Merge pull request #1699 from glotzerlab/remove_custom_methods

Deprecate custom action methods

hoomd/custom/custom_operation.py

@@ -216,9 +216,6 @@ def __init__(self, trigger, *args, **kwargs):
             key: value.update_cls(self.__class__)
             for key, value in self._export_dict.items()
         }
-        # Wrap action act method with operation appropriate one.
-        wrapping_method = getattr(self, self._operation_func).__func__
-        setattr(wrapping_method, "__doc__", self._action.act.__doc__)
 
     def __dir__(self):
         """Expose all attributes for dynamic querying in notebooks and IDEs."""

hoomd/md/pytest/test_hdf5.py

@@ -88,37 +88,6 @@ def test_write(create_md_sim, tmp_path):
             assert np.allclose(fh[key], kinetic_energy_list)
 
 
-def test_write_method(create_md_sim, tmp_path):
-    filename = tmp_path / "temporary_test_file.h5"
-
-    sim = create_md_sim
-    thermo = hoomd.md.compute.ThermodynamicQuantities(filter=hoomd.filter.All())
-    sim.operations.computes.append(thermo)
-
-    logger = hoomd.logging.Logger(["scalar", "particle", "sequence"])
-    logger.add(thermo)
-
-    # Writer should never run on its own.
-    hdf5_writer = hoomd.write.HDF5Log(filename=filename,
-                                      trigger=hoomd.trigger.Periodic(100),
-                                      mode='w',
-                                      logger=logger)
-    sim.operations.writers.append(hdf5_writer)
-
-    kinetic_energy_list = []
-    for _ in range(5):
-        sim.run(1)
-        kinetic_energy_list.append(thermo.kinetic_energy)
-        hdf5_writer.write()
-
-    hdf5_writer.flush()
-
-    if sim.device.communicator.rank == 0:
-        key = 'hoomd-data/md/compute/ThermodynamicQuantities/kinetic_energy'
-        with h5py.File(filename, mode='r') as fh:
-            assert np.allclose(fh[key], kinetic_energy_list)
-
-
 def test_mode(tmp_path, create_md_sim):
     logger = hoomd.logging.Logger(categories=['scalar'])
     sim = create_md_sim

hoomd/tune/custom_tuner.py

@@ -15,7 +15,6 @@ def act(self, timestep):
 
 from hoomd.custom import (CustomOperation, _InternalCustomOperation, Action)
 from hoomd.operation import Tuner
-import warnings
 
 
 class _TunerProperty:
@@ -72,14 +71,3 @@ class _InternalCustomTuner(_InternalCustomOperation, Tuner):
     _cpp_list_name = 'tuners'
     _cpp_class_name = 'PythonTuner'
     _operation_func = "tune"
-
-    def tune(self, timestep):
-        return self._action.act(timestep)
-        """
-        .. deprecated:: 4.5.0
-
-           Use `Simulation` to call the operation.
-        """
-        warnings.warn(
-            "`_InternalCustomTuner.tune` is deprecated,"
-            "use `Simulation` to call the operation.", FutureWarning)

hoomd/update/custom_updater.py

@@ -15,7 +15,6 @@ def act(self, timestep):
 
 from hoomd.custom import (CustomOperation, _InternalCustomOperation, Action)
 from hoomd.operation import Updater
-import warnings
 
 
 class _UpdaterProperty:
@@ -71,14 +70,3 @@ class _InternalCustomUpdater(_InternalCustomOperation, Updater):
     _cpp_list_name = 'updaters'
     _cpp_class_name = 'PythonUpdater'
     _operation_func = "update"
-
-    def update(self, timestep):
-        return self._action.act(timestep)
-        """
-        .. deprecated:: 4.5.0
-
-            Use `Simulation` to call the operation.
-        """
-        warnings.warn(
-            "`_InternalCustomUpdater.update` is deprecated,"
-            "use `Simulation` to call the operation.", FutureWarning)

hoomd/write/custom_writer.py

@@ -15,7 +15,6 @@ def act(self, timestep):
 
 from hoomd.custom import (CustomOperation, _InternalCustomOperation, Action)
 from hoomd.operation import Writer
-import warnings
 
 
 class _WriterProperty:
@@ -72,14 +71,3 @@ class _InternalCustomWriter(_InternalCustomOperation, Writer):
     _cpp_list_name = 'analyzers'
     _cpp_class_name = 'PythonAnalyzer'
     _operation_func = "write"
-
-    def write(self, timestep):
-        return self._action.act(timestep)
-        """
-        .. deprecated:: 4.5.0
-
-            Use `Simulation` to call the operation.
-        """
-        warnings.warn(
-            "`_InternalCustomWriter.write` is deprecated,"
-            "use `Simulation` to call the operation.", FutureWarning)

hoomd/write/hdf5.py

@@ -37,7 +37,6 @@
 
 from hoomd.write.custom_writer import _InternalCustomWriter
 from hoomd.data.parameterdicts import ParameterDict
-import warnings
 
 try:
     import h5py
@@ -332,30 +331,5 @@ class HDF5Log(_InternalCustomWriter):
     _internal_class = _HDF5LogInternal
     _wrap_methods = ("flush",)
 
-    def write(self, timestep=None):
-        """Write out data to the HDF5 file.
-
-        Writes out a frame at the current timestep from the composed logger.
-
-        Warning:
-            This may not be able to write out quantities which require the
-            pressure tensor, rotational kinetic energy, or external field
-            virial.
-
-        .. rubric:: Example:
-
-        .. code-block:: python
-
-            hdf5_writer.write()
-
-        .. deprecated:: 4.5.0
-
-            Use `Simulation` to call the operation.
-        """
-        warnings.warn(
-            "`HDF5Log.writer` is deprecated,"
-            "use `Simulation` to call the operation.", FutureWarning)
-        self._action.act(timestep)
-
 
 __all__ = ["HDF5Log"]

sphinx-doc/migrating.rst

@@ -4,6 +4,20 @@
 Migrating to the latest version
 ===============================
 
+Migrating to HOOMD v5
+---------------------
+
+Removed functionalities
+^^^^^^^^^^^^^^^^^^^^^^^
+
+HOOMD-blue v5 removes functionalities deprecated in v4.x releases:
+
+* ``_InternalCustomUpdater.update``
+* ``_InternalCustomTuner.tune``
+* ``_InternalCustomWriter.write``
+* ``HDF5Log.write``
+
+
 Migrating to HOOMD v4
 ---------------------