condaVenv.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# How to setup conda virtual env from notebook.\n",
    "\n",
    "Its best practice to always work from isolated virtual environments with python. This notebook demonstrates how to create such an environment for use with jupyter lab.\n",
    "\n",
    "### Steps:\n",
    "1. Create your environment, I named this one here after myself. \n",
    "1. Install the ipykernel package into your environment.\n",
    "1. Activate your environment and install the kernel for jupyter to pick up. \n",
    "1. Install a package into that environment, this is how you could install all the dependencies you need. \n",
    "\n",
    "That is it! Give Jupyter a few minutes to pick up the new kernel, then you can hit the plus sign, create notebook, and choose the new kernel that is pointing to your virtual env. \n",
    "\n",
    "![](http://dpo0hxkzjoxim.cloudfront.net/venv.gif) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Collecting package metadata: done\n",
      "Solving environment: done\n",
      "\n",
      "## Package Plan ##\n",
      "\n",
      "  environment location: /opt/cortex-installs/miniconda/envs/benchmark_syndi\n",
      "\n",
      "  added / updated specs:\n",
      "    - python=3.6\n",
      "\n",
      "\n",
      "The following NEW packages will be INSTALLED:\n",
      "\n",
      "  _libgcc_mutex      conda/linux-64::_libgcc_mutex-0.1-conda_forge\n",
      "  _openmp_mutex      conda/linux-64::_openmp_mutex-4.5-0_gnu\n",
      "  ca-certificates    conda/linux-64::ca-certificates-2021.10.26-h06a4308_2\n",
      "  ld_impl_linux-64   conda/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2\n",
      "  libffi             conda/linux-64::libffi-3.4.2-h7f98852_5\n",
      "  libgcc-ng          conda/linux-64::libgcc-ng-11.2.0-h1d223b6_11\n",
      "  libgomp            conda/linux-64::libgomp-11.2.0-h1d223b6_11\n",
      "  libnsl             conda/linux-64::libnsl-2.0.0-h7f98852_0\n",
      "  libstdcxx-ng       conda/linux-64::libstdcxx-ng-11.2.0-he4da1e4_11\n",
      "  libzlib            conda/linux-64::libzlib-1.2.11-h36c2ea0_1013\n",
      "  ncurses            conda/linux-64::ncurses-6.2-h58526e2_4\n",
      "  openssl            conda/linux-64::openssl-1.1.1m-h7f8727e_0\n",
      "  pip                conda/noarch::pip-21.3.1-pyhd8ed1ab_0\n",
      "  python             conda/linux-64::python-3.6.15-hb7a2778_0_cpython\n",
      "  python_abi         conda/linux-64::python_abi-3.6-2_cp36m\n",
      "  readline           conda/linux-64::readline-8.1-h46c0cb4_0\n",
      "  setuptools         conda/linux-64::setuptools-58.0.4-py36h5fab9bb_2\n",
      "  sqlite             conda/linux-64::sqlite-3.37.0-hc218d9a_0\n",
      "  tk                 conda/linux-64::tk-8.6.11-h27826a3_1\n",
      "  wheel              conda/noarch::wheel-0.37.1-pyhd3eb1b0_0\n",
      "  xz                 conda/linux-64::xz-5.2.5-h516909a_1\n",
      "  zlib               conda/linux-64::zlib-1.2.11-h36c2ea0_1013\n",
      "\n",
      "\n",
      "Preparing transaction: done\n",
      "Verifying transaction: done\n",
      "Executing transaction: done\n",
      "#\n",
      "# To activate this environment, use:\n",
      "# > conda activate benchmark_syndi\n",
      "#\n",
      "# To deactivate an active environment, use:\n",
      "# > conda deactivate\n",
      "#\n",
      "\n",
      "\n",
      "Note: you may need to restart the kernel to use updated packages.\n"
     ]
    }
   ],
   "source": [
    "conda create -n benchmark_syndi python=3.6 -y"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "rm -fr build/\n",
      "rm -fr dist/\n",
      "rm -fr .eggs/\n",
      "find . -name '*.egg-info' -exec rm -fr {} +\n",
      "find . -name '*.egg' -exec rm -f {} +\n",
      "find . -name '*.pyc' -exec rm -f {} +\n",
      "find . -name '*.pyo' -exec rm -f {} +\n",
      "find . -name '*~' -exec rm -f {} +\n",
      "find . -name '__pycache__' -exec rm -fr {} +\n",
      "pip install -e .[dev]\n",
      "Looking in indexes: https://cran-pull:****@lmdatalab.jfrog.io/artifactory/api/pypi/pypi/simple\n",
      "Obtaining file:///mnt/LM3F245CF8CD4A/benchmark/syndi\n",
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      "  Using cached https://lmdatalab.jfrog.io/artifactory/api/pypi/pypi/packages/packages/a8/07/946d5a9431bae05a776a59746ec385fbb79b526738d25e4202d3e0bbf7f4/argon2_cffi-21.3.0-py3-none-any.whl (14 kB)\n",
      "Collecting terminado>=0.8.3\n",
      "  Using cached https://lmdatalab.jfrog.io/artifactory/api/pypi/pypi/packages/packages/cb/17/b1162b39786c44e14d30ee557fbf41276c4a966dab01106c15fb70f5c27a/terminado-0.12.1-py3-none-any.whl (15 kB)\n",
      "Collecting PyWavelets\n",
      "  Downloading https://lmdatalab.jfrog.io/artifactory/api/pypi/pypi/packages/packages/59/bb/d2b85265ec9fa3c1922210c9393d4cdf7075cc87cce6fe671d7455f80fbc/PyWavelets-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (4.4 MB)\n",
      "     |████████████████████████████████| 4.4 MB 26.2 MB/s            \n",
      "\u001b[?25hCollecting pycparser\n",
      "  Using cached https://lmdatalab.jfrog.io/artifactory/api/pypi/pypi/packages/packages/62/d5/5f610ebe421e85889f2e55e33b7f9a6795bd982198517d912eb1c76e1a53/pycparser-2.21-py2.py3-none-any.whl (118 kB)\n",
      "Collecting argon2-cffi-bindings\n",
      "  Using cached https://lmdatalab.jfrog.io/artifactory/api/pypi/pypi/packages/packages/ec/f7/378254e6dd7ae6f31fe40c8649eea7d4832a42243acaf0f1fff9083b2bed/argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (86 kB)\n",
      "Building wheels for collected packages: aiobotocore, idna-ssl\n",
      "  Building wheel for aiobotocore (setup.py) ... \u001b[?25ldone\n",
      "\u001b[?25h  Created wheel for aiobotocore: filename=aiobotocore-2.1.0-py3-none-any.whl size=52068 sha256=9349b52e873073c17ccb255da988e5cc33abd39e1b078c1481ce98162db66ae6\n",
      "  Stored in directory: /mnt/LM3F245CF8CD4A/.cache/pip/wheels/c5/3e/2c/79aa5ee215b59cf94ac91261006577d58a6805a02589cddf27\n",
      "  Building wheel for idna-ssl (setup.py) ... \u001b[?25ldone\n",
      "\u001b[?25h  Created wheel for idna-ssl: filename=idna_ssl-1.1.0-py3-none-any.whl size=3178 sha256=148413ad30ed827873df44d3de3987cfb6ba0418a1bfbdcf8249795229c8ff77\n",
      "  Stored in directory: /mnt/LM3F245CF8CD4A/.cache/pip/wheels/44/33/d6/6d70b848da76de0dfb47cf684f64943f3b7dabfdaf6211d651\n",
      "Successfully built aiobotocore idna-ssl\n",
      "Installing collected packages: zipp, typing-extensions, six, ipython-genutils, decorator, traitlets, pyrsistent, importlib-metadata, attrs, wcwidth, tornado, pyzmq, python-dateutil, pyparsing, pycparser, ptyprocess, parso, nest-asyncio, jupyter-core, jsonschema, entrypoints, webencodings, pygments, prompt-toolkit, pickleshare, pexpect, packaging, nbformat, MarkupSafe, jupyter-client, jedi, cffi, backcall, async-generator, testpath, pandocfilters, nbclient, mistune, jupyterlab-pygments, jinja2, ipython, defusedxml, dataclasses, bleach, argon2-cffi-bindings, terminado, Send2Trash, pytz, prometheus-client, pillow, numpy, nbconvert, kiwisolver, ipykernel, cycler, argon2-cffi, Werkzeug, urllib3, threadpoolctl, tangled-up-in-unicode, smmap, scipy, PyWavelets, patsy, pandas, notebook, networkx, murmurhash, multimethod, multidict, matplotlib, llvmlite, joblib, itsdangerous, idna, greenlet, frozenlist, cymem, click, charset-normalizer, certifi, yarl, widgetsnbextension, websocket-client, wasabi, visions, tqdm, torch, tenacity, tabulate, statsmodels, srsly, sqlalchemy, seaborn, scikit-learn, requests, regex, python-editor, psutil, preshed, plac, numba, Mako, jupyterlab-widgets, jmespath, imagehash, idna-ssl, gitdb, Flask, catalogue, blis, asynctest, async-timeout, aiosignal, wrapt, torchvision, thinc, text-unidecode, sqlparse, smart-open, sktime, rdt, querystring-parser, pyyaml, pynndescent, pydantic, protobuf, prometheus-flask-exporter, plotly, phik, numexpr, nltk, missingno, jeepney, ipywidgets, htmlmin, gunicorn, gitpython, future, funcy, docker, databricks-cli, cryptography, copulas, colorlover, cloudpickle, botocore, alembic, aioitertools, aiohttp, yellowbrick, wordcloud, umap-learn, tomli, toml, textblob, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, spacy, soupsieve, snowballstemmer, SecretStorage, sdmetrics, scikit-plot, pyod, pyLDAvis, py, pluggy, platformdirs, pandas-profiling, mlxtend, mlflow, markdown, lightgbm, kmodes, iniconfig, importlib-resources, imbalanced-learn, imagesize, graphviz, gensim, fsspec, filelock, Faker, docutils, distlib, deepecho, cufflinks, ctgan, coverage, cached-property, Boruta, babel, alabaster, aiobotocore, virtualenv, Sphinx, sdv, s3fs, rfc3986, requests-toolbelt, readme-renderer, pyts, pytest, pyflakes, pycodestyle, pycaret, pkginfo, mccabe, markdown-rundoc, keyring, h5py, colorama, bump2version, beautifulsoup4, watchdog, twine, tox, syndi, rundoc, pytest-cov, pydocstyle, pydata-sphinx-theme, nbsphinx, m2r2, isort, flake8, bumpversion, autopep8, autoflake, autodocsumm\n",
      "  Running setup.py develop for syndi\n",
      "Successfully installed Boruta-0.3 Faker-4.14.2 Flask-2.0.2 Mako-1.1.6 MarkupSafe-2.0.1 PyWavelets-1.1.1 SecretStorage-3.3.1 Send2Trash-1.8.0 Sphinx-3.2.1 Werkzeug-2.0.2 aiobotocore-2.1.0 aiohttp-3.8.1 aioitertools-0.8.0 aiosignal-1.2.0 alabaster-0.7.12 alembic-1.4.1 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 async-generator-1.10 async-timeout-4.0.2 asynctest-0.13.0 attrs-21.4.0 autodocsumm-0.2.7 autoflake-1.4 autopep8-1.6.0 babel-2.9.1 backcall-0.2.0 beautifulsoup4-4.10.0 bleach-4.1.0 blis-0.7.5 botocore-1.23.24 bump2version-1.0.1 bumpversion-0.6.0 cached-property-1.5.2 catalogue-1.0.0 certifi-2021.10.8 cffi-1.15.0 charset-normalizer-2.0.10 click-7.1.2 cloudpickle-2.0.0 colorama-0.4.4 colorlover-0.3.0 copulas-0.5.1 coverage-6.2 cryptography-36.0.1 ctgan-0.4.3 cufflinks-0.17.3 cycler-0.11.0 cymem-2.0.6 databricks-cli-0.16.2 dataclasses-0.8 decorator-4.4.2 deepecho-0.2.1 defusedxml-0.7.1 distlib-0.3.4 docker-5.0.3 docutils-0.18.1 entrypoints-0.3 filelock-3.4.1 flake8-4.0.1 frozenlist-1.2.0 fsspec-2022.1.0 funcy-1.17 future-0.18.2 gensim-3.8.3 gitdb-4.0.9 gitpython-3.1.18 graphviz-0.19.1 greenlet-1.1.2 gunicorn-20.1.0 h5py-3.1.0 htmlmin-0.1.12 idna-3.3 idna-ssl-1.1.0 imagehash-4.2.1 imagesize-1.3.0 imbalanced-learn-0.7.0 importlib-metadata-4.2.0 importlib-resources-5.4.0 iniconfig-1.1.1 ipykernel-5.5.6 ipython-7.4.0 ipython-genutils-0.2.0 ipywidgets-7.6.5 isort-5.10.1 itsdangerous-2.0.1 jedi-0.18.1 jeepney-0.7.1 jinja2-3.0.3 jmespath-0.10.0 joblib-1.0.1 jsonschema-3.2.0 jupyter-client-7.1.1 jupyter-core-4.9.1 jupyterlab-pygments-0.1.2 jupyterlab-widgets-1.0.2 keyring-23.4.1 kiwisolver-1.3.1 kmodes-0.11.1 lightgbm-3.3.2 llvmlite-0.36.0 m2r2-0.2.8 markdown-2.6.11 markdown-rundoc-0.3.1 matplotlib-3.3.4 mccabe-0.6.1 missingno-0.5.0 mistune-0.8.4 mlflow-1.22.0 mlxtend-0.19.0 multidict-5.2.0 multimethod-1.5 murmurhash-1.0.6 nbclient-0.5.9 nbconvert-6.0.7 nbformat-5.1.3 nbsphinx-0.6.1 nest-asyncio-1.5.4 networkx-2.5.1 nltk-3.6.7 notebook-6.4.7 numba-0.53.1 numexpr-2.8.1 numpy-1.19.5 packaging-21.3 pandas-1.1.4 pandas-profiling-3.1.0 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.2 pexpect-4.8.0 phik-0.12.0 pickleshare-0.7.5 pillow-8.4.0 pkginfo-1.8.2 plac-1.1.3 platformdirs-2.4.0 plotly-5.5.0 pluggy-1.0.0 preshed-3.0.6 prometheus-client-0.12.0 prometheus-flask-exporter-0.18.7 prompt-toolkit-2.0.10 protobuf-3.19.3 psutil-5.9.0 ptyprocess-0.7.0 py-1.11.0 pyLDAvis-3.2.2 pycaret-2.3.6 pycodestyle-2.8.0 pycparser-2.21 pydantic-1.9.0 pydata-sphinx-theme-0.7.2 pydocstyle-3.0.0 pyflakes-2.4.0 pygments-2.11.2 pynndescent-0.5.5 pyod-0.9.7 pyparsing-3.0.6 pyrsistent-0.18.0 pytest-6.2.5 pytest-cov-3.0.0 python-dateutil-2.8.2 python-editor-1.0.4 pyts-0.12.0 pytz-2021.3 pyyaml-5.4.1 pyzmq-22.3.0 querystring-parser-1.2.4 rdt-0.5.3 readme-renderer-32.0 regex-2021.11.10 requests-2.27.1 requests-toolbelt-0.9.1 rfc3986-1.5.0 rundoc-0.4.5 s3fs-2022.1.0 scikit-learn-0.23.2 scikit-plot-0.3.7 scipy-1.5.4 sdmetrics-0.3.2 sdv-0.12.1 seaborn-0.11.2 six-1.16.0 sktime-0.5.3 smart-open-5.2.1 smmap-5.0.0 snowballstemmer-2.2.0 soupsieve-2.3.1 spacy-2.3.7 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 sqlalchemy-1.4.29 sqlparse-0.4.2 srsly-1.0.5 statsmodels-0.12.2 syndi-0.1.0.dev0 tabulate-0.8.9 tangled-up-in-unicode-0.1.0 tenacity-8.0.1 terminado-0.12.1 testpath-0.5.0 text-unidecode-1.3 textblob-0.17.1 thinc-7.4.5 threadpoolctl-3.0.0 toml-0.10.2 tomli-1.2.3 torch-1.7.1 torchvision-0.8.2 tornado-6.1 tox-3.24.5 tqdm-4.62.3 traitlets-4.3.3 twine-3.7.1 typing-extensions-4.0.1 umap-learn-0.5.2 urllib3-1.26.8 virtualenv-20.13.0 visions-0.7.4 wasabi-0.9.0 watchdog-2.1.6 wcwidth-0.2.5 webencodings-0.5.1 websocket-client-1.2.3 widgetsnbextension-3.5.2 wordcloud-1.8.1 wrapt-1.13.3 yarl-1.7.2 yellowbrick-1.3.post1 zipp-3.6.0\n",
      "Installed kernelspec benchmark_syndi in /mnt/LM3F245CF8CD4A/.local/share/jupyter/kernels/benchmark_syndi\n"
     ]
    }
   ],
   "source": [
    "!source /opt/cortex-installs/miniconda/bin/activate benchmark_syndi && make install-develop && ipython kernel install --user --name=benchmark_syndi"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Collecting package metadata: done\n",
      "Solving environment: done\n",
      "\n",
      "## Package Plan ##\n",
      "\n",
      "  environment location: /opt/cortex-installs/miniconda/envs/benchmark_syndi\n",
      "\n",
      "  added / updated specs:\n",
      "    - s3fs\n",
      "\n",
      "\n",
      "The following NEW packages will be INSTALLED:\n",
      "\n",
      "  aiobotocore        conda/noarch::aiobotocore-2.1.0-pyhd8ed1ab_0\n",
      "  aiohttp            conda/linux-64::aiohttp-3.7.4.post0-py36h7f8727e_2\n",
      "  aioitertools       conda/noarch::aioitertools-0.8.0-pyhd8ed1ab_0\n",
      "  async-timeout      conda/noarch::async-timeout-3.0.1-py_1000\n",
      "  attrs              conda/noarch::attrs-21.4.0-pyhd8ed1ab_0\n",
      "  botocore           conda/noarch::botocore-1.23.24-pyhd8ed1ab_0\n",
      "  brotlipy           conda/linux-64::brotlipy-0.7.0-py36h27cfd23_1003\n",
      "  certifi            conda/linux-64::certifi-2021.5.30-py36h06a4308_0\n",
      "  cffi               conda/linux-64::cffi-1.14.6-py36hd8eec40_1\n",
      "  chardet            conda/linux-64::chardet-4.0.0-py36h06a4308_1003\n",
      "  cryptography       conda/linux-64::cryptography-35.0.0-py36hd23ed53_0\n",
      "  fsspec             conda/noarch::fsspec-2022.1.0-pyhd8ed1ab_0\n",
      "  idna               conda/noarch::idna-3.3-pyhd3eb1b0_0\n",
      "  idna_ssl           conda/noarch::idna_ssl-1.1.0-pyhd8ed1ab_1002\n",
      "  jmespath           conda/noarch::jmespath-0.10.0-pyhd3eb1b0_0\n",
      "  multidict          conda/linux-64::multidict-5.2.0-py36h8f6f2f9_0\n",
      "  pycparser          conda/noarch::pycparser-2.21-pyhd3eb1b0_0\n",
      "  pyopenssl          conda/noarch::pyopenssl-21.0.0-pyhd3eb1b0_1\n",
      "  pysocks            conda/linux-64::pysocks-1.7.1-py36h5fab9bb_3\n",
      "  python-dateutil    conda/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0\n",
      "  s3fs               conda/noarch::s3fs-2022.1.0-pyhd8ed1ab_0\n",
      "  six                conda/noarch::six-1.16.0-pyhd3eb1b0_0\n",
      "  typing-extensions  conda/noarch::typing-extensions-4.0.1-hd8ed1ab_0\n",
      "  typing_extensions  conda/noarch::typing_extensions-4.0.1-pyha770c72_0\n",
      "  urllib3            conda/noarch::urllib3-1.26.8-pyhd8ed1ab_1\n",
      "  wrapt              conda/linux-64::wrapt-1.13.1-py36h8f6f2f9_0\n",
      "  yarl               conda/linux-64::yarl-1.6.3-py36h8f6f2f9_2\n",
      "\n",
      "\n",
      "Preparing transaction: done\n",
      "Verifying transaction: done\n",
      "Executing transaction: done\n",
      "\n",
      "Note: you may need to restart the kernel to use updated packages.\n"
     ]
    }
   ],
   "source": [
    "conda install -n benchmark_syndi s3fs -y"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Cortex-Python3",
   "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": "3.9.7"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}