Merge branch 'main' into add_pack_seed

.github/workflows/pytest.yml

@@ -29,8 +29,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-latest, macOS-13, ubuntu-latest]
-        python-version: ['3.10', '3.11']
+        os: [macos-14, ubuntu-24.04]
+        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: ${{ matrix.python-version }}
-        miniforge-variant: Mambaforge
-        miniforge-version: 4.9.2-4
-        use-mamba: true
+        create-args: >-
+          python=${{ matrix.python-version }}
 
     - name: Install package
       shell: bash -l {0}
@@ -56,14 +54,14 @@ 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
 
   test-tutorials:
     if: ${{ github.event.issue.pull_request && github.event.comment.body== '/testtutorials'}}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
     - name: Put a reaction to the comment
       run: gh api graphql --silent --raw-field query="mutation AddReaction {addReaction(input:{subjectId:\"$NODE_ID\",content:EYES}){reaction{content}subject{id}}}"
@@ -96,15 +94,14 @@ jobs:
         PR_NUMBER: ${{ github.event.issue.number }}
 
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Build environment
-      uses: conda-incubator/setup-miniconda@v2
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: environment-dev.yml
-        miniforge-variant: Mambaforge
-        miniforge-version: 4.9.2-4
-        use-mamba: true
+        create-args: >-
+          python=3.12
 
     - name: Install package
       shell: bash -l {0}

.pre-commit-config.yaml

@@ -9,14 +9,14 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.6 # Ruff version
+    rev: v0.9.3 # 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

environment-dev.yml

@@ -8,7 +8,7 @@ dependencies:
   - gmso >=0.12.0
   - gsd >=3.0
   - grits >=0.5.0
-  - hoomd >=4.5
+  - hoomd >=4.5, <5.0
   - mbuild >=0.17.0
   - numpy <2.0
   - openbabel >=3
@@ -18,6 +18,6 @@ dependencies:
   - pytest
   - pytest-cov
   - nbmake
-  - python >=3.10, <3.12
+  - python >=3.10, <3.13
   - fresnel >=0.13.5
   - cmeutils >=1.3

environment.yml

@@ -8,12 +8,12 @@ dependencies:
   - gmso >=0.12.0
   - gsd >=3.0
   - grits >=0.5.0
-  - hoomd >=4.5
+  - hoomd >=4.5, <5.0
   - mbuild >=0.17.0
   - numpy <2.0
   - openbabel >=3
   - pip
   - py3Dmol
-  - python >=3.10, <3.12
+  - python >=3.10, <3.13
   - fresnel >=0.13.5
   - cmeutils >=1.3

flowermd/__init__.py

@@ -10,3 +10,5 @@
     Simulation,
     System,
 )
+
+__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

@@ -665,8 +665,7 @@ def __init__(
         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."
             )
         else:
             self.density = density

flowermd/modules/surface_wetting/surface_wetting.py

@@ -102,8 +102,7 @@ def run_droplet(
             shrink_density, u.array.unyt_quantity
         ) and not isinstance(final_density, u.array.unyt_quantity):
             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 * (u.g / (u.cm**3)),

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 = "[email protected]"},
+  {name = "Marjan Albooyeh", email = "[email protected]"},
+  {name = "Eric Jankowski", email = "[email protected]"}
+]
+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__"}