JSS autowig examples

basic.ipynb

{
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Wrapping a basic library\n",
    "\n",
    "We here aim at presenting the interactive wrapping workflow.\n",
    "For the sake of simplicity, we consider a basic example of *C++* library."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Preamble\n",
    "\n",
    "The source code is available in the `basic` directory."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "!pygmentize basic/src/cpp/binomial.h"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This directory already contains wrappers, we therefore need to remove them."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from path import path\n",
    "srcdir = path('basic')/'src'/'py'\n",
    "for wrapper in srcdir.walkfiles('*.cpp'):\n",
    "    wrapper.unlink()\n",
    "for wrapper in srcdir.walkfiles('*.h'):\n",
    "    wrapper.unlink()\n",
    "wrapper = srcdir/'basic'/'_basic.py'\n",
    "if wrapper.exists():\n",
    "    wrapper.unlink()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Then, we need to install and compile the *C++* library.\n",
    "This is done using available **Conda** recipes."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
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   },
   "outputs": [],
   "source": [
    "!conda build basic/conda/libbasic -c statiskit -c conda-forge\n",
    "!conda install libbasic --use-local -c statiskit -c conda-forge"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Wrapping the *C++* library\n",
    "\n",
    "Once these preliminaries done, we can proceed to the actual generation of wrappers for the **Basic** *C++* library.\n",
    "For this, we import **AutoWIG** and create an empty Abstract Semantic Graph (ASG)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import autowig\n",
    "asg = autowig.AbstractSemanticGraph()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Then, we parse headers with relevant compilation flags."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%time\n",
    "import sys\n",
    "prefix = path(sys.prefix)\n",
    "asg = autowig.parser(asg, [prefix/'include'/'basic'/'overload.h',\n",
    "                           prefix/'include'/'basic'/'binomial.h'],\n",
    "                          ['-x', 'c++', '-std=c++11',  '-I' + str((prefix/'include').abspath())],\n",
    "                          silent = True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Since most of **AutoWIG** guidelines are respected, the `default` `controller` implementation is suitable."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%time\n",
    "autowig.controller.plugin = 'default'\n",
    "asg = autowig.controller(asg)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In order to wrap the library we need to select the `boost_python_internal` `generator` implementation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%time\n",
    "autowig.generator.plugin = 'boost_python_internal'\n",
    "wrappers = autowig.generator(asg,\n",
    "                             module = 'basic/src/py/_basic.cpp',\n",
    "                             decorator = 'basic/src/py/basic/_basic.py',\n",
    "                             prefix = 'wrapper_')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The wrappers are only generated in-memory.\n",
    "It is therefore needed to write them on the disk to complete the process."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%time\n",
    "wrappers.write()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here is an example of the generated wrappers."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "!pygmentize basic/src/py/_basic.cpp"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Once the wrappers are written on disk, we need to compile and install the *Python* bindings."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "!conda build basic/conda/python-basic -c statiskit -c conda-forge\n",
    "!conda install python-basic --use-local -c statiskit -c conda-forge"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Using the *C++* library *Python* bindings\n",
    "\n",
    "Finally, we can hereafter use the *C++* library in the *Python* interpreter."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import basic\n",
    "binomial = basic.BinomialDistribution(1, .5)\n",
    "binomial"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "binomial.pmf(0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "binomial.pmf(1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "binomial.n = 0\n",
    "binomial"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "binomial.pmf(0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "binomial.set_pi(1.1)"
   ]
  }
 ],
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  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.12"
  }
 },
 "nbformat": 4,
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}

dependent.ipynb

index.ipynb

run.bat

echo OFF

echo "AutoWIG Examples"
echo "================"
echo ""
echo "This script will run the four examples presented in the"
echo "accompanying paper. Corresponding Jupyter notebooks can"
echo "also be run individually, echo using, the following"
echo "commands,"
echo ""

echo ON

jupyter nbconvert --to notebook --execute basic.ipynb --allow-errors --inplace --ExecutePreprocessor.timeout=3600 --NotebookApp.kernel_spec_manager_class='environment_kernels.EnvironmentKernelSpecManager'
jupyter nbconvert --to notebook --execute subset.ipynb --allow-errors --inplace --ExecutePreprocessor.timeout=3600 --NotebookApp.kernel_spec_manager_class='environment_kernels.EnvironmentKernelSpecManager'
jupyter nbconvert --to notebook --execute template.ipynb --allow-errors --inplace --ExecutePreprocessor.timeout=3600 --NotebookApp.kernel_spec_manager_class='environment_kernels.EnvironmentKernelSpecManager'
jupyter nbconvert --to notebook --execute dependent.ipynb --allow-errors --inplace --ExecutePreprocessor.timeout=3600 --NotebookApp.kernel_spec_manager_class='environment_kernels.EnvironmentKernelSpecManager'

echo OFF

echo "In order to visualize the Jupyter notebooks execute the "
echo "folowing command"
echo ""
echo "jupyter notebook index.ipynb"

run.sh

set +x
set +e

echo "AutoWIG Examples"
echo "================"
echo ""
echo "This script will run the four examples presented in the"
echo "accompanying paper. Corresponding Jupyter notebooks can"
echo "also be run individually, echo using, the following"
echo "commands,"
echo ""

set -x

# git clone http://github.com/StatisKit/AutoWIG.git --depth=1
# mv AutoWIG/doc/examples/basic basic
# rm -rf AutoWIG
# jupyter nbconvert --to notebook --execute basic.ipynb --allow-errors --inplace --ExecutePreprocessor.timeout=3600 --NotebookApp.kernel_spec_manager_class='environment_kernels.EnvironmentKernelSpecManager'
# git clone http://github.com/StatisKit/PyClangLite.git --depth=1
# jupyter nbconvert --to notebook --execute subset.ipynb --allow-errors --inplace --ExecutePreprocessor.timeout=3600 --NotebookApp.kernel_spec_manager_class='environment_kernels.EnvironmentKernelSpecManager'
# rm -rf PySTL
# git clone http://github.com/StatisKit/PySTL.git --depth=1
# jupyter nbconvert --to notebook --execute template.ipynb --allow-errors --inplace --ExecutePreprocessor.timeout=3600 --NotebookApp.kernel_spec_manager_class='environment_kernels.EnvironmentKernelSpecManager'
git clone http://github.com/pfernique/StructureAnalysis.git
cd StructureAnalysis
git checkout -b remove_tool origin/remove_tool
cd ..
jupyter nbconvert --to notebook --execute dependent.ipynb --allow-errors --inplace --ExecutePreprocessor.timeout=3600 --NotebookApp.kernel_spec_manager_class='environment_kernels.EnvironmentKernelSpecManager'

set -e
set +x

echo "In order to visualize the Jupyter notebooks execute the "
echo "folowing command"
echo ""
echo "jupyter notebook index.ipynb"

subset.ipynb

template.ipynb