Migrating packaging system from setup.py to pyproject.toml

[ganow]

Changes

• Migrated packaging system from setup.py (setuptools) to pyproject.toml
• Added missing package import threadpoolctl for Python >= 3.5
• Added a simple contribution guide
• Reorganized a directory structure:
  • from flat-layout to src-layout
  • test files are now located in tests/path/to/test_<src-file-name>.py
• Specified the requires-python parameter to ">=3.1". (at this moment I'm not sure whether this specification is appropriate or not)

Verification

I have tested the following procedures work in the local environment.

Package building

$ git clone https://github.com/KamitaniLab/PyFastL2LiR.git
$ cd PyFastL2LiR && git fetch && git checkout update-packaging
$ uv build
Building source distribution (uv build backend)...
Building wheel from source distribution (uv build backend)...
Successfully built dist/fastl2lir-0.10.tar.gz
Successfully built dist/fastl2lir-0.10-py3-none-any.whl

Unit testing

$ uv run pytest .
======================================================= test session starts ========================================================
platform darwin -- Python 3.9.6, pytest-8.4.2, pluggy-1.6.0
rootdir: /path/to/PyFastL2LiR
configfile: pyproject.toml
collected 6 items

tests/test_fastl2lir.py ......                                                                                               [100%]

========================================================= warnings summary =========================================================
...
================================================ 6 passed, 27824 warnings in 0.50s =================================================