Anaconda Environments
Overview
Teaching: 15 min
Exercises: 15 minQuestions
How do I install new python libraries?
How are Anaconda Environments useful to my research?
Objectives
Create an Anaconda Environment
Add packages to that environment
Share environments
Change environments
Anaconda allows you to create environments that use different versions of Python and/or packages installed in them. This allows you to create a different environment for every project, switch between environments and share environments. Anaconda environments are independent of python used by the operating system so updates or changes to the system python or packages will not impact your environment. Anaconda environments retain package version information which aids in research repeatability. This is a brief overview of how to use Anaconda environments, for a more complete tutorial please visit Conda’s Managing Environments user guide.
Creating an Environment
For this module we will be working in the terminal. Create a new environment
with conda create. By default it will set the environment up
with the latest version of Python and only the necessary packages.
$ conda create --name testEnv
You may be prompted to install new packages. Hit Y [Enter] to proceed
Note: at this time you can also specify which version of python you would like to use ex:
$ conda create --name testEnv2 python=2.7
Now activate your environment with:
$ conda activate testEnv
(testEnv) $
Notice the command prompt has changed slightly to include the name of the active environment in parentheses
Installing Packages
Now install a new package to your environment:
(testEnv) $ conda install scipy
Fetching package metadata ...........
Solving package specifications: .
Package plan for installation in environment /home/user/.conda/envs/testEnv:
The following NEW packages will be INSTALLED:
libgfortran-ng: 7.2.0-h9f7466a_2
scipy: 1.0.0-py36hbf646e7_0
Proceed ([y]/n)? y
scipy-1.0.0-py 100% |###################| Time: 0:00:04 4.45 MB/s
Let’s view the packages currently installed in our environment:
(testEnv) $ conda list
# packages in environment at /home/user/.conda/envs/testEnv:
#
asn1crypto 0.23.0 py36h4639342_0
ca-certificates 2017.08.26 h1d4fec5_0
certifi 2017.11.5 py36hf29ccca_0
cffi 1.11.2 py36h2825082_0
chardet 3.0.4 py36h0f667ec_1
cryptography 2.1.4 py36hd09be54_0
idna 2.6 py36h82fb2a8_1
intel-openmp 2018.0.0 hc7b2577_8
libedit 3.1 heed3624_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 7.2.0 h7cc24e2_2
libgfortran-ng 7.2.0 h9f7466a_2
libstdcxx-ng 7.2.0 h7a57d05_2
mkl 2018.0.1 h19d6760_4
ncurses 6.0 h9df7e31_2
numpy 1.13.3 py36ha12f23b_0
openssl 1.0.2n hb7f436b_0
pandas 0.22.0 py36hf484d3e_0
pandas-datareader 0.5.0 py36_0
pip 9.0.1 py36h6c6f9ce_4
pycparser 2.18 py36hf9f622e_1
pyopenssl 17.5.0 py36h20ba746_0
pysocks 1.6.7 py36hd97a5b1_1
python 3.6.4 hc3d631a_0
python-dateutil 2.6.1 py36h88d3b88_1
pytz 2017.3 py36h63b9c63_0
readline 7.0 ha6073c6_4
requests 2.18.4 py36he2e5f8d_1
requests-file 1.4.1 py36_0
requests-ftp 0.3.1 py36_0
scipy 1.0.0 py36hbf646e7_0
setuptools 36.5.0 py36he42e2e1_0
six 1.11.0 py36h372c433_1
sqlite 3.20.1 hb898158_2
tk 8.6.7 hc745277_3
urllib3 1.22 py36hbe7ace6_0
wheel 0.30.0 py36hfd4bba0_1
xz 5.2.3 h55aa19d_2
zlib 1.2.11 ha838bed_2
Notice scipy is installed and for future reference the python version is 3.6.4
Sharing Environments
Now let’s try sharing our environment. Environments are shared using yaml files which, among other things, include the name of the environment and the environments dependencies. Export your environment with:
(testEnv) $ conda env export > testEnv.yml
Exporting Environments in PowerShell
In windows powershell I found using
>to save my output to file saved the data in an odd format. Instead I had to useconda env export | Out-File -FilePath .\environment.yml -Encoding ASCIIto force an encoding that would work
You could then share this yaml file with others so they could load the same python environment you have been working in. To simplify sharing I have provided a yaml file to share with you: python102.yml (linux) or python102.yml (windows) or python102.yml (OSX) Right click and select “save link as” to download and save the file to your current working directory.
Exit your current environment with:
$ conda deactivate
Notice the command prompt has changed back and no longer shows the environment name.
To load and activate the environment I have shared with you:
$ conda env create -f python102.yml
Using Anaconda API: https://api.anaconda.org
Fetching package metadata ...........
Solving package specifications: .
#
# To activate this environment, use:
# > conda activate python102
#
# To deactivate an active environment, use:
# > conda deactivate
#
$ conda activate python102
(python102) $
View Environments
If you have created a new environment from a file and are unsure of the name you can look at a list of all of your environments with:
(python102) $ conda info --envs
# conda environments:
#
python102 * /home/user/.conda/envs/python102
testEnv /home/user/.conda/envs/testEnv
testEnv2 /home/user/.conda/envs/testEnv2
root /software/anaconda/3
Note: the asterisks indicates the active environment.
Key Points
Anaconda Environments