fix make file, add README, add CI check (#25)

* add contrib info

* run pre-commit hooks

* remove make.bat

* update structure relax

* update notebook

* glob and update notebook

.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]

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/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/notebooks/combine.ipynb

@@ -0,0 +1,195 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/basf/mlipx/blob/main/docs/source/notebooks/combine.ipynb)\n",
+    "\n",
+    "# Combine Multiple Nodes\n",
+    "\n",
+    "The `mlipx` command line interface provides you with recipes for specific tasks.\n",
+    "In this notebook, we will write a script to include different aspects from different recipes into a single workflow."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Only install the packages if they are not already installed\n",
+    "!pip show mlipx > /dev/null 2>&1 || pip install mlipx\n",
+    "!pip show rdkit2ase > /dev/null 2>&1 || pip install rdkit2ase"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# We will create a GIT and DVC repository in a temporary directory\n",
+    "import os\n",
+    "import tempfile\n",
+    "\n",
+    "temp_dir = tempfile.TemporaryDirectory()\n",
+    "os.chdir(temp_dir.name)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Like all `mlipx` Nodes we will use a GIT and DVC repository to run experiments.\n",
+    "To make our custom code available, we structure our project like\n",
+    "\n",
+    "```\n",
+    "relaxation/\n",
+    "   ├── .git/\n",
+    "   ├── .dvc/\n",
+    "   ├── src/__init__.py\n",
+    "   ├── src/relaxation.py\n",
+    "   ├── models.py\n",
+    "   └── main.py\n",
+    "```\n",
+    "\n",
+    "to allow us to import our code `from src.relaxation import Relax`.\n",
+    "Alternatively, you can package your code and import it like any other Python package."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!git init\n",
+    "!dvc init --quiet"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Let us configure now configure a workflow, creating a structure from `SMILES`, relax it, run molecular dynamics and compute the homonuclear diatomics."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import mlipx\n",
+    "\n",
+    "project = mlipx.Project()\n",
+    "\n",
+    "emt = mlipx.GenericASECalculator(\n",
+    "    module=\"ase.calculators.emt\",\n",
+    "    class_name=\"EMT\",\n",
+    ")\n",
+    "\n",
+    "with project.group(\"initialize\"):\n",
+    "    confs = mlipx.Smiles2Conformers(smiles=\"CCCC\", num_confs=1)\n",
+    "\n",
+    "with project.group(\"structure-optimization\"):\n",
+    "    struct_optim = mlipx.StructureOptimization(\n",
+    "        data=confs.frames, data_id=-1, optimizer=\"LBFGS\", model=emt\n",
+    "    )\n",
+    "\n",
+    "thermostat = mlipx.LangevinConfig(\n",
+    "    timestep=0.5,\n",
+    "    temperature=300,\n",
+    "    friction=0.001,\n",
+    ")\n",
+    "\n",
+    "with project.group(\"molecular-dynamics\"):\n",
+    "    md = mlipx.MolecularDynamics(\n",
+    "        data=struct_optim.frames,\n",
+    "        data_id=-1,\n",
+    "        model=emt,\n",
+    "        thermostat=thermostat,\n",
+    "        steps=1000,\n",
+    "    )\n",
+    "\n",
+    "with project.group(\"homonuclear-diatomics\"):\n",
+    "    ev = mlipx.HomonuclearDiatomics(\n",
+    "        data=confs.frames,\n",
+    "        model=emt,\n",
+    "        n_points=100,\n",
+    "        min_distance=0.75,\n",
+    "        max_distance=2.0,\n",
+    "        elements=[],\n",
+    "    )\n",
+    "\n",
+    "project.repro()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Once the graph has been executed, we can look at the resulting structures."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "struct_optim.figures[\"energy_vs_steps\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "md.figures[\"energy\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(ev.figures.keys())\n",
+    "ev.figures[\"C-C bond\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "temp_dir.cleanup()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "mlipx",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}