Installation

Reshapr uses Pixi for dependency and environment management. If you don’t already have Pixi installed, please follow its installation instructions to do so.

Get the Code

Clone the code and documentation repository from GitHub with:

$ git clone git@github.com:UBC-MOAD/Reshapr.git

or copy the URI (the stuff after git clone above) from the Code button on the repository page.

Note

The git clone command above assumes that your are connecting to GitHub using SSH. If it fails, please follow the instructions in our Secure Remote Access docs to set up your SSH keys and Copy Your Public ssh Key to GitHub.

Package Installation

Use Pixi to create an isolated environment for Reshapr to avoid conflicts with other Python packages installed on your system. That environment will have all of the Python packages necessary to use the reshapr command that is provided by the Reshapr package.

$ cd Reshapr
$ pixi install

When you are in the Reshapr/ directory (or a sub-directory) you can run the reshapr command with with the pixi run command. Example:

$ pixi run reshapr help

You can show the version of Reshapr that you have installed and other important information with:

$ pixi run reshapr info

A common use-case is to execute the reshapr extract command in the directory containing your extraction configuration YAML file. To accomplish that, you have to tell Pixi where to find the Reshapr/ directory so that it can use the correct environment. You do that by using the -m or --manifest option of pixi run. Example:

$ cd $HOME/MEOPAR/analysis-doug/notebooks/SHEM/
$ pixi run -m $HOME/MOAD/Reshapr reshapr extract extract_SHEM_heterotrophic_bacteria.yaml

For doing development, testing, and documentation of the Reshapr package, please see the Development Environment section.

Updating Your Installation

In general, all you need to do to update your Reshapr installation is pull the latest updates from GitHub:

$ cd Reshapr
$ git pull
$ pixi install

Uninstalling

If you want to uninstall Reshapr, you can remove your clone of the repository and the Pixi environment with:

$ cd Reshapr/..
$ rm -rf Reshapr/