No-python files#

Find below a description of no-python files and folders inside pyHiM repository.

diagram of high-level

Left side - Files#

.gitignore: Basic text file used by the Git versioning tool to identify files that should not be shared.
.readthedocs.yaml: Read the Docs configuration file, used when RTD build online the documentation.
COPYRIGHT.txt: File containing the information of each contributor to this software.
environment.yml: Instructions to create a conda environment
LICENSE: Legal information on the code usage
pyproject.toml: Used for PyPI
README.md: Short description of pyHiM repository.

tests: Directory containing files that test the functions in the src folder.
docs: Main directory containing the files describing the software and those configuring compilation with the Sphinx tool for reading the documentation in the form of HTML web pages.
dist (local file): Generate by build to publish on PyPI with twine.
1. Install these 2 tools usefull for pip
```
pip install build twine
```
1. Move to the root of your source code and create the files for pip
```
python -m build
```
1. Check locally the consistency of files created inside dist folder
```
twine check dist/*
```
1. Upload your package on test.pypi
```
twine upload -r testpypi dist/*
```
1. Test installation from test.pypi
```
python -m pip install -i https://test.pypi.org/simple <your_package_name>
```
1. If everything seems good, upload on pypi server:
```
twine upload dist/*
```
1. To install your package:
```
pip install <your_package_name>
```
apiFISH (submodule): Use to help developer for the pyHiM function migration inside apiFISH library.
pyhim-small-dataset (submodule): Use to run pyHiM tests because of the github memory size limit (~500Mo).

This command will make automatically git submodule update --recursive after your git pull.