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Merged
PythonFZ merged 1 commit into from
Nov 15, 2025
Merged

release preperation #85

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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
[![Docs](https://github.com/zincware/rdkit2ase/actions/workflows/pages.yaml/badge.svg)](https://zincware.github.io/rdkit2ase/)
[![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/).
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8 changes: 7 additions & 1 deletion docs/source/index.rst
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Expand Up @@ -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
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11 changes: 9 additions & 2 deletions pyproject.toml
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@@ -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"
Expand Down Expand Up @@ -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/"
Comment on lines +43 to +47

@coderabbitai coderabbitai Bot Nov 15, 2025

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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

Project URLs follow PyPI best practices.

The new [project.urls] section provides standard metadata for PyPI listings, improving project discoverability and user access to resources.

Please verify that the Discord invite link and documentation URL are active and current:

🌐 Web query:

Verify zincware molify project URLs on PyPI and GitHub

💡 Result:

Confirmed:

Sources: PyPI project page for molify [1] and the zincware documentation which points to the GitHub repo (rdkit2ase) [2].

I need to gather more specific information. The initial search results show a potential repository mismatch (molify vs rdkit2ase) and don't verify the Discord or documentation URLs. Let me search for more details:

Repository URL is incorrect in pyproject.toml.

The package is installed via "pip install molify", but the actual GitHub repository is https://github.com/zincware/rdkit2ase, not https://github.com/zincware/molify. Update line 44:

Repository = "https://github.com/zincware/rdkit2ase"

The Discord invite link and ReadTheDocs documentation URL could not be verified through web searches and should be manually confirmed to ensure they are active and accessible.

🤖 Prompt for AI Agents 
In pyproject.toml around lines 43 to 47, the Repository URL is incorrect (points
to /molify) and should be updated to the actual GitHub repo for the package;
change the Repository entry to "https://github.com/zincware/rdkit2ase". Also
verify the Discord invite and Documentation (ReadTheDocs) URLs—if you cannot
confirm they are valid, remove or replace them with verified links or add a TODO
comment to have the maintainer supply the correct URLs.



[tool.ruff.lint]
select = ["E", "F", "N", "C", "I"]
extend-ignore = [
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2 changes: 1 addition & 1 deletion uv.lock
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