Merge branch 'main' into ml-forces

.github/workflows/pytest.yml

@@ -30,7 +30,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-14, ubuntu-24.04]
-        python-version: ['3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
 
     runs-on: ${{ matrix.os }}
 
@@ -39,13 +39,11 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Build environment
-      uses: conda-incubator/setup-miniconda@v3
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: environment-dev.yml
-        python-version: ${{ matrix.python-version }}
-        miniforge-variant: Mambaforge
-        #miniforge-version: 24.11.0
-        use-mamba: true
+        create-args: >-
+          python=${{ matrix.python-version }}
 
     - name: Install package
       shell: bash -l {0}
@@ -56,7 +54,7 @@ jobs:
       run: python -m pytest -rs -v --cov=./ --cov-report=xml
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -99,17 +97,16 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Build environment
-      uses: conda-incubator/setup-miniconda@v3
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: environment-dev.yml
-        miniforge-variant: Mambaforge
-        #miniforge-version: 24.11.0
-        use-mamba: true
+        create-args: >-
+          python=3.12
 
     - name: Install package
       shell: bash -l {0}
       run: pip install .
 
     - name: Run pytest on tutorials
       shell: bash -l {0}
-      run: python -m pytest -rs -v --nbmake tutorials/
+      run: python -m pytest -rs -v --nbmake tutorials/

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.4 # Ruff version
+    rev: v0.9.6 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]
@@ -23,7 +23,7 @@ repos:
       - id: trailing-whitespace
         exclude: 'flowermd/tests/assets/.* | flowermd/assets/.*'
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 6.0.0
     hooks:
       - id: isort
         name: isort (python)

environment-dev.yml

@@ -19,6 +19,6 @@ dependencies:
   - pytest
   - pytest-cov
   - nbmake
-  - python >=3.10, <3.12
+  - python >=3.10, <3.13
   - fresnel >=0.13.5
   - cmeutils >=1.3

environment.yml

@@ -14,6 +14,6 @@ dependencies:
   - openbabel >=3
   - pip
   - py3Dmol
-  - python >=3.10, <3.12
+  - python >=3.10, <3.13
   - fresnel >=0.13.5
   - cmeutils >=1.3

flowermd/__init__.py

@@ -11,3 +11,4 @@
     System,
 )
 from .internal.units import Units
+

flowermd/base/molecule.py

@@ -525,8 +525,7 @@ def _build(self, length):
                 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'"
+                    "Valid choices for a `periodic_bond_axis` are 'x', 'y', 'z'"
                 )
             add_hydrogens = False
         else:

flowermd/base/simulation.py

@@ -74,8 +74,7 @@ def __init__(
     ):
         if not isinstance(forcefield, Iterable) or isinstance(forcefield, str):
             raise ValueError(
-                "forcefield must be a sequence of "
-                "hoomd.md.force.Force objects."
+                "forcefield must be a sequence of hoomd.md.force.Force objects."
             )
         else:
             for obj in forcefield:

flowermd/base/system.py

@@ -3,7 +3,7 @@
 import pickle
 import warnings
 from abc import ABC, abstractmethod
-from typing import List, Union
+from typing import List
 
 import gsd
 import mbuild as mb
@@ -14,7 +14,7 @@
 
 from flowermd.base.forcefield import BaseHOOMDForcefield, BaseXMLForcefield
 from flowermd.base.molecule import Molecule
-from flowermd.internal import Units, check_return_iterable, validate_unit
+from flowermd.internal import check_return_iterable, validate_ref_value
 from flowermd.internal.exceptions import ForceFieldError, MoleculeLoadError
 from flowermd.utils import (
     get_target_box_mass_density,
@@ -48,6 +48,8 @@ class System(ABC):
         Dictionary of base units to use for scaling.
         Dictionary keys are "length", "mass", and "energy". Values should be an
         unyt array of the desired base unit.
+    kwargs
+        See classes that inherit from System for kwargs
 
     Warnings
     --------
@@ -68,6 +70,7 @@ def __init__(
         self,
         molecules,
         base_units=dict(),
+        **kwargs,
     ):
         self._molecules = check_return_iterable(molecules)
         self.all_molecules = []
@@ -123,7 +126,7 @@ def __init__(
                 self.n_mol_types += 1
 
         # Create mBuild system
-        self.system = self._build_system()
+        self.system = self._build_system(**kwargs)
         # Create GMSO topology
         self.gmso_system = self._convert_to_gmso()
 
@@ -208,10 +211,12 @@ def reference_length(self, length):
 
         Parameters
         ----------
-        length : reference length * `flowermd.Units`, required
+        length : string or unyt.unyt_quantity, required
             The reference length of the system.
-            It can be provided in the following form of:
-            value * `flowermd.Units`, for example 1 * `flowermd.Units.angstrom`.
+            It can be provided in the following forms:
+            1) A string with the format of "value unit", for example "1 nm".
+            2) A unyt.unyt_quantity object with the correct dimension. For
+            example, unyt.unyt_quantity(1, "nm").
 
         """
         if self.auto_scale:
@@ -220,7 +225,7 @@ def reference_length(self, length):
                 "Setting reference length manually disables auto "
                 "scaling."
             )
-        validated_length = validate_unit(length, u.dimensions.length)
+        validated_length = validate_ref_value(length, u.dimensions.length)
         self._reference_values["length"] = validated_length
 
     @reference_energy.setter
@@ -229,10 +234,12 @@ def reference_energy(self, energy):
 
         Parameters
         ----------
-        energy : reference energy * `flowermd.Units`, required
+        energy : string or unyt.unyt_quantity, required
             The reference energy of the system.
-            It can be provided in the following form of:
-            value * `flowermd.Units`, for example 1 * `flowermd.Units.kcal/mol`.
+            It can be provided in the following forms:
+            1) A string with the format of "value unit", for example "1 kJ/mol".
+            2) A unyt.unyt_quantity object with the correct dimension. For
+            example, unyt.unyt_quantity(1, "kJ/mol").
 
         """
         if self.auto_scale:
@@ -241,7 +248,7 @@ def reference_energy(self, energy):
                 "Setting reference energy manually disables auto "
                 "scaling."
             )
-        validated_energy = validate_unit(energy, u.dimensions.energy)
+        validated_energy = validate_ref_value(energy, u.dimensions.energy)
         self._reference_values["energy"] = validated_energy
 
     @reference_mass.setter
@@ -250,18 +257,21 @@ def reference_mass(self, mass):
 
         Parameters
         ----------
-        mass : reference mass * `flowermd.Units`, required
+        mass : string or unyt.unyt_quantity, required
             The reference mass of the system.
-            It can be provided in the following form of:
-            value * `flowermd.Units`, for example 1 * `flowermd.Units.amu`.
+            It can be provided in the following forms:
+            1) A string with the format of "value unit", for example "1 amu".
+            2) A unyt.unyt_quantity object with the correct dimension. For
+            example, unyt.unyt_quantity(1, "amu").
+
         """
         if self.auto_scale:
             warnings.warn(
                 "`auto_scale` was set to True for this system. "
                 "Setting reference mass manually disables auto "
                 "scaling."
             )
-        validated_mass = validate_unit(mass, u.dimensions.mass)
+        validated_mass = validate_ref_value(mass, u.dimensions.mass)
         self._reference_values["mass"] = validated_mass
 
     @reference_values.setter
@@ -397,23 +407,6 @@ def to_gsd(self, file_name):
         with gsd.hoomd.open(file_name, "w") as traj:
             traj.append(self.hoomd_snapshot)
 
-    def save_reference_values(self, file_path="reference_values.pickle"):
-        """Save the reference values of the system to a pickle file.
-
-        Parameters
-        ----------
-        file_path : str, default "reference_values.pickle"
-            The path to save the pickle file to.
-
-        """
-        if not self.reference_values:
-            raise ValueError(
-                "Reference values have not been set. "
-                "See System.reference_values"
-            )
-        f = open(file_path, "wb")
-        pickle.dump(self.reference_values, f)
-
     def _convert_to_gmso(self):
         """Convert the mbuild system to a gmso system."""
         topology = from_mbuild(self.system)
@@ -625,18 +618,21 @@ class Pack(System):
 
     Parameters
     ----------
-    density : float or unyt_quantity or flowermd.internal.Units, required
-        The desired density of the system. Used to set the
+    density : float, required
+        The desired density of the system (g/cm^3). Used to set the
         target_box attribute. Can be useful when initializing
         systems at low density and running a shrink simulation
-        to achieve a target density. If no unit is provided, assuming the
-        density is in g/cm**3.
+        to achieve a target density.
     packing_expand_factor : int, default 5
         The factor by which to expand the box for packing.
     edge : float, default 0.2
         The space (nm) between the edge of the box and the molecules.
     overlap : float, default 0.2
         Minimum separation (nm) between particles of different molecules.
+    seed : int, default 12345
+        Change seed to be passed to PACKMOL for different starting positions
+    kwargs
+        Arguments to be passed into mbuild.packing.fill_box
 
 
     .. warning::
@@ -661,30 +657,34 @@ class Pack(System):
     def __init__(
         self,
         molecules,
-        density: Union[int, float, u.unyt_quantity, u.unyt_array, Units],
+        density: float,
         base_units=dict(),
         packing_expand_factor=5,
         edge=0.2,
         overlap=0.2,
+        seed=12345,
         fix_orientation=False,
+        **kwargs,
     ):
-        if isinstance(density, (int, float)):
+        if not isinstance(density, u.array.unyt_quantity):
+            self.density = density * u.Unit("g") / u.Unit("cm**3")
             warnings.warn(
-                "Units for density were not given, assuming "
-                "units of g/cm**3."
+                "Units for density were not given, assuming units of g/cm**3."
             )
-            self.density = density * Units.g_cm3
         else:
             self.density = density
         self.packing_expand_factor = packing_expand_factor
         self.edge = edge
         self.overlap = overlap
+        self.seed = seed
         self.fix_orientation = fix_orientation
-        super(Pack, self).__init__(molecules=molecules, base_units=base_units)
+        super(Pack, self).__init__(
+            molecules=molecules, base_units=base_units, **kwargs
+        )
 
-    def _build_system(self):
-        mass_density = Units.kg_m3
-        number_density = Units.n_m3
+    def _build_system(self, **kwargs):
+        mass_density = u.Unit("kg") / u.Unit("m**3")
+        number_density = u.Unit("m**-3")
         if self.density.units.dimensions == mass_density.dimensions:
             target_box = get_target_box_mass_density(
                 density=self.density, mass=self.mass
@@ -706,8 +706,10 @@ def _build_system(self):
             n_compounds=[1 for i in self.all_molecules],
             box=list(target_box * self.packing_expand_factor),
             overlap=self.overlap,
+            seed=self.seed,
             edge=self.edge,
             fix_orientation=self.fix_orientation,
+            **kwargs,
         )
         return system
 
@@ -794,4 +796,4 @@ def _build_system(self):
         system.translate_to(
             (system.box.Lx / 2, system.box.Ly / 2, system.box.Lz / 2)
         )
-        return system
+        return system

flowermd/modules/surface_wetting/surface_wetting.py

@@ -105,8 +105,7 @@ def run_droplet(
             final_density, (u.array.unyt_quantity, u.unyt_quantity, Units)
         ):
             warnings.warn(
-                "Units for density were not given, assuming "
-                "units of g/cm**3."
+                "Units for density were not given, assuming units of g/cm**3."
             )
             target_box_shrink = get_target_box_mass_density(
                 density=shrink_density * Units.g_cm3,

flowermd/tests/base/test_molecule.py

@@ -207,8 +207,8 @@ def test_polymer_different_chain_lengths(self, dimethylether_smiles):
             bond_orientation=[None, None],
         )
         assert polymer.n_particles == 53
-        assert len(polymer.molecules[0].children) == 3
-        assert len(polymer.molecules[1].children) == 4
+        assert len(polymer.molecules[0].labels["all-monomers"]) == 3
+        assert len(polymer.molecules[1].labels["all-monomers"]) == 4
 
     def test_polymer_different_num_mol(self, dimethylether_smiles):
         polymer = Polymer(
@@ -220,9 +220,9 @@ def test_polymer_different_num_mol(self, dimethylether_smiles):
             bond_orientation=[None, None],
         )
         assert polymer.n_particles == 55
-        assert len(polymer.molecules[0].children) == 3
-        assert len(polymer.molecules[1].children) == 2
-        assert len(polymer.molecules[2].children) == 2
+        assert len(polymer.molecules[0].labels["all-monomers"]) == 3
+        assert len(polymer.molecules[1].labels["all-monomers"]) == 2
+        assert len(polymer.molecules[2].labels["all-monomers"]) == 2
 
     def test_polymer_unequal_num_mol_length(self, dimethylether_smiles):
         with pytest.raises(ValueError):
@@ -324,4 +324,4 @@ def test_periodic_bond_bad_axis(self, polyethylene):
         with pytest.raises(ValueError):
             polyethylene(num_mols=1, lengths=20, periodic_bond_axis=1)
         with pytest.raises(ValueError):
-            polyethylene(num_mols=1, lengths=20, periodic_bond_axis="a")
+            polyethylene(num_mols=1, lengths=20, periodic_bond_axis="a")