How can you "clone" a conda environment into the root environment?
Question:
I’d like the root environment of conda to copy all of the packages in another environment. How can this be done?
Answers:
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’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 envfor 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) andsource activate(Linux/Mac OS). Newer versions of conda can useconda activate(this may require some setup with your shell configuration viaconda 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