Merge branch 'main' into 563-box-enh

.github/workflows/CI.yaml

@@ -19,8 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macOS-latest, ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-        pydantic-version: ["2"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     defaults:
       run:
@@ -36,7 +35,6 @@ jobs:
           environment-file: environment-dev.yml
           create-args: >-
             python=${{ matrix.python-version }}
-            pydantic=${{ matrix.pydantic-version }}
 
       - name: Install Package
         run: python -m pip install -e .
@@ -66,7 +64,7 @@ jobs:
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment-dev.yml
-          python-version: python="3.10"
+          create-args: python=3.10
 
       - name: Clone mBuild and Foyer and forcefield-utilities
         run: |
@@ -95,34 +93,34 @@ jobs:
     runs-on: ubuntu-latest
     needs: test
     name: Build Docker Image
-    if: ${{ false }}
+    if: github.event_name != 'pull_request'
 
     steps:
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
 
       - name: Login to DockerHub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
 
       - name: Get Tagged Version
         run: |
-          echo "DOCKER_TAGS=mosdef-gmso-${CI_COMMIT_REF_SLUG}, mosdef-gmso-stable" >> $GITHUB_ENV
+          echo "DOCKER_TAGS=mosdef/gmso:${GITHUB_REF_NAME}, mosdef/gmso:stable" >> $GITHUB_ENV
         if: github.ref_type == 'tag'
 
       - name: Get Push Version
         run: |
-          echo "DOCKER_TAGS=mosdef-gmso-${CI_COMMIT_REF_SLUG}, mosdef-gmso-latest" >> $GITHUB_ENV
+          echo "DOCKER_TAGS=mosdef/gmso:${GITHUB_REF_NAME}, mosdef/gmso:latest" >> $GITHUB_ENV
         if: github.ref_type == 'branch'
 
       - name: Docker Image Info
         run: |
           echo Docker Image tags: ${DOCKER_TAGS}
 
       - name: Build and Push
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: ${{ env.DOCKER_TAGS }}

.pre-commit-config.yaml

@@ -9,19 +9,19 @@ ci:
     submodules: false
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
       exclude: 'setup.cfg|gmso/tests/files/.*'
 - repo: https://github.com/psf/black
-  rev: 23.9.1
+  rev: 24.2.0
   hooks:
     - id: black
       args: [--line-length=80]
 - repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
     - id: isort
       name: isort (python)

Dockerfile

@@ -1,4 +1,5 @@
-FROM mambaorg/micromamba:1.4.3
+ARG PY_VERSION=3.10
+FROM continuumio/miniconda3:4.10.3-alpine AS builder
 
 EXPOSE 8888
 
@@ -13,17 +14,34 @@ ADD . /gmso
 
 WORKDIR /gmso
 
-RUN apt-get update && apt-get install -y git
+# Create a group and user
+RUN addgroup -S anaconda && adduser -S anaconda -G anaconda
+
+RUN apk update && apk add libarchive &&\
+  conda update conda -yq && \
+  conda config --set always_yes yes --set changeps1 no && \
+  . /opt/conda/etc/profile.d/conda.sh && \
+  sed -i -E "s/python.*$/python="$(PY_VERSION)"/" environment-dev.yml && \
+  conda install -c conda-forge mamba && \
+  mamba env create --file environment-dev.yml && \
+  conda activate gmso-dev && \
+  mamba install -c conda-forge jupyter python="$PY_VERSION" && \
+  python setup.py install && \
+  echo "source activate gmso-dev" >> \
+  /home/anaconda/.profile && \
+  conda clean -afy && \
+  mkdir -p /home/anaconda/data && \
+  chown -R anaconda:anaconda /gmso && \
+  chown -R anaconda:anaconda /opt && \
+  chown -R anaconda:anaconda /home/anaconda
 
-RUN micromamba create --file environment-dev.yml && \
-  micromamba clean -afy
-ARG MAMBA_DOCKERFILE_ACTIVATE=1  # (otherwise python will not be found)
+WORKDIR /home/anaconda
 
-RUN  micromamba install -c conda-forge nomkl jupyter python="3.10" && \
-  python setup.py install && \
-  echo "source activate gmso-dev" >> /home/.bashrc && \
-  mkdir -p /home/data
+COPY devtools/docker-entrypoint.sh /entrypoint.sh
+
+RUN chmod a+x /entrypoint.sh
 
+USER anaconda
 
 ENTRYPOINT ["/entrypoint.sh"]
 CMD ["jupyter"]

codecov.yml

@@ -1,5 +1,6 @@
 ignore:
   - "gmso/examples"
   - "gmso/tests"
+  - "gmso/paper"
   - "gmso/formats/networkx.py"
   - "gmso/external/convert_foyer_xml.py"

docs/conf.py

@@ -23,8 +23,8 @@
 author = "Matt Thompson, Alex Yang, Ray Matsumoto, Parashara Shamaprasad, Umesh Timalsina, Co Quach, Ryan S. DeFever, Justin Gilmer"
 
 # The full version, including alpha/beta/rc tags
-version = "0.11.2"
-release = "0.11.2"
+version = "0.12.0"
+release = "0.12.0"
 
 
 # -- General configuration ---------------------------------------------------

docs/index.rst

@@ -5,10 +5,75 @@
 
 GMSO: Flexible storage of chemical topology for molecular simulation
 ====================================================================
+`GMSO`is a flexible storage of chemical topology for molecular simulation.
+With a few lines of `GMSO` code, together with [`mBuild`](https://mbuild.mosdef.org) and [`foyer`](https://foyer.mosdef.org), users can rapidly prototype arbitrary parameterized chemical systems and generate data files for a wide variety of simulation engines.
+
+
+GMSO is a part of the MoSDeF ecosystem
+-----------------------------------------
+`GMSO` is designed to be a general and flexible representation of chemical topolgies for molecular simulation.
+With an emphasis on assuming as little as possible about the chemical system, model, or engine, `GMSO` can enable support for a variety of systems.
+`GMSO` is a part of the [MoSDeF (Molecular Simulation and Design Framework)](https://mosdef.org) ecosystem, and is intended to be the backend replacement for the [`foyer` package](https://foyer.mosdef.org).
+Libraries in the MoSDeF ecosystem are designed to provide utilities neccessary to streamline
+a researcher's simulation workflow. When setting up simulation studies,
+we also recommend users to follow the [TRUE](https://www.tandfonline.com/doi/full/10.1080/00268976.2020.1742938)
+(Transparent, Reproducible, Usable-by-others, and Extensible) standard, which is a set of common
+practices meant to improve the reproducibility of computational simulation research.
+
+
+Goals and Features
+------------------
+
+`GMSO`'s goal is to provide a flexible backend framework to store topological information of a chemical system in a reproducible fashion.
+**Topology** in this case is defined as the information needed to initialize a molecular simulation.
+Depending on the type of simulation performed, this ranges from:
+* particle positions
+* particle connectivity
+* box information
+* forcefield data
+    - functional forms defined as [`sympy` expressions](https://www.sympy.org)
+    - parameters with defined units
+    - partial charges
+    - tabulated data
+    - etc.
+* Other optional data
+    - particle mass
+    - elemental data
+    - etc.
+
+With these driving goals for `GMSO`, the following features are enabled:
+1. __Supporting a variety of models__ in the molecular simulation/computational
+  chemistry community_:
+  No assumptions are made about an interaction site
+  representing an atom or bead, instead these can be atomistic,
+  united-atom/coarse-grained, polarizable, and other models!
+
+1. __Greater flexibility for exotic potentials__: The [`AtomType`](./gmso/core/atom_type.py) (and [analogue
+  classes for intramolecular interactions](./gmso/core)) uses [`sympy`](https://www.sympy.org) to store any
+  potential that can be represented by a mathematical expression.
+
+1. __Adaptable for new engines__: by not being designed for
+  compatibility with any particular molecular simulation engine or ecosystem,
+  it becomes more tractable for developers in the community to add glue for
+  engines that are not currently supported.
+
+1. __Compatibility with existing community tools__: No single molecular simulation
+  tool will ever be a silver bullet, so ``GMSO`` includes functions to convert
+  between various file formats and libraries. These can be used in their own right to convert between objects in-memory
+  and also to support conversion to file formats not natively supported at
+  any given time. Currently supported conversions include:
+    * [`ParmEd`](./gmso/external/convert_parmed.py)
+    * [`OpenMM`](./gmso/external/convert_openmm.py)
+    * [`mBuild`](./gmso/external/convert_mbuild.py)
+    * more in the future!
+
+1. __Native support for reading and writing many common file formats__: We natively have support for:
+    * [`XYZ`](./gmso/formats/xyz.py)
+    * [`GRO`](./gmso/formats/gro.py)
+    * [`TOP`](gmso/formats/top.py)
+    * [`LAMMPSDATA`](gmso/formats/lammpsdata.py)
+    * indirect support, through other libraries, for many more!
 
-This is the documentation for ``GMSO``, the General Molecular Simulation Object.
-It is a part of the `MoSDeF <http://mosdef.org>`_, the Molecular Simulation
-Design Framework.
 
 .. toctree::
    :hidden:

environment-dev.yml

@@ -9,7 +9,7 @@ dependencies:
   - unyt>=2.9.5
   - boltons
   - lxml
-  - pydantic
+  - pydantic>=2
   - networkx
   - pytest
   - mbuild>=0.11.0

environment.yml

@@ -9,7 +9,7 @@ dependencies:
   - unyt>=2.9.5
   - boltons
   - lxml
-  - pydantic
+  - pydantic>=2
   - networkx
   - ele >= 0.2.0
   - molbox

gmso/__init__.py

@@ -1,4 +1,5 @@
 """GMSO: General Molecular Simulation Object."""
+
 from .core.angle import Angle
 from .core.angle_type import AngleType
 from .core.atom import Atom
@@ -15,4 +16,4 @@
 from .core.pairpotential_type import PairPotentialType
 from .core.topology import Topology
 
-__version__ = "0.11.2"
+__version__ = "0.12.0"

gmso/abc/__init__.py

@@ -1 +1 @@
-from gmso.abc.serialization_utils import GMSOJSONHandler, unyt_to_dict
+from gmso.abc.serialization_utils import unyt_to_dict

gmso/abc/abstract_connection.py

@@ -1,14 +1,11 @@
 from typing import Optional, Sequence
 
+from pydantic import ConfigDict, Field, model_validator
+
 from gmso.abc.abstract_site import Site
 from gmso.abc.gmso_base import GMSOBase
 from gmso.exceptions import GMSOError
 
-try:
-    from pydantic.v1 import Field, root_validator
-except ImportError:
-    from pydantic import Field, root_validator
-
 
 class Connection(GMSOBase):
     __base_doc__ = """An abstract class that stores data about connections between sites.
@@ -18,12 +15,21 @@ class Connection(GMSOBase):
     """
 
     name_: str = Field(
-        default="", description="Name of the connection. Defaults to class name"
+        default="",
+        description="Name of the connection. Defaults to class name.",
+        alias="name",
     )
 
     connection_members_: Optional[Sequence[Site]] = Field(
         default=None,
         description="A list of constituents in this connection, in order.",
+        alias="connection_members",
+    )
+    model_config = ConfigDict(
+        alias_to_fields={
+            "name": "name_",
+            "connection_members": "connection_members_",
+        }
     )
 
     @property
@@ -37,12 +43,12 @@ def name(self):
     @property
     def member_types(self):
         """Return the atomtype of the connection members as a list of string."""
-        return self._get_members_types_or_classes("member_types_")
+        return self._get_members_types_or_classes("member_types")
 
     @property
     def member_classes(self):
         """Return the class of the connection members as a list of string."""
-        return self._get_members_types_or_classes("member_classes_")
+        return self._get_members_types_or_classes("member_classes")
 
     def _has_typed_members(self):
         """Check if all the members of this connection are typed."""
@@ -53,24 +59,29 @@ def _has_typed_members(self):
 
     def _get_members_types_or_classes(self, to_return):
         """Return types or classes for connection members if they exist."""
-        assert to_return in {"member_types_", "member_classes_"}
+        assert to_return in {"member_types", "member_classes"}
         ctype = getattr(self, "connection_type")
         ctype_attr = getattr(ctype, to_return) if ctype else None
 
         if ctype_attr:
             return list(ctype_attr)
         elif self._has_typed_members():
             tc = [
-                member.atom_type.name
-                if to_return == "member_types_"
-                else member.atom_type.atomclass
+                (
+                    member.atom_type.name
+                    if to_return == "member_types"
+                    else member.atom_type.atomclass
+                )
                 for member in self.__dict__.get("connection_members_")
             ]
             return tc if all(tc) else None
 
-    @root_validator(pre=True)
+    @model_validator(mode="before")
     def validate_fields(cls, values):
-        connection_members = values.get("connection_members")
+        if "connection_members" in values:
+            connection_members = values.get("connection_members")
+        else:
+            connection_members = values.get("connection_members_")
 
         if all(isinstance(member, dict) for member in connection_members):
             connection_members = [
@@ -103,11 +114,3 @@ def __repr__(self):
 
     def __str__(self):
         return f"<{self.__class__.__name__} {self.name}, id: {id(self)}> "
-
-    class Config:
-        fields = {"name_": "name", "connection_members_": "connection_members"}
-
-        alias_to_fields = {
-            "name": "name_",
-            "connection_members": "connection_members_",
-        }