molify 0.2.0__tar.gz → 0.2.1__tar.gz

molify-0.2.1/.github/workflows/build-wheels.yaml

@@ -0,0 +1,25 @@
+name: Build and upload to PyPI
+
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/molify
+    permissions:
+      id-token: write
+    steps:
+    - uses: actions/checkout@v5
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+    - name: Build
+      run: |
+          uv build
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

{molify-0.2.0 → molify-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: molify
-Version: 0.2.0
+Version: 0.2.1
 Summary: Molecular Structure Interface with RDKit, ASE, Packmol and NetworkX
 Project-URL: Repository, https://github.com/zincware/molify
 Project-URL: Releases, https://github.com/zincware/molify/releases
@@ -13,6 +13,7 @@ Requires-Python: >=3.10
 Requires-Dist: ase>=3.25.0
 Requires-Dist: matplotlib>=3.10.1
 Requires-Dist: networkx>=3.4.2
+Requires-Dist: packmol>=21.1.2
 Requires-Dist: rdkit>=2024
 Provides-Extra: vesin
 Requires-Dist: vesin>=0.3.7; extra == 'vesin'

{molify-0.2.0 → molify-0.2.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "molify"
-version = "0.2.0"
+version = "0.2.1"
 description = "Molecular Structure Interface with RDKit, ASE, Packmol and NetworkX"
 readme = "README.md"
 license = "Apache-2.0"
@@ -12,6 +12,7 @@ dependencies = [
     "ase>=3.25.0",
     "matplotlib>=3.10.1",
     "networkx>=3.4.2",
+    "packmol>=21.1.2",
     "rdkit>=2024",
 ]
 
@@ -37,9 +38,6 @@ vesin = [
     "vesin>=0.3.7",
 ]
 
-[project.scripts]
-packmol = "molify.packmol:packmol_cli"
-
 [project.urls]
 Repository = "https://github.com/zincware/molify"
 Releases = "https://github.com/zincware/molify/releases"
@@ -57,11 +55,5 @@ extend-ignore = [
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
-[tool.hatch.build.hooks.custom]
-path = "hatch_build.py"
-
-[tool.hatch.build.targets.wheel]
-packages = ["src/molify"]
-
 [tool.codespell]
 skip = "*.ipynb"

{molify-0.2.0 → molify-0.2.1}/src/molify/pack.py

@@ -9,7 +9,6 @@ import numpy as np
 from ase.io.proteindatabank import write_proteindatabank
 from rdkit import Chem
 
-from molify.packmol import get_packmol_binary
 from molify.utils import calculate_box_dimensions
 
 log = logging.getLogger(__name__)
@@ -147,7 +146,7 @@ def pack(
     seed: int = 42,
     tolerance: float = 2,
     verbose: bool = False,
-    packmol: str | None = None,
+    packmol: str = "packmol",
     pbc: bool = True,
     output_format: FORMAT = "pdb",
     ratio: tuple[float, float, float] = (1.0, 1.0, 1.0),
@@ -169,11 +168,8 @@ def pack(
         The tolerance for the packing algorithm, by default 2.
     verbose : bool, optional
         If True, enables logging of the packing process, by default False.
-    packmol : str or None, optional
-        The path to the packmol executable. If None (default), uses the bundled
-        packmol binary shipped with molify. You can provide a custom path to
-        use a different packmol installation (e.g., "packmol" to use system
-        PATH, or "/path/to/custom/packmol").
+    packmol : str, optional
+        The path to the packmol executable.
     pbc : bool, optional
         Ensure tolerance across periodic boundaries, by default True.
     output_format : str, optional
@@ -199,10 +195,6 @@ def pack(
     >>> print(packed_system)
     Atoms(symbols='C10H44O12', pbc=True, cell=[8.4, 8.4, 8.4])
     """
-    # Use bundled packmol binary if not specified
-    if packmol is None:
-        packmol = str(get_packmol_binary())
-
     selected_images = _select_conformers(data, counts, seed)
     cell = calculate_box_dimensions(images=selected_images, density=density)