merge changes from upstream.

.github/workflows/pytest.yml

@@ -2,7 +2,6 @@ name: pytest
 
 on:
   push:
-    # Action will run when any changes to these paths are pushed or pr'ed to master
     branches: [ main ]
     paths:
       - flowermd/**
@@ -26,6 +25,7 @@ on:
 
 jobs:
   pytest:
+    if: github.event.pull_request.draft == false
     strategy:
       fail-fast: false
       matrix:
@@ -36,10 +36,10 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Build environment
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         environment-file: environment-dev.yml
         python-version: ${{ matrix.python-version }}
@@ -56,7 +56,7 @@ jobs:
       run: python -m pytest -rs -v --cov=./ --cov-report=xml
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml

.pre-commit-config.yaml

@@ -1,48 +1,32 @@
 ci:
   autofix_commit_msg: |
     [pre-commit.ci] auto fixes from pre-commit.com hooks
-
     for more information, see https://pre-commit.ci
   autofix_prs: true
   autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
   autoupdate_schedule: weekly
   skip: [ ]
   submodules: false
-
 repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.4 # Ruff version
+    hooks:
+      - id: ruff
+        args: [--fix, --extend-ignore=E203]
+      - id: ruff-format
+        args: [ --line-length=80 ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
         exclude: 'flowermd/tests/assets/.* | flowermd/assets/.*'
-  - repo: https://github.com/psf/black
-    rev: 24.4.2
-    hooks:
-      - id: black
-        args: [ --line-length=80 ]
   - repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)
         args:
           [ --profile=black, --line-length=80 ]
-        exclude: 'flowermd/tests/assets/.* | */__init__.py'
-
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
-    hooks:
-      - id: flake8
-        args:
-          - --max-line-length=80
-          - --extend-ignore=E203
-        exclude: '__init__.py'
-
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: '6.3.0'
-    hooks:
-      - id: pydocstyle
-        exclude: ^(flowermd/tests/|flowermd/internal/|flowermd/utils|setup.py|flowermd/__version__.py|docs/)
-        args: [ --convention=numpy ]
+        exclude: 'flowermd/tests/assets/.* '

environment-dev.yml

@@ -4,13 +4,13 @@ channels:
 dependencies:
   - foyer >=0.12.0
   - fresnel
-  - freud >=2.13.1
-  - gmso >=0.11.2
+  - freud >=3.0
+  - gmso >=0.12.0
   - gsd >=3.0
-  - grits=0.4.1
-  - hoomd=4.3
+  - grits >=0.5.0
+  - hoomd >=4.5
   - mbuild >=0.17.0
-  - numpy
+  - numpy <2.0
   - openbabel >=3
   - pip
   - pre-commit
@@ -20,4 +20,4 @@ dependencies:
   - nbmake
   - python >=3.10, <3.12
   - fresnel >=0.13.5
-  - cmeutils >=1.1.1
+  - cmeutils >=1.3

environment.yml

@@ -4,16 +4,16 @@ channels:
 dependencies:
   - foyer >=0.12.0
   - fresnel
-  - freud >=2.13.1
-  - gmso >=0.11.2
+  - freud >=3.0
+  - gmso >=0.12.0
   - gsd >=3.0
-  - hoomd=4.3
+  - grits >=0.5.0
+  - hoomd >=4.5
   - mbuild >=0.17.0
-  - numpy
+  - numpy <2.0
   - openbabel >=3
   - pip
   - py3Dmol
   - python >=3.10, <3.12
   - fresnel >=0.13.5
-  - cmeutils >=1.1.1
-  - grits =0.4.1
+  - cmeutils >=1.3

flowermd/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F401
 """flowerMD package."""
 
 from .internal.units import Units

flowermd/__version__.py

@@ -1,3 +1,3 @@
-VERSION = (1, 3, 0)
+VERSION = (1, 3, 1)
 
 __version__ = ".".join(map(str, VERSION))

flowermd/assets/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F401
 """Paths to the assets used by flowerMD."""
 
 from .forcefields import FF_DIR

flowermd/base/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F401
 """Base classes for flowerMD."""
 
 from .forcefield import BaseHOOMDForcefield, BaseXMLForcefield

flowermd/base/molecule.py

@@ -314,7 +314,7 @@ def _identify_bond_types(self, gmso_molecule):
                 or bond.connection_members[1].name
             )
             bond_connections = [p1_name, p2_name]
-            if not tuple(bond_connections[::-1]) in self.bond_types:
+            if tuple(bond_connections[::-1]) not in self.bond_types:
                 self.bond_types.add(tuple(bond_connections))
 
     def _identify_angle_types(self, gmso_molecule):
@@ -341,7 +341,7 @@ def _identify_angle_types(self, gmso_molecule):
                 or angle.connection_members[2].name
             )
             angle_connections = [p1_name, p2_name, p3_name]
-            if not tuple(angle_connections[::-1]) in self.angle_types:
+            if tuple(angle_connections[::-1]) not in self.angle_types:
                 self.angle_types.add(tuple(angle_connections))
 
     def _identify_dihedral_types(self, gmso_molecule):
@@ -372,7 +372,7 @@ def _identify_dihedral_types(self, gmso_molecule):
                 or dihedral.connection_members[3].name
             )
             dihedral_connections = [p1_name, p2_name, p3_name, p4_name]
-            if not tuple(dihedral_connections[::-1]) in self.dihedral_types:
+            if tuple(dihedral_connections[::-1]) not in self.dihedral_types:
                 self.dihedral_types.add(tuple(dihedral_connections))
 
     def _identify_improper_types(self, gmso_molecule):
@@ -403,7 +403,7 @@ def _identify_improper_types(self, gmso_molecule):
                 or improper.connection_members[3].name
             )
             improper_connections = [p1_name, p2_name, p3_name, p4_name]
-            if not tuple(improper_connections[::-1]) in self.improper_types:
+            if tuple(improper_connections[::-1]) not in self.improper_types:
                 self.improper_types.add(tuple(improper_connections))
 
     def _identify_topology_information(self, gmso_molecule):
@@ -477,6 +477,11 @@ class Polymer(Molecule):
         The bond length between connected atoms (units: nm)
     bond_orientation: list, default None
         The orientation of the bond between connected atoms.
+    periodic_bond_axis : str, default None
+        Axis which to orient the polymer backbone along.
+        Once the chain is aligned, a periodic bond between
+        head and tail atoms is formed.
+        Options are "x", "y", or "z"
 
     """
 
@@ -490,12 +495,14 @@ def __init__(
         bond_indices=None,
         bond_length=None,
         bond_orientation=None,
+        periodic_bond_axis=None,
         **kwargs,
     ):
         self.lengths = check_return_iterable(lengths)
         self.bond_indices = bond_indices
         self.bond_length = bond_length
         self.bond_orientation = bond_orientation
+        self.periodic_bond_axis = periodic_bond_axis
         num_mols = check_return_iterable(num_mols)
         if len(num_mols) != len(self.lengths):
             raise ValueError("Number of molecules and lengths must be equal.")
@@ -513,14 +520,27 @@ def monomer(self):
         return self._mb_molecule
 
     def _build(self, length):
+        if self.periodic_bond_axis:
+            if not isinstance(
+                self.periodic_bond_axis, str
+            ) or self.periodic_bond_axis.lower() not in ["x", "y", "z"]:
+                raise ValueError(
+                    "Valid choices for a `periodic_bond_axis` are "
+                    "'x', 'y', 'z'"
+                )
+            add_hydrogens = False
+        else:
+            add_hydrogens = True
         chain = mbPolymer()
         chain.add_monomer(
             self.monomer,
             indices=self.bond_indices,
             separation=self.bond_length,
             orientation=self.bond_orientation,
         )
-        chain.build(n=length, sequence="A")
+        chain.build(n=length, sequence="A", add_hydrogens=add_hydrogens)
+        if self.periodic_bond_axis:
+            chain.create_periodic_bond(axis=self.periodic_bond_axis)
         return chain
 
     def _generate(self):