molify 0.0.1a2__tar.gz → 0.2.0__tar.gz

{molify-0.0.1a2 → molify-0.2.0}/.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-0.2.0}/PKG-INFO

@@ -1,7 +1,11 @@
 Metadata-Version: 2.4
 Name: molify
-Version: 0.0.1a2
-Summary: Interface between rdkit and ASE
+Version: 0.2.0
+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
@@ -15,16 +19,16 @@ 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-0.2.0}/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-0.2.0}/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-0.2.0}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "molify"
-version = "0.0.1a2"
-description = "Interface between rdkit and ASE"
+version = "0.2.0"
+description = "Molecular Structure Interface with RDKit, ASE, Packmol and NetworkX"
 readme = "README.md"
 license = "Apache-2.0"
 requires-python = ">=3.10"
@@ -40,6 +40,13 @@ vesin = [
 [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"]
 extend-ignore = [

{molify-0.0.1a2 → molify-0.2.0}/uv.lock

@@ -950,7 +950,7 @@ wheels = [
 
 [[package]]
 name = "molify"
-version = "0.0.1a2"
+version = "0.2.0"
 source = { editable = "." }
 dependencies = [
     { name = "ase" },