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Template-Python-Singularity

A template to build executable Singularity images for Python projects

Objective

This repo contains a template to create a Python app that will run in an executable Singularity container. A Singularity container can typically be used in data science projects to provide transparency and support of reproducibility.

Content

  • utils/ : utility scripts. The code in this directory is not included in the singularity container.
    • build_image.sh : a script to build a container image based on singularity/recipe.txt. The corresponding Singularity image is executable, and contains the scripts in src/. By default, the execution of the container image runs src/model.py (edit recipe.txt to change this behavior).
    • test_container.sh : a script to test if the execution of the container image works properly.
  • singularity/: contains the singularity image built with build_image.sh
    • singularity_test : a directory where a singularity image is copied and tested.
  • src/: the code that is included in the container.
  • data/ : input data
  • output/ : where code output is stored

Instruction to build the singularity container from the recipe.txt

To create an executable singularity container (which contains the code in /src) from singularity/recipe.txt, run :

./utils/build_container.sh

This will create a container image /singularity/container.sif. To test the executable singularity container image, run :

./utils/test_container.sh

This will output the results of src/model.py in singularity/test_singularity/output.

Instructions to execute the image

The singularity container image container.sif is executable, you can execute it by running:

singularity run ./singularity/container.sif <Argument for input path>

Note: <Argument for input path> is optional, default is ./

Instructions to run a custom model in the same environment

By default, the script called model.py is executed upon execution of the image. To run a specific Python script locally on synthetic data in the container environment, activate the singularity container in Terminal using:

singularity shell ./singularity/container.sif

This will allow you to have an environment (Singularity>) to run the model without installing any additional package. In order to run the model, run the following command :

Singularity> python3 src/script.py <Argument for input path>

This command can also be used to run the singularity without accessing the singularity shell:

singularity exec container.sif python3 src/script.py <Argument for input path>

License

This software is distributed under the GNU GENERAL PUBLIC LICENSE. Please refer to the file LICENCE.txt included for details.