Move ConverterBase out of coordinates/base.py

package/CHANGELOG

@@ -13,7 +13,7 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/?? IAlibay, hmacdope, pillose, jaclark5, tylerjereddy
+??/??/?? IAlibay, hmacdope, pillose, jaclark5, tylerjereddy, ianmkenney
 
  * 2.7.0
 
@@ -29,8 +29,11 @@ Changes
     (Issue #4247)
   * Cython DEF statments have been replaced with compile time integer constants
     as DEF is deprecated as of Cython>=3.0 (Issue #4237, PR #4246)
+  * ConverterBase class moved from coordinates/base.py to converters/base.py (Issue #3404)
 
 Deprecations
+  * coordinates.base.ConverterBase has been deprecated and will be removed in 3.0.0;
+    use converters.base.ConvertBase instead (Issue #3404)
 
 
 08/15/23 IAlibay, jaclark5, MohitKumar020291, orionarcher, xhgchen,

package/MDAnalysis/converters/ParmEd.py

@@ -81,13 +81,14 @@
 import itertools
 import warnings
 
-from ..coordinates import base
+from . import base
+from ..coordinates.base import SingleFrameReaderBase
 from ..topology.tables import SYMB2Z
 from ..core.universe import Universe
 from ..exceptions import NoDataError
 
 
-class ParmEdReader(base.SingleFrameReaderBase):
+class ParmEdReader(SingleFrameReaderBase):
     """Coordinate reader for ParmEd."""
     format = 'PARMED'
 

package/MDAnalysis/converters/RDKit.py

@@ -88,7 +88,8 @@
 
 import numpy as np
 
-from ..coordinates import base, memory
+from . import base
+from ..coordinates import memory
 from ..coordinates.PDB import PDBWriter
 from ..core.topologyattrs import _TOPOLOGY_ATTRS
 from ..exceptions import NoDataError

package/MDAnalysis/converters/base.py

@@ -0,0 +1,61 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+#
+# MDAnalysis --- https://www.mdanalysis.org
+# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
+# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
+# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
+# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
+# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
+# doi: 10.25080/majora-629e541a-00e
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+
+""" Base classes --- :mod:`MDAnalysis.converters.base`
+======================================================
+
+Converters output information to other libraries.
+
+.. autoclass:: ConverterBase
+   :members:
+   :inherited-members:
+"""
+
+from .. import _CONVERTERS
+from ..coordinates.base import IOBase
+from ..lib.util import asiterable
+
+
+class _Convertermeta(type):
+    # Auto register upon class creation
+    def __init__(cls, name, bases, classdict):
+        type.__init__(type, name, bases, classdict)
+        try:
+            fmt = asiterable(classdict['lib'])
+        except KeyError:
+            pass
+        else:
+            for f in fmt:
+                f = f.upper()
+                _CONVERTERS[f] = cls
+
+
+class ConverterBase(IOBase, metaclass=_Convertermeta):
+    """Base class for converting to other libraries.
+    """
+
+    def __repr__(self):
+        return "<{cls}>".format(cls=self.__class__.__name__)
+
+    def convert(self, obj):
+        raise NotImplementedError

package/MDAnalysis/coordinates/base.py

@@ -1,6 +1,6 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
 # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
-#
+
 # MDAnalysis --- https://www.mdanalysis.org
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
@@ -101,17 +101,18 @@
    :members:
    :inherited-members:
 
-
 Converters
 ----------
-
 Converters output information to other libraries.
 
+.. deprecated:: 2.7.0
+    All converter code has been moved to :mod:`MDAnalysis.converters` and will
+    be removed from the :mod:`MDAnalysis.coordinates.base` module in 3.0.0.
+
 .. autoclass:: ConverterBase
    :members:
    :inherited-members:
 
-
 Helper classes
 --------------
 
@@ -134,7 +135,7 @@
     _READERS, _READER_HINTS,
     _SINGLEFRAME_WRITERS,
     _MULTIFRAME_WRITERS,
-    _CONVERTERS
+    _CONVERTERS,  # remove in 3.0.0 (Issue #3404)
 )
 from .. import units
 from ..auxiliary.base import AuxReader
@@ -1783,7 +1784,10 @@ def range_length(start, stop, step):
         # The range is empty.
         return 0
 
-
+# Verbatim copy of code from converters/base.py
+# Needed to avoid circular imports before removal in
+# MDAnalysis 3.0.0
+# Remove in 3.0.0
 class _Convertermeta(type):
     # Auto register upon class creation
     def __init__(cls, name, bases, classdict):
@@ -1797,14 +1801,27 @@ def __init__(cls, name, bases, classdict):
                 f = f.upper()
                 _CONVERTERS[f] = cls
 
+
+# Verbatim copy of code from converters/base.py
+# Needed to avoid circular imports before removal in
+# MDAnalysis 3.0.0
+# Remove in 3.0.0
 class ConverterBase(IOBase, metaclass=_Convertermeta):
     """Base class for converting to other libraries.
 
-    See Also
-    --------
-    :mod:`MDAnalysis.converters`
+    .. deprecated:: 2.7.0
+        This class has been moved to
+        :class:`MDAnalysis.converters.base.ConverterBase` and will be removed
+        from :mod:`MDAnalysis.coordinates.base` in 3.0.0.
     """
 
+    def __init_subclass__(cls):
+        wmsg = ("ConverterBase moved from coordinates.base."
+                "ConverterBase to converters.base.ConverterBase "
+                "and will be removed from coordinates.base "
+                "in MDAnalysis release 3.0.0")
+        warnings.warn(wmsg, DeprecationWarning, stacklevel=2)
+
     def __repr__(self):
         return "<{cls}>".format(cls=self.__class__.__name__)
 

package/doc/sphinx/source/documentation_pages/converters.rst

@@ -52,3 +52,11 @@ Another syntax is also available for tab-completion support::
 
     core/accessors
 
+
+Developers may find the :mod:`MDAnaylsis.converters.base` module helpful for
+creating new converter classes.
+
+.. toctree::
+   :maxdepth: 1
+
+   converters/base

package/doc/sphinx/source/documentation_pages/converters/base.rst

@@ -0,0 +1 @@
+.. automodule:: MDAnalysis.converters.base

testsuite/MDAnalysisTests/converters/test_base.py

@@ -0,0 +1,56 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
+#
+# MDAnalysis --- https://www.mdanalysis.org
+# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
+# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
+# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
+# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
+# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
+# doi: 10.25080/majora-629e541a-00e
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+
+import pytest
+import warnings
+
+
+def test_coordinate_converterbase_warning():
+    from MDAnalysis.coordinates.base import ConverterBase
+    import MDAnalysis.converters.base
+
+    wmsg = ("ConverterBase moved from coordinates.base."
+            "ConverterBase to converters.base.ConverterBase "
+            "and will be removed from coordinates.base "
+            "in MDAnalysis release 3.0.0")
+
+    with pytest.warns(DeprecationWarning, match=wmsg):
+        class DerivedConverter(ConverterBase):
+            pass
+
+    assert issubclass(DerivedConverter, ConverterBase)
+    assert not issubclass(DerivedConverter,
+                          MDAnalysis.converters.base.ConverterBase)
+
+
+def test_converters_converterbase_no_warning():
+    from MDAnalysis.converters.base import ConverterBase
+
+    # check that no warning is issued at all
+    # when subclassing converters.base.ConverterBase
+    with warnings.catch_warnings():
+        warnings.simplefilter("error")
+
+        class DerivedConverter(ConverterBase):
+            pass
+
+    assert issubclass(DerivedConverter, ConverterBase)