Installation

Requirements

Python Packages:

  • Python 3.7 (or later)

  • pandas

  • numpy (1.18)

  • matplotlib

  • seaborn

  • pytorch

  • scikit-learn

  • xlsxwriter

  • wxpython (4.0.7)

  • networkx

  • pypubsub

  • python.app (for MacOS X)

  • setuptools_scm

Creating a Conda environment

The code Git repository https://github.com/uvaKCCI/flimanalyzer.git contains an environment.yml file defining required Python packages. The python.app package, only required for MacOS X, is not included in the environment file and has to be installed manually, see below.

Run the following commands to create a flimenv Conda environment based on the environemnt.yml file:

git clone https://github.com/uvaKCCI/flimanalyzer.git
cd flimanalyzer
conda env create -f environment.yml
conda activate flimenv-0.4.0
python setup.py install

Installations on Windows and MacOS require a couple additional steps.

Windows Installation

Install VS Code.

MacOS X Installation

Activate the Conda environment, install the MacOS specific python.app package, and patch the shebang of the flimanalyzer console script.

conda activate flimenv-0.4.0
conda install python.app
sed -i '' -e 's/bin\/python/python\.app\/Contents\/MacOS\/python/' $(which flimanalyzer)

Run the application

From the command line

On Mac and Linux, run this command:

conda activate flimenv-0.4.0 
export PREFECT__FLOWS__CHECKPOINTING=true 
flimanalyzer

On Windows, run this command:

conda activate flimenv-0.4.0 
set PREFECT__FLOWS__CHECKPOINTING=true
flimanalyzer.exe

On Powershell, run this command:

conda activate flimenv-0.4.0
$env:PREFECT__FLOWS__CHECKPOINTING='true'
flimanalyzer.exe

From Anaconda Spyder

  1. Launch the Anaconda Navigator

  2. In the Applications on drop-down, select the name of the conda environment, e.g. flimenv.

  3. Launch Spyder (you may have to install it in your custom flimenv environment).

  4. In the Spyder editor, open the analyzerapp.py file.

  5. Go to Run–> Configuration per file... and check the box Execute in external system terminal.

  6. Go to Run –>Run or click the button with the green triangle in the Spyder toolbar.