From 8eaa2f888536fab9d743008e1ff8362675ac0a9a Mon Sep 17 00:00:00 2001
From: Michael Blaschek <michael.blaschek@univie.ac.at>
Date: Tue, 24 Nov 2020 17:43:01 +0100
Subject: [PATCH] Upload New File
---
Python/QA-003-Conda-Environment.ipynb | 383 ++++++++++++++++++++++++++
1 file changed, 383 insertions(+)
create mode 100644 Python/QA-003-Conda-Environment.ipynb
diff --git a/Python/QA-003-Conda-Environment.ipynb b/Python/QA-003-Conda-Environment.ipynb
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+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Setting up a user environment with conda\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Currently Loaded Modulefiles:\u001b[m\n",
+ " 1) miniconda3/4.8.2-gcc-8.3.1-3m7b6t2 \u001b[m\n",
+ "\u001b[K\u001b[?1l\u001b>"
+ ]
+ }
+ ],
+ "source": [
+ "!module list"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ " active environment : None\n",
+ " user config file : /jetfs/home/mblaschek/.condarc\n",
+ " populated config files : /jetfs/home/mblaschek/.condarc\n",
+ " conda version : 4.8.5\n",
+ " conda-build version : not installed\n",
+ " python version : 3.8.1.final.0\n",
+ " virtual packages : __glibc=2.28\n",
+ " base environment : /jetfs/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.3.1/miniconda3-4.8.2-3m7b6t2kgedyr3jnd2nasmgiq7wm27iv (read only)\n",
+ " channel URLs : https://repo.anaconda.com/pkgs/main/linux-64\n",
+ " https://repo.anaconda.com/pkgs/main/noarch\n",
+ " https://repo.anaconda.com/pkgs/r/linux-64\n",
+ " https://repo.anaconda.com/pkgs/r/noarch\n",
+ " package cache : /jetfs/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.3.1/miniconda3-4.8.2-3m7b6t2kgedyr3jnd2nasmgiq7wm27iv/pkgs\n",
+ " /jetfs/home/mblaschek/.conda/pkgs\n",
+ " envs directories : /jetfs/home/mblaschek/.conda/envs\n",
+ " /jetfs/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.3.1/miniconda3-4.8.2-3m7b6t2kgedyr3jnd2nasmgiq7wm27iv/envs\n",
+ " platform : linux-64\n",
+ " user-agent : conda/4.8.5 requests/2.22.0 CPython/3.8.1 Linux/4.18.0-147.el8.x86_64 centos/8.2.2004 glibc/2.28\n",
+ " UID:GID : 54212:100\n",
+ " netrc file : None\n",
+ " offline mode : False\n",
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "!conda info"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Collecting package metadata (current_repodata.json): done\n",
+ "Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.\n",
+ "Collecting package metadata (repodata.json): done\n",
+ "Solving environment: done\n",
+ "\n",
+ "\n",
+ "==> WARNING: A newer version of conda exists. <==\n",
+ " current version: 4.8.5\n",
+ " latest version: 4.9.2\n",
+ "\n",
+ "Please update conda by running\n",
+ "\n",
+ " $ conda update -n base -c defaults conda\n",
+ "\n",
+ "\n",
+ "\n",
+ "## Package Plan ##\n",
+ "\n",
+ " environment location: /jetfs/home/mblaschek/.conda/envs/myenv\n",
+ "\n",
+ " added / updated specs:\n",
+ " - ipykernel\n",
+ " - numpy\n",
+ " - python=3.7\n",
+ "\n",
+ "\n",
+ "The following packages will be downloaded:\n",
+ "\n",
+ " package | build\n",
+ " ---------------------------|-----------------\n",
+ " certifi-2020.11.8 | py37h06a4308_0 148 KB\n",
+ " ipython-7.19.0 | py37hb070fc8_0 978 KB\n",
+ " jupyter_core-4.7.0 | py37h06a4308_0 68 KB\n",
+ " numpy-1.19.2 | py37h54aff64_0 22 KB\n",
+ " numpy-base-1.19.2 | py37hfa32c7d_0 4.1 MB\n",
+ " pexpect-4.8.0 | pyhd3eb1b0_3 53 KB\n",
+ " pip-20.2.4 | py37h06a4308_0 1.7 MB\n",
+ " ptyprocess-0.6.0 | pyhd3eb1b0_2 20 KB\n",
+ " pygments-2.7.2 | pyhd3eb1b0_0 674 KB\n",
+ " setuptools-50.3.1 | py37h06a4308_1 711 KB\n",
+ " six-1.15.0 | py37h06a4308_0 27 KB\n",
+ " wheel-0.35.1 | pyhd3eb1b0_0 38 KB\n",
+ " ------------------------------------------------------------\n",
+ " Total: 8.5 MB\n",
+ "\n",
+ "The following NEW packages will be INSTALLED:\n",
+ "\n",
+ " _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main\n",
+ " backcall pkgs/main/noarch::backcall-0.2.0-py_0\n",
+ " blas pkgs/main/linux-64::blas-1.0-mkl\n",
+ " ca-certificates pkgs/main/linux-64::ca-certificates-2020.10.14-0\n",
+ " certifi pkgs/main/linux-64::certifi-2020.11.8-py37h06a4308_0\n",
+ " decorator pkgs/main/noarch::decorator-4.4.2-py_0\n",
+ " intel-openmp pkgs/main/linux-64::intel-openmp-2020.2-254\n",
+ " ipykernel pkgs/main/linux-64::ipykernel-5.3.4-py37h5ca1d4c_0\n",
+ " ipython pkgs/main/linux-64::ipython-7.19.0-py37hb070fc8_0\n",
+ " ipython_genutils pkgs/main/linux-64::ipython_genutils-0.2.0-py37_0\n",
+ " jedi pkgs/main/linux-64::jedi-0.17.2-py37_0\n",
+ " jupyter_client pkgs/main/noarch::jupyter_client-6.1.7-py_0\n",
+ " jupyter_core pkgs/main/linux-64::jupyter_core-4.7.0-py37h06a4308_0\n",
+ " ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7\n",
+ " libedit pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1\n",
+ " libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2\n",
+ " libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0\n",
+ " libsodium pkgs/main/linux-64::libsodium-1.0.18-h7b6447c_0\n",
+ " libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0\n",
+ " mkl pkgs/main/linux-64::mkl-2020.2-256\n",
+ " mkl-service pkgs/main/linux-64::mkl-service-2.3.0-py37he904b0f_0\n",
+ " mkl_fft pkgs/main/linux-64::mkl_fft-1.2.0-py37h23d657b_0\n",
+ " mkl_random pkgs/main/linux-64::mkl_random-1.1.1-py37h0573a6f_0\n",
+ " ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1\n",
+ " numpy pkgs/main/linux-64::numpy-1.19.2-py37h54aff64_0\n",
+ " numpy-base pkgs/main/linux-64::numpy-base-1.19.2-py37hfa32c7d_0\n",
+ " openssl pkgs/main/linux-64::openssl-1.1.1h-h7b6447c_0\n",
+ " parso pkgs/main/noarch::parso-0.7.0-py_0\n",
+ " pexpect pkgs/main/noarch::pexpect-4.8.0-pyhd3eb1b0_3\n",
+ " pickleshare pkgs/main/linux-64::pickleshare-0.7.5-py37_1001\n",
+ " pip pkgs/main/linux-64::pip-20.2.4-py37h06a4308_0\n",
+ " prompt-toolkit pkgs/main/noarch::prompt-toolkit-3.0.8-py_0\n",
+ " ptyprocess pkgs/main/noarch::ptyprocess-0.6.0-pyhd3eb1b0_2\n",
+ " pygments pkgs/main/noarch::pygments-2.7.2-pyhd3eb1b0_0\n",
+ " python pkgs/main/linux-64::python-3.7.9-h7579374_0\n",
+ " python-dateutil pkgs/main/noarch::python-dateutil-2.8.1-py_0\n",
+ " pyzmq pkgs/main/linux-64::pyzmq-19.0.2-py37he6710b0_1\n",
+ " readline pkgs/main/linux-64::readline-8.0-h7b6447c_0\n",
+ " setuptools pkgs/main/linux-64::setuptools-50.3.1-py37h06a4308_1\n",
+ " six pkgs/main/linux-64::six-1.15.0-py37h06a4308_0\n",
+ " sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0\n",
+ " tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0\n",
+ " tornado pkgs/main/linux-64::tornado-6.0.4-py37h7b6447c_1\n",
+ " traitlets pkgs/main/noarch::traitlets-5.0.5-py_0\n",
+ " wcwidth pkgs/main/noarch::wcwidth-0.2.5-py_0\n",
+ " wheel pkgs/main/noarch::wheel-0.35.1-pyhd3eb1b0_0\n",
+ " xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0\n",
+ " zeromq pkgs/main/linux-64::zeromq-4.3.3-he6710b0_3\n",
+ " zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3\n",
+ "\n",
+ "\n",
+ "\n",
+ "Downloading and Extracting Packages\n",
+ "numpy-1.19.2 | 22 KB | ##################################### | 100% \n",
+ "pip-20.2.4 | 1.7 MB | ##################################### | 100% \n",
+ "numpy-base-1.19.2 | 4.1 MB | ##################################### | 100% \n",
+ "certifi-2020.11.8 | 148 KB | ##################################### | 100% \n",
+ "wheel-0.35.1 | 38 KB | ##################################### | 100% \n",
+ "ipython-7.19.0 | 978 KB | ##################################### | 100% \n",
+ "pexpect-4.8.0 | 53 KB | ##################################### | 100% \n",
+ "pygments-2.7.2 | 674 KB | ##################################### | 100% \n",
+ "ptyprocess-0.6.0 | 20 KB | ##################################### | 100% \n",
+ "jupyter_core-4.7.0 | 68 KB | ##################################### | 100% \n",
+ "setuptools-50.3.1 | 711 KB | ##################################### | 100% \n",
+ "six-1.15.0 | 27 KB | ##################################### | 100% \n",
+ "Preparing transaction: done\n",
+ "Verifying transaction: done\n",
+ "Executing transaction: done\n",
+ "#\n",
+ "# To activate this environment, use\n",
+ "#\n",
+ "# $ conda activate myenv\n",
+ "#\n",
+ "# To deactivate an active environment, use\n",
+ "#\n",
+ "# $ conda deactivate\n",
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Create a environment with conda\n",
+ "!conda create -y -n myenv python=3.7 numpy ipykernel"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Add the new environment to your active kernels\n",
+ "This way you can choose the kernel from the Jupyterlab launcher."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Installed kernelspec MYENV in /jetfs/home/mblaschek/.local/share/jupyter/kernels/myenv\n"
+ ]
+ }
+ ],
+ "source": [
+ "!~/.conda/envs/myenv/bin/python -m ipykernel install --user --name MYENV --display-name \"Py3.7\""
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Available kernels:\n",
+ " myenv /jetfs/home/mblaschek/.local/share/jupyter/kernels/myenv\n",
+ " python3 /jetfs/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.3.1/miniconda3-4.8.2-3m7b6t2kgedyr3jnd2nasmgiq7wm27iv/share/jupyter/kernels/python3\n"
+ ]
+ }
+ ],
+ "source": [
+ "# List available Kernels\n",
+ "!jupyter kernelspec list"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Custom Environment Python Environment"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Setup a virtual Environment for your Python in the directoy: myfancyenv\n",
+ "!python -m venv myfancyenv "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "bin include lib lib64 pyvenv.cfg\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Creates a directory with new environment\n",
+ "!ls myfancyenv/"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\u001b[33mWARNING: You are using pip version 19.2.3, however version 20.2.4 is available.\n",
+ "You should consider upgrading via the 'pip install --upgrade pip' command.\u001b[0m\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Install some package into that environment\n",
+ "# important is ipykernel to use it within jupyterlab/notebook\n",
+ "!./myfancyenv/bin/pip -q install numpy scipy pandas ipykernel"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Installed kernelspec fancy in /jetfs/home/mblaschek/.local/share/jupyter/kernels/fancy\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Allow this environment to be available on the LAUNCHERS (+) sign on the left\n",
+ "!./myfancyenv/bin/python -m ipykernel install --user --name fancy --display-name \"My Python\""
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Wait a bit and the new python environment should be available on your launchers."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Available kernels:\n",
+ " fancy /jetfs/home/mblaschek/.local/share/jupyter/kernels/fancy\n",
+ " myenv /jetfs/home/mblaschek/.local/share/jupyter/kernels/myenv\n",
+ " python3 /jetfs/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.3.1/miniconda3-4.8.2-3m7b6t2kgedyr3jnd2nasmgiq7wm27iv/share/jupyter/kernels/python3\n"
+ ]
+ }
+ ],
+ "source": [
+ "!jupyter kernelspec list"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Finished"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Miniconda3 (4.8.2)",
+ "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": 4
+}
--
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