Remove more deprecated names.

hoomd/device.py

@@ -115,18 +115,6 @@ def message_filename(self):
         """
         return self._message_filename
 
-    @property
-    def msg_file(self):
-        """str: Filename to write messages to.
-
-        .. deprecated:: v3.10.0
-           ``msg_file`` will be renamed to ``message_Filename`` in v4.
-        """
-        warnings.warn(
-            "msg_file is deprecated since v3.10.0. Use message_filename.",
-            FutureWarning)
-        return self.message_filename
-
     @message_filename.setter
     def message_filename(self, filename):
         self._message_filename = filename
@@ -135,13 +123,6 @@ def message_filename(self, filename):
         else:
             self._cpp_msg.openStd()
 
-    @msg_file.setter
-    def msg_file(self, filename):
-        warnings.warn(
-            "msg_file is deprecated since v3.10.0. Use message_filename.",
-            FutureWarning)
-        self.message_filename = filename
-
     @property
     def devices(self):
         """list[str]: Descriptions of the active hardware devices."""
@@ -202,23 +183,6 @@ def _create_messenger(mpi_config, notice_level, message_filename):
     return msg
 
 
-def _get_message_filename(msg_file, message_file):
-    if msg_file is None and message_file is None:
-        return None
-
-    if msg_file is not None and message_file is not None:
-        raise ValueError("Pass in msg_file or message_file, not both")
-
-    if message_file is not None:
-        return message_file
-
-    if msg_file is not None:
-        warnings.warn(
-            "msg_file is deprecated since v3.10.0. Use message_filename.",
-            FutureWarning)
-        return msg_file
-
-
 class GPU(Device):
     """Select a GPU or GPU(s) to execute simulations.
 
@@ -232,17 +196,12 @@ class GPU(Device):
         communicator (hoomd.communicator.Communicator): MPI communicator object.
             When `None`, create a default communicator that uses all MPI ranks.
 
-        msg_file (str): Alias for ``message_filename``.
-
-            .. deprecated:: v3.10.0
-               ``msg_file`` will be renamed to ``message_filename`` in v4.
-
-        notice_level (int): Minimum level of messages to print.
-
         message_filename (str): Filename to write messages to. When `None`, use
             `sys.stdout` and `sys.stderr`. Messages from multiple MPI
             ranks are collected into this file.
 
+        notice_level (int): Minimum level of messages to print.
+
     Tip:
         Call `GPU.get_available_devices` to get a human readable list of
         devices. ``gpu_ids = [0]`` will select the first device in this list,
@@ -277,16 +236,16 @@ class GPU(Device):
 
     """
 
-    def __init__(self,
-                 gpu_ids=None,
-                 num_cpu_threads=None,
-                 communicator=None,
-                 msg_file=None,
-                 notice_level=2,
-                 message_filename=None):
+    def __init__(
+        self,
+        gpu_ids=None,
+        num_cpu_threads=None,
+        communicator=None,
+        message_filename=None,
+        notice_level=2,
+    ):
 
-        super().__init__(communicator, notice_level,
-                         _get_message_filename(msg_file, message_filename))
+        super().__init__(communicator, notice_level, message_filename)
 
         if gpu_ids is None:
             gpu_ids = []
@@ -382,31 +341,26 @@ class CPU(Device):
         communicator (hoomd.communicator.Communicator): MPI communicator object.
             When `None`, create a default communicator that uses all MPI ranks.
 
-        msg_file (str): Alias for ``message_filename``.
-
-            .. deprecated:: v3.10.0
-               ``msg_file`` will be renamed to ``message_filename`` in v4.
-
-        notice_level (int): Minimum level of messages to print.
-
         message_filename (str): Filename to write messages to. When `None`, use
             `sys.stdout` and `sys.stderr`. Messages from multiple MPI
             ranks are collected into this file.
 
+        notice_level (int): Minimum level of messages to print.
+
     .. rubric:: MPI
 
     In MPI execution environments, create a `CPU` device on every rank.
     """
 
-    def __init__(self,
-                 num_cpu_threads=None,
-                 communicator=None,
-                 msg_file=None,
-                 notice_level=2,
-                 message_filename=None):
+    def __init__(
+        self,
+        num_cpu_threads=None,
+        communicator=None,
+        message_filename=None,
+        notice_level=2,
+    ):
 
-        super().__init__(communicator, notice_level,
-                         _get_message_filename(msg_file, message_filename))
+        super().__init__(communicator, notice_level, message_filename)
 
         self._cpp_exec_conf = _hoomd.ExecutionConfiguration(
             _hoomd.ExecutionConfiguration.executionMode.CPU, [],
@@ -416,37 +370,29 @@ def __init__(self,
             self.num_cpu_threads = num_cpu_threads
 
 
-def auto_select(communicator=None,
-                msg_file=None,
-                notice_level=2,
-                message_filename=None):
+def auto_select(
+    communicator=None,
+    message_filename=None,
+    notice_level=2,
+):
     """Automatically select the hardware device.
 
     Args:
 
         communicator (hoomd.communicator.Communicator): MPI communicator object.
             When `None`, create a default communicator that uses all MPI ranks.
 
-        msg_file (str): Alias for ``message_filename``.
-
-            .. deprecated:: v3.10.0
-               ``msg_file`` will be renamed to ``message_filename`` in v4.
-
-        notice_level (int): Minimum level of messages to print.
-
         message_filename (str): Filename to write messages to. When `None`, use
             `sys.stdout` and `sys.stderr`. Messages from multiple MPI
             ranks are collected into this file.
 
+        notice_level (int): Minimum level of messages to print.
+
     Returns:
         Instance of `GPU` if availabile, otherwise `CPU`.
     """
     # Set class according to C++ object
     if len(GPU.get_available_devices()) > 0:
-        return GPU(None, None, communicator,
-                   _get_message_filename(msg_file, message_filename),
-                   notice_level)
+        return GPU(None, None, communicator, message_filename, notice_level)
     else:
-        return CPU(None, communicator,
-                   _get_message_filename(msg_file, message_filename),
-                   notice_level)
+        return CPU(None, communicator, message_filename, notice_level)

hoomd/md/external/wall.py

@@ -282,20 +282,20 @@ def __init__(self, walls):
         self._add_typeparam(params)
 
 
-class Gauss(WallPotential):
+class Gaussian(WallPotential):
     r"""Gaussian wall force.
 
     Args:
         walls (`list` [`hoomd.wall.WallGeometry` ]): A list of wall definitions
             to use for the force.
 
-    Wall force evaluated using the Gaussian force.  See `hoomd.md.pair.Gauss`
+    Wall force evaluated using the Gaussian force.  See `hoomd.md.pair.Gaussian`
     for the functional form of the force and parameter definitions.
 
     Example::
 
         walls = [hoomd.wall.Sphere(radius=4.0)]
-        gaussian_wall = hoomd.md.external.wall.Gauss(walls=walls)
+        gaussian_wall = hoomd.md.external.wall.Gaussian(walls=walls)
         gaussian_wall.params['A'] = {"epsilon": 1.0, "sigma": 1.0, "r_cut": 2.5}
         gaussian_wall.params[['A','B']] = {
             "epsilon": 2.0, "sigma": 1.0, "r_cut": 1.0}

hoomd/md/pair/__init__.py

@@ -133,7 +133,7 @@
 """
 
 from . import aniso
-from .pair import (Pair, LJ, Gauss, Gaussian, ExpandedLJ, Yukawa, Ewald, Morse,
-                   DPD, DPDConservative, DPDLJ, ForceShiftedLJ, Moliere, ZBL,
-                   Mie, ExpandedMie, ReactionField, DLVO, Buckingham, LJ1208,
-                   LJ0804, Fourier, OPP, Table, TWF, LJGauss)
+from .pair import (Pair, LJ, Gaussian, ExpandedLJ, Yukawa, Ewald, Morse, DPD,
+                   DPDConservative, DPDLJ, ForceShiftedLJ, Moliere, ZBL, Mie,
+                   ExpandedMie, ReactionField, DLVO, Buckingham, LJ1208, LJ0804,
+                   Fourier, OPP, Table, TWF, LJGauss)

hoomd/md/pair/pair.py

@@ -236,7 +236,7 @@ class Gaussian(Pair):
         default_r_on (float): Default turn-on radius :math:`[\mathrm{length}]`.
         mode (str): Energy shifting/smoothing mode.
 
-    `Gauss` computes the Gaussian pair force should on every particle in the
+    `Gaussian` computes the Gaussian pair force should on every particle in the
     simulation state:
 
     .. math::
@@ -279,20 +279,6 @@ def __init__(self, nlist, default_r_cut=None, default_r_on=0., mode='none'):
         self._add_typeparam(params)
 
 
-class Gauss(Gaussian):
-    """Gaussian pair force.
-
-    .. deprecated:: v3.10.0
-        Use `Gaussian`.
-    """
-
-    def __init__(self, nlist, default_r_cut=None, default_r_on=0., mode='none'):
-        warnings.warn(
-            "Gauss is deprecated and will be removed in hoomd 4.0. Use "
-            "Gaussian instead.", FutureWarning)
-        super().__init__(nlist, default_r_cut, default_r_on, mode)
-
-
 class ExpandedLJ(Pair):
     r"""Expanded Lennard-Jones pair force.
 

hoomd/md/pytest/forces_and_energies.json

@@ -64,7 +64,7 @@
       ]
     ]
   },
-  "Gauss": {
+  "Gaussian": {
     "params": [
       {
         "sigma": 0.5,

hoomd/md/pytest/test_half_step_hook.py

@@ -42,7 +42,7 @@ def sim_factory(particle_types=['A'], dimensions=3, d=1, L=20):
 def integrator_elements():
     nlist = md.nlist.Cell(buffer=0.4)
     lj = md.pair.LJ(nlist=nlist, default_r_cut=2.5)
-    gauss = md.pair.Gauss(nlist, default_r_cut=3.0)
+    gauss = md.pair.Gaussian(nlist, default_r_cut=3.0)
     lj.params[("A", "A")] = {"epsilon": 1.0, "sigma": 1.0}
     gauss.params[("A", "A")] = {"epsilon": 1.0, "sigma": 1.0}
     return {

hoomd/md/pytest/test_integrate.py

@@ -27,7 +27,7 @@ def sim_factory(particle_types=['A'], dimensions=3, d=1, L=20):
 def integrator_elements():
     nlist = md.nlist.Cell(buffer=0.4)
     lj = md.pair.LJ(nlist=nlist, default_r_cut=2.5)
-    gauss = md.pair.Gauss(nlist, default_r_cut=3.0)
+    gauss = md.pair.Gaussian(nlist, default_r_cut=3.0)
     lj.params[("A", "A")] = {"epsilon": 1.0, "sigma": 1.0}
     gauss.params[("A", "A")] = {"epsilon": 1.0, "sigma": 1.0}
     return {

hoomd/md/pytest/test_potential.py

@@ -183,7 +183,7 @@ def _invalid_params():
     gauss_valid_dict = {'sigma': 0.05, 'epsilon': 0.05}
     gauss_invalid_dicts = _make_invalid_param_dict(gauss_valid_dict)
     invalid_params_list.extend(
-        _make_invalid_params(gauss_invalid_dicts, md.pair.Gauss, {}))
+        _make_invalid_params(gauss_invalid_dicts, md.pair.Gaussian, {}))
 
     yukawa_valid_dict = {"epsilon": 0.0005, "kappa": 1}
     yukawa_invalid_dicts = _make_invalid_param_dict(yukawa_valid_dict)
@@ -396,7 +396,7 @@ def _valid_params(particle_types=['A', 'B']):
     gauss_arg_dict = {'epsilon': [0.025, 0.05, 0.075], 'sigma': [0.5, 1.0, 1.5]}
     gauss_valid_param_dicts = _make_valid_param_dicts(gauss_arg_dict)
     valid_params_list.append(
-        paramtuple(md.pair.Gauss, dict(zip(combos, gauss_valid_param_dicts)),
+        paramtuple(md.pair.Gaussian, dict(zip(combos, gauss_valid_param_dicts)),
                    {}))
 
     yukawa_arg_dict = {
@@ -1167,11 +1167,12 @@ def test_lrc_non_lj(simulation_factory, two_particle_snapshot_factory):
     # test we can't pass in tail_correction to non-LJ pair potential
     cell = md.nlist.Cell(buffer=0.4)
     with pytest.raises(TypeError):
-        # flake8 complains about unused variable with gauss = md.pair.Gauss(...)
-        md.pair.Gauss(nlist=cell,
-                      default_r_cut=2.5,
-                      mode='none',
-                      tail_correction=True)
+        # flake8 complains about unused variable with
+        # gauss = md.pair.Gaussian(...)
+        md.pair.Gaussian(nlist=cell,
+                         default_r_cut=2.5,
+                         mode='none',
+                         tail_correction=True)
 
 
 def test_tail_corrections(simulation_factory, two_particle_snapshot_factory):

hoomd/md/pytest/test_wall_potential.py

@@ -63,7 +63,7 @@ def generate_n(cls, N):
 
 _potential_cls = (
     md.external.wall.LJ,
-    md.external.wall.Gauss,
+    md.external.wall.Gaussian,
     md.external.wall.Yukawa,
     md.external.wall.Morse,
     md.external.wall.ForceShiftedLJ,

hoomd/pytest/test_custom_writer.py

@@ -49,7 +49,7 @@ def test_flags(self, simulation_factory, two_particle_snapshot_factory):
         action = WriteTimestep()
         action.flags = [hoomd.custom.Action.Flags.PRESSURE_TENSOR]
         sim.operations += hoomd.write.CustomWriter(2, action)
-        gauss = hoomd.md.pair.Gauss(hoomd.md.nlist.Cell(0.5))
+        gauss = hoomd.md.pair.Gaussian(hoomd.md.nlist.Cell(0.5))
         gauss.params[("A", "A")] = {"sigma": 1.0, "epsilon": 1.0}
         gauss.r_cut[("A", "A")] = 2.0
         sim.operations += hoomd.md.Integrator(