Environment

Source code

Code and issues are hosted on GitHub in marcnol/pyHiM repository. If you want to contribute with code, checkout: development process page.

Dependencies

pyHiM relies on apiFISH for the 3D localization of barcodes. In future, more pyHiM common functions will be progressively moved to apiFISH to provide a commnon API for FISH-based analysis. If you develop pyHiM, you will need to install apiFISH using the following guide: how work with apiFISH.

Main pyHiM dependencies:

• Astropy

• scikit-image

• starDist

Dependencies needed to locally build the readthedocs documentation website:

• Sphinx

• Read the Docs

Development editor

The development editor choice is up to you, we list here two editors suitable for pyHiM development in Python:

• Spyder is popular in scientist community

• VSCode is popular in developer community

Analysis tools

• black: Linter to apply an auto format for PEP8.

• pylint: A Python static code analysis tool.