Prepare SpectrumPY for pip packaging

[eayari21]

Summary

• move all SpectrumPY source, data, and assets into a src/spectrumpy_flight package and add packaging metadata
• update imports, launchers, and tests to use the new package namespace and entry points
• refresh documentation and add instructions for cutting a pip release

Testing

• pytest

---

https://chatgpt.com/codex/tasks/task_e_6902449889348320ad0b5875b57eb4e1

[chatgpt-codex-connector]

💡 Codex Review

SpectrumPY-Flight/src/spectrumpy_flight/spectrum_launcher.py

Lines 590 to 593 in b2564a2

	def _convert_packet_file(self, path: Path) -> Optional[Path]:
	output_dir = REPO_ROOT / "HDF5"
	output_dir.mkdir(parents=True, exist_ok=True)
	produced_path = output_dir / f"{path.name}.h5"

Packet converter stores HDF5 into read‑only package path

_convert_packet_file() now runs from the packaged module, but it still creates output_dir = REPO_ROOT / "HDF5". After pip installation that location is inside site-packages and cannot be created or written by normal users, so converting a packet downloaded via the launcher will fail even before subprocess.run is invoked. Use the new cache directory (e.g. ~/.spectrumpy_flight/HDF5) or another user‑writable location instead of the package directory.

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[chatgpt-codex-connector]

Avoid writing ImpactBook output into package directory

When running the GUI from an installed wheel, REPO_ROOT points to the package inside site-packages, which is typically read‑only for normal users. run_impactbook() writes results to REPO_ROOT / "HDF5" / <experiment>.h5, so a pip‑installed copy will raise PermissionError before any processing completes. The output directory should be moved to a user‑writable cache (as done for API downloads) rather than the package installation folder.

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[chatgpt-codex-connector]

Replace unsupported importlib.resources exists check

The new _collect_olivine_inputs() uses resources.files("spectrumpy_flight").joinpath(default) and then calls resource.exists(). Traversable objects returned by importlib.resources do not implement exists, so the test will raise an AttributeError before any assertions run. Use resource.is_dir()/is_file() or as_file instead of exists to keep the test runnable.

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