Merge branch 'main' into pandas-simplification-v2

.github/workflows/CI.yaml

@@ -13,20 +13,20 @@ on:
 jobs:
   test:
     if: github.event.pull_request.draft == false
-    name: GMSO Tests
+    name: GMSO Tests (python)
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, macOS-13, ubuntu-latest]
+        os: [ubuntu-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba
@@ -43,11 +43,42 @@ jobs:
         run: python -m pytest -v --cov=gmso --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs gmso
 
       - name: Upload Coverage Report
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v4
         with:
           name: GMSO-Coverage
           verbose: true
 
+  arch-test:
+    if: github.event.pull_request.draft == false
+    name: GMSO Tests (arch)
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macOS-latest, macOS-13, ubuntu-latest]
+        python-version: ["3.12"]
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v4
+        name: Checkout Branch / Pull Request
+
+      - name: Install Mamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment-dev.yml
+          create-args: >-
+            python=${{ matrix.python-version }}
+
+      - name: Install Package
+        run: python -m pip install -e .
+
+      - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
+        run: python -m pytest -v --color yes --pyargs gmso
+
   bleeding-edge-test:
     if: github.event.pull_request.draft == false
     name: Bleeding Edge mosdef Tests for GMSO
@@ -57,14 +88,14 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment-dev.yml
-          create-args: python=3.10
+          create-args: python=3.12
 
       - name: Clone mBuild and Foyer and forcefield-utilities
         run: |
@@ -120,7 +151,7 @@ jobs:
           echo Docker Image tags: ${DOCKER_TAGS}
 
       - name: Build and Push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           push: true
           tags: ${{ env.DOCKER_TAGS }}

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ ci:
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.4.5
+  rev: v0.5.7
   hooks:
     # Run the linter.
     - id: ruff

docs/conf.py

@@ -20,11 +20,11 @@
 
 project = "gmso"
 copyright = "2024, mosdef-hub, Vanderbilt University"
-author = "Matt Thompson, Alex Yang, Ray Matsumoto, Parashara Shamaprasad, Umesh Timalsina, Co D. Quach, Ryan S. DeFever, Justin Gilmer"
+author = "Matt Thompson, Alex Yang, Ray Matsumoto, Parashara Shamaprasad, Umesh Timalsina, Co D. Quach, Ryan S. DeFever, Justin Gilmer, Nicholas C. Craven, Christopher R. Iacovella, Brad Crawford, and Chris Jones"
 
 # The full version, including alpha/beta/rc tags
-version = "0.12.1"
-release = "0.12.1"
+version = "0.12.4"
+release = "0.12.4"
 
 
 # -- General configuration ---------------------------------------------------

gmso/__init__.py

@@ -17,4 +17,4 @@
 from .core.pairpotential_type import PairPotentialType
 from .core.topology import Topology
 
-__version__ = "0.12.1"
+__version__ = "0.12.4"

gmso/abc/abstract_site.py

@@ -1,14 +1,13 @@
 """Basic interaction site in GMSO that all other sites will derive from."""
 
 import warnings
-from typing import Any, ClassVar, NamedTuple, Optional, Sequence, TypeVar, Union
+from typing import Any, ClassVar, Optional, Sequence, TypeVar, Union
 
 import numpy as np
 import unyt as u
 from pydantic import (
     ConfigDict,
     Field,
-    StrictInt,
     StrictStr,
     field_serializer,
     field_validator,
@@ -20,8 +19,124 @@
 from gmso.exceptions import GMSOError
 
 PositionType = Union[Sequence[float], np.ndarray, u.unyt_array]
-MoleculeType = NamedTuple("Molecule", name=StrictStr, number=StrictInt)
-ResidueType = NamedTuple("Residue", name=StrictStr, number=StrictInt)
+
+
+class Molecule(GMSOBase):
+    def __repr__(self):
+        return (
+            f"Molecule(name={self.name}, residue={self.residue}, isrigid={self.isrigid}"
+        )
+
+    __iterable_attributes__: ClassVar[set] = {
+        "name",
+        "number",
+        "isrigid",
+    }
+
+    __base_doc__: ClassVar[str] = "Molecule label for interaction sites."
+
+    name_: str = Field(
+        "",
+        validate_default=True,
+        description="Name of the molecule",
+        alias="name",
+    )
+    number_: int = Field(
+        0,
+        description="The index/number of the molecule",
+        alias="number",
+    )
+    isrigid_: bool = Field(
+        False,
+        description="Indicate whether the molecule is rigid",
+    )
+    model_config = ConfigDict(
+        alias_to_fields={
+            "name": "name_",
+            "number": "number_",
+            "isrigid": "isrigid_",
+        }
+    )
+
+    @property
+    def name(self) -> str:
+        """Return the name of the molecule."""
+        return self.__dict__.get("name_")
+
+    @property
+    def number(self) -> int:
+        """Return the index/number of the moleucle."""
+        return self.__dict__.get("number_")
+
+    @property
+    def isrigid(self) -> bool:
+        """Return the rigid label of the molecule."""
+        return self.__dict__.get("isrigid_")
+
+    def __hash__(self):
+        return hash(tuple([(name, val) for name, val in self.__dict__.items()]))
+
+    def __eq__(self, other):
+        """Test if two objects are equivalent."""
+        if isinstance(other, (list, tuple)):
+            return all(
+                [val1 == val2 for val1, val2 in zip(self.__dict__.values(), other)]
+            )
+        else:
+            return self.__dict__ == other.__dict__
+
+
+class Residue(GMSOBase):
+    def __repr__(self):
+        return f"Residue(name={self.name}, residue={self.residue}"
+
+    __iterable_attributes__: ClassVar[set] = {
+        "name",
+        "number",
+    }
+
+    __base_doc__: ClassVar[str] = "Residue label for interaction sites."
+
+    name_: str = Field(
+        "",
+        validate_default=True,
+        description="Name of the residue",
+        alias="name",
+    )
+    number_: int = Field(
+        0,
+        description="The index/number of the residue",
+        alias="number",
+    )
+    model_config = ConfigDict(
+        alias_to_fields={
+            "name": "name_",
+            "number": "number_",
+        }
+    )
+
+    @property
+    def name(self) -> str:
+        """Return the name of the residue."""
+        return self.__dict__.get("name_")
+
+    @property
+    def number(self) -> int:
+        """Return the index/number of the residue."""
+        return self.__dict__.get("number_")
+
+    def __hash__(self):
+        return hash(tuple([(name, val) for name, val in self.__dict__.items()]))
+
+    def __eq__(self, other):
+        """Test if two objects are equivalent."""
+        if isinstance(other, (list, tuple)):
+            return all(
+                [val1 == val2 for val1, val2 in zip(self.__dict__.values(), other)]
+            )
+        else:
+            return self.__dict__ == other.__dict__
+
 
 SiteT = TypeVar("SiteT", bound="Site")
 
@@ -76,13 +191,13 @@ class Site(GMSOBase):
         alias="group",
     )
 
-    molecule_: Optional[MoleculeType] = Field(
+    molecule_: Optional[Union[Molecule, list, tuple]] = Field(
         None,
         description="Molecule label for the site, format of (molecule_name, molecule_number)",
         alias="molecule",
     )
 
-    residue_: Optional[ResidueType] = Field(
+    residue_: Optional[Union[Residue, list, tuple]] = Field(
         None,
         description="Residue label for the site, format of (residue_name, residue_number)",
         alias="residue",
@@ -126,7 +241,7 @@ def group(self) -> str:
         return self.__dict__.get("group_")
 
     @property
-    def molecule(self) -> tuple:
+    def molecule(self):
         """Return the molecule of the site."""
         return self.__dict__.get("molecule_")
 
@@ -185,12 +300,28 @@ def is_valid_position(cls, position):
         return position
 
     @field_validator("name_")
-    def inject_name(cls, value):
+    def parse_name(cls, value):
         if value == "" or value is None:
             return cls.__name__
         else:
             return value
 
+    @field_validator("residue_")
+    def parse_residue(cls, value):
+        if isinstance(value, (tuple, list)):
+            assert len(value) == 2
+            value = Residue(name=value[0], number=value[1])
+        return value
+
+    @field_validator("molecule_")
+    def parse_molecule(cls, value):
+        if isinstance(value, (tuple, list)):
+            if len(value) == 2:
+                value = Molecule(name=value[0], number=value[1])
+            elif len(value) == 3:
+                value = Molecule(name=value[0], number=value[1], isrigid=value[2])
+        return value
+
     @classmethod
     def __new__(cls, *args: Any, **kwargs: Any) -> SiteT:
         if cls is Site:

gmso/core/element.py

@@ -254,14 +254,22 @@ def element_by_smarts_string(smarts_string, verbose=False):
     GMSOError
         If no matching element is found for the provided smarts string
     """
+    from lark import UnexpectedCharacters
+
     from gmso.utils.io import import_
 
     foyer = import_("foyer")
     SMARTS = foyer.smarts.SMARTS
 
     PARSER = SMARTS()
 
-    symbols = PARSER.parse(smarts_string).iter_subtrees_topdown()
+    try:
+        symbols = PARSER.parse(smarts_string).iter_subtrees_topdown()
+    except UnexpectedCharacters:
+        raise GMSOError(
+            f"Failed to find an element from SMARTS string {smarts_string}. "
+            f"The SMARTS string contained unexpected characters."
+        )
 
     first_symbol = None
     for symbol in symbols: