Merge branch 'main' into main

.github/workflows/pytest.yml

@@ -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: ${{ matrix.python-version }}
-        miniforge-variant: Miniforge3
-        miniforge-version: 24.11.0-0
-        use-mamba: true
+        create-args: >-
+          python=${{ 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
@@ -99,12 +97,11 @@ 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
-        miniforge-variant: Miniforge3
-        miniforge-version: 24.11.0-0
-        use-mamba: true
+        create-args: >-
+          python=3.12
 
     - name: Install package
       shell: bash -l {0}

.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: v0.9.2 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

flowermd/__init__.py

@@ -10,4 +10,7 @@
     Simulation,
     System,
 )
+
 from .internal.units import Units
+
+__version__ = "1.3.1"

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

@@ -73,8 +73,7 @@ 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

@@ -670,8 +670,7 @@ def __init__(
     ):
         if isinstance(density, (int, float)):
             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:

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,

pyproject.toml

@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools>=61.2", "versioningit"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "flowermd"
+description = "Framework for building and running coplex simulaiton workflows with MosDeF and HOOMD-Blue."
+readme = "README.md"
+authors = [
+  {name = "Chris Jones", email = "chrisjones4@u.boisestate.edu"},
+  {name = "Marjan Albooyeh", email = "marjanalbooyeh@u.boisestate.edu"},
+  {name = "Eric Jankowski", email = "ericjankowski@boisestate.edu"}
+]
+license= {text = "GPLv3"}
+classifiers=[
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+]
+urls = {Homepage = "https://github.com/cmelab/flowermd"}
+requires-python = ">=3.10"
+dynamic = ["version"]
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+license-files = ["LICENSE"]
+
+[tool.setuptools.packages]
+find = {namespaces = false}
+
+[tool.setuptools.package-data]
+flowermd = [
+  '"modules/**"',
+  '"library/**"',
+  '"assets/forcefields/**"',
+  '"assets/molecule_files/**"',
+  '"utils/**"',
+  '"internal/**"',
+]
+
+[tool.setuptools.dynamic]
+version = {attr = "flowermd.__version__"}