Add python bindings for some commands

[dkhofer]

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[dkhofer]

Just pacifying clippy with a lot of this

[dkhofer]

I couldn't get to everything, so I focused on the existing operations that I think Bob wants python bindings for, mainly derive_chunks and make_stitch. I refactored those so we can pass in arguments directly from python instead of reading them from files. I also did the same for update_with_fasta, so you can call update_with_sequence from python and just pass in a sequence you want to have added to the graph.

Bob, let me know if there are operations that I missed, or other operations that don't exist yet that you'd like to see implemented for python.

[bobvh]

The functions you have added is a good start. The ergonomics look a bit clunky, but that could be handled on the python side (setting up a gen_api_client that hides many of the arguments). I did want to try what it feels like and I can't figure out how you are building / testing the Python module.

The Makefile in the main project dir causes the old python bindings to be built, not your new workspace. The idea is to supersede /src/python-api, correct? So we could remove /src/python-api when merging this into main?

Calling maturin directly from gen-python says it installed something, but under what name?

> maturin develop
🔗 Found pyo3 bindings
🐍 Found CPython 3.13 at <my gen repo>/gen-python/.venv/bin/python
    Finished `dev` profile [unoptimized + debuginfo] target(s) in 0.11s
📦 Built wheel for CPython 3.13 to /var/folders/f8/8zf8xczs0pxf9_vfnlmqlx9h0000gn/T/.tmpHFSTAY/gen_python-0.1.0-cp313-cp313-macosx_11_0_arm64.whl
✏️ Setting installed package as editable
🛠 Installed gen-python-0.1.0

> which python
<my gen repo>/gen-python/.venv/bin/python

> python
Python 3.13.3 (main, Apr 25 2025, 01:23:04) [Clang 17.0.0 (clang-1700.0.13.3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import gen
Traceback (most recent call last):
  File "<python-input-0>", line 1, in <module>
    import gen
ModuleNotFoundError: No module named 'gen'
>>>

I know we can't keep the name "gen", did we decide on the alternative?

I also tried just building it with cargo build from gen-python, but that gives the usual linker issues from pyo3.