Drop support for Python <3.7

.github/workflows/tests.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04]
-        python-version: ["2.7", "3.6", "3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
         include:
           - os: windows-2019
             python-version: "3.8"

examples/indexes.py

@@ -14,4 +14,4 @@
 
 print("Atoms with x < 5: ")
 for i in less_than_five:
-    print("  - {}".format(i))
+    print(f"  - {i}")

src/chemfiles/__init__.py

@@ -1,6 +1,3 @@
-# -*- coding=utf-8 -*-
-from __future__ import absolute_import, print_function, unicode_literals
-
 from .atom import Atom
 from .cell import CellShape, UnitCell
 from .frame import Frame

src/chemfiles/_c_lib.py

@@ -1,4 +1,3 @@
-# -* coding: utf-8 -*
 import os
 import sys
 from ctypes import POINTER, c_double, cdll

src/chemfiles/atom.py

@@ -1,11 +1,8 @@
-# -*- coding=utf-8 -*-
-from __future__ import absolute_import, print_function, unicode_literals
-
 from ctypes import c_char_p, c_double, c_uint64
 
 from .misc import ChemfilesError
 from .property import Property
-from .utils import CxxPointer, _call_with_growing_buffer, string_type
+from .utils import CxxPointer, _call_with_growing_buffer
 
 
 class Atom(CxxPointer):
@@ -38,12 +35,10 @@ def __copy__(self):
         return Atom.from_mutable_ptr(None, self.ffi.chfl_atom_copy(self.ptr))
 
     def __repr__(self):
-        name = self.name
-        type = self.type
-        if type == name:
-            return "Atom('{}')".format(name)
+        if self.type == self.name:
+            return f"Atom('{self.name}')"
         else:
-            return "Atom('{}', '{}')".format(name, type)
+            return f"Atom('{self.name}', '{self.type}')"
 
     @property
     def mass(self):
@@ -150,10 +145,11 @@ def __getitem__(self, name):
         Get a property of this atom with the given ``name``, or raise an error
         if the property does not exists.
         """
-        if not isinstance(name, string_type):
+        if not isinstance(name, str):
             raise ChemfilesError(
-                "Invalid type {} for an atomic property name".format(type(name))
+                f"Invalid type {type(name)} for an atomic property name"
             )
+
         ptr = self.ffi.chfl_atom_get_property(self.ptr, name.encode("utf8"))
         return Property.from_mutable_ptr(self, ptr).get()
 
@@ -162,10 +158,9 @@ def __setitem__(self, name, value):
         Set a property of this atom, with the given ``name`` and ``value``.
         The new value overwrite any pre-existing property with the same name.
         """
-        if not isinstance(name, string_type):
-            raise ChemfilesError(
-                "invalid type {} for a property name".format(type(name))
-            )
+        if not isinstance(name, str):
+            raise ChemfilesError(f"invalid type {type(name)} for a property name")
+
         property = Property(value)
         self.ffi.chfl_atom_set_property(self.mut_ptr, name.encode("utf8"), property.ptr)
 

src/chemfiles/cell.py

@@ -1,6 +1,3 @@
-# -*- coding=utf-8 -*-
-from __future__ import absolute_import, print_function, unicode_literals
-
 from ctypes import ARRAY, c_double
 from enum import IntEnum
 
@@ -63,9 +60,7 @@ def __init__(self, lengths, angles=(90.0, 90.0, 90.0)):
         else:
             if lengths.shape != (3, 3):
                 raise ChemfilesError(
-                    "expected the cell matrix to have 3x3 shape, got {}".format(
-                        lengths.shape
-                    )
+                    f"expected the cell matrix to have 3x3 shape, got {lengths.shape}"
                 )
             matrix = ARRAY(chfl_vector3d, (3))()
             matrix[0][0] = lengths[0, 0]

src/chemfiles/frame.py

@@ -1,6 +1,3 @@
-# -*- coding=utf-8 -*-
-from __future__ import absolute_import, print_function, unicode_literals
-
 from ctypes import POINTER, c_bool, c_char_p, c_double, c_uint64
 
 import numpy as np
@@ -11,7 +8,7 @@
 from .misc import ChemfilesError
 from .property import Property
 from .topology import Topology
-from .utils import CxxPointer, string_type
+from .utils import CxxPointer
 
 
 class FrameAtoms(object):
@@ -32,9 +29,7 @@ def __getitem__(self, index):
         associated :py:class:`Frame`.
         """
         if index >= len(self):
-            raise IndexError(
-                "atom index ({}) out of range for this frame".format(index)
-            )
+            raise IndexError(f"atom index ({index}) out of range for this frame")
         else:
             ptr = self.frame.ffi.chfl_atom_from_frame(
                 self.frame.mut_ptr, c_uint64(index)
@@ -68,7 +63,7 @@ def __copy__(self):
         return Frame.from_mutable_ptr(None, self.ffi.chfl_frame_copy(self.ptr))
 
     def __repr__(self):
-        return "Frame with {} atoms".format(len(self.atoms))
+        return f"Frame with {len(self.atoms)} atoms"
 
     @property
     def atoms(self):
@@ -325,10 +320,9 @@ def __getitem__(self, name):
         Get a property of this frame with the given ``name``, or raise an error
         if the property does not exists.
         """
-        if not isinstance(name, string_type):
-            raise ChemfilesError(
-                "Invalid type {} for a frame property name".format(type(name))
-            )
+        if not isinstance(name, str):
+            raise ChemfilesError(f"Invalid type {type(name)} for a frame property name")
+
         ptr = self.ffi.chfl_frame_get_property(self.ptr, name.encode("utf8"))
         return Property.from_mutable_ptr(self, ptr).get()
 
@@ -337,10 +331,9 @@ def __setitem__(self, name, value):
         Set a property of this frame, with the given ``name`` and ``value``.
         The new value overwrite any pre-existing property with the same name.
         """
-        if not isinstance(name, string_type):
-            raise ChemfilesError(
-                "Invalid type {} for a frame property name".format(type(name))
-            )
+        if not isinstance(name, str):
+            raise ChemfilesError(f"Invalid type {type(name)} for a frame property name")
+
         property = Property(value)
         self.ffi.chfl_frame_set_property(
             self.mut_ptr, name.encode("utf8"), property.ptr

src/chemfiles/misc.py

@@ -1,6 +1,3 @@
-# -*- coding=utf-8 -*-
-from __future__ import absolute_import, print_function, unicode_literals
-
 import warnings
 from ctypes import POINTER, c_uint64, create_string_buffer
 
@@ -82,43 +79,28 @@ def _set_from_c(self, c_format_metadata):
         self.residues = c_format_metadata.residues
 
     def __repr__(self):
-        return """
-FormatMetadata for {name}
--------------------{name_underline}
-{description}
+        return f"""
+FormatMetadata for {self.name}
+-------------------{"-" * len(self.name)}
+{self.description}
 
-name      = {name}
-extension = {extension}
-reference = {reference}
+name      = {self.name}
+extension = {self.extension}
+reference = {self.reference}
 
 Capacities:
 -----------
 
-read        = {read}
-write       = {write}
-memory      = {memory}
-positions   = {positions}
-velocities  = {velocities}
-unit_cell   = {unit_cell}
-atoms       = {atoms}
-bonds       = {bonds}
-residues    = {residues}
-""".format(
-            name=self.name,
-            name_underline="-" * len(self.name),
-            description=self.description,
-            extension=self.extension,
-            reference=self.reference,
-            read=self.read,
-            write=self.write,
-            memory=self.memory,
-            positions=self.positions,
-            velocities=self.velocities,
-            unit_cell=self.unit_cell,
-            atoms=self.atoms,
-            bonds=self.bonds,
-            residues=self.residues,
-        )
+read        = {self.read}
+write       = {self.write}
+memory      = {self.memory}
+positions   = {self.positions}
+velocities  = {self.velocities}
+unit_cell   = {self.unit_cell}
+atoms       = {self.atoms}
+bonds       = {self.bonds}
+residues    = {self.residues}
+"""
 
 
 def formats_list():
@@ -162,7 +144,7 @@ def callback(message):
         try:
             function(message.decode("utf8"))
         except Exception as e:
-            message = "exception raised in warning callback: {}".format(e)
+            message = f"exception raised in warning callback: {e}"
             warnings.warn(message, ChemfilesWarning)
 
     global _CURRENT_CALLBACK

src/chemfiles/property.py

@@ -1,14 +1,10 @@
-# -*- coding=utf-8 -*-
-from __future__ import absolute_import, print_function, unicode_literals
-
-import sys
 from ctypes import c_bool, c_double
 
 import numpy as np
 
 from ._c_api import chfl_property_kind, chfl_vector3d
 from .misc import ChemfilesError
-from .utils import CxxPointer, _call_with_growing_buffer, string_type
+from .utils import CxxPointer, _call_with_growing_buffer
 
 
 class Property(CxxPointer):
@@ -26,16 +22,14 @@ def __init__(self, value):
             ptr = self.ffi.chfl_property_bool(c_bool(value))
         elif isinstance(value, (float, int)):
             ptr = self.ffi.chfl_property_double(c_double(value))
-        elif isinstance(value, string_type):
+        elif isinstance(value, str):
             ptr = self.ffi.chfl_property_string(value.encode("utf8"))
         elif _is_vector3d(value):
             value = chfl_vector3d(value[0], value[1], value[2])
             ptr = self.ffi.chfl_property_vector3d(value)
         else:
             raise ChemfilesError(
-                "can not create a Property with a value of type '{}'".format(
-                    type(value)
-                )
+                f"can not create a Property with a value of type '{type(value)}'"
             )
 
         super(Property, self).__init__(ptr, is_const=False)

src/chemfiles/residue.py

@@ -1,13 +1,10 @@
-# -*- coding=utf-8 -*-
-from __future__ import absolute_import, print_function, unicode_literals
-
 from ctypes import c_bool, c_char_p, c_int64, c_uint64
 
 import numpy as np
 
 from .misc import ChemfilesError
 from .property import Property
-from .utils import CxxPointer, _call_with_growing_buffer, string_type
+from .utils import CxxPointer, _call_with_growing_buffer
 
 
 class ResidueAtoms(object):
@@ -90,7 +87,7 @@ def __copy__(self):
         return Residue.from_mutable_ptr(None, self.ffi.chfl_residue_copy(self.ptr))
 
     def __repr__(self):
-        return "Residue('{}') with {} atoms".format(self.name, len(self.atoms))
+        return f"Residue('{self.name}') with {len(self.atoms)} atoms"
 
     @property
     def name(self):
@@ -120,10 +117,11 @@ def __getitem__(self, name):
         Get a property of this residude with the given ``name``, or raise an
         error if the property does not exists.
         """
-        if not isinstance(name, string_type):
+        if not isinstance(name, str):
             raise ChemfilesError(
-                "Invalid type {} for a residue property name".format(type(name))
+                f"Invalid type {type(name)} for a residue property name"
             )
+
         ptr = self.ffi.chfl_residue_get_property(self.ptr, name.encode("utf8"))
         return Property.from_mutable_ptr(self, ptr).get()
 
@@ -132,10 +130,11 @@ def __setitem__(self, name, value):
         Set a property of this residue, with the given ``name`` and ``value``.
         The new value overwrite any pre-existing property with the same name.
         """
-        if not isinstance(name, string_type):
+        if not isinstance(name, str):
             raise ChemfilesError(
-                "Invalid type {} for a residue property name".format(type(name))
+                f"Invalid type {type(name)} for a residue property name"
             )
+
         property = Property(value)
         self.ffi.chfl_residue_set_property(
             self.mut_ptr, name.encode("utf8"), property.ptr

src/chemfiles/selection.py

@@ -1,6 +1,3 @@
-# -*- coding=utf-8 -*-
-from __future__ import absolute_import, print_function, unicode_literals
-
 from ctypes import c_uint64
 
 import numpy as np
@@ -33,7 +30,7 @@ def __copy__(self):
         return Selection.from_mutable_ptr(None, self.ffi.chfl_selection_copy(self.ptr))
 
     def __repr__(self):
-        return "Selection('{}')".format(self.string)
+        return f"Selection('{self.string}')"
 
     @property
     def size(self):

src/chemfiles/topology.py

@@ -1,6 +1,3 @@
-# -*- coding=utf-8 -*-
-from __future__ import absolute_import, print_function, unicode_literals
-
 from ctypes import c_bool, c_uint64
 from enum import IntEnum
 
@@ -54,9 +51,7 @@ def __getitem__(self, index):
         associated :py:class:`Topology`.
         """
         if index >= len(self):
-            raise IndexError(
-                "atom index ({}) out of range for this topology".format(index)
-            )
+            raise IndexError(f"atom index ({index}) out of range for this topology")
         else:
             ptr = self.topology.ffi.chfl_atom_from_topology(
                 self.topology.mut_ptr, c_uint64(index)
@@ -110,9 +105,7 @@ def __getitem__(self, index):
         topology does not necessarily match the residue id.
         """
         if index >= len(self):
-            raise IndexError(
-                "residue index ({}) out of range for this topology".format(index)
-            )
+            raise IndexError(f"residue index ({index}) out of range for this topology")
         else:
             ptr = self.topology.ffi.chfl_residue_from_topology(
                 self.topology.ptr, c_uint64(index)
@@ -151,7 +144,7 @@ def __copy__(self):
         return Topology.from_mutable_ptr(None, self.ffi.chfl_topology_copy(self.ptr))
 
     def __repr__(self):
-        return "Topology with {} atoms".format(len(self.atoms))
+        return f"Topology with {len(self.atoms)} atoms"
 
     @property
     def atoms(self):
@@ -186,9 +179,8 @@ def residue_for_atom(self, index):
         atom is not part of a residue.
         """
         if index >= len(self.atoms):
-            raise IndexError(
-                "residue index ({}) out of range for this topology".format(index)
-            )
+            raise IndexError(f"residue index ({index}) out of range for this topology")
+
         ptr = self.ffi.chfl_residue_for_atom(self.ptr, c_uint64(index))
         if ptr:
             return Residue.from_const_ptr(self, ptr)