refactor: fix wrong type Residue -> DefinitionResidue

[kiyoon]

The Residue type doesn't have altnames, so it must have been documented with the wrong type. The correct type seems to be DefinitionResidue.

I'm fixing the type issue with a type checker. Untyped code makes it vulnerable to random crashes thus making it hard to develop. Below is an example of errors that need to be addressed in the future:

For now, I want to keep each PR simple. I didn't fix all issues but I'm slowly trying to.

FYI: adding types is usually safe because they are ignored on runtime. Even if you pass an object with a different type by mistake, it won't error out during runtime (only in the IDE it will show an error.) It just helps the IDE to figure out what they are.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 66.36%. Comparing base (be4e943) to head (27eb2a7).
Report is 9 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #412      +/-   ##
==========================================
+ Coverage   66.22%   66.36%   +0.14%     
==========================================
  Files          30       30              
  Lines        7765     7742      -23     
==========================================
- Hits         5142     5138       -4     
+ Misses       2623     2604      -19     

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[kiyoon]

I think we should remove setup.py and use pyproject.toml to configure the build. Ruff didn't detect the python version, thus it reported error. While we can specifically configure ruff, this means we have two locations for the configuration.

A little bit of background:

setup.py is old because it requires users to "run" the python program in order to know the spec of the package. What packages does it require? Which python version user is using to install it? Is it even compatible with the current system? Nothing can be known unless you try it and fail.

However, pyproject.toml resolves this by specifying all specs in a config file rather than python. This way, other tools like ruff can even know what the program requires etc.

[kiyoon]

OK, I've made the change. I think you would like this.

1. No setup.py, setup.cfg, MANIFEST.in

   • it used to be confusing how to include files in the distribution tarballs or wheel.
   • Now, you simply specify some directories and everything except .gitignored items will be included.

2. Not generating pdb2pqr.egg-info files in the project folder.

Test building the package using

# option 1. uv (recommended)
pip install uv
uv build

# option 2. pyproject-build (slower)
pip install build
python -m build

Unpack the wheel and tarball to see what they include

pip install wheel
wheel unpack dist/pdb2pqr-3.6.2-py3-none-any.whl