## Installing Miniconda

I generally use miniconda to avoid installing tons of packages that I don’t need. It’s important to download the installer for whichever python distro you want as default; you can always make an environment with a different flavor of python. As of 2020, it probably makes sense to install with the Python 3 binary, and then make environments for using Python 2.

Currently, you can install Anaconda or Miniconda simply by downloading and running a bash script from the project website

 $ bash ./[some long file name].sh

You can also a GUI installer for Anaconda, but I found the bash script easier to use.

Making and using virtual environments

Now try making a new virtual environment via conda

$ conda create -n cenv python=2.7
(cenv) $ conda activate cenv
(cenv) $ conda deactivate

Note: before 2018, source activate and source deactivate were used instead of conda activate. Some older clusters still use these commands.

Updating conda

 $ conda update conda

Duplicating an environment

 $ conda list --export > exported-packages.txt
 $ conda create -n py3clone --file exported-packages.txt

-OR-

 $ conda create -n newname --clone oldname

Removing an environment

 $ conda remove -n myenv --all

Installing packages

$ conda install numpy

It is sometimes difficult to decide whether to install a package using pip or conda. As a rule of thumb, I only use conda to install binaries from the main Anaconda channels (ie, not from a forge channel), and I use pip for everything else.

Distributing a package on Anaconda cloud

Create an online Anaconda cloud account here

You need to install two additional command line utilities

conda install anaconda-client conda-build

Now login locally from the terminal, entering your username and password when prompted

anaconda login

Upload the package to Anaconda cloud

Disable automatic uploading and then build

conda config --set anaconda_upload no
conda build .

Now find out where the build was stored

conda build . --output

This directory will be somewhere weird on your system, depending on where Miniconda is installed. Now that you know the path, run

anaconda upload /path/to/file/somename.tar.bz2

Now you can distribute and install the package using

conda install -c username my_package

Updating a package on Anaconda cloud

Edit ‘devtools/conda-recipe/meta.yaml’ to the latest version number

Now re-build

conda build .

Now check the output location

conda build . --output

Upload to anaconda cloud

anaconda upload /path/to/file/somename.tar.bz2

For a package that is already being distributed using PyPI

Note: this should only be done if direct uploading to Anaconda cloud isn’t working—otherwise, this conflicts. Create a tarball for the package

python setup.py sdist

Upload the package to Anaconda Cloud

anaconda upload dist/*.tar.gz

Broken conda installation

Here are some fixes I’ve used when my conda installation stops working.

Revert your environment

Some packages install a mess of dependencies, which can break parts of your code. To revert, enter your environment and then view your environment’s revision history

conda list --revisions

Pick which revision you want to go back to. For revision N, run

conda install --revision N

Found this tip here

Attempt a partial re-installation

During an update after several months without use, conda stopped working. To recover the installation without deleting all the environments follow the guide here

Download the same installer as your original install (mine was Python 2.7) and then run it with the -f option:

bash Miniconda3-latest-MacOSX-x86_64.sh -f

Make sure you install to the same location as your previous installation. You will have a chance to pick your path; I had to purposely change mine to the location of the previous install:

/Users/william/miniconda

You may need to edit your bash settings to help get the paths correct

emacs /Users/william/.bash_profile

Completely re-installing

Occasionally, I’ve found that conda on OSX will break with no meaningful way of recovering. These issues can be too difficult to troubleshoot on a case-by-case basis, and the easiest solution is a clean re-installation.

The question is whether it is at all possible to recover one’s existing environments. I am under the impression that this is very difficult to do because of the way that internal links to moved filed are built into conda. Instead I opted for a clean re-install, which unfortunately meant that I had to re-install various packages piecemeal as I required them.

If you still have access to your old, broken conda installation, a list of what was installed can be found in a path that looks something like

/Users/username/miniconda/envs/example_env/lib/python3.4/site-packages

You can export a list of the dependencies using

cd ~/miniconda_broken/envs/example_env/lib/python3.4//site-packages/
ls -d */ > ~/example_env_dependencies.txt

Packages install through conda, but don’t show up correctly in iPython

For example, conda successfully runs

$ conda install matplotlib

However, in a jupyter notebook (or iPython terminal), the following returns a ModuleNotFound exception

$ import matplotlib

Try checking in a bare python terminal

$ python
>>> import matplotlib

If this works, then you don’t have jupyter correctly installed in your environment, so just run

$ conda install jupyter

Broken conda installation in an HPC without sudo priveleges

I had an issue in which all conda operations would fail, but I could not reinstall conda. I found that the culprit was my .bashrc and .bash_profile files. I removed all references to conda from both, and then reloaded the module on the cluster.

I did need to delete and re-create all of my environments, however.