Managing Conda, Miniconda, and Anaconda, Environments, Python, Configuration, Packages. Removing Packages or Environments
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda%%bash
MINICONDA_INSTALLER_SCRIPT=Miniconda3-latest-Linux-x86_64.sh
MINICONDA_PREFIX=/usr/local
wget https://repo.continuum.io/miniconda/$MINICONDA_INSTALLER_SCRIPT
chmod +x $MINICONDA_INSTALLER_SCRIPT
./$MINICONDA_INSTALLER_SCRIPT -b -f -p $MINICONDA_PREFIX%%bash
conda install --channel defaults conda python=3.9 --yes
conda update --channel defaults --all --yes!conda --version
!python --version conda --version Check conda version
conda info Verify conda is installed, check version
conda update conda Update conda package and environment manager
conda update anaconda Update the anaconda meta package
conda update --all Update all packages in the environment
conda update --all -y Update all packages in the environment
conda info --envs Verify environment you are right now
conda info -e Get a list of all my environmentsActive environment shown with *
conda create --name snowflakes biopython
conda create -n snowflakes biopython Create an environment and install program(s)
conda activate snowflakes Activate the new environment to use it
conda deactivate Deactivate the environment
conda create -n bunnies python=3.9 astroid Create a new environment, specify Python version
conda create -n foo instrain awscli samtools python=3.8 Create a new environment with a set of packages and specific version of Python
conda create -n flowers --clone snowflakes Make exact copy of an environment
conda remove -n flowers --all Delete an environment
conda env list List all envs
conda env export > env.yml Save the current Package-specific environment to a file
conda env export --file env.yml Saving an entire environment to a file
conda env export --from-history > env.yml Save the current Cross-platform compitible environment to a file
conda env create -f env.yml Load the Package-specific environment from a file
conda env update -n coolbase --file environment.yml install and/or update packages from environment.yml
conda env remove --name bamqc Remove Virtual Environment
CONDA_SUBDIR=osx-arm64 conda create -n test_env --dry-run python=3.8 llvm-openmp cython numpy pip "matplotlib-base>=3.0.3" "protobuf >=3.11.2,<4.0.0" "scipy >=1.3.2,<2.0.0" Conda dry run environment on a specific platform
for py in 3.8 3.9 3.10; do echo -e "\n***** python $py *****"; conda create --dry-run --quiet -n __test__ python=$py pandas=1.4.2; done Conda dry run creating an environment and installing packages (pandas 1.4.2) for different python versions
conda search --full-name python
conda search -f python Check versions of Python available to install
conda search ipython=8.3.0 --info | sed '/file name/,/timestamp/d' For quick checking package dependencies (for example, for all python versions)
conda create -n snakes python=3.4 Install different version of Python in new environment
conda config --get Get all keys and values from my .condarc file
conda config --get channels Get value of the key channels from .condarc file
conda config --show channels Knowing the active channels
conda config --add channels pandas Add a new value to channels so conda looks for packages in this location
conda config --add channels defaults Adding a default channel
conda config --add channels conda-forge Adding a channel
conda config --add channels bioconda Adding a channel
conda config --set anaconda_upload yes Enable uploading to Anaconda Cloud
conda config --set anaconda_upload no Disable uploading to Anaconda Cloud
conda config --set auto_activate_base false Deactivating the activation of the base environment in Python
conda list View list of packages and versions installed in active environment
conda list | grep pandas Search package in the list
conda list --show-channel-urls List all installed packages along its channels
conda list --export > env.txt Save to a Requirements file all packages in an environment
conda list > env.txt Save a package list an a file
conda search beautiful-soup Search for a package to see if it is available to conda install
conda search -c conda-forge black Search Alternate Channels specify different channels as well, with the use of the -c flag
conda search conda-forge::black Search Alternate Channels
conda install -n bunnies beautiful-soup Install a new package NOTE: If you do not include the name of the environment, it will install in the current active environment.
conda update beautiful-soup Update a package in the current environment
conda search --override-channels -c pandas bottleneck Search for a package in a specific location (the pandas channel on Anaconda.org)
conda install -c conda-forge black Installing black from the conda-forge channel
conda install -c pandas bottleneck Install a package from a specific channel
conda install scipy --channel conda-forge --channel bioconda Specifying multiple channels when installing a package
conda search --override-channels -c defaults beautiful-soup Search for a package to see if it is available from the Anaconda repository
conda install iopro accelerate Install commercial Continuum packages
conda install black isort flake8 install python linter
conda install conda-build Install conda-build
conda install matplotlib=1.4.3 Install a certain package version
conda install m2-patch posix Windows only
conda install --use-local click
conda skeleton pypi pyinstrument
conda build pyinstrument Build a package from a Python Package Index (PyPi) Package
conda remove --name bunnies beautiful-soup Remove one package from any named environment
conda remove beautiful-soup Remove one package from the active environment
conda remove --name bunnies beautiful-soup astroid Remove multiple packages from any environment
conda remove --name snakes --all Remove an environment (remove all packages)
conda uninstall packagename Remove one package. Alias for conda remove
conda clean --all Delete unused packages and caches
anaconda login Login in to Anaconda Cloud
anaconda upload C:\ProgramData\Anaconda3\conda-bld\win-64\conda_gc_test-1.2.1-3.tar.bz2 Upload artifact for win64 to your own channel in Anaconda Cloud
anaconda upload my-notebook.ipynb Upload my-notebook.ipynb to http://notebooks.anaconda.org/<USERNAME>/my-notebook
conda-build . Build a recipe from the current folder
conda build --test /home/user/miniconda3/conda-bld/noarch/pytest-cov-2.12.1-py_0.tar.bz2 test the package in your environment (for regression testing)
conda build gdal-feedstock
conda build sep
conda-build --python 2.7 click
conda build gdal-feedstock --variant-config-file conda_build_config.yaml
conda convert --platform all ~/anaconda/conda-bld/linux-64/click-7.0-py37_0.tar.bz2 -o outputdir/
conda convert package-1.0-py33.tar.bz2 -p win-64
conda skeleton pypi --pypi-url <mirror-url> package_name
conda skeleton pypi <package name on pypi>
conda skeleton pypi click
conda skeleton pypi --recursive pyinstrument
conda install -y conda-forge::jake && conda list | jake ddt A helpful oneliner to check your conda environments for vulnerable Open Source packages
conda install boa -c conda-forge Install boa. Use the mamba solver through mambabuild. It not only has a faster solve speed but also prints better error messages that make debugging simpler.
conda mambabuild . build the recipe with mambasolver
conda mambabuild myrecipe build the recipe with mambasolver