A ready to use example: generate polymer and run simulation

.devcontainer/Dockerfile

@@ -0,0 +1,4 @@
+FROM mcr.microsoft.com/devcontainers/miniconda:1-3
+
+RUN sh -c "$(wget -O- https://github.com/deluan/zsh-in-docker/releases/download/v1.2.0/zsh-in-docker.sh)" -- \
+    -t nanotech 

.devcontainer/devcontainer.json

@@ -0,0 +1,34 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/anaconda
+{
+  "name": "MolExp",
+  "build": {
+    "context": ".",
+    "dockerfile": "Dockerfile"
+  },
+  // Features to add to the dev container. More info: https://containers.dev/features.
+  // "features": {
+  //   "ghcr.io/devcontainers/features/conda:1": {}
+  // },
+  // Use 'forwardPorts' to make a list of ports inside the container available locally.
+  // "forwardPorts": [],
+  // Use 'postCreateCommand' to run commands after the container is created.
+  "postCreateCommand": "pip install -e \".[dev]\"",
+  // Configure tool-specific properties.
+  // "customizations": {},
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "ms-python.python",
+        "ms-python.black-formatter",
+        "ms-python.isort",
+        "ms-toolsai.jupyter",
+        "github.copilot",
+        "ms-vscode.test-adapter-converter",
+        "njpwerner.autodocstr"
+      ]
+    }
+  },
+  // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+  "remoteUser": "root"
+}

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "python.analysis.autoImportCompletions": true
+}

README.md

@@ -1,2 +1,31 @@
-# molexp
-[WIP] Molecular experiment managerment
+# molexp: a computational chemistry workflow and experiment management package
+
+`molexp` is a comprehensive computational chemistry workflow and experiment management package, designed to streamline and enhance the efficiency of chemistry-related research and experimentation. At its core, `molexp` leverages the robust capabilities of [Hamilton](https://github.com/DAGWorks-Inc/hamilton), allowing users to define workflows in a manner that is testable, modular, and self-documenting. This ensures that all workflows are easy to understand, maintain, and share, as they are written in pure Python code.
+
+One of the standout features of `molexp` is its advanced experiment management system. This system is meticulously designed to facilitate self-explanatory task organization, making it simple for researchers to manage and document their experiments effectively. Users can perform Create, Read, Update, and Delete (CRUD) operations directly from the command line, using specific variables to tailor the management process to their unique requirements.
+
+## Features
+
+1. **Integration with Hamilton**: By utilizing Hamilton, `molexp` ensures that workflows are not only powerful and flexible but also maintain high standards of code quality and reusability.
+
+2. **Modular Workflow Design**: Workflows in `molexp` are built in a modular fashion, promoting reusability and ease of testing. This modularity allows for individual components to be tested and debugged independently, significantly reducing the time and effort required to ensure the reliability of complex workflows.
+
+3. **Self-Documenting Code**: The use of pure Python code means that all workflows and experiments are inherently self-documenting. This transparency is crucial for collaborative research environments, where clear documentation and easy-to-follow code are essential for effective teamwork.
+
+4. **Comprehensive Experiment Management**: The experiment management system in `molexp` is designed to simplify the organization of tasks. It supports comprehensive CRUD operations via the command line, allowing users to create, view, modify, and delete experiments with ease.
+
+5. **Customizable Variables**: The system’s flexibility is further enhanced by the ability to use specific variables to manage experiments. This feature allows users to tailor their workflow management processes to suit their specific needs and preferences.
+
+6. **User-Friendly Command Line Interface**: The command line interface of `molexp` is intuitive and user-friendly, ensuring that even users with minimal programming experience can effectively manage their computational chemistry workflows and experiments.
+
+7. **Scalability and Flexibility**: `molexp` is designed to handle projects of varying sizes and complexities. Whether you are managing a small-scale experiment or a large, multifaceted research project, `molexp` scales to meet your needs.
+
+8. **Community and Support**: As an open-source package, `molexp` benefits from a growing community of users and contributors. This ensures continuous improvements, updates, and a wealth of shared knowledge and resources.
+
+## Concepts
+
+`project`: a project represents a stand alone research topic, and contains necessary index and doc files
+
+`Experiment`: an experiment is new science trial with new variable
+
+`Task`: several tasks in an experiment, each task is a complete workflow or graph or executation.

docs/getting_started.ipynb

@@ -0,0 +1,141 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Getting Startted with MolExp\n",
+    "\n",
+    "let's we start from hierarchy "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Three level "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import molexp as me\n",
+    "\n",
+    "proj = me.Project(\n",
+    "    name='tutorial_proj',\n",
+    "    description='A tutorial project',\n",
+    "    root='.'\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "exp1 = proj.def_exp(\n",
+    "    name = 'exp_1',\n",
+    "    description = 'test exp',\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<Asset: global_asset>"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "proj.add_asset(\n",
+    "    'global_asset'\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<Task: task_1>"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "exp1.def_task(\n",
+    "    name = 'task_1',\n",
+    "    description = 'test task'\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "proj.init()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "exp2 = exp1.clone()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "base",
+   "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": "3.12.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/index.md

@@ -0,0 +1,2 @@
+# Welcome to MolExp
+

mkdocs.yml

@@ -0,0 +1,19 @@
+site_name: MolExp
+
+site_url: https://github.com/MolCrafts/molexp
+theme:
+  name: material
+  features:
+    - navigation.instant
+    - navigation.instant.progress
+    - navigation.tracking
+    - navigation.tabs
+
+markdown_extensions:
+  - pymdownx.arithmatex:
+      generic: true
+
+extra_javascript:
+  - javascripts/mathjax.js
+  - https://polyfill.io/v3/polyfill.min.js?features=es6
+  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js