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Simple workflow platform used in scientific applications, initially developed within the Scipion framework for image processing in Electron Microscopy.

Project description

pyworkflow is a simple workflow platform used in scientific applications. It has been initially developed within the Scipion framework for image processing in Electron Microscopy.

pyworkflow allows you to define a working Domain by defining the following group of classes:

  • Objects: input/outputs that will be generated by different programs
  • Protocols: special type of Objects that have defined input parameters and will produce some output
  • Viewers: Entities that provide graphical analysis of results.
  • Wizards: Small GUIs that can be develop to help users to select given parameter values.


We are now fully going toward Python 3!

To install pyworkflow for development purposes, one can do:

# Create a clean virtual environment
python -m venv ~/myenv
source ~/myenv/bin/activate
git clone
cd scipion-pyworkflow
python -m pip install -e .  # Install in the environment as development

Running tests

First make sure that pyworkflow is available as a Python module in your current Python environment. During development, I tend to set the PYTHONPATH:

cd scipion-pyworkflow
# Either you have installed as mentioned above, or modify the PYTHONPATH
# After pyworkflow is accesible as a module, then:
cd pyworkflow/tests

python -m unittest discover

# Simple project GUI can be shown after running tests:
cd scipion-pyworkflow

# At the moment you need to specify SCIPION_DOMAIN and SCIPION_VERSION
export SCIPION_DOMAIN=scipion-pyworkflow/pyworkflow/tests/mock_domain
export SCIPION_VERSION=3.0.0

python pyworkflow/apps/ TestProtocolOutputs


Using a python virtual environment you might need: # For virtual env in ubuntu: # sudo apt-get install python3-dev # sudo apt-get install python3-tk

Project details

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