Example flowws-based workflow in a notebook

README.md

Launch a binder notebook with the button below:

apt.txt

povray
xvfb
libglu1-mesa
libgl1-mesa-dri

environment.yml

# specify dependencies for myblender.org operation (see also apt.txt
# for the full set)
channels:
    - conda-forge
dependencies:
    - fresnel
    - pyglet
    - pip
    - pip:
      - freud-analysis
      - matplotlib
      - pythreejs
      - vispy
      - pyriodic-aflow
      - git+https://github.com/glotzerlab/plato@copy_from
      - git+https://github.com/klarh/flowws
      - git+https://github.com/klarh/flowws-analysis
      - git+https://github.com/klarh/flowws-freud

flowws structure analysis workflow.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Overview\n",
    "\n",
    "This notebook demonstrates a very barebones structure analysis workflow using `flowws`. \n",
    "\n",
    "You'll need vispy installed and functional to see the vispy widgets. Note that vispy's implementation of jupyter widgets is not currently robust enough for us to be able to properly control their layout, but in theory we have somewhat detailed control over the display configuration of other types of widgets. Another option is to enable a desktop backend of vispy (`%gui qt5` and then `vispy.app.use_app('pyside2')`, for example) and vispy displays can pop up on your desktop."
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "# this cell can be used to get rid of some of the margins on the side of the notebook\n",
    "from IPython.display import display, HTML\n",
    "\n",
    "display(HTML(data=\"\"\"\n",
    "<style>\n",
    "    div#notebook-container    { width: 98%; }\n",
    "    div#menubar-container     { width: 65%; }\n",
    "    div#maintoolbar-container { width: 99%; }\n",
    "</style>\n",
    "\"\"\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import flowws"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "860d42f8dcaf4896811e1e227b14833a",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "GridBox(children=(VBox(children=(HTML(value='<center><b>Pyriodic</b></center>'), Dropdown(description='structu…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c95bd684be0c46ae8a68969199520ffe",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Output()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "798b7463ccac479abd03dd80a3d99374",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VispyWidget(height=600, width=800)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "bf74c7117d0a436ca7f2422931927c0e",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Output()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "236fa0ad5294467f81d0739064c942ea",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VispyWidget(height=300, width=300)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "d3583d5aa327488e93d7f10347315396",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Output()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "flowws.Workflow.from_command(\"\"\"\n",
    "Pyriodic -s tP30-CrFe -n 256 --noise 1e-2\n",
    "Plato\n",
    "SmoothBOD\n",
    "flowws_freud.RDF --r-max 2\n",
    "ViewNotebook\n",
    "\"\"\".split()).run()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "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": "3.8.1"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}

start

#!/bin/bash

xvfb-run -a -s "-screen 0 1600x1200x24 +extension GLX +render +iglx" "${@}"