameters = kwargs.pop('parameters', {})
         if len(args) > 0 and isinstance(args[0], string_types) or isinstance(kwargs.get('grid', None), string_types):
@@ -718,10 +714,11 @@ def density_from_Universe(universe, delta=1.0, atomselection='name OH2',
        defined boxes
     .. versionchanged:: 0.13.0
        *update_selection* and *quiet* keywords added
-
     .. deprecated:: 0.16
        The keyword argument *quiet* is deprecated in favor of *verbose*.
-
+    .. versionchanged:: 0.21.0
+       time_unit and length_unit default to ps and Angstrom now flags have
+       been removed (same as previous flag defaults)
     """
     u = universe
 
@@ -815,7 +812,7 @@ def current_coordinates():
     metadata['n_frames'] = n_frames
     metadata['totaltime'] = round(u.trajectory.n_frames * u.trajectory.dt, 3)
     metadata['dt'] = u.trajectory.dt
-    metadata['time_unit'] = MDAnalysis.core.flags['time_unit']
+    metadata['time_unit'] = 'ps'
     try:
         metadata['trajectory_skip'] = u.trajectory.skip_timestep  # frames
     except AttributeError:
@@ -832,7 +829,7 @@ def current_coordinates():
     parameters['isDensity'] = False  # must override
 
 
-    g = Density(grid=grid, edges=edges, units={'length': MDAnalysis.core.flags['length_unit']},
+    g = Density(grid=grid, edges=edges, units={'length': 'Angstrom'},
                 parameters=parameters, metadata=metadata)
     g.make_density()
     logger.info("Density completed (initial density in Angstrom**-3)")

package/MDAnalysis/coordinates/DCD.py

@@ -66,7 +66,6 @@
 import types
 import warnings
 
-from ..core import flags
 from .. import units as mdaunits  # use mdaunits instead of units to avoid a clash
 from ..exceptions import NoDataError
 from . import base, core

package/MDAnalysis/coordinates/GRO.py

@@ -116,7 +116,6 @@
 
 from . import base
 from .core import triclinic_box, triclinic_vectors
-from ..core import flags
 from ..exceptions import NoDataError
 from ..lib import util
 
@@ -301,21 +300,17 @@ class GROWriter(base.WriterBase):
     }
     fmt['xyz_v'] = fmt['xyz'][:-1] + "{vel[0]:8.4f}{vel[1]:8.4f}{vel[2]:8.4f}\n"
 
-    def __init__(self, filename, convert_units=None, n_atoms=None, **kwargs):
+    def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs):
         """Set up a GROWriter with a precision of 3 decimal places.
 
         Parameters
         -----------
         filename : str
             output filename
-
         n_atoms : int (optional)
             number of atoms
-
-        convert_units : str (optional)
-            units are converted to the MDAnalysis base format; ``None`` selects
-            the value of :data:`MDAnalysis.core.flags` ['convert_lengths']
-
+        convert_units : bool (optional)
+            units are converted to the MDAnalysis base format; [``True``]
         reindex : bool (optional)
             By default, all the atoms were reindexed to have a atom id starting
             from 1. [``True``] However, this behaviour can be turned off by
@@ -342,8 +337,6 @@ def __init__(self, filename, convert_units=None, n_atoms=None, **kwargs):
         self.n_atoms = n_atoms
         self.reindex = kwargs.pop('reindex', True)
 
-        if convert_units is None:
-            convert_units = flags['convert_lengths']
         self.convert_units = convert_units  # convert length and time to base units
 
     def write(self, obj):

package/MDAnalysis/coordinates/LAMMPS.py

@@ -128,7 +128,6 @@
 import os
 import numpy as np
 
-from ..core import flags
 from ..core.groups import requires
 from ..lib import util, mdamath, distances
 from ..lib.util import cached
@@ -254,18 +253,18 @@ class DATAWriter(base.WriterBase):
     """
     format = 'DATA'
 
-    def __init__(self, filename, convert_units=None, **kwargs):
+    def __init__(self, filename, convert_units=True, **kwargs):
         """Set up a DATAWriter
 
         Parameters
         ----------
         filename : str
             output filename
+        convert_units : bool, optional
+            units are converted to the MDAnalysis base format; [``True``]
         """
         self.filename = util.filename(filename, ext='data')
 
-        if convert_units is None:
-            convert_units = flags['convert_lengths']
         self.convert_units = convert_units
 
         self.units = {'time': 'fs', 'length': 'Angstrom'}

package/MDAnalysis/coordinates/MOL2.py

@@ -117,7 +117,6 @@
 import numpy as np
 
 from . import base
-from ..core import flags
 from ..lib import util
 
 
@@ -281,20 +280,17 @@ class MOL2Writer(base.WriterBase):
     multiframe = True
     units = {'time': None, 'length': 'Angstrom'}
 
-    def __init__(self, filename, n_atoms=None, convert_units=None):
+    def __init__(self, filename, n_atoms=None, convert_units=True):
         """Create a new MOL2Writer
 
         Parameters
         ----------
         filename: str
             name of output file
         convert_units: bool (optional)
-            units are converted to the MDAnalysis base format; ``None`` selects
-            the value of :data:`MDAnalysis.core.flags` ['convert_lengths']
+            units are converted to the MDAnalysis base format; [``True``]
         """
         self.filename = filename
-        if convert_units is None:
-            convert_units = flags['convert_lengths']
         self.convert_units = convert_units  # convert length and time to base units
 
         self.frames_written = 0

package/MDAnalysis/coordinates/PDB.py

@@ -155,7 +155,6 @@
 import collections
 import numpy as np
 
-from ..core import flags
 from ..lib import util
 from . import base
 from ..topology.core import guess_atom_element
@@ -542,7 +541,7 @@ class PDBWriter(base.WriterBase):
 
     def __init__(self, filename, bonds="conect", n_atoms=None, start=0, step=1,
                  remarks="Created by PDBWriter",
-                 convert_units=None, multiframe=None):
+                 convert_units=True, multiframe=None):
         """Create a new PDBWriter
 
         Parameters
@@ -559,9 +558,8 @@ def __init__(self, filename, bonds="conect", n_atoms=None, start=0, step=1,
            any remarks from the trajectory that serves as input are
            written to REMARK records with lines longer than :attr:`remark_max_length` (66
            characters) being wrapped.
-        convert_units: str (optional)
-           units are converted to the MDAnalysis base format; ``None`` selects
-           the value of :data:`MDAnalysis.core.flags` ['convert_lengths']
+        convert_units: bool (optional)
+           units are converted to the MDAnalysis base format; [``True``]
         bonds : {"conect", "all", None} (optional)
            If set to "conect", then only write those bonds that were already
            defined in an input PDB file as PDB CONECT_ record. If set to "all",
@@ -585,8 +583,6 @@ def __init__(self, filename, bonds="conect", n_atoms=None, start=0, step=1,
         #       - additional title keyword could contain line for TITLE
 
         self.filename = filename
-        if convert_units is None:
-            convert_units = flags['convert_lengths']
         # convert length and time to base units
         self.convert_units = convert_units
         self._multiframe = self.multiframe if multiframe is None else multiframe

package/MDAnalysis/coordinates/PQR.py

@@ -105,7 +105,6 @@
 import numpy as np
 import warnings
 
-from ..core import flags
 from ..lib import util
 from . import base
 
@@ -197,23 +196,21 @@ class PQRWriter(base.WriterBase):
                 " {pos[2]:-8.3f} {charge:-7.4f} {radius:6.4f}\n")
     fmt_remark = "REMARK   {0} {1}\n"
 
-    def __init__(self, filename, convert_units=None, **kwargs):
+    def __init__(self, filename, convert_units=True, **kwargs):
         """Set up a PQRWriter with full whitespace separation.
 
         Parameters
         ----------
         filename : str
              output filename
+        convert_units: bool (optional)
+            units are converted to the MDAnalysis base format; [``True``]
         remarks : str (optional)
              remark lines (list of strings) or single string to be added to the
              top of the PQR file
         """
         self.filename = util.filename(filename, ext='pqr')
-
-        if convert_units is None:
-            convert_units = flags['convert_lengths']
         self.convert_units = convert_units  # convert length and time to base units
-
         self.remarks = kwargs.pop('remarks', "PQR file written by MDAnalysis")
 
     def write(self, selection, frame=None):

package/MDAnalysis/coordinates/ParmEd.py

@@ -77,11 +77,9 @@
 
 from . import base
 from ..topology.tables import SYMB2Z
-from ..core import flags
 from ..core.universe import Universe
 
 
-
 class ParmEdReader(base.SingleFrameReaderBase):
     """Coordinate reader for ParmEd."""
     format = 'PARMED'
@@ -339,4 +337,4 @@ def convert(self, obj):
                         if isinstance(p.type, clstype):
                             typelist.append(p.type)
                             p.type.list = typelist
-        return struct
+        return struct

package/MDAnalysis/coordinates/TRJ.py

@@ -163,7 +163,6 @@
 import logging
 
 import MDAnalysis
-from ..core import flags
 from . import base
 from ..lib import util
 
@@ -776,9 +775,7 @@ class NCDFWriter(base.WriterBase):
     dt : float (optional)
         timestep
     convert_units : bool (optional)
-        ``True``: units are converted to the AMBER base format; ``None``
-        selects the value of :data:`MDAnalysis.core.flags`
-        ['convert_lengths'] (see :ref:`flags-label`).
+        ``True``: units are converted to the AMBER base format; [``True``]
     velocities : bool (optional)
         Write velocities into the trajectory [``False``]
     forces : bool (optional)
@@ -864,14 +861,12 @@ def __init__(self,
                  step=1,
                  dt=1.0,
                  remarks=None,
-                 convert_units=None,
+                 convert_units=True,
                  **kwargs):
         self.filename = filename
         if n_atoms == 0:
             raise ValueError("NCDFWriter: no atoms in output trajectory")
         self.n_atoms = n_atoms
-        if convert_units is None:
-            convert_units = flags['convert_lengths']
         # convert length and time to base units on the fly?
         self.convert_units = convert_units
 

package/MDAnalysis/coordinates/TRZ.py

@@ -95,7 +95,6 @@
 import errno
 
 from . import base
-from ..core import flags
 from ..lib import util
 from ..lib.util import cached
 from .core import triclinic_box, triclinic_vectors
@@ -447,7 +446,7 @@ class TRZWriter(base.WriterBase):
 
     units = {'time': 'ps', 'length': 'nm', 'velocity': 'nm/ps'}
 
-    def __init__(self, filename, n_atoms, title='TRZ', convert_units=None):
+    def __init__(self, filename, n_atoms, title='TRZ', convert_units=True):
         """Create a TRZWriter
 
         Parameters
@@ -460,9 +459,7 @@ def __init__(self, filename, n_atoms, title='TRZ', convert_units=None):
             title of the trajectory; the title must be 80 characters or
             shorter, a longer title raises a ValueError exception.
         convert_units : bool (optional)
-            units are converted to the MDAnalysis base format; ``None`` selects
-            the value of :data:`MDAnalysis.core.flags` ['convert_lengths'].
-            (see :ref:`flags-label`)
+            units are converted to the MDAnalysis base format; [``True``]
         """
         self.filename = filename
         if n_atoms is None:
@@ -474,8 +471,6 @@ def __init__(self, filename, n_atoms, title='TRZ', convert_units=None):
         if len(title) > 80:
             raise ValueError("TRZWriter: 'title' must be 80 characters of shorter")
 
-        if convert_units is None:
-            convert_units = flags['convert_lengths']
         self.convert_units = convert_units
 
         self.trzfile = util.anyopen(self.filename, 'wb')

package/MDAnalysis/coordinates/XYZ.py

@@ -93,7 +93,6 @@
 logger = logging.getLogger('MDAnalysis.coordinates.XYZ')
 
 from . import base
-from ..core import flags
 from ..lib import util
 from ..lib.util import cached
 from ..exceptions import NoDataError
@@ -118,7 +117,7 @@ class XYZWriter(base.WriterBase):
     # these are assumed!
     units = {'time': 'ps', 'length': 'Angstrom'}
 
-    def __init__(self, filename, n_atoms=None, atoms=None, convert_units=None,
+    def __init__(self, filename, n_atoms=None, atoms=None, convert_units=True,
                  remark=None, **kwargs):
         """Initialize the XYZ trajectory writer
 
@@ -148,10 +147,8 @@ def __init__(self, filename, n_atoms=None, atoms=None, convert_units=None,
         """
         self.filename = filename
         self.n_atoms = n_atoms
-        if convert_units is not None:
-            self.convert_units = convert_units
-        else:
-            self.convert_units = flags['convert_lengths']
+        self.convert_units = convert_units
+
         self.atomnames = self._get_atoms_elements_or_names(atoms)
         default_remark = "Written by {0} (release {1})".format(
             self.__class__.__name__, __version__)