update IPSuite docs

.readthedocs.yaml

@@ -9,14 +9,14 @@ submodules:
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-lts-latest
   tools:
     python: "3.11"
   jobs:
     post_install:
       # see https://github.com/astral-sh/uv/issues/10074
       - pip install uv
-      - UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv sync --all-extras --link-mode=copy --group=docs
+      - UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv sync --link-mode=copy --group=docs
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

docs/source/_examples/01_relaxation.rst

@@ -0,0 +1,59 @@
+Geometry Relaxation
+===================
+
+In this example we will setup a simulation box and relax the structure using an :term:`MLIP`.
+
+.. tip::
+
+    Setup a new project in an empty directory by calling
+
+    .. code::
+
+        git init
+        dvc init
+        touch main.py
+
+
+Add the following to your main.py file:
+
+.. code::
+
+    import ipsuite as ips
+
+    project = ips.Project()
+    # create the main project to handle the workflow
+
+    with project:
+    # add new nodes to the project within the project context manager
+        ips.Smiles2Conformers(smiles="O", numConfs=1) # add our first node
+
+    project.build()
+
+To build the project, run the file using :code:`python main.py`.
+
+.. note::
+
+    This will construct the workflow, but not execute.
+
+To execute the workflow now constructed, run :code:`dvc repro`.
+
+
+.. code::
+
+    import ipsuite as ips
+
+    project = ips.Project()
+    # create the main project to handle the workflow
+
+    with project:
+    # add new nodes to the project within the project context manager
+        water = ips.Smiles2Conformers(smiles="O", numConfs=1) # add our first node
+        ammonia = ips.Smiles2Conformers(smiles="N", numConfs=1) # add another node
+        box = ips.MultiPackmol(
+            data=[water.frames, ammonia.frames],
+            count=[10, 3],
+            density=997,
+            n_configurations=3
+        )
+
+    project.build()

docs/source/_get_started/installation.rst

@@ -0,0 +1,39 @@
+Installation
+============
+
+From PyPI
+---------
+
+To use :code:`ipsuite`, first install it using pip:
+
+.. code-block:: console
+
+   (.venv) $ pip install ipsuite
+
+.. note::
+
+   The :code:`ipsuite` package installation does not contain any :term:`MLIP` packages.
+   Due to different dependencies, it is highly recommended to install your preferred :term:`MLIP` package individually into the same environment.
+
+.. note::
+
+   If you encounter en error like :code:`Permission denied '/var/cache/dvc'` you might want to reinstall :code:`pip install platformdirs==3.11.0` or :code:`pip install platformdirs==3.10.0` as discussed at https://github.com/iterative/dvc/issues/9184
+
+From Source
+-----------
+
+To install and develop :code:`ipsuite` from source we recommend using :code:`https://docs.astral.sh/uv`.
+More information and installation instructions can be found at https://docs.astral.sh/uv/getting-started/installation/ .
+
+.. code:: console
+
+   (.venv) $ git clone https://github.com/zincware/ipsuite
+   (.venv) $ cd ipsuite
+   (.venv) $ uv sync
+   (.venv) $ source .venv/bin/activate
+
+In a file :code:`main.py` try importing IPS to check if everything is working correctly
+
+.. code-block:: python
+
+    import ipsuite as ips

docs/source/_get_started/quickstart.rst

@@ -1,55 +1,13 @@
 .. _getting_started:
 
-Getting started
-===============
-
-Installation
-------------
-
-The IPS package can be downloaded via the package-management system pip.
-We recommend the usage of an python environment with the python version 3.10. Other versions might not currently work.
-
-.. code-block:: bash
-
-    pip install ipsuite
-
-Alternatively the latest version of IPSuite can be downloaded from `GitHub <https://github.com/zincware/IPSuite>`_,
-using `Poetry <https://python-poetry.org/>`_ to install the python dependencies.
-
-.. code-block:: bash
-
-    git clone https://github.com/zincware/IPSuite.git
-    cd IPSuite
-    poetry install
-
-For IPSuite to work, it is necessary for an IPS Project to be in a git as well as DVC initialized directory.
-Create a folder for your project and initialize git and DVC to start working with IPS.
-
-.. code-block:: bash
-
-    mkdir project
-    cd project
-    git init
-    dvc init
-
-In a file :code:`main.py` try importing IPS to check if everything is working correctly
-
-.. code-block:: python
-
-    import ipsuite as ips
-
+Quickstart
+==========
 
 
 To get to know the IPS procedures we will do an example problem.
 
-
-The First Project
-=================
-
 Initial Data Generation
 -----------------------
-This project will show the basic creation of an IPS Project using an additional piece of software
-called `Packmol <https://m3g.github.io/packmol/>`_.
 The goal is to place water molecules inside a box at a specified density.
 
 .. code-block:: python
@@ -58,20 +16,20 @@ The goal is to place water molecules inside a box at a specified density.
 
     with ips.Project() as project:
         # Generate a single water molecule
-        mol = ips.Smiles2Atoms(smiles="O")
+        mol = ips.Smiles2Conformers(smiles="O")
         # Duplicate water molecules
         packmol = ips.Packmol(
             data=[mol.frames], count=[10], density=876
             )
 
     project.build()
 
-The *Smiles2Atoms* node takes the `SMILES <https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system>`_ string for water ("O"),
+The :class:`ipsuite.Smiles2Conformers` node takes the `SMILES <https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system>`_ string for water ("O"),
 and generates an an `ASE atoms object <https://wiki.fysik.dtu.dk/ase/ase/atoms.html>`_ from it.
-This atom from the Smiles2Atoms instance can be accessd by calling `mol.atoms`.
+This atom from the :class:`ipsuite.Smiles2Conformers` instance can be accessd by calling `mol.frames`.
 This instance attribute is then handed over to the Packmol node in the `data` attribute.
 It is possible to hand over multiple different types of ASE atoms,
-so `mol.atoms` as to be given as a list. The next attribute we need to set is the amount of molecules we want to place in the box.
+so `mol.frames` as to be given as a list. The next attribute we need to set is the amount of molecules we want to place in the box.
 This also has to be a list with each entry being the amount for other ASE atoms object in the `data` list. Lastly the density has
 to be provided. Calling `project.build()` will save the workflow into DVC graph configuration and parameter files.
 After executing the code, the entire workflow is constructed and can be visualised
@@ -80,7 +38,7 @@ used with `Mermaid <https://mermaid.js.org/>`_ to better visualise the workflows
 
 The parameters files, namely `params.yaml` can be viewed and parameters can be changed without rerunning the python script.
 
-By calling `dvc repro` the workflow consisting of the nodes is executed, which results in the generation of firstly a single water molecule by the Smiles2Atoms node and then the placement
+By calling `dvc repro` the workflow consisting of the nodes is executed, which results in the generation of firstly a single water molecule by the :class:`ipsuite.Smiles2Conformers` node and then the placement
 of multiple water molecules in a box by the Packmol node.
 After running `dvc repro` a new folder `nodes` is created which each node having their own subfolder. These folders
 contain the results from the Nodes.
@@ -90,9 +48,9 @@ we can visualise the H5MD files generated by the nodes.
 
 .. code-block:: bash
 
-    zndraw nodes/Smiles2Atoms/structures.h5
+    zndraw nodes/Smiles2Conformers/structures.h5
 
-will visualise the single water molecule generated by Smiles2Atoms. There will also be a H5MD file in the Packmol folder
+will visualise the single water molecule generated by :class:`ipsuite.Smiles2Conformers`. There will also be a H5MD file in the Packmol folder
 
 .. figure:: ../images/water_packmol.png
     :alt: ZnDraw Screenshot