Installation

PoreSpy depends heavily on SciPy and its dependencies. The best way to get a fully functional environment is the Anaconda distribution. Be sure to get the Python 3.8+ version.

Once you’ve installed Anaconda you can then install porespy. It is available on conda-forge and can be installed by typing the following at the conda prompt:

$ conda install -c conda-forge porespy

It’s possible to use pip install porespy, but this will not result in a full installation and some features won’t work (i.e. outputing to paraview and calling imagej functions).

Installing the dev version

We frequently publish new releases every couple of months, but if you still want to use the latest features available on the dev branch, (but not yet officially released), you have two options:

The easy way

If you’re looking for an easy way to install the development version of porespy and use the latest features, you can install it using:

$ pip install git+https://github.com/PMEAL/[email protected]

Warning

This approach is not recommended if you are a porespy contributor or want to frequently get new updates as they roll in. If you insist on using this approach, to get the latest version at any point, you need to first uninstall your porespy and then rerun the command above.

The hard (but correct) way

If you are a porespy contributor or want to easily get the new updates as they roll in, you need to properly clone our repo and install it locally. It’s not as difficult as it sounds, just follow these steps:

Open up the terminal/cmd and cd to the directory you want to clone porespy.

Clone the repo somewhere in your disk using:

$ git clone https://github.com/PMEAL/porespy

cd to the root folder of porespy:

$ cd porespy

Install porespy dependencies:

$ conda install --file=requirements/conda.txt
$ pip install -r requirements.txt

Install porespy in “editable” mode:

$ pip install --no-deps -e .

Voila! You can now use the latest features available on the dev branch. To keep your “local” porespy installation up to date, every now and then, cd to the root folder of porespy and pull the latest changes:

$ git pull

Warning

For the development version of porespy to work, you need to first remove the porespy that you’ve previously installed using pip or conda.

Where’s my conda prompt?

All the commands in this page need to be typed in the conda prompt.

Windows

On Windows you should have a shortcut to the “Anaconda prompt” in the Anaconda program group in the start menu. This will open a Windows command console with access to the Python features added by conda, such as installing things via conda.

Mac and Linux

On Mac or Linux, you need to open a normal terminal window, then type source activate env where you replace env with the name of the environment you want to install PoreSpy. If you don’t know what this means, then use source activate base, which will install PoreSpy in the base environment which is the default.