Anaconda.ipynb

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   "source": "# Anaconda and (Other) Python Distributions\n<br />\n### DesertPy Lightning Talk, May 2015\n<br />\n### Ashley Anderson\n[@aganders3](twitter.com/aganders3) on Twitter or [email protected]"
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   "source": "## Anaconda : Python :: Debian : Linux\n\nAnaconda is a Python distribution. A Python distribution is analagous to a Linux distribution.\n\nOther distributions:\n* \"Python\" aka \"CPython\" (from python.org)\n* Enthought Canopy (formerly EPD)\n* Python(x,y)\n\n<div style=\"margin:auto\"><img src=\"images/anaconda-logo.png\" style=\"height:128px;float:left\"><img src=\"images/psf-logo.png\" style=\"height:128px;float:left\"><img src=\"images/canopy-logo.png\" style=\"height:128px;float:left\"><img src=\"images/pythonxy-logo.png\" style=\"height:128px;float:left\"></div>\n<div style=\"clear: both;\"></div>"
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   "cell_type": "markdown",
   "source": "## It's nothing new\n\nA Python *distribution* is distinct from an alternative *implementation* (e.g. PyPy). It's (likely) just a re-packaged version of CPython, with additional libraries or programs.\n"
  },
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   "metadata": {
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   "cell_type": "markdown",
   "source": "## Yes, they're selling stuff\nMany distributions are a foot-in-the-door for upselling add-ons (e.g. MKL Optimizations), training, or consulting services."
  },
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   "source": "## What's in the box?\n\nMost distributions aim to enable \"scientific\" computing. Scientists often need tools for computation, but many don't have prior development experience. Distributions provide them a ready-to-use environment.\n\nIncluded in Anaconda (~280 MB vs. ~25 MB for vanilla Python):\n* Python and the standard library\n* [\"Full SciPy Stack\"](http://www.scipy.org/stackspec.html#stackspec) aka the PyData Stack\n    * NumPy\n    * SciPy\n    * Matplotlib\n    * IPython\n    * Pandas\n* [SciKit-*, tornado, flask, PyQT, spyder, Cython, Numba, ...](http://docs.continuum.io/anaconda/pkg-docs.html)\n* `conda`"
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   "metadata": {
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   "cell_type": "markdown",
   "source": "##[`conda`](http://conda.pydata.org) : a package and environment manager\n* Install/manage binary packages - not just Python libs\n* Implemented in Python, BSD license\n* Create your own packages\n* Manage dependencies in environments\n* Works alongside `pip`\n* Comes with Anaconda, or standalone as Miniconda (~20 MB)"
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   "cell_type": "markdown",
   "source": "[<img src=\"images/xkcd-standards.png\" style=\"width:90%;margin:auto\" title=\"Fortunately, the charging one has been solved now that we've all standardized on mini-USB. Or is it micro-USB? Shit.\">](https://xkcd.com/927/)"
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   "cell_type": "code",
   "source": "!conda",
   "execution_count": 2,
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "usage: conda [-h] [-V] [--debug] command ...\n\nconda is a tool for managing and deploying applications, environments and packages.\n\nOptions:\n\npositional arguments:\n  command\n    info         Display information about current conda install.\n    help         Displays a list of available conda commands and their help strings.\n    list         List linked packages in a conda environment.\n    search       Search for packages and display their information. The input is a regular expression. To perform a search\n                 with a search string that starts with a -, separate the search from the options with --, like 'conda search\n                 -- -h'. A * in the results means that package is installed in the current environment. A . means that\n                 package is not installed but is cached in the pkgs directory.\n    create       Create a new conda environment from a list of specified packages.\n    install      Install a list of packages into a specified conda environment.\n    update       Update conda packages to the current version.\n    remove       Remove a list of packages from a specified conda environment.\n    uninstall    Alias for conda remove. See conda remove --help.\n    run          Launches an application installed with Conda.\n    config       Modify configuration values in .condarc. This is modeled after the git config command. Writes to the user\n                 .condarc file (/Users/ash/.condarc) by default.\n    init         Initialize conda into a regular environment (when conda was installed as a Python package, e.g. using pip).\n                 (DEPRECATED)\n    clean        Remove unused packages and caches.\n    package      Low-level conda package utility. (EXPERIMENTAL)\n    bundle       Create or extract a \"bundle package\" (EXPERIMENTAL)\n\noptional arguments:\n  -h, --help     Show this help message and exit.\n  -V, --version  Show the conda version number and exit.\n  --debug        Show debug output.\n\nexternal commands:\n    build        tool for building conda packages\n    convert      various tools to convert conda packages\n    develop      Install a Python package in 'development mode'. This works by creating a conda.pth file in site-packages, and using setup.py\n                 to determine any entry-points to install.\n    env          positional arguments:\n                   {create,export,list,remove,update}\n                     create              Create an environment based on an environment file\n                     export              Export a given environment\n                     list                List the Conda environments\n                     remove              Remove an environment\n                     update              Update the current environment based on environment file\n    index        Update package index metadata files in given directories\n    metapackage  tool for building conda metapackages. A metapackage is a package with no files, only metadata\n    pipbuild     tool for building conda packages just using pip install\n    skeleton     create skeleton recipes for packages from hosting sites\n"
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    "collapsed": false,
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   "cell_type": "code",
   "source": "!conda search pyqt",
   "execution_count": 1,
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "Fetching package metadata: ....\npyqt                         4.10.4                   py34_0  defaults        \n                             4.10.4                   py33_0  defaults        \n                          *  4.10.4                   py27_0  defaults        \n                             4.10.4                   py26_0  defaults        \n                             4.11.3                   py34_0  defaults        \n                             4.11.3                   py33_0  defaults        \n                             4.11.3                   py27_0  defaults        \n                             4.11.3                   py26_0  defaults        \n"
    }
   ]
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   "cell_type": "markdown",
   "source": "<sup>The `*` indicates the currently installed version</sup>"
  },
  {
   "metadata": {
    "collapsed": false,
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   "cell_type": "code",
   "source": "!conda list",
   "execution_count": 11,
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "# packages in environment at /opt/gpi/local/anaconda:\n#\n_license                  1.1                      py27_0  \nabstract-rendering        0.5.1                np19py27_0  \nanaconda                  2.1.0                np19py27_0  \nargcomplete               0.8.1                    py27_0  \nastropy                   0.4.2                np19py27_0  \natom                      0.3.9                    py27_0  \nautopep8                  1.0.4                     <pip>\nbackports.ssl-match-hostname 3.4.0.2                   <pip>\nbeautiful-soup            4.3.2                    py27_0  \nbeautifulsoup4            4.3.2                     <pip>\nbinstar                   0.7.1                    py27_0  \nbitarray                  0.8.1                    py27_0  \nblaze                     0.6.3                np19py27_0  \nblz                       0.6.2                np19py27_0  \nbokeh                     0.8.2                np19py27_0  \nboto                      2.32.1                   py27_0  \ncasuarius                 1.1                      py27_0  \ncdecimal                  2.3                      py27_0  \ncffi                      0.8.6                    py27_0  \nchaco                     4.4.1                np19py27_0  \ncolorama                  0.3.3                    py27_0  \nconda                     3.12.0                   py27_0  \nconda-build               1.8.2                    py27_0  \nconda-env                 2.1.4                    py27_0  \nconfigobj                 5.0.6                    py27_0  \ncryptography              0.5.4                    py27_0  \ncurl                      7.38.0                        0  \ncython                    0.21                     py27_0  \ncytoolz                   0.7.0                    py27_0  \ndatashape                 0.3.0                np19py27_1  \ndateutil                  2.1                      py27_2  \ndecorator                 3.4.0                    py27_0  \ndocutils                  0.12                     py27_0  \ndynd-python               0.6.5                np19py27_0  \nenable                    4.3.0                np19py27_2  \nenaml                     0.9.8                    py27_0  \nflask                     0.10.1                   py27_1  \nfreetype                  2.4.10                        1  \nfuture                    0.13.1                   py27_0  \nfutures                   2.1.6                    py27_0  \ngevent                    1.0.1                    py27_0  \ngevent-websocket          0.9.3                    py27_0  \ngreenlet                  0.4.5                    py27_0  \ngrin                      1.2.1                    py27_1  \nh5py                      2.3.1                np19py27_0  \nhdf5                      1.8.13                        0  \nipython                   3.1.0                    py27_0  \nipython-notebook          3.1.0                    py27_1  \nipython-qtconsole         2.2.0                    py27_0  \nitsdangerous              0.24                     py27_0  \njdcal                     1.0                      py27_0  \njinja2                    2.7.3                    py27_1  \njpeg                      8d                            1  \njsonschema                2.4.0                    py27_0  \nkiwisolver                0.1.3                    py27_0  \nlabjackpython-4-24        2014                      <pip>\nlauncher                  1.0.0                         1  \nlcms                      1.19                          0  \nlibdynd                   0.6.5                         0  \nlibpng                    1.5.13                        1  \nlibsodium                 0.4.5                         0  \nlibtiff                   4.0.2                         1  \nlibxml2                   2.9.0                         1  \nlibxslt                   1.1.28                        2  \nllvm                      3.3                           0  \nllvmpy                    0.12.7                   py27_0  \nlxml                      3.4.0                    py27_0  \nmarkupsafe                0.23                     py27_0  \nmatplotlib                1.4.0                np19py27_0  \nmistune                   0.5.1                    py27_1  \nmock                      1.0.1                    py27_0  \nmultipledispatch          0.4.7                    py27_0  \nnetworkx                  1.9.1                    py27_0  \nnibabel                   2.0.0                     <pip>\nnipype                    0.10.0                    <pip>\nnltk                      3.0.0                np19py27_0  \nnode-webkit               0.10.1                        0  \nnose                      1.3.4                    py27_0  \nnumba                     0.14.0               np19py27_0  \nnumexpr                   2.3.1                np19py27_0  \nnumpy                     1.9.2                    py27_0  \nopencv                    2.4.8                np17py27_2  \nopenpyxl                  1.8.5                    py27_0  \nopenssl                   1.0.1k                        1  \npandas                    0.16.0               np19py27_1  \npatsy                     0.3.0                np19py27_0  \npep8                      1.5.7                    py27_0  \npil                       1.1.7                    py27_1  \npip                       6.1.1                    py27_0  \nply                       3.4                      py27_0  \npsutil                    2.1.1                    py27_0  \nptyprocess                0.4                      py27_0  \npy                        1.4.25                   py27_0  \npyaudio                   0.2.7                    py27_0  \npycosat                   0.6.1                    py27_0  \npycparser                 2.10                     py27_0  \npycrypto                  2.6.1                    py27_0  \npycurl                    7.19.5                   py27_1  \npyface                    4.4.0                    py27_0  \npyflakes                  0.8.1                    py27_0  \npygments                  2.0.2                    py27_0  \npyopengl                  3.0.2                    py27_0  \npyopenssl                 0.14                     py27_0  \npyparsing                 2.0.1                    py27_0  \npyqt                      4.10.4                   py27_0  \npytables                  3.1.1                np19py27_0  \npytest                    2.6.3                    py27_0  \npython                    2.7.9                         1  \npython-dateutil           2.4.2                    py27_0  \npython.app                1.2                      py27_3  \npytz                      2015.2                   py27_0  \npyyaml                    3.11                     py27_0  \npyzmq                     14.6.0                   py27_0  \nqimage2ndarray            1.4                       <pip>\nqt                        4.8.5                         3  \nreadline                  6.2                           2  \nredis                     2.6.9                         0  \nredis-py                  2.9.1                    py27_0  \nrequests                  2.7.0                    py27_0  \nrope                      0.9.4                    py27_1  \nrunipy                    0.1.1                    py27_0  \nscikit-image              0.10.1               np19py27_0  \nscikit-learn              0.15.2               np19py27_0  \nscipy                     0.14.0               np19py27_0  \nsetuptools                15.2                     py27_0  \nsimpleitk                 0.8.1                    py27_0  \nsip                       4.15.5                   py27_0  \nsix                       1.9.0                    py27_0  \nsockjs-tornado            1.0.1                    py27_0  \nsphinx                    1.2.3                    py27_0  \nspyder                    2.3.1                    py27_1  \nspyder-app                2.3.1                    py27_0  \nsqlalchemy                0.9.7                    py27_0  \nsqlite                    3.8.4.1                       1  \nssl_match_hostname        3.4.0.2                  py27_0  \nstatsmodels               0.5.0                np19py27_2  \nsympy                     0.7.5                    py27_0  \ntables                    3.1.1                     <pip>\nterminado                 0.5                      py27_0  \ntk                        8.5.18                        0  \ntoolz                     0.7.0                    py27_0  \ntornado                   4.1                      py27_0  \ntraits                    4.4.0                    py27_0  \ntraitsui                  4.4.0                    py27_0  \nujson                     1.33                     py27_0  \nunicodecsv                0.9.4                    py27_0  \nwerkzeug                  0.10.4                   py27_0  \nwxpython                  3.0                      py27_0  \nwxpython-common           3.0.0.0                   <pip>\nxlrd                      0.9.3                    py27_0  \nxlsxwriter                0.5.7                    py27_0  \nxlwt                      0.7.5                    py27_0  \nyaml                      0.1.4                         1  \nzeromq                    4.0.5                         0  \nzlib                      1.2.8                         0  \n"
    }
   ]
  },
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     "slide_type": "slide"
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   },
   "cell_type": "markdown",
   "source": "## Conda Environments"
  },
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    "collapsed": false,
    "slideshow": {
     "slide_type": "subslide"
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    "trusted": true
   },
   "cell_type": "code",
   "source": "!source activate tempura",
   "execution_count": 40,
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "discarding /opt/gpi/local/anaconda/bin from PATH\nprepending /opt/gpi/local/anaconda/envs/tempura/bin to PATH\n"
    }
   ]
  },
  {
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "cell_type": "markdown",
   "source": "A `conda` environment is just a directory. Activating it adds it to your `PATH`.\n<br />\nHere's what's in it:"
  },
  {
   "metadata": {
    "collapsed": false,
    "slideshow": {
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    "trusted": true
   },
   "cell_type": "code",
   "source": "!ls /opt/gpi/local/anaconda/envs/tempura",
   "execution_count": 36,
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "\u001b[1m\u001b[36mExamples\u001b[m\u001b[m   \u001b[1m\u001b[36mbin\u001b[m\u001b[m        \u001b[1m\u001b[36mconda-meta\u001b[m\u001b[m \u001b[1m\u001b[36minclude\u001b[m\u001b[m    \u001b[1m\u001b[36mlib\u001b[m\u001b[m        \u001b[1m\u001b[36mpython.app\u001b[m\u001b[m \u001b[1m\u001b[36mshare\u001b[m\u001b[m      \u001b[1m\u001b[36mssl\u001b[m\u001b[m\r\n"
    }
   ]
  },
  {
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "cell_type": "markdown",
   "source": "Shared packages are hardlinked into each environment to save space, etc."
  },
  {
   "metadata": {
    "collapsed": false,
    "slideshow": {
     "slide_type": "fragment"
    },
    "trusted": true
   },
   "cell_type": "code",
   "source": "!ls /opt/gpi/local/anaconda/envs/tempura/lib/python2.7/site-packages",
   "execution_count": 37,
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "Flask-0.10.1-py2.7.egg-info                         numpy-1.9.2-py2.7.egg-info\r\n\u001b[1m\u001b[36mIPython\u001b[m\u001b[m                                             \u001b[1m\u001b[36mpandas\u001b[m\u001b[m\r\nJinja2-2.7.3-py2.7.egg-info                         pandas-0.16.0-py2.7-macosx-10.5-x86_64.egg-info\r\n\u001b[1m\u001b[36mLabJackPython-4_24_2014-py2.7.egg-info\u001b[m\u001b[m              \u001b[1m\u001b[36mpip\u001b[m\u001b[m\r\nLabJackPython.py                                    pip-6.1.1-py2.7.egg-info\r\nLabJackPython.pyc                                   \u001b[1m\u001b[36mpygments\u001b[m\u001b[m\r\nMarkupSafe-0.23-py2.7-macosx-10.5-x86_64.egg-info   \u001b[1m\u001b[36mpython_dateutil-2.4.2-py2.7.egg-info\u001b[m\u001b[m\r\nModbus.py                                           \u001b[1m\u001b[36mpytz\u001b[m\u001b[m\r\nModbus.pyc                                          pytz-2015.2-py2.7.egg-info\r\nPyYAML-3.11-py2.7.egg-info                          pyzmq-14.6.0-py2.7.egg-info\r\nPygments-2.0.2-py2.7.egg-info                       \u001b[1m\u001b[36mrequests\u001b[m\u001b[m\r\nREADME                                              requests-2.7.0-py2.7.egg-info\r\nWerkzeug-0.10.4-py2.7.egg-info                      setuptools-15.2-py2.7.egg\r\n_yaml.so\u001b[m\u001b[m                                            setuptools.pth\r\n\u001b[1m\u001b[36mbackports\u001b[m\u001b[m                                           six-1.9.0-py2.7.egg-info\r\nbackports.ssl_match_hostname-3.4.0.2-py2.7.egg-info six.py\r\n\u001b[1m\u001b[36mbokeh\u001b[m\u001b[m                                               six.pyc\r\nbokeh-0.8.2-py2.7.egg-info                          skymote.py\r\n\u001b[1m\u001b[36mcolorama\u001b[m\u001b[m                                            skymote.pyc\r\ncolorama-0.3.3-py2.7.egg-info                       \u001b[1m\u001b[36mtornado\u001b[m\u001b[m\r\n\u001b[1m\u001b[36mdateutil\u001b[m\u001b[m                                            tornado-4.1-py2.7.egg-info\r\n\u001b[1m\u001b[36mflask\u001b[m\u001b[m                                               u12.py\r\n\u001b[1m\u001b[36mgevent\u001b[m\u001b[m                                              u12.pyc\r\ngevent-1.0.1-py2.7.egg-info                         u3.py\r\ngevent_websocket-0.9.3-py2.7.egg-info               u3.pyc\r\n\u001b[1m\u001b[36mgeventwebsocket\u001b[m\u001b[m                                     u6.py\r\ngreenlet-0.4.6-py2.7.egg-info                       u6.pyc\r\ngreenlet.so\u001b[m\u001b[m                                         ue9.py\r\nipython-3.1.0-py2.7.egg-info                        ue9.pyc\r\nitsdangerous-0.24-py2.7.egg-info                    ujson-1.33-py2.7.egg-info\r\nitsdangerous.py                                     ujson.so\u001b[m\u001b[m\r\nitsdangerous.pyc                                    \u001b[1m\u001b[36mwerkzeug\u001b[m\u001b[m\r\n\u001b[1m\u001b[36mjinja2\u001b[m\u001b[m                                              \u001b[1m\u001b[36myaml\u001b[m\u001b[m\r\n\u001b[1m\u001b[36mmarkupsafe\u001b[m\u001b[m                                          \u001b[1m\u001b[36mzmq\u001b[m\u001b[m\r\n\u001b[1m\u001b[36mnumpy\u001b[m\u001b[m\r\n"
    }
   ]
  },
  {
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
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   },
   "cell_type": "markdown",
   "source": "What executables are added in the `bin` directory?"
  },
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    "collapsed": false,
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     "slide_type": "fragment"
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    "trusted": true
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   "cell_type": "code",
   "source": "!ls /opt/gpi/local/anaconda/envs/tempura/bin",
   "execution_count": 38,
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "2to3\u001b[m\u001b[m                easy_install\u001b[m\u001b[m        ipcontroller2\u001b[m\u001b[m       ipython2\u001b[m\u001b[m            \u001b[32mpython\u001b[m\u001b[m              pythonw\u001b[m\u001b[m\r\n\u001b[32mactivate\u001b[m\u001b[m            \u001b[32measy_install-2.7\u001b[m\u001b[m    ipengine\u001b[m\u001b[m            irunner\u001b[m\u001b[m             \u001b[32mpython-config\u001b[m\u001b[m       smtpd.py\u001b[m\u001b[m\r\nbokeh-server\u001b[m\u001b[m        f2py\u001b[m\u001b[m                ipengine2\u001b[m\u001b[m           openssl\u001b[m\u001b[m             python.app\u001b[m\u001b[m          sqlite3\u001b[m\u001b[m\r\nc_rehash\u001b[m\u001b[m            idle\u001b[m\u001b[m                iplogger\u001b[m\u001b[m            pip\u001b[m\u001b[m                 \u001b[32mpython2\u001b[m\u001b[m             tclsh8.5\u001b[m\u001b[m\r\n\u001b[32mconda\u001b[m\u001b[m               ipcluster\u001b[m\u001b[m           iptest\u001b[m\u001b[m              pycolor\u001b[m\u001b[m             \u001b[32mpython2-config\u001b[m\u001b[m      websocket_worker.py\u001b[m\u001b[m\r\ncurve_keygen\u001b[m\u001b[m        ipcluster2\u001b[m\u001b[m          iptest2\u001b[m\u001b[m             pydoc\u001b[m\u001b[m               python2.7\u001b[m\u001b[m           wish8.5\u001b[m\u001b[m\r\n\u001b[32mdeactivate\u001b[m\u001b[m          ipcontroller\u001b[m\u001b[m        ipython\u001b[m\u001b[m             pygmentize\u001b[m\u001b[m          python2.7-config\u001b[m\u001b[m\r\n"
    }
   ]
  },
  {
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "cell_type": "markdown",
   "source": "Oh hey, `pip` is in there!\n<br />\nUse `pip install` and the package will be installed in your current `conda` environment.\n<br />\n`conda` recognizes `pip` installed packages, but can't manage or move them."
  },
  {
   "metadata": {
    "collapsed": false,
    "slideshow": {
     "slide_type": "fragment"
    },
    "trusted": true
   },
   "cell_type": "code",
   "source": "!conda list labjack",
   "execution_count": 39,
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "# packages in environment at /opt/gpi/local/anaconda:\n#\nlabjackpython-4-24        2014                      <pip>\n"
    }
   ]
  },
  {
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "cell_type": "markdown",
   "source": "## Additional Links For the Curious or Enthusiastic\n\n* [Continuum Analytics](http://continuum.io) - The people who make Anaconda\n* [Binstar](http://www.binstar.com) - Public (free) and private hosting for `conda` packages\n* [Alternative Implementations and Distributions](https://www.python.org/download/alternatives/) - Listed on Python.org\n"
  }
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