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The big picture

The following graph shows the contents of the example project root directory after executing pytask:

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Files and directories in yellow are constructed by pytask; those with a bluish background are added directly by the researcher. You immediately see the separation of inputs and outputs (one of our guiding principles) at work:

  • All source code is in the src directory
  • All outputs are constructed in the bld directory

The contents of both the root/bld and the root/src directories directly follow the steps of the analysis from the workflow section.

The idea is that everything that needs to be run during the, say, analysis step, is specified in root/src/analysis and all its output is placed in root/bld/analysis.

Some differences:

  • Because they are accessed frequently, figures and the like get extra directories in root/bld

  • The directory root/src contains many more subdirectories and files:

    • utilities.py provides code that may be used by different steps of the project. Little code snippets for input / output or stuff that is not directly related to the model would go here.

Zooming in

Lets go one step deeper and consider the root/src directory in more detail:

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It is imperative that you do all the task handling inside the task_xxx.py-scripts, using the pathlib library. This ensures that your project can be used on different machines and it minimises the potential for cross-platform errors.

For running Python source code from pytask, simply include depends_on and produces as inputs to your function.

For running scripts in other languages, pass all required files (inputs, log files, outputs) as arguments to the @pytask.mark.[x]-decorator. You can then read them in. Check the sections on different programming languages for examples.