To save a conda environment and re-create it, I use:
# Save the environment
conda env export > my_conda_env.yml
# Re-create the environment
conda env create --file my_conda_env.yml
# Reactivate the environment
conda activate pytorch
However, when I do so, in the new environment the pip freeze lists some python packages that were not specified in the my_conda_env.yml but instead comes from the pip from the conda default environment. How can I prevent my newly created conda environment from containing pip packages inherited from pip from the conda default environment?
I notice that my_conda_env.yml contains prefix: /home/franck/anaconda3/envs/pytorch on the last line. What's the point of it?
> echo $PYTHONPATH
/home/code-base/runtime/app:/home/code-base/runtime/app/python:/home/code-base/runtime/app/python/dev:/app/python:/app/plugins:/app/plugins/jupyterlab-zip
> echo $PATH
/opt/conda/bin:/opt/conda/condabin:/opt/conda/bin:/app/python/bin:/opt/conda/bin:/usr/local/mpi/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
My .gitlab-ci.yml file looks like this:
anomalydetector:
image: continuumio/miniconda:4.7.10
stage: build
tags:
- docker
script:
- conda env create -f environment.yml
- conda activate my-env
- pytest tests/.
On Gitlab, this job starts fine, and the logs read
$ conda env create -f environment.yml
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.7.10
latest version: 4.7.11
Ok, so I'm using a conda version later than 4.4, so conda activate should work. However, the job fails with the following:
# To activate this environment, use
#
# $ conda activate my-env
#
# To deactivate an active environment, use
#
# $ conda deactivate
$ conda activate my-env
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
I have then tried editing my .gitlab-ci.yml file so that there is a command
conda init bash
but then get the message
==> For changes to take effect, close and re-open your current shell. <==
How can I activate my conda environment in the gitlab CI process?
conda init touches the .bashrc file. To reinitialize the shell you can source it:
- conda create --name myenv
- conda init bash
- source ~/.bashrc # <- !!!
- conda activate myenv
Whether this is better or worse than source activate myenv is a separate discussion, I guess.
Similarly to Tommy's answer, this needs to be done for the Windows Powershell as well. Contrary to bash conda activate myenv does not fail in the powershell. It just has no effect (i.e. the environment is not switched) without calling conda init powershell which makes it even more awkward. Reloading the profile in the powershell is more complicated since there are six of them [1]. I used:
- conda create --name myenv
- conda init powershell
- "if (test-path $PROFILE.CurrentUserAllHosts) { & $PROFILE.CurrentUserAllHosts}"
- conda activate myenv
Why Conda uses the $PROFILE.CurrentUserAllHosts profile has been asked in an issue [2].
references:
[1] https://devblogs.microsoft.com/scripting/understanding-the-six-powershell-profiles/
[2] https://github.com/conda/conda/issues/8608
Another possibility that you might find more succinct and elegant: source directly the code needed for conda to run run with bash. This also has the effect of adding conda to the PATH, if it's not the case.
This is done with
- source <anaconda_root>/etc/profile.d/conda.sh
- conda activate myenv
(Stolen from https://stackoverflow.com/a/60523131/11343)
Somehow all of these answers failed me. I ended up using conda run instead of activating an environment. That allowed me to run pytest without activating the environment
- conda run -n <environment-name> python -m pytest <addl-pytest-args>
I want to remove a certain environment created with conda. How can I achieve that? Let's say I have an active testenv environment. I tried, by following documentation, with:
$ conda env remove
CondaEnvironmentError: cannot remove current environment. deactivate and run conda remove again
I then deactivate it:
$ source deactivate
I try running again the command to remove it and I still get the same error. What is going wrong here?
You probably didn't fully deactivate the Conda environment - remember, the command you need to use with Conda is conda deactivate (for older versions, use source deactivate). So it may be wise to start a new shell and activate the environment in that before you try. Then deactivate it.
You can use the command
conda env remove -n ENV_NAME
to remove the environment with that name. (--name is equivalent to -n)
Note that you can also place environments anywhere you want using -p /path/to/env instead of -n ENV_NAME when both creating and deleting environments, if you choose. They don't have to live in your conda installation.
UPDATE, 30 Jan 2019: From Conda 4.6 onwards the conda activate command becomes the new official way to activate an environment across all platforms. The changes are described in this Anaconda blog post
After making sure your environment is not active, type:
$ conda env remove --name ENVIRONMENT
Official documentation way worked for me:
conda remove --name myenv --all
Or just conda env remove --name myenv.
To verify that the environment was removed, in your terminal window or an Anaconda Prompt, run:
conda info --envs
The environments list that displays should not show the removed environment.
You anaconda3 enviroments folder might list an empty folder of deleted environment in your anaconda3 installation folder, like:
/opt/anaconda3/envs
If you are in base:
(base) HP-Compaq-Elite-8300-CMT:~$
remove env_name by:
conda env remove -n env_name
if you are already in env_name environment :
(env_name) HP-Compaq-Elite-8300-CMT:~$
deactivate then remove by :
conda deactivate
conda env remove -n env_name
In my windows 10 Enterprise edition os this code works fine:
(suppose for environment namely testenv)
conda env remove --name testenv
Environments created with the --prefix or -p flag must be removed with the -p flag (not -n).
For example:
conda remove -p </filepath/myenvironment> --all, in which </filepath/myenvironment> is substituted with a complete or relative path to the environment.
There're 3 ways to achieve this in total. Assuming you have a environment named myenv,
conda env remove --name myenv, -n is shortcut for --name.
conda remove --name myenv --all.
Delete the env folder directly. (Not recommended)
# list environments and their locations
conda env list
# or
# conda info --envs
# delete the folder listed
rm -rf /Users/username/.local/share/conda/envs/myenv
If you wanna delete the environment without a prompt to let you check again. Use -y, shortcut for --yes. (For global use check silent prompt in conda)
conda env remove -n myenv -y
conda remove -n myenv --all -y
References
conda env --help
conda remove --help
First deactivate the environment that you wish to remove.
Then type the following code:
conda env remove -n <your environment name>
To make sure you have deleted it, you can use the following code.
conda info --envs or conda env list
4.If you wan to remove all the dependencies along with the installed packages, you can use:
conda remove -n <environment name> --all
You may try the following: Open anaconda command prompt and type
conda remove --name myenv --all
This will remove the entire environment.
Further reading: docs.conda.io > Manage Environments
To remove complete conda environment :
conda remove --name YOUR_CONDA_ENV_NAME --all
First you have to deactivate your environment before removing it. You can remove conda environment by using the following command
Suppose your environment name is "sample_env" , you can remove this environment by using
source deactivate
conda remove -n sample_env --all
'--all' will be used to remove all the dependencies
My environment name is: test
conda remove -n test --all
Use source deactivate to deactivate the environment before removing it, replace ENV_NAME with the environment you wish to remove:
source deactivate
conda env remove -n ENV_NAME
First I checkout from the environment (tensorflow):
conda deactivate
Then I removed the environment by:
conda remove -n tensorflow --all
The tensorflow is the name of my environment
You can check your env name using this command:
conda env list
First deactivate the environment and come back to the base environment. From the base, you should be able to run the command conda env remove -n <envname>. This will give you the message
Remove all packages in environment
C:\Users\<username>\AppData\Local\Continuum\anaconda3\envs\{envname}:
This worked for me:
conda env remove --name tensorflow
if you are unfamiliar with the command line , you can remove it using the anaconda dashboard
View the environments in Anaconda or miniconda:
conda env list
If you have created an environment using name then use:
conda remove -n envname --all
if you have created an environment using prefix then use:
conda remove -p [path] --all
Change the envname with your environment name and in case of prefix provide the complete path of the environment eg: C:/Users/techv/Desktop/project/env.
--all will remove all the dependencies of the target environment.
I hope this answer will be helpful.
Because you can only deactivate the active environment, so conda deactivate does not need nor accept arguments. The error message is very explicit here.
Just call conda deactivate
https://github.com/conda/conda/issues/7296#issuecomment-389504269
on terminal it's showing
(base) [root#localhost ~]#
simply hit command : conda deactivate
and you are out of conda env , now your prompt will look like
[root#localhost ~]#
I create a virtual environment with conda
$ conda create test_env numpy .....
It gets created successfully.
$ conda env list
# conda environments:
#
base * /home/myname/anaconda3
my_project_env /home/myname/anaconda3/envs/my_project_env
test_env /home/myname/anaconda3/envs/test_env
but I can not activate it
$ source activate my_project_env
returns - activate: No such file or directory
The only place I find activate is within the whole anaconda3 is in /common folder
source anaconda3/envs/my_project_env/lib/python3.6/venv/scripts/common/activate my_project_env
When I run it with this path I get VENV_PROMPT "kind of environment" but when I check libraries with pip list it returns a global list of installed libraries instead of the selected few.
$ source anaconda3/envs/my_project_env/lib/python3.6/venv/scripts/common/activate my_project_env
__VENV_PROMPT__myname#box:~$ pip3 list
I met with the same problem. It is because I have changed the system's $PATH variable from anaconda's main bin directory to the environment's bin directory. Actually, the activate's path is under /home/users/anaconda3/bin/. So I just use the following command to make a link between the two bin directories:
ln -s /home/userName/anaconda3/bin/activate /home/userName/anaconda3/envs/envName/bin/activate
ln -s /home/userName/anaconda3/bin/deactivate /home/userName/anaconda3/envs/envName/bin/deactivate
Try to use this command activate your conda environment:
source activate /home/myname/anaconda3/envs/my_project_env
Recommended command to create environment with python version 2.7 :
conda create -n my_project_env python=2.7
Check your conda version
conda -V
Create virtual environment for your project
conda create -n yourenvname python=x.x anaconda
To activate your virtual environment
source activate yourenvname
As others have mentioned, it may be a PATH issue. However, if you're still able to run other conda commands then you may need to either conda update conda or delete conda and reinstall. In my case, I was running miniconda which I believe simply did not contain the activate binary.
Running conda activate instead of source activate solved my issues.
I have been using Anaconda(4.3.23) on my GuestOS ubuntu 14.04 which is installed on Vmware on HostOS windows 8.1. I have setup an environment in anaconda and have installed many libraries, some of which were very hectic to install (not straight forward pip installs). few libraries had inner dependencies and had to be build together and from their git source.
Problem
I am going to use Cloud based VM (Azure GPU instance) to use GPU. but I don't want to get into the hectic installation again as i don't want to waste money on the time it will take me to install all the packages and libraries again
Is there any way to transfer/copy my existing env (which has everything already installed) to the Cloud VM?
From the very end of this documentation page:
Save packages for future use:
conda list --export > package-list.txt
Reinstall packages from an export file:
conda create -n myenv --file package-list.txt
If conda list --export failes like this ...
Executing conda list --export > package-list.txt creates a file which looks like this:
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: win-64
_tflow_1100_select=0.0.1=gpu
absl-py=0.5.0=py_0
astor=0.7.1=py_0
...
But creating a new environment by executing conda create -n myenv --file package-list.txt gives me this error:
Solving environment: ...working... failed
PackagesNotFoundError: The following packages are not available from current channels:
- markdown==2.6.11=py_0
...
... then try to use conda env export
According to this discussion execute the following command on your source machine:
source activate yourEnvironment
conda env export --no-builds > file.txt
On the target machine execute:
conda env create --file /path/to/file.txt
The file generated by conda env export looks a bit different, but it contains pip packages as well:
name: yourEnvironment
channels:
- conda-forge
- defaults
dependencies:
- absl-py=0.5.0
...
- pip:
- astroid==2.0.4
...
## You can try below approach to move all the package from one machine to other :
## Note : Machine that packages are being moved should be same and python version also should be same
$ pip install conda-pack
# To package an environment:
## Pack environment my_env into my_env.tar.gz
$ conda pack -n my_env
## Pack environment my_env into out_name.tar.gz
$ conda pack -n my_env -o out_name.tar.gz
## Pack environment located at an explicit path into my_env.tar.gz
$ conda pack -p /explicit/path/to/my_env
# After following above approach, you will end up with a tar.gz file. Now to install package from this zip file follow below approach.
## To install the environment:
## Unpack environment into directory `my_env`
$ mkdir -p my_env
$ tar -xzf my_env.tar.gz -C my_env
## Use Python without activating or fixing the prefixes. Most Python
## libraries will work fine, but things that require prefix cleanups
## will fail.
$ ./my_env/bin/python
## Activate the environment. This adds `my_env/bin` to your path
$ source my_env/bin/activate
## Run Python from in the environment
(my_env) $ python
## Cleanup prefixes from in the active environment.
## Note that this command can also be run without activating the environment
## as long as some version of Python is already installed on the machine.
(my_env) $ conda-unpack
You can probably get away with copying the whole Anaconda installation to your cloud instance.
According to github thread execute the following command on your source machine:
https://github.com/conda/conda/issues/3847
source activate yourEnvironment
conda env export --no-builds > environment.yml
On the target machine execute:
conda env create -f environment.yml
The file generated by conda env export looks a bit different, but it contains pip packages as well:
name: yourEnvironment
channels:
conda-forge
defaults
dependencies:
absl-py=0.5.0
...
pip:
astroid==2.0.4
...
I found the answer from this
you can export your Anaconda environment using:
conda env export > environment.yml
In order to recreate it on another machine using:
conda env create -f environment.yml
You can modify the environment.yml as required because some of the python libraries may be obsolete or due to version conflict in future releases.