Tom Ordonez

Data Science, Machine Learning, Software Engineering

Install Miniconda on Linux


I loved virtualenv and then I found Miniconda. It's pretty similar to RVM for Ruby.

You can create a Python environment with a specific Python version and/or specific library versions.

Before installing Miniconda. Create the .conda directory in your home folder:

$ mkdir ~/.conda

Then use the script to install Miniconda. Find your install file from here: https://docs.conda.io/en/latest/miniconda.html

For Linux:

$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh

Welcome to Miniconda3 4.7.10 In order to continue the installation process, please review the license agreement. Please, press ENTER to continue

=================================== Miniconda End User License Agreement

... Cryptography Notice

This distribution includes cryptographic software. The country in which you currently reside may have restrictions on the import, possession, use, and/or re-export to anothe r country, of encryption software. BEFORE using any encryption software, please check your country's laws, regulations and policies concerning the import, possession, or use , and re-export of encryption software, to see if this is permitted. See the Wassenaar Arrangement http://www.wassenaar.org/ for more information. Anaconda, Inc. has self-classified this software as Export Commodity Control Number (ECCN) 5D992b, which includes mass market information security software using or performi ng cryptographic functions with asymmetric algorithms. No license is required for export of this software to non-embargoed countries. In addition, the Intel(TM) Math Kernel Library contained in Anaconda, Inc.'s software is classified by Intel(TM) as ECCN 5D992b with no license required for export to non-embargoed countries. The following packages are included in this distribution that relate to cryptography:

openssl The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolkit implementing the Transport Layer Security (TL S) and Secure Sockets Layer (SSL) protocols as well as a full-strength general purpose cryptography library.

pycrypto A collection of both secure hash functions (such as SHA256 and RIPEMD160), and various encryption algorithms (AES, DES, RSA, ElGamal, etc.).

pyopenssl A thin Python wrapper around (a subset of) the OpenSSL library.

kerberos (krb5, non-Windows platforms) A network authentication protocol designed to provide strong authentication for client/server applications by using secret-key cryptography.

cryptography A Python library which exposes cryptographic recipes and primitives.

Do you accept the license terms? [yes|no]

[no] >>> yes

Miniconda3 will now be installed into this location:

/home/tom/miniconda3
  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below

[/home/tom/miniconda3] >>>

PREFIX=/home/tom/miniconda3
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /home/tom/miniconda3 added / updated specs:

- _libgcc_mutex==0.1=main
- asn1crypto==0.24.0=py37_0
- bzip2==1.0.8=h7b6447c_0
- ca-certificates==2019.5.15=0
- certifi==2019.6.16=py37_0
- cffi==1.12.3=py37h2e261b9_0
- chardet==3.0.4=py37_1
- conda-package-handling==1.3.11=py37_0
- conda==4.7.10=py37_0
- cryptography==2.7=py37h1ba5d50_0
- idna==2.8=py37_0
- idna==2.8=py37_0
- libarchive==3.3.3=h5d8350f_5
- libedit==3.1.20181209=hc058e9b_0
- libffi==3.2.1=hd88cf55_4
- libgcc-ng==9.1.0=hdf63c60_0
- libstdcxx-ng==9.1.0=hdf63c60_0
- libxml2==2.9.9=hea5a465_1
- lz4-c==1.8.1.2=h14c3975_0
- lzo==2.10=h49e0be7_2
- ncurses==6.1=he6710b0_1
- openssl==1.1.1c=h7b6447c_1
- pip==19.1.1=py37_0
- pycosat==0.6.3=py37h14c3975_0
- pycparser==2.19=py37_0
- pyopenssl==19.0.0=py37_0
- pysocks==1.7.0=py37_0
- python-libarchive-c==2.8=py37_11
- python==3.7.3=h0371630_0
- readline==7.0=h7b6447c_5
- requests==2.22.0=py37_0
- ruamel_yaml==0.15.46=py37h14c3975_0
- setuptools==41.0.1=py37_0
- six==1.12.0=py37_0
- sqlite==3.29.0=h7b6447c_0
- tk==8.6.8=hbc83047_0
- tqdm==4.32.1=py_0
- urllib3==1.24.2=py37_0
- wheel==0.33.4=py37_0
- xz==5.2.4=h14c3975_4
- yaml==0.1.7=had09818_2
- zlib==1.2.11=h7b6447c_3
- zstd==1.3.7=h0b5b093_0

The following NEW packages will be INSTALLED:

_libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
asn1crypto         pkgs/main/linux-64::asn1crypto-0.24.0-py37_0
bzip2              pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0
ca-certificates    pkgs/main/linux-64::ca-certificates-2019.5.15-0
certifi            pkgs/main/linux-64::certifi-2019.6.16-py37_0
cffi               pkgs/main/linux-64::cffi-1.12.3-py37h2e261b9_0
chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1
conda              pkgs/main/linux-64::conda-4.7.10-py37_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.3.11-py37_0
cryptography       pkgs/main/linux-64::cryptography-2.7-py37h1ba5d50_0
idna               pkgs/main/linux-64::idna-2.8-py37_0
libarchive         pkgs/main/linux-64::libarchive-3.3.3-h5d8350f_5
libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
libxml2            pkgs/main/linux-64::libxml2-2.9.9-hea5a465_1
lz4-c              pkgs/main/linux-64::lz4-c-1.8.1.2-h14c3975_0
lzo                pkgs/main/linux-64::lzo-2.10-h49e0be7_2
ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
openssl            pkgs/main/linux-64::openssl-1.1.1c-h7b6447c_1
pip                pkgs/main/linux-64::pip-19.1.1-py37_0
pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h14c3975_0
pycparser          pkgs/main/linux-64::pycparser-2.19-py37_0
pyopenssl          pkgs/main/linux-64::pyopenssl-19.0.0-py37_0
pysocks            pkgs/main/linux-64::pysocks-1.7.0-py37_0
python             pkgs/main/linux-64::python-3.7.3-h0371630_0
python-libarchive~ pkgs/main/linux-64::python-libarchive-c-2.8-py37_11
readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
requests           pkgs/main/linux-64::requests-2.22.0-py37_0
ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.46-py37h14c3975_0
setuptools         pkgs/main/linux-64::setuptools-41.0.1-py37_0
six                pkgs/main/linux-64::six-1.12.0-py37_0
sqlite             pkgs/main/linux-64::sqlite-3.29.0-h7b6447c_0
tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
tqdm               pkgs/main/noarch::tqdm-4.32.1-py_0
urllib3            pkgs/main/linux-64::urllib3-1.24.2-py37_0
wheel              pkgs/main/linux-64::wheel-0.33.4-py37_0
xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
zstd               pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0

Preparing transaction: done Executing transaction: done installation finished.

Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no]

[no] >>> yes

no change /home/tom/miniconda3/condabin/conda no change /home/tom/miniconda3/bin/conda no change /home/tom/miniconda3/bin/conda-env no change /home/tom/miniconda3/bin/activate no change /home/tom/miniconda3/bin/deactivate no change /home/tom/miniconda3/etc/profile.d/conda.sh no change /home/tom/miniconda3/etc/fish/conf.d/conda.fish no change /home/tom/miniconda3/shell/condabin/Conda.psm1 no change /home/tom/miniconda3/shell/condabin/conda-hook.ps1 no change /home/tom/miniconda3/lib/python3.7/site-packages/xontrib/conda.xsh no change /home/tom/miniconda3/etc/profile.d/conda.csh modified /home/tom/.bashrc

==> For changes to take effect, close and re-open your current shell. <==

If you'd prefer that conda's base environment not be activated on startup,

set the auto_activate_base parameter to false:

conda config --set auto_activate_base false

Thank you for installing Miniconda3!

Reopen Terminal

Then try:

$ conda --version
conda 4.7.10

After reopening the Terminal, the prompt changes to this:

(base) $

This shows that your current conda environment is base. If you don't wish to see this in your Terminal. For instance, if you write in other languages. You can disable this:

conda config --set auto_activate_base false

Update conda

Use this:

$ conda update conda

Output:

Collecting package metadata (current_repodata.json): done Solving environment: done

environment location: /home/tom/miniconda3

added / updated specs: - conda

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
ca-certificates-2019.5.15  |                1         134 KB
certifi-2019.6.16          |           py37_1         156 KB
chardet-3.0.4              |        py37_1003         173 KB
conda-4.7.11               |           py37_0         3.0 MB
pip-19.2.2                 |           py37_0         1.9 MB
python-libarchive-c-2.8    |          py37_13          23 KB
------------------------------------------------------------
                                       Total:         5.4 MB

The following packages will be UPDATED:

ca-certificates                               2019.5.15-0 --> 2019.5.15-1
certifi                                  2019.6.16-py37_0 --> 2019.6.16-py37_1
chardet                                      3.0.4-py37_1 --> 3.0.4-py37_1003
conda                                       4.7.10-py37_0 --> 4.7.11-py37_0
pip                                         19.1.1-py37_0 --> 19.2.2-py37_0
python-libarchive~                            2.8-py37_11 --> 2.8-py37_13

Create a conda environment

As seen on the official docs: https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html

You could try this:

$ conda create --name snowflakes pandas

It will show an output with these headers:

  • The following packages will be downloaded
  • The following NEW packages will be INSTALLED

Activate:

$ conda activate snowflakes

Go back to base:

$ conda activate

Create a conda environment with a yml file

This is a yml file for a class I was taking:

name: ml4t
dependencies:
- python=3.6
- cycler=0.10.0
- kiwisolver=1.1.0
- matplotlib=3.0.3
- numpy=1.16.3
- pandas=0.24.2
- pyparsing=2.4.0
- python-dateutil=2.8.0
- pytz=2019.1
- scipy=1.2.1
- seaborn=0.9.0
- six=1.12.0
- joblib=0.13.2
- pytest=5.0
- future=0.17.1
- pip
- pip:
  - pprofile==2.0.2
  - jsons==0.8.8

Save the file as environment.yml.

If you run this:

$ conda create --file environment.yml

You will get an error that the target is the base.

Instead run like this:

$ conda env create --file environment.yml

Then activate:

$ conda activate ml4t

Check where python is located and the version to confirm that this is set correctly:

$ which python
$ python --version

To deactivate and go back to base:

$ conda activate

To list your conda environments:

$ conda info --envs

Conda cheat sheet

Get it here: https://docs.conda.io/projects/conda/en/latest/user-guide/cheatsheet.html

Troubleshooting installation

Executing transaction:

WARNING conda.core.envs_manager:register_env(46): Unable to register environment.
  Path not writable or missing.

environment location: /home/tom/miniconda3
registry file: /home/tom/.conda/environments.txt

As seen here: https://github.com/ContinuumIO/anaconda-issues/issues/11148

If you see this error try this:

  • Remove your miniconda folder such as: rm -rf miniconda3
  • Remove what the install added to your bashrc
  • Create the .conda directory.
  • Reinstall.