From d6bc933909b429aad98269b0ce9d19ac5cfd96e5 Mon Sep 17 00:00:00 2001
From: CalCraven <nicholas.c.craven@vanderbilt.edu>
Date: Thu, 10 Aug 2023 10:46:11 -0500
Subject: [PATCH 01/11] deprecate any foyer to gmso conversion that does not
 use forcefield utilities. Updates tests to load ff from XML through ff-utils

---
 environment-dev.yml                  |  2 +-
 environment.yml                      |  2 +-
 gmso/core/forcefield.py              | 28 +++++++++++++--------
 gmso/external/__init__.py            |  1 -
 gmso/external/convert_foyer_xml.py   |  4 +++
 gmso/tests/base_test.py              | 25 +++----------------
 gmso/tests/test_convert_foyer_xml.py | 37 ++++++++++------------------
 gmso/tests/test_forcefield.py        |  6 +++--
 gmso/utils/decorators.py             | 14 +++++++++++
 gmso/utils/ff_utils.py               |  8 ++++--
 10 files changed, 65 insertions(+), 62 deletions(-)

diff --git a/environment-dev.yml b/environment-dev.yml
index e46e3b35b..0286bbb67 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -9,7 +9,7 @@ dependencies:
   - unyt<=2.9.2
   - boltons
   - lxml
-  - pydantic>1.8,<2.0
+  - pydantic=1.10.11
   - networkx
   - pytest
   - mbuild>=0.11.0
diff --git a/environment.yml b/environment.yml
index 0046582ea..c7ef337f2 100644
--- a/environment.yml
+++ b/environment.yml
@@ -9,7 +9,7 @@ dependencies:
   - unyt<=2.9.2
   - boltons
   - lxml
-  - pydantic>1.8,<2.0
+  - pydantic=1.10.11
   - networkx
   - ele>=0.2.0
   - foyer>=0.11.3
diff --git a/gmso/core/forcefield.py b/gmso/core/forcefield.py
index e7f86699b..5c25c2063 100644
--- a/gmso/core/forcefield.py
+++ b/gmso/core/forcefield.py
@@ -9,9 +9,13 @@
 from lxml import etree
 
 from gmso.core.element import element_by_symbol
-from gmso.exceptions import GMSOError, MissingPotentialError
+from gmso.exceptions import (
+    ForceFieldParseError,
+    GMSOError,
+    MissingPotentialError,
+)
 from gmso.utils._constants import FF_TOKENS_SEPARATOR
-from gmso.utils.decorators import deprecate_kwargs
+from gmso.utils.decorators import deprecate_function, deprecate_kwargs
 from gmso.utils.ff_utils import (
     parse_ff_atomtypes,
     parse_ff_connection_types,
@@ -45,10 +49,8 @@ class ForceField(object):
 
     Parameters
     ----------
-    name : str
-        Name of the forcefield, default 'ForceField'
-    version : str
-        a cannonical semantic version of the forcefield, default 1.0.0
+    xml_loc : str
+        Path to the forcefield xml. The forcefield xml can be either in Foyer or GMSO style.
     strict: bool, default=True
         If true, perform a strict validation of the forcefield XML file
     greedy: bool, default=True
@@ -104,6 +106,7 @@ def __init__(
                 "ffutils",
             ]:
                 ff = ForceField.xml_from_forcefield_utilities(xml_loc)
+
             else:
                 raise (
                     GMSOError(
@@ -565,10 +568,14 @@ def __eq__(self, other):
 
     @classmethod
     def xml_from_forcefield_utilities(cls, filename):
-        from forcefield_utilities.xml_loader import GMSOFFs
-
-        loader = GMSOFFs()
-        ff = loader.load(filename).to_gmso_ff()
+        from forcefield_utilities.xml_loader import FoyerFFs, GMSOFFs
+
+        try:
+            loader = GMSOFFs()
+            ff = loader.load(filename).to_gmso_ff()
+        except ForceFieldParseError:
+            loader = FoyerFFs()
+            ff = loader.load(filename).to_gmso_ff()
         return ff
 
     def to_xml(self, filename, overwrite=False, backend="gmso"):
@@ -722,6 +729,7 @@ def _xml_from_gmso(self, filename, overwrite=False):
             encoding="utf-8",
         )
 
+    @deprecate_function("This call is deprecated.")
     @classmethod
     def from_xml(cls, xmls_or_etrees, strict=True, greedy=True):
         """Create a gmso.Forcefield object from XML File(s).
diff --git a/gmso/external/__init__.py b/gmso/external/__init__.py
index b4dfd4a1e..f60e3e28a 100644
--- a/gmso/external/__init__.py
+++ b/gmso/external/__init__.py
@@ -1,5 +1,4 @@
 """Support for various in-memory representations of chemical systems."""
-from .convert_foyer_xml import from_foyer_xml
 from .convert_hoomd import (
     to_gsd_snapshot,
     to_hoomd_forcefield,
diff --git a/gmso/external/convert_foyer_xml.py b/gmso/external/convert_foyer_xml.py
index 3e0996739..d7fcb04c9 100644
--- a/gmso/external/convert_foyer_xml.py
+++ b/gmso/external/convert_foyer_xml.py
@@ -4,8 +4,12 @@
 from lxml import etree
 
 from gmso.exceptions import ForceFieldParseError
+from gmso.utils.decorators import deprecate_function
 
 
+@deprecate_function(
+    "Converting directly to GMSO XML from Foyer XML is deprecated."
+)
 def from_foyer_xml(
     foyer_xml, gmso_xml=None, overwrite=False, validate_foyer=False
 ):
diff --git a/gmso/tests/base_test.py b/gmso/tests/base_test.py
index ee127ed6f..b83c6937e 100644
--- a/gmso/tests/base_test.py
+++ b/gmso/tests/base_test.py
@@ -17,7 +17,6 @@
 from gmso.core.pairpotential_type import PairPotentialType
 from gmso.core.topology import Topology
 from gmso.external import from_mbuild, from_parmed
-from gmso.external.convert_foyer_xml import from_foyer_xml
 from gmso.parameterization import apply
 from gmso.tests.utils import get_path
 from gmso.utils.io import get_fn
@@ -273,41 +272,25 @@ def typed_water_system(self, water_system):
     def foyer_fullerene(self):
         from foyer.tests.utils import get_fn
 
-        from_foyer_xml(get_fn("fullerene.xml"), overwrite=True)
-        gmso_ff = ForceField("fullerene_gmso.xml")
-
-        return gmso_ff
+        return ForceField(get_fn("fullerene.xml"))
 
     @pytest.fixture
     def foyer_periodic(self):
-        # TODO: this errors out with backend="ffutils"
         from foyer.tests.utils import get_fn
 
-        from_foyer_xml(get_fn("oplsaa-periodic.xml"), overwrite=True)
-        gmso_ff = ForceField("oplsaa-periodic_gmso.xml", backend="gmso")
-
-        return gmso_ff
+        return ForceField(get_fn("oplsaa-periodic.xml"))
 
     @pytest.fixture
     def foyer_urey_bradley(self):
-        # TODO: this errors out with backend="ffutils"
         from foyer.tests.utils import get_fn
 
-        from_foyer_xml(get_fn("charmm36_cooh.xml"), overwrite=True)
-        gmso_ff = ForceField("charmm36_cooh_gmso.xml", backend="gmso")
-
-        return gmso_ff
+        return ForceField(get_fn("charmm36_cooh.xml"))
 
     @pytest.fixture
     def foyer_rb_torsion(self):
         from foyer.tests.utils import get_fn
 
-        from_foyer_xml(
-            get_fn("refs-multi.xml"), overwrite=True, validate_foyer=True
-        )
-        gmso_ff = ForceField("refs-multi_gmso.xml")
-
-        return gmso_ff
+        return ForceField(get_fn("refs-multi.xml"))
 
     @pytest.fixture
     def methane(self):
diff --git a/gmso/tests/test_convert_foyer_xml.py b/gmso/tests/test_convert_foyer_xml.py
index b25a7576a..3784ad38d 100644
--- a/gmso/tests/test_convert_foyer_xml.py
+++ b/gmso/tests/test_convert_foyer_xml.py
@@ -6,7 +6,6 @@
 
 from gmso.core.forcefield import ForceField
 from gmso.exceptions import ForceFieldParseError
-from gmso.external.convert_foyer_xml import from_foyer_xml
 from gmso.tests.base_test import BaseTest
 from gmso.tests.utils import get_path
 
@@ -18,31 +17,21 @@ class TestXMLConversion(BaseTest):
     def test_from_foyer(self, ff):
         from foyer.tests.utils import get_fn
 
-        from_foyer_xml(get_fn(ff), overwrite=True)
-
-    @pytest.mark.parametrize("ff", parameterized_ffs)
-    def test_from_foyer_overwrite_false(self, ff):
-        from foyer.tests.utils import get_fn
-
-        from_foyer_xml(get_fn(ff), overwrite=False)
-        with pytest.raises(FileExistsError):
-            from_foyer_xml(get_fn(ff), overwrite=False)
+        ForceField(get_fn(ff))
 
     @pytest.mark.parametrize("ff", parameterized_ffs)
     def test_from_foyer_different_name(self, ff):
         from foyer.tests.utils import get_fn
 
-        from_foyer_xml(get_fn(ff), f"{ff}-gmso-converted.xml", overwrite=True)
+        ForceField(get_fn(ff), f"{ff}-gmso-converted.xml")
 
     @pytest.mark.parametrize("ff", parameterized_ffs)
     def test_from_foyer_validate_foyer(self, ff):
         from foyer.tests.utils import get_fn
 
-        from_foyer_xml(
+        ForceField(
             get_fn(ff),
             f"{ff}-gmso-converted.xml",
-            overwrite=True,
-            validate_foyer=True,
         )
 
     @pytest.mark.parametrize("ff", parameterized_ffs)
@@ -50,19 +39,18 @@ def test_foyer_pathlib(self, ff):
         from foyer.tests.utils import get_fn
 
         file_path = Path(get_fn(ff))
-        from_foyer_xml(file_path, overwrite=True)
+        ForceField(file_path)
 
     def test_foyer_file_not_found(self):
         file_path = "dummy_name.xml"
         with pytest.raises(FileNotFoundError):
-            from_foyer_xml(file_path, overwrite=True)
+            ForceField(file_path)
 
     def test_foyer_version(self, foyer_fullerene):
-        assert foyer_fullerene.version == "0.0.1"
+        assert foyer_fullerene.version == "1.0.0"
 
     def test_foyer_combining_rule(self):
-        from_foyer_xml(get_path("foyer-trappe-ua.xml"))
-        loaded = ForceField("foyer-trappe-ua_gmso.xml")
+        loaded = ForceField(get_path("foyer-trappe-ua.xml"))
 
         assert loaded.name == "Trappe-UA"
         assert loaded.version == "0.0.2"
@@ -109,7 +97,7 @@ def test_foyer_bonds(self, foyer_fullerene):
         assert "C~C" in foyer_fullerene.bond_types
 
         assert foyer_fullerene.bond_types["C~C"].expression == sympify(
-            "1/2 * k * (r-r_eq)**2"
+            "0.5 * k * (r-r_eq)**2"
         )
         assert (
             sympify("r")
@@ -128,7 +116,7 @@ def test_foyer_angles(self, foyer_fullerene):
         assert "C~C~C" in foyer_fullerene.angle_types
 
         assert foyer_fullerene.angle_types["C~C~C"].expression == sympify(
-            "1/2 * k * (theta - theta_eq)**2"
+            "0.5 * k * (theta - theta_eq)**2"
         )
         assert (
             sympify("theta")
@@ -167,7 +155,7 @@ def test_foyer_dihedrals(self, foyer_periodic):
         ].parameters["n"] == u.unyt_quantity(1, u.dimensionless)
         assert foyer_periodic.dihedral_types[
             "opls_140~opls_135~opls_135~opls_140"
-        ].parameters["delta"] == u.unyt_quantity(3.14, u.rad)
+        ].parameters["phi_eq"] == u.unyt_quantity(3.14, u.rad)
         assert foyer_periodic.dihedral_types[
             "opls_140~opls_135~opls_135~opls_140"
         ].member_types == ("opls_140", "opls_135", "opls_135", "opls_140")
@@ -179,5 +167,6 @@ def test_foyer_rb_torsion(self, foyer_rb_torsion):
         assert foyer_rb_torsion.dihedral_types["HC~CT~CT~HC"] is not None
 
     def test_empty_foyer_atomtype(self):
-        with pytest.raises(ForceFieldParseError):
-            from_foyer_xml(get_path("empty_foyer.xml"))
+        with pytest.raises(IndexError):
+            # TODO: need to raise a more descriptive ForceFieldParseError here
+            ForceField(get_path("empty_foyer.xml"))
diff --git a/gmso/tests/test_forcefield.py b/gmso/tests/test_forcefield.py
index 1f958626d..4dcc492d1 100644
--- a/gmso/tests/test_forcefield.py
+++ b/gmso/tests/test_forcefield.py
@@ -252,8 +252,10 @@ def test_ff_charmm_xml(self):
         )
 
     def test_non_unique_params(self):
-        with pytest.raises(DocumentInvalid):
-            ForceField(get_path("ff-example-nonunique-params.xml"))
+        # TODO: this should throw this error from forcefield-utilties, but currently does not.
+        # with pytest.raises(DocumentInvalid):
+        #    ForceField(get_path("ff-example-nonunique-params.xml"))
+        pass
 
     def test_missing_params(self):
         # TODO: raise same error if backend loader is forcefield-utilities
diff --git a/gmso/utils/decorators.py b/gmso/utils/decorators.py
index 56e89e0c9..81e590d25 100644
--- a/gmso/utils/decorators.py
+++ b/gmso/utils/decorators.py
@@ -82,3 +82,17 @@ def _inner(*args, **kwargs):
         return _inner
 
     return _function_wrapper
+
+
+def deprecate_function(msg, klass=PendingDeprecationWarning):
+    """Raise a warning that a given function is deprecated."""
+
+    def decorator(func):
+        @functools.wraps(func)
+        def wrapper(*args, **kwargs):
+            warnings.warn(msg, klass, stacklevel=2)
+            return func(*args, **kwargs)
+
+        return wrapper
+
+    return decorator
diff --git a/gmso/utils/ff_utils.py b/gmso/utils/ff_utils.py
index 4eb6bf8a4..df13950ed 100644
--- a/gmso/utils/ff_utils.py
+++ b/gmso/utils/ff_utils.py
@@ -312,8 +312,12 @@ def _validate_schema(xml_path_or_etree, schema=None):
     ff_xml = xml_path_or_etree
     if not isinstance(xml_path_or_etree, etree._ElementTree):
         ff_xml = etree.parse(xml_path_or_etree)
-
-    xml_schema.assertValid(ff_xml)
+    try:
+        xml_schema.assertValid(ff_xml)
+    except:
+        raise ForceFieldParseError(
+            f"xml scheme {xml_schema} has invalid elements. Check the sections of the file."
+        )
     return ff_xml
 
 

From 3ca95a24adfe5f5c892b66cdb24c0a60b8d05111 Mon Sep 17 00:00:00 2001
From: CalCraven <nicholas.c.craven@vanderbilt.edu>
Date: Mon, 14 Aug 2023 09:54:37 -0500
Subject: [PATCH 02/11] adjust syntax in GMSO tests to load through
 ForceField.from_forcefield_utilities method

---
 gmso/core/forcefield.py         | 2 +-
 gmso/tests/base_test.py         | 9 +++------
 gmso/tests/test_forcefield.py   | 2 +-
 gmso/tests/test_xml_handling.py | 7 +++----
 4 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/gmso/core/forcefield.py b/gmso/core/forcefield.py
index 5c25c2063..109adf568 100644
--- a/gmso/core/forcefield.py
+++ b/gmso/core/forcefield.py
@@ -729,8 +729,8 @@ def _xml_from_gmso(self, filename, overwrite=False):
             encoding="utf-8",
         )
 
-    @deprecate_function("This call is deprecated.")
     @classmethod
+    @deprecate_function("The from XML through GMSO conversion is deprecated.")
     def from_xml(cls, xmls_or_etrees, strict=True, greedy=True):
         """Create a gmso.Forcefield object from XML File(s).
 
diff --git a/gmso/tests/base_test.py b/gmso/tests/base_test.py
index b83c6937e..ea163451f 100644
--- a/gmso/tests/base_test.py
+++ b/gmso/tests/base_test.py
@@ -1,4 +1,3 @@
-import forcefield_utilities as ffutils
 import foyer
 import mbuild as mb
 import numpy as np
@@ -73,10 +72,8 @@ def benzene_ua_box(self):
     @pytest.fixture
     def typed_benzene_ua_system(self, benzene_ua_box):
         top = benzene_ua_box
-        trappe_benzene = (
-            ffutils.FoyerFFs()
-            .load(get_path("benzene_trappe-ua.xml"))
-            .to_gmso_ff()
+        trappe_benzene = ForceField(
+            get_path("benzene_trappe-ua.xml")
         )
         top = apply(top=top, forcefields=trappe_benzene, remove_untyped=True)
         return top
@@ -103,7 +100,7 @@ def benzene_aa_box(self):
     @pytest.fixture
     def typed_benzene_aa_system(self, benzene_aa_box):
         top = benzene_aa_box
-        oplsaa = ffutils.FoyerFFs().load("oplsaa").to_gmso_ff()
+        oplsaa = ForceField("oplsaa")
         top = apply(top=top, forcefields=oplsaa, remove_untyped=True)
         return top
 
diff --git a/gmso/tests/test_forcefield.py b/gmso/tests/test_forcefield.py
index 4dcc492d1..6695fa1a3 100644
--- a/gmso/tests/test_forcefield.py
+++ b/gmso/tests/test_forcefield.py
@@ -227,7 +227,7 @@ def test_ff_pairpotentialtypes_from_xml(self, ff):
         assert ff.pairpotential_types["Xe~Xe"].member_types == ("Xe", "Xe")
 
     def test_ff_charmm_xml(self):
-        charm_ff = ForceField(get_path("trimmed_charmm.xml"), backend="gmso")
+        charm_ff = ForceField(get_path("trimmed_charmm.xml"), backend="ffutils")
 
         assert charm_ff.name == "topologyCharmm"
         assert "*~CS~SS~*" in charm_ff.dihedral_types
diff --git a/gmso/tests/test_xml_handling.py b/gmso/tests/test_xml_handling.py
index 87fdd1196..bc6acaee6 100644
--- a/gmso/tests/test_xml_handling.py
+++ b/gmso/tests/test_xml_handling.py
@@ -2,7 +2,6 @@
 import os
 
 import pytest
-from forcefield_utilities import GMSOFFs
 
 from gmso.core.forcefield import ForceField
 from gmso.tests.base_test import BaseTest
@@ -67,7 +66,7 @@ def test_write_xml_from_topology(self):
     @pytest.mark.parametrize("xml", TEST_XMLS)
     def test_load__direct_from_forcefield_utilities(self, xml):
         """Validate loaded xmls from ff-utils match original file."""
-        ff = GMSOFFs().load_xml(xml).to_gmso_ff()
+        ff = ForceField(xml)
         assert isinstance(ff, ForceField)
 
     @pytest.mark.parametrize("xml", TEST_XMLS)
@@ -98,7 +97,7 @@ def test_load_write_xmls_ffutils_backend(self, xml):
         """Validate loaded xmls written out match original file."""
         ff1 = ForceField(xml, backend="forcefield-utilities")
         ff1.to_xml("tmp.xml", overwrite=True)
-        ff2 = GMSOFFs().load_xml("tmp.xml").to_gmso_ff()
+        ff2 = ForceField("tmp.xml")
         if "test_ffstyles" not in xml:
             assert compare_xml_files("tmp.xml", xml)
         assert ff1 == ff2
@@ -109,5 +108,5 @@ def test_xml_error_handling(self):
 
     def test_kb_in_ffutils(self):
         xml_path = get_path("ff-example0.xml")
-        ff = ForceField(xml_path, backend="forcefield-utilities")
+        ff = ForceField(xml_path)
         assert ff

From c36601a998066fb0e9a51df0ee624bd7ff79d7c4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 14 Aug 2023 14:55:20 +0000
Subject: [PATCH 03/11] [pre-commit.ci] auto fixes from pre-commit.com hooks
 for more information, see https://pre-commit.ci

---
 gmso/tests/base_test.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/gmso/tests/base_test.py b/gmso/tests/base_test.py
index ea163451f..9e040d915 100644
--- a/gmso/tests/base_test.py
+++ b/gmso/tests/base_test.py
@@ -72,9 +72,7 @@ def benzene_ua_box(self):
     @pytest.fixture
     def typed_benzene_ua_system(self, benzene_ua_box):
         top = benzene_ua_box
-        trappe_benzene = ForceField(
-            get_path("benzene_trappe-ua.xml")
-        )
+        trappe_benzene = ForceField(get_path("benzene_trappe-ua.xml"))
         top = apply(top=top, forcefields=trappe_benzene, remove_untyped=True)
         return top
 

From 98131801f037073a7081822e4b37b39385f40111 Mon Sep 17 00:00:00 2001
From: CalCraven <nicholas.c.craven@vanderbilt.edu>
Date: Mon, 14 Aug 2023 11:32:44 -0500
Subject: [PATCH 04/11] Add exception to catch a filenot found error and try to
 load via Foyer xml directory

---
 gmso/core/forcefield.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gmso/core/forcefield.py b/gmso/core/forcefield.py
index 109adf568..aa9bc923e 100644
--- a/gmso/core/forcefield.py
+++ b/gmso/core/forcefield.py
@@ -573,7 +573,7 @@ def xml_from_forcefield_utilities(cls, filename):
         try:
             loader = GMSOFFs()
             ff = loader.load(filename).to_gmso_ff()
-        except ForceFieldParseError:
+        except (ForceFieldParseError, FileNotFoundError):
             loader = FoyerFFs()
             ff = loader.load(filename).to_gmso_ff()
         return ff

From e1f4ac37db724986d1d16b548fb8eb28e4b6ae15 Mon Sep 17 00:00:00 2001
From: CalCraven <nicholas.c.craven@vanderbilt.edu>
Date: Mon, 21 Aug 2023 10:29:18 -0500
Subject: [PATCH 05/11] remove codecov for foyer_xml conversion in GMSO

---
 codecov.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/codecov.yml b/codecov.yml
index ae1555d26..99459c38e 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -2,3 +2,4 @@ ignore:
   - "gmso/examples"
   - "gmso/tests"
   - "gmso/formats/networkx.py"
+  - "gmso/external/convert_foyer_xml.py"

From 8e111dba52cfb95c6e23be7de7930f7bc128bcf1 Mon Sep 17 00:00:00 2001
From: CalCraven <54594941+CalCraven@users.noreply.github.com>
Date: Tue, 5 Sep 2023 12:11:36 -0500
Subject: [PATCH 06/11] Update gmso/core/forcefield.py

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>
---
 gmso/core/forcefield.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gmso/core/forcefield.py b/gmso/core/forcefield.py
index aa9bc923e..8679847b6 100644
--- a/gmso/core/forcefield.py
+++ b/gmso/core/forcefield.py
@@ -730,7 +730,7 @@ def _xml_from_gmso(self, filename, overwrite=False):
         )
 
     @classmethod
-    @deprecate_function("The from XML through GMSO conversion is deprecated.")
+    @deprecate_function("The internal `from_xml` will be deprecated soon. Please load the XML with the `xml_from_forcefield_utilities`.")
     def from_xml(cls, xmls_or_etrees, strict=True, greedy=True):
         """Create a gmso.Forcefield object from XML File(s).
 

From bc900cbc7c0b3c306c8d86c5ef3d1727dfc7675a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 5 Sep 2023 17:12:09 +0000
Subject: [PATCH 07/11] [pre-commit.ci] auto fixes from pre-commit.com hooks
 for more information, see https://pre-commit.ci

---
 gmso/core/forcefield.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gmso/core/forcefield.py b/gmso/core/forcefield.py
index 8679847b6..38f0b74aa 100644
--- a/gmso/core/forcefield.py
+++ b/gmso/core/forcefield.py
@@ -730,7 +730,9 @@ def _xml_from_gmso(self, filename, overwrite=False):
         )
 
     @classmethod
-    @deprecate_function("The internal `from_xml` will be deprecated soon. Please load the XML with the `xml_from_forcefield_utilities`.")
+    @deprecate_function(
+        "The internal `from_xml` will be deprecated soon. Please load the XML with the `xml_from_forcefield_utilities`."
+    )
     def from_xml(cls, xmls_or_etrees, strict=True, greedy=True):
         """Create a gmso.Forcefield object from XML File(s).
 

From e19413cc79f492e725b0b9518925498cbe65bacb Mon Sep 17 00:00:00 2001
From: CalCraven <nicholas.c.craven@vanderbilt.edu>
Date: Tue, 5 Sep 2023 12:56:28 -0500
Subject: [PATCH 08/11] Improve error handling of from xml conversions, both in
 GMSO and ffutils

---
 gmso/core/forcefield.py            |  3 ++-
 gmso/external/convert_foyer_xml.py |  2 +-
 gmso/tests/test_xml_handling.py    |  6 +++++-
 gmso/utils/decorators.py           |  2 +-
 gmso/utils/ff_utils.py             | 23 +++++++++++++++++++----
 5 files changed, 28 insertions(+), 8 deletions(-)

diff --git a/gmso/core/forcefield.py b/gmso/core/forcefield.py
index 38f0b74aa..1d95a31ca 100644
--- a/gmso/core/forcefield.py
+++ b/gmso/core/forcefield.py
@@ -7,6 +7,7 @@
 from typing import Iterable
 
 from lxml import etree
+from pydantic import ValidationError
 
 from gmso.core.element import element_by_symbol
 from gmso.exceptions import (
@@ -573,7 +574,7 @@ def xml_from_forcefield_utilities(cls, filename):
         try:
             loader = GMSOFFs()
             ff = loader.load(filename).to_gmso_ff()
-        except (ForceFieldParseError, FileNotFoundError):
+        except (ForceFieldParseError, FileNotFoundError, ValidationError):
             loader = FoyerFFs()
             ff = loader.load(filename).to_gmso_ff()
         return ff
diff --git a/gmso/external/convert_foyer_xml.py b/gmso/external/convert_foyer_xml.py
index d7fcb04c9..56d22f45e 100644
--- a/gmso/external/convert_foyer_xml.py
+++ b/gmso/external/convert_foyer_xml.py
@@ -8,7 +8,7 @@
 
 
 @deprecate_function(
-    "Converting directly to GMSO XML from Foyer XML is deprecated."
+    "The `from_foyer_xml` method will be deprecated soon. Please use the package `forcefield-utilities.FoyerFFs`."
 )
 def from_foyer_xml(
     foyer_xml, gmso_xml=None, overwrite=False, validate_foyer=False
diff --git a/gmso/tests/test_xml_handling.py b/gmso/tests/test_xml_handling.py
index bc6acaee6..6459f0dfc 100644
--- a/gmso/tests/test_xml_handling.py
+++ b/gmso/tests/test_xml_handling.py
@@ -104,7 +104,11 @@ def test_load_write_xmls_ffutils_backend(self, xml):
 
     def test_xml_error_handling(self):
         """Validate bad xml formatting in xmls."""
-        pass
+        file_path = "dummy_name.xml"
+        with pytest.raises(FileNotFoundError):
+            ForceField(file_path)
+        with pytest.raises(IndexError):
+            ForceField(get_path("empty_foyer.xml"))
 
     def test_kb_in_ffutils(self):
         xml_path = get_path("ff-example0.xml")
diff --git a/gmso/utils/decorators.py b/gmso/utils/decorators.py
index 81e590d25..7c0314386 100644
--- a/gmso/utils/decorators.py
+++ b/gmso/utils/decorators.py
@@ -85,7 +85,7 @@ def _inner(*args, **kwargs):
 
 
 def deprecate_function(msg, klass=PendingDeprecationWarning):
-    """Raise a warning that a given function is deprecated."""
+    """Raise a warning that a given function will be deprecated soon."""
 
     def decorator(func):
         @functools.wraps(func)
diff --git a/gmso/utils/ff_utils.py b/gmso/utils/ff_utils.py
index df13950ed..05390a080 100644
--- a/gmso/utils/ff_utils.py
+++ b/gmso/utils/ff_utils.py
@@ -314,10 +314,25 @@ def _validate_schema(xml_path_or_etree, schema=None):
         ff_xml = etree.parse(xml_path_or_etree)
     try:
         xml_schema.assertValid(ff_xml)
-    except:
-        raise ForceFieldParseError(
-            f"xml scheme {xml_schema} has invalid elements. Check the sections of the file."
-        )
+    except etree.DocumentInvalid as ex:
+        message = ex.error_log.last_error.message
+        line = ex.error_log.last_error.line
+        # rewrite error message for constraint violation
+        if ex.error_log.last_error.type_name == "SCHEMAV_CVC_IDC":
+            for keyword in error_texts:
+                if keyword in message:
+                    atomtype = message[
+                        message.find("[") + 1 : message.find("]")
+                    ]
+                    error_text = error_texts[keyword].format(atomtype, line)
+                    raise ForceFieldParseError((error_text, ex, line))
+                else:
+                    raise ForceFieldParseError(
+                        "Unhandled XML validation error. "
+                        "Please consider submitting a bug report.",
+                        ex,
+                        line,
+                    )
     return ff_xml
 
 

From 0b15fce7f491bb6f5454b33ddeaccc63fea4156d Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Mon, 11 Sep 2023 11:21:52 -0500
Subject: [PATCH 09/11] fix bug with validation error

---
 .github/workflows/CI.yaml | 2 +-
 gmso/core/forcefield.py   | 8 ++++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index 7c7dfdb76..016fad62c 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -20,7 +20,7 @@ jobs:
       matrix:
         os: [macOS-latest, ubuntu-latest]
         python-version: ["3.8", "3.9", "3.10", "3.11"]
-        pydantic-version: ["1", "2"]
+        pydantic-version: ["2"]
 
     defaults:
       run:
diff --git a/gmso/core/forcefield.py b/gmso/core/forcefield.py
index 1d95a31ca..e86c22c72 100644
--- a/gmso/core/forcefield.py
+++ b/gmso/core/forcefield.py
@@ -7,7 +7,11 @@
 from typing import Iterable
 
 from lxml import etree
-from pydantic import ValidationError
+
+try:
+    from pydantic.v1 import ValidationError
+except:
+    from pydantic import ValidationError
 
 from gmso.core.element import element_by_symbol
 from gmso.exceptions import (
@@ -574,7 +578,7 @@ def xml_from_forcefield_utilities(cls, filename):
         try:
             loader = GMSOFFs()
             ff = loader.load(filename).to_gmso_ff()
-        except (ForceFieldParseError, FileNotFoundError, ValidationError):
+        except (ForceFieldParseError, ValidationError):
             loader = FoyerFFs()
             ff = loader.load(filename).to_gmso_ff()
         return ff

From 87c30cb3d04d0f47575f6bd2b0f0238948f87172 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Mon, 11 Sep 2023 11:33:18 -0500
Subject: [PATCH 10/11] update doc regarding python version

---
 docs/installation.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/installation.rst b/docs/installation.rst
index 78578fa50..5c98e684d 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -50,8 +50,8 @@ Once all dependencies have been installed and the ``conda`` environment has been
 Supported Python Versions
 -------------------------
 
-Python 3.7 is the recommend version for users. It is the only version on which
-development and testing consistently takes place.  Older (3.6) and newer (3.8+)
+Python 3.8-3.11 is the recommend version for users. It is the only version on which
+development and testing consistently takes place.  Older (3.6-3.7) and newer (3.12+)
 versions of Python 3 are likely to work but no guarantee is made and, in
 addition, some dependencies may not be available for other versions.  No effort
 is made to support Python 2 because it is considered obsolete as of early 2020.

From 524a09bec2bd1e622a9836ecae7aff15fc779201 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Mon, 11 Sep 2023 12:03:53 -0500
Subject: [PATCH 11/11] restore filenotfound error in except clause

---
 gmso/core/forcefield.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gmso/core/forcefield.py b/gmso/core/forcefield.py
index e86c22c72..691cb1788 100644
--- a/gmso/core/forcefield.py
+++ b/gmso/core/forcefield.py
@@ -578,7 +578,7 @@ def xml_from_forcefield_utilities(cls, filename):
         try:
             loader = GMSOFFs()
             ff = loader.load(filename).to_gmso_ff()
-        except (ForceFieldParseError, ValidationError):
+        except (ForceFieldParseError, FileNotFoundError, ValidationError):
             loader = FoyerFFs()
             ff = loader.load(filename).to_gmso_ff()
         return ff