Add warnings for deprecated file formats (protobuf, hoomdxml, Hoomd-B…

…lue and LAMMPS simulation writers) (#1188) * add return statement for deprecation decorator, add dep warnings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * import deprecated method * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add path to writers --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Co Quach <[email protected]>
mosdef-hub · Jun 17, 2024 · cd53189 · cd53189
1 parent 3ceeda2
commit cd53189
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Showing 6 changed files with 44 additions and 3 deletions.
diff --git a/mbuild/formats/hoomd_forcefield.py b/mbuild/formats/hoomd_forcefield.py
@@ -10,6 +10,7 @@
 
 import mbuild as mb
 from mbuild.utils.conversion import RB_to_OPLS
+from mbuild.utils.decorators import deprecated
 from mbuild.utils.io import import_
 from mbuild.utils.sorting import natural_sort
 
@@ -18,6 +19,16 @@
 hoomd = import_("hoomd")
 
 
+dep_msg = """
+Support for Hoomd-Blue writers will be removed in mBuild 1.0.
+See GMSO (https://github.com/mosdef-hub/gmso/tree/main/gmso/external/convert_hoomd) for
+Hoomd-Blue 3.x and 4.x format support.
+To convert to GMSO, use the method `Compound.to_gmso()`.
+"""
+print(dep_msg)
+
+
+@deprecated(dep_msg)
 def create_hoomd_forcefield(
     structure,
     r_cut,

diff --git a/mbuild/formats/hoomd_simulation.py b/mbuild/formats/hoomd_simulation.py
@@ -10,6 +10,7 @@
 
 import mbuild as mb
 from mbuild.utils.conversion import RB_to_OPLS
+from mbuild.utils.decorators import deprecated
 from mbuild.utils.io import import_
 from mbuild.utils.sorting import natural_sort
 
@@ -21,6 +22,16 @@
 hoomd.md = import_("hoomd.md")
 
 
+dep_msg = """
+Support for Hoomd-Blue 2.0 will be removed in mBuild 1.0.
+See GMSO (https://github.com/mosdef-hub/gmso/tree/main/gmso/external/convert_hoomd) for
+Hoomd-Blue 3.x and 4.x format support.
+To convert to GMSO, use the method `Compound.to_gmso()`.
+"""
+print(dep_msg)
+
+
+@deprecated(dep_msg)
 def create_hoomd_simulation(
     structure,
     r_cut,

diff --git a/mbuild/formats/hoomdxml.py b/mbuild/formats/hoomdxml.py
@@ -7,13 +7,13 @@
 import numpy as np
 
 from mbuild.utils.conversion import RB_to_OPLS
-from mbuild.utils.decorators import breaking_change
+from mbuild.utils.decorators import deprecated
 from mbuild.utils.geometry import coord_shift
 
 __all__ = ["write_hoomdxml"]
 
 
-@breaking_change("See PR#463 on github")
+@deprecated("The .hoomdxml file format will be removed in mBuild 1.0.")
 def write_hoomdxml(
     structure,
     filename,

diff --git a/mbuild/formats/lammpsdata.py b/mbuild/formats/lammpsdata.py
@@ -11,6 +11,7 @@
 
 from mbuild import Box
 from mbuild.utils.conversion import RB_to_OPLS
+from mbuild.utils.decorators import deprecated
 from mbuild.utils.orderedset import OrderedSet
 from mbuild.utils.sorting import natural_sort
 
@@ -22,6 +23,16 @@
 ELEM_TO_COUL = 1.602176634e-19
 
 
+dep_msg = """
+Support for writing out LAMMPS data files will be removed
+in mbuild 1.0.
+See GMSO (https://github.com/mosdef-hub/gmso/tree/main/gmso/formats/lammpsdata) for
+continued support for LAMMPS.
+"""
+print(dep_msg)
+
+
+@deprecated(dep_msg)
 def write_lammpsdata(
     structure,
     filename,

diff --git a/mbuild/formats/protobuf.py b/mbuild/formats/protobuf.py
@@ -10,10 +10,18 @@
 
 from mbuild import Box, Compound
 from mbuild.formats import compound_pb2
+from mbuild.utils.decorators import deprecated
 
 __all__ = ["write_pb2", "read_pb2"]
 
 
+dep_msg = """
+Support for the Protobuf file format will be removed in mBuild 1.0.
+"""
+print(dep_msg)
+
+
+@deprecated(dep_msg)
 def write_pb2(cmpd, filename, binary=True):
     """Convert mb.Compound to Protobuf Message file.
 

diff --git a/mbuild/utils/decorators.py b/mbuild/utils/decorators.py
@@ -30,7 +30,7 @@ def wrapper(*args, **kwargs):
                 fcn.__name__, warning_string
             )
             warn(printed_message, DeprecationWarning)
-            fcn(*args, **kwargs)
+            return fcn(*args, **kwargs)
 
         return wrapper