molify 0.0.1a2__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-0.0.1a2 → molify-0.2.1}/.pre-commit-config.yaml

@@ -26,7 +26,7 @@ repos:
         additional_dependencies: ["tomli"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.12.12
+    rev: v0.14.4
     hooks:
       # Run the linter.
       - id: ruff
@@ -34,7 +34,7 @@ repos:
       # Run the formatter.
       - id: ruff-format
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.22
+    rev: 1.0.0
     hooks:
     - id: mdformat
       args: ["--wrap=80"]

{molify-0.0.1a2 → molify-0.2.1}/PKG-INFO

@@ -1,7 +1,11 @@
 Metadata-Version: 2.4
 Name: molify
-Version: 0.0.1a2
-Summary: Interface between rdkit and ASE
+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
+Project-URL: Discord, https://discord.gg/7ncfwhsnm4
+Project-URL: Documentation, https://molify.readthedocs.io/
 Author-email: Fabian Zills <fzills@icp.uni-stuttgart.de>
 License-Expression: Apache-2.0
 License-File: LICENSE
@@ -9,22 +13,23 @@ 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'
 Description-Content-Type: text/markdown
 
 [![zincware](https://img.shields.io/badge/Powered%20by-zincware-darkcyan)](https://github.com/zincware)
-[![codecov](https://codecov.io/gh/zincware/rdkit2ase/graph/badge.svg?token=Q0VIN03185)](https://codecov.io/gh/zincware/rdkit2ase)
+[![codecov](https://codecov.io/gh/zincware/molify/graph/badge.svg?token=Q0VIN03185)](https://codecov.io/gh/zincware/molify)
 [![PyPI version](https://badge.fury.io/py/molify.svg)](https://badge.fury.io/py/molify)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15423477.svg)](https://doi.org/10.5281/zenodo.15423477)
-[![Docs](https://github.com/zincware/rdkit2ase/actions/workflows/pages.yaml/badge.svg)](https://zincware.github.io/rdkit2ase/)
+[![Docs](https://github.com/zincware/molify/actions/workflows/pages.yaml/badge.svg)](https://zincware.github.io/molify/)
 [![status](https://joss.theoj.org/papers/4c1ec2a0b66ed6baaf3fe93066696d5f/status.svg)](https://joss.theoj.org/papers/4c1ec2a0b66ed6baaf3fe93066696d5f)
 
-# molify - Interface between the rdkit and ASE package.
+# molify - Molecular Structure Interface with RDKit, ASE, Packmol and NetworkX
 
 Installation via `pip install molify`. For more information please visit the
-[documentation](https://zincware.github.io/rdkit2ase/).
+[documentation](https://zincware.github.io/molify/).
 
 A common use case is to create 3D structures from SMILES strings. This can be
 achieved using the `molify.rdkit2ase` function.

{molify-0.0.1a2 → molify-0.2.1}/README.md

@@ -1,14 +1,14 @@
 [![zincware](https://img.shields.io/badge/Powered%20by-zincware-darkcyan)](https://github.com/zincware)
-[![codecov](https://codecov.io/gh/zincware/rdkit2ase/graph/badge.svg?token=Q0VIN03185)](https://codecov.io/gh/zincware/rdkit2ase)
+[![codecov](https://codecov.io/gh/zincware/molify/graph/badge.svg?token=Q0VIN03185)](https://codecov.io/gh/zincware/molify)
 [![PyPI version](https://badge.fury.io/py/molify.svg)](https://badge.fury.io/py/molify)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15423477.svg)](https://doi.org/10.5281/zenodo.15423477)
-[![Docs](https://github.com/zincware/rdkit2ase/actions/workflows/pages.yaml/badge.svg)](https://zincware.github.io/rdkit2ase/)
+[![Docs](https://github.com/zincware/molify/actions/workflows/pages.yaml/badge.svg)](https://zincware.github.io/molify/)
 [![status](https://joss.theoj.org/papers/4c1ec2a0b66ed6baaf3fe93066696d5f/status.svg)](https://joss.theoj.org/papers/4c1ec2a0b66ed6baaf3fe93066696d5f)
 
-# molify - Interface between the rdkit and ASE package.
+# molify - Molecular Structure Interface with RDKit, ASE, Packmol and NetworkX
 
 Installation via `pip install molify`. For more information please visit the
-[documentation](https://zincware.github.io/rdkit2ase/).
+[documentation](https://zincware.github.io/molify/).
 
 A common use case is to create 3D structures from SMILES strings. This can be
 achieved using the `molify.rdkit2ase` function.

{molify-0.0.1a2 → molify-0.2.1}/docs/source/index.rst

@@ -156,11 +156,17 @@ More information and installation instructions can be found in the `UV documenta
 
 .. code-block:: console
 
-   (.venv) $ git clone https://github.com/zincware/molify
+   (.venv) $ git clone --recursive https://github.com/zincware/molify
    (.venv) $ cd molify
    (.venv) $ uv sync
    (.venv) $ source .venv/bin/activate
 
+If you haven't used `--recursive` you can also initialize the submodules later:
+
+.. code-block:: console
+
+   (.venv) $ git submodule update --init --recursive
+
 
 .. toctree::
    :maxdepth: 2

{molify-0.0.1a2 → molify-0.2.1}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "molify"
-version = "0.0.1a2"
-description = "Interface between rdkit and ASE"
+version = "0.2.1"
+description = "Molecular Structure Interface with RDKit, ASE, Packmol and NetworkX"
 readme = "README.md"
 license = "Apache-2.0"
 requires-python = ">=3.10"
@@ -12,6 +12,7 @@ dependencies = [
     "ase>=3.25.0",
     "matplotlib>=3.10.1",
     "networkx>=3.4.2",
+    "packmol>=21.1.2",
     "rdkit>=2024",
 ]
 
@@ -37,8 +38,12 @@ 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"
+Discord = "https://discord.gg/7ncfwhsnm4"
+Documentation = "https://molify.readthedocs.io/"
+
 
 [tool.ruff.lint]
 select = ["E", "F", "N", "C", "I"]
@@ -50,11 +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-0.0.1a2 → 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)