sdssdb v1

[albireox]

This PR includes changes described in #267 and sub-issues to bring sdssdb to stable development. The main changes includes:

• Support for SQLA 2.
• Support for connection pooling with Peewee.
• Update the style of the documentation and remove outdated text.
• Increase coverage in tests.
• Improve Python packaging and linting with uv and ruff.
• Update GitHub actions and workflows.

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[havok2063]

Oh yeah that's right. Is this only in the new catalogdb schema? I think you can switch to Optional, and that should work. I used Optional in the models following https://docs.sqlalchemy.org/en/20/changelog/whatsnew_20.html#migrating-an-existing-mapping. They use Optional to imply the mapped types so you can reduce fullname: Mapped[Optional[str]] = mapped_column(String) to just fullname: Mapped[Optional[str]]. I don't know if it does that with Mapped[str | None].

[havok2063]

Admittedly, I did not follow their complete guide, because I wanted to a.) finish this work, and b.) keep some readability in the models

[albireox]

Yes, actually Optional may work there and be not too painful. Other unions may require changing to Union[A, B] which is a bit ugly but probably ok. I think this happens with any migrated module in sdss5db.

[havok2063]

I also noticed catalogdb has a lot of Mapped[Any]. These should probably be updated to match the actual db column type.

[albireox]

Yes, that worked and it was only catalogdb. I also typed most of the Mapped[Any].

[havok2063]

Sounds good. What is left to do in the list for v1? We can also discuss in a breakout on Thursday.

[albireox]

Yes, let's discuss it on Thursday but I think we are basically done.

[Copilot]

Pull request overview

This PR upgrades sdssdb to version 1.0, including major dependency updates and code style improvements.

Changes:

• Upgraded SQLAlchemy from 1.x to 2.0 and psycopg2 to psycopg3
• Updated Python version requirements (3.9-4.0) and migrated build system to uv
• Standardized code style by converting all string literals from single to double quotes

Reviewed changes

Copilot reviewed 91 out of 96 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
pyproject.toml	Updated version to 1.0.0a1, upgraded dependencies (SQLAlchemy 2.0, psycopg3), migrated to uv build system
python/sdssdb/connection.py	Updated SQLAlchemy API calls for 2.0 compatibility (URL.create, future flags)
python/sdssdb/sqlalchemy/sdss5db/init.py	Replaced declarative_base with DeclarativeBase for SQLAlchemy 2.0
schema/sdss5db/vizdb/*.py	Added new sdss_id_to_astra_pipeline table and helper script
tests/**/*.py	Converted string quotes to double quotes throughout test files
.github/workflows/*.yml	Updated CI/CD workflows to use uv package manager
docs/sphinx/*.rst	Updated documentation for SQLAlchemy 2.0 syntax changes
readthedocs.yml	Updated OS version and removed deprecated configuration

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[albireox]

@copilot write a description for this pull request.

[Copilot]

@albireox I've opened a new pull request, #306, to work on those changes. Once the pull request is ready, I'll request review from you.