When creating conda virtual environment with YAML file for the first time, I unknowingly ran:
conda env update -f environment.yml
call activate process_name
which successfully created a venv in: C:\Users\userName\AppData\Local\Continuum\anaconda3\envs.
Should I have ran the following instead?
conda env create -f environment.yml
call activate process_name
Does conda env update create a new venv if no existing venv is found in the anaconda envs directory?
How stable is conda env update in defaulting to creating a new venv if no existing venv is found?
Both should work to create the new venv if such an environment doesn't exists. You can easily try this with a sample environment.yml
Create the following environment.yml file in a directory of your choice:
name: testenv123
dependencies:
- python
- pytorch
and then run this:
conda env update
activate testenv123
Does conda env update create a new venv if no existing venv is found
in the anaconda envs directory?
Yes
How stable is conda env update in defaulting to creating a new venv if
no existing venv is found?
I could not find any documentation stating that it will create a new environment if the environment does not already exist. Therefore I think that there are no guarantees about this behavior staying the same in the future.
Related
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
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 installed anaconda in C:\Program Files\Anaconda3. Every time to create a new env, I just do cmd and write:
conda create --name envname python=3.5
But how can i install a new env from the "environments.yml" file
conda env create allows an option --file for an environment file:
conda env create --name envname --file=environments.yml
The above answers did not work for me with conda 4.7.12, but this (from the Anaconda documentation) did:
conda env create -f environment.yml
conda env create --file environment.yml
To sum up (as of conda 4.8.4) conda env create and conda create are two fundamentally different commands.
conda create
this is the official (quasi-recommended) command to create envs, listed in the general commands section of the docs
conda create --file expects a requirements.txt, not an environment.yml, each line in the given file is treated as a package-reference
conda env create
instead, this command is needed to create an environment from a given environment.yml
environment.yml files have a specific syntax (e.g. for env name, source channels, packages)
e.g. conda env create --file environment.yml
some flags available with conda create are not available with conda env create, such as --strict-channel-priority, which may result in some confusion
conda env create is only mentioned deep into the docs of conda (although I think it is the more common command to use)
Worked for me on anaconda, mini conda Replace the .yml file path to location of environment.yml file.
conda env create --prefix ./env -f ../yml file path/environment.yml
I'd like the root environment of conda to copy all of the packages in another environment. How can this be done?
There are options to copy dependency names/urls/versions to files.
Recommendation
Normally it is safer to work from a new environment rather than changing root. However, consider backing up your existing environments before attempting changes. Verify the desired outcome by testing these commands in a demo environment. To backup your root env for example:
λ conda activate root
λ conda env export > environment_root.yml
λ conda list --explicit > spec_file_root.txt
Options
Option 1 - YAML file
Within the second environment (e.g. myenv), export names+ to a yaml file:
λ activate myenv
λ conda env export > environment.yml
then update the first environment+ (e.g. root) with the yaml file:
λ conda env update --name root --file environment.yml
Option 2 - Cloning an environment
Use the --clone flag to clone environments (see #DevC's post):
λ conda create --name myclone --clone root
This basically creates a direct copy of an environment.
Option 3 - Spec file
Make a spec-file++ to append dependencies from an env (see #Ormetrom):
λ activate myenv
λ conda list --explicit > spec_file.txt
λ conda install --name root --file spec_file.txt
Alternatively, replicate a new environment (recommended):
λ conda create --name myenv2 --file spec_file.txt
See Also
conda env for more details on the env sub-commands.
Anaconada Navigator desktop program for a more graphical experience.
Docs on updated commands. With older conda versions use activate (Windows) and source activate (Linux/Mac OS). Newer versions of conda can use conda activate (this may require some setup with your shell configuration via conda init).
Discussion on keeping conda env
Extras
There appears to be an undocumented conda run option to help execute commands in specific environments.
# New command
λ conda run --name myenv conda list --explicit > spec_file.txt
The latter command is effective at running commands in environments without the activation/deactivation steps. See the equivalent command below:
# Equivalent
λ activate myenv
λ conda list --explicit > spec_file.txt
λ deactivate
Note, this is likely an experimental feature, so this may not be appropriate in production until official adoption into the public API.
+Conda docs have changed since the original post; links updated.
++Spec-files only work with environments created on the same OS. Unlike the first two options, spec-files only capture links to conda dependencies; pip dependencies are not included.
To make a copy of your root environment (named base), you can use following command; worked for me with Anaconda3-5.0.1:
conda create --name <env_name> --clone base
you can list all the packages installed in conda environment with following command
conda list -n <env_name>
When setting up a new environment and I need the packages from the base environment in my new one (which is often the case) I am building in the prompt a identical conda environment by using a spec-file.txt with:
conda list --explicit > spec-file.txt
The spec-file includes the packages of for example the base environment.
Then using the prompt I install the the packages into the new environment:
conda create --name myenv --file spec-file.txt
The packages from base are then available in the new environment.
The whole process is describe in the doc:
https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#building-identical-conda-environments
I also ran into the trouble of cloning an environment onto another machine and wanted to provide an answer. The key issue I had was addressing errors when the current environment contains development packages which cannot be obtained directly from conda install or pip install. For these cases I highly recommend conda-pack (see this answer):
pip install conda-pack
or,
conda install conda-pack
then back up the environment, to use the current environment just omit the my_env name,
# 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
and restoring,
# 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
I can create a new conda environment, with program biopython with this:
conda create --name snowflakes biopython
What if I do not want to install any program? It seems I can not do that:
» conda create --name tryout
Error: too few arguments, must supply command line package specs or --file
You can specify one or more default packages to install when creating
an environment. Doing so allows you to call conda create without
explicitly providing any package names.
To set the provided packages, call conda config like this:
conda config --add create_default_packages PACKAGE_NAME
You can give a package name of just "python" to get a base, empty install.
conda create --name myenv python
conda create --name myenv python=3.4
If you've created a create_default_packages block in your .condarc file, #joelion's answer will install those packages. If you don't want those, use the --no-default-packages flag. For example:
conda create --name myenv python --no-default-packages
This is how to create a truly empty (light) conda_env with 0 packages:
conda create --name myenv --no-default-packages
it will take a few seconds to create and finish.
To create an environment that is absolutely empty, without python and/or any other default package, just make a new folder in envs directory in your Anaconda installation (Anaconda3 in this example):.
~\Anaconda3\envs>mkdir empy_env
The first time that you activate this environment a directory named Scripts in Windows, bin in Linux, with a few batch files are created. At the time of this post this works for Anaconda version 4.3.30 both in Windows and Linux.
I have noticed that #cel has suggested the same thing in the first comment under the question, but obviously it hasn't got the attention it deserves!
For Conda 2020.11 Linux, the following command will create an empty environment.
conda create --name your-env-name