Merge branch 'main' into update-ref-forces

.github/workflows/pre-comit.yaml

@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/[email protected]

.readthedocs.yaml

@@ -16,10 +16,7 @@ build:
       # See https://github.com/readthedocs/readthedocs.org/pull/11152/
       - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
       # Navigate to the examples directory and perform DVC operations
-      - cd examples
-      - poetry run dvc remote modify origin endpointurl $AWS_ENDPOINT_URL
-      - poetry run dvc pull --allow-missing
-      - cd ..
+      - cd examples && poetry run dvc remote modify origin endpointurl $AWS_ENDPOINT_URL && poetry run dvc pull --allow-missing
 
 sphinx:
   configuration: docs/source/conf.py

README.md

@@ -1,20 +1,19 @@
 <div align="center">
 
-![Logo](./docs/source/_static/mlipx-dark.svg#gh-dark-mode-only)
-![Logo](./docs/source/_static/mlipx-light.svg#gh-light-mode-only)
+![Logo](https://raw.githubusercontent.com/basf/mlipx/refs/heads/main/docs/source/_static/mlipx-light.svg#gh-light-mode-only)
+![Logo](https://raw.githubusercontent.com/basf/mlipx/refs/heads/main/docs/source/_static/mlipx-dark.svg#gh-dark-mode-only)
 
 
 [![PyPI version](https://badge.fury.io/py/mlipx.svg)](https://badge.fury.io/py/mlipx)
 [![ZnTrack](https://img.shields.io/badge/Powered%20by-ZnTrack-%23007CB0)](https://zntrack.readthedocs.io/en/latest/)
-[![ZnDraw](https://img.shields.io/badge/works_with-ZnDraw-orange)
-](https://github.com/zincware/zndraw)
+[![ZnDraw](https://img.shields.io/badge/works_with-ZnDraw-orange)](https://github.com/zincware/zndraw)
 [![open issues](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/basf/mlipx/issues)
-
+[![Documentation Status](https://readthedocs.org/projects/mlipx/badge/?version=latest)](https://mlipx.readthedocs.io/en/latest/?badge=latest)
 
 [📘Documentation](https://mlipx.readthedocs.io) |
 [🛠️Installation](https://mlipx.readthedocs.io/en/latest/installation.html) |
-[📜Recipes](https://mambular.readthedocs.io/en/latest/recipes.html) |
-[🚀Quickstart](https://mambular.readthedocs.io/en/latest/quickstart.html)
+[📜Recipes](https://mlipx.readthedocs.io/en/latest/recipes.html) |
+[🚀Quickstart](https://mlipx.readthedocs.io/en/latest/quickstart.html)
 </div>
 
 <div style="text-align: center;">

docs/Makefile

@@ -6,15 +6,15 @@
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = source
-BUILDDIR      = build
+BUILDDIR      = ../build
 
 # Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@cd "$(SOURCEDIR)" && $(SPHINXBUILD) -M help "." "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 .PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@cd "$(SOURCEDIR)" && $(SPHINXBUILD) -M $@ "." "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/authors.rst

@@ -1,14 +1,61 @@
-Authors
-=======
+Authors and Contributing
+========================
+
 .. note::
 
     Every contribution is welcome and you will be included in this ever growing list.
 
-The creation of mlipx began during Fabian Zills internship at BASF SE, where he worked under the guidance of Sandip De. The foundational concepts and designs were initially developed by Sandip, while the current version of the code is a product of contributions from various members of the BASF team. Fabian Zills integrated several of his previous projects and lead the technical development of the initial release of this code. The code has been released with the intention of fostering community involvement in future developments.  We acknowledge support from:
+Authors
+-------
+The creation of ``mlipx`` began during Fabian Zills internship at BASF SE, where he worked under the guidance of Sandip De. The foundational concepts and designs were initially developed by Sandip, while the current version of the code is a product of contributions from various members of the BASF team. Fabian Zills integrated several of his previous projects and lead the technical development of the initial release of this code. The code has been released with the intention of fostering community involvement in future developments.  We acknowledge support from:
 
 - Fabian Zills
 - Sheena Agarwal
 - Sandip De
 - Shuang Han
 - Srishti Gupta
 - Tiago Joao Ferreira Goncalves
+
+
+Contribution Guidelines
+-----------------------
+
+We welcome contributions to :code:`mlipx`!
+With the inclusion of your contributions, we can make :code:`mlipx` better for everyone.
+
+To ensure code quality and consistency, we use :code:`pre-commit` hooks.
+To install the pre-commit hooks, run the following command:
+
+.. code:: console
+
+   (.venv) $ pre-commit install
+
+All pre-commit hooks have to pass before a pull request can be merged.
+
+For new recipes, we recommend adding an example to the ``\examples`` directory of this repository and updating the documentation accordingly.
+
+**Plugins**
+
+It is further possible, to add new recipes to ``mlipx`` by writing plugins.
+We use the entry point ``mlipx.recipes`` to load new recipes.
+You can find more information on entry points `here <https://setuptools.pypa.io/en/latest/userguide/entry_point.html>`_.
+
+Given the following file ``yourpackage/recipes.py`` in your package:
+
+.. code:: python
+
+    from mlipx.recipes import app
+
+    @app.command()
+    def my_recipe():
+        # Your recipe code here
+
+you can add the following to your ``pyproject.toml``:
+
+.. code:: toml
+
+    [project.entry-points."mlipx.recipes"]
+    yourpackage = "yourpackage.recipes"
+
+
+and when your package is installed together with ``mlipx``, the recipe will be available in the CLI via ``mlipx recipes my_recipe``.

docs/source/build_graph.rst

@@ -8,5 +8,6 @@ You will learn how to include :term:`MLIP` that can not be interfaced with the :
 With your own custom Nodes you can build more comprehensive test cases or go even beyond :term:`MLIP` testing and build workflows for other scenarios, such as :term:`MLIP` training with :code:`mlipx` and :term:`IPSuite`.
 
 .. toctree::
+    :glob:
 
-    notebooks/structure_relaxation.ipynb
+    notebooks/*

docs/source/conf.py

@@ -3,19 +3,17 @@
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-import pathlib
-import sys
 import typing as t
 
-sys.path.insert(0, pathlib.Path(__file__).parents[2].resolve().as_posix())
+import mlipx
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = "mlipx"
 copyright = "2024, Fabian Zills, Sheena Agarwal, Sandip De"
 author = "Fabian Zills, Sheena Agarwal, Sandip De"
-release = "v0.1.0"
+release = mlipx.__version__
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -54,19 +52,21 @@
         {
             "name": "GitHub",
             "url": "https://github.com/basf/mlipx",
-            "html": """
-                <svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16">
-                    <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
-                </svg>
-            """,  # noqa: E501
-            "class": "",
+            "html": "",
+            "class": "fa-brands fa-github fa-2x",
         },
     ],
     "source_repository": "https://github.com/basf/mlipx/",
     "source_branch": "main",
     "source_directory": "docs/source/",
+    "navigation_with_keys": True,
 }
 
+# font-awesome logos
+html_css_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/brands.min.css",
+]
+
 # -- Options for hoverxref extension -----------------------------------------
 # https://sphinx-hoverxref.readthedocs.io/en/latest/
 

docs/source/glossary.rst

@@ -46,7 +46,7 @@ Glossary
             }
 
     packmol
-        Packmol is a software package used for building initial configurations for molecular dynamics or Monte Carlo simulations. It can generate a random collection of molecules using the specified density and composition. TODO add cite
+        Packmol is a software package used for building initial configurations for molecular dynamics or Monte Carlo simulations. It can generate a random collection of molecules using the specified density and composition. More information can be found at https://m3g.github.io/packmol/ .
 
     rdkit2ase
         A package for converting RDKit molecules to ASE atoms.

docs/source/installation.rst

@@ -35,17 +35,3 @@ More information and installation instructions can be found at https://python-po
 
    You can also use :code:`pip install -e .` for a editable installation.
    This does not ensure that all dependencies are handled correctly and for adding new requirements it is mandatory to update the :code:`poetry.lock` file.
-
-Contributing
-------------
-We welcome contributions to :code:`mlipx`!
-With the inclusion of your contributions, we can make :code:`mlipx` better for everyone.
-
-To ensure code quality and consistency, we use :code:`pre-commit` hooks.
-To install the pre-commit hooks, run the following command:
-
-.. code:: console
-
-   (.venv) $ pre-commit install
-
-All pre-commit hooks have to pass before a pull request can be merged.