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Installation

poreFlow is written in Python and C++, and is published as a Python package. We recommend to use a Python virtual environment when installing with pip or with uv. Both options automatically install all necessary dependencies alongside Zensical.

Below, you'll find instructions to install poreFlow on your personal computer.

Prerequisites

Operating system

poreFlow is officially supported for macOS Tahoe 26 and Windows 11. For these operating systems, there are pre-built binary distributions of poreFlow wheels

I have a different OS/version

If you are using another OS version, don't worry, you can use poreFlow too. Instead of using the pre-built binary, you can build from source.

  • For MacOS, just follow the instructions below.
  • If you are using Windows 10, or Windows on an ARM machine, check out the Developer Install
  • For general Linux distributions, install uv and follow steps below.

Python

To install poreFlow you will need Python installed. If you do not have Python on your computer, we recommend you follow the Python Setup and Usage instructions for your operating system provided on the Python website. Here, follow the instructions for just installing Python.

If you are using Anaconda/Miniconda

...Dont? No just kidding.

If you already have Anaconda/Miniconda installed on your system, Python is already available on your computer. You can skip this step.

Note that we do not officially support installing on machines with conda, but members of the Cees Dekker lab are welcome to contact us for assistance to make it work.

Some tips on installing

In your Terminal Window, run source deactivate to first deactivate conda before installing.

In your Anaconda Prompt, run deactivate before installing. Alternatively, just use Windows PowerShell.

In your Terminal Window, run source deactivate to first deactivate conda before installing.

A package manager

We recommend installing the uv package manager, which is a modern and fast package/project manager. This will handle the installation of poreFlow, and allow for you to easily add extra packages needed for your use case. Install uv by following the installation instructions.

Using just pip

Installing poreFlow using pip only is supported, so go ahead. It is the simplest option to install poreFlow on your system, but we recommend users in the Cees Dekker lab to use uv.

Creating a virtual environment

We recommend installing in a virtual environment which isolates the packages used in a project from the overall Python installation.

About virtual environments

Typically, this virtual environment is created in the folder of your project:

username
└─ my-project
    ├─  .venv
    │     └─ # Packages go here
    ├─  README.md
    ├─  my-code.py
    └─  my-notebook.ipynb

To create a virtual environment, make sure your working directory is set to your project folder. In the example above, the project folder my-project is in the home directory, so we set the working directory to the project folder using:

cd my-project

Follow the instructions below to create the virtual environment.

You only need to create the virtual environment once. After creating, you will only need to activate it each time you work in a new terminal.

Initializing a project and creating a virtual environment
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2
uv init --python 3.11
uv venv

WIP, supported Python versions

poreFlow has been released on PyPi, but for now we are only creating pre-built binaries for Python 3.11. Versions for python 3.11+ coming soon!

Activating the virtual environment

To activate the virtual environment:

Activating a virtual environment
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source .venv/bin/activate
Activating a virtual environment
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.venv\Scripts\activate
Activating a virtual environment
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source .venv/bin/activate

Installing poreFlow

Poreflow can now be installed stand-alone using uv

Installing poreFlow
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uv add poreflow

Using poreFlow

The next section describes typical workflows with poreFlow.

Upgrading poreFlow

poreFlow can be upgraded by specifying the version in uv. To find the latest version number, check out poreFlow on PyPI.

Upgrading poreFlow
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uv add "poreflow>=0.3.5"

Developer install

If you want to develop, extend, or modify poreFlow, install as a developer using the instructions on Installation from source.